[apophenia] 02/02: Primary Debian patch 0.999a+ds-1
Jerome Benoit
calculus-guest at moszumanska.debian.org
Fri Aug 15 08:52:38 UTC 2014
This is an automated email from the git hooks/post-receive script.
calculus-guest pushed a commit to branch master
in repository apophenia.
commit 2acff203797cbd4aa9320ce2056b6ee6647cd8e8
Author: Jerome Benoit <calculus at rezozer.net>
Date: Fri Aug 15 10:51:03 2014 +0200
Primary Debian patch 0.999a+ds-1
---
debian/adhoc/examples/build.sh | 78 +
debian/adhoc/images/structs.png | Bin 0 -> 80016 bytes
debian/apophenia-bin.install | 1 +
debian/apophenia-bin.manpages | 1 +
debian/apophenia-doc.doc-base | 17 +
debian/apophenia-doc.docs | 1 +
debian/apophenia-doc.examples | 4 +
debian/apophenia-doc.links | 2 +
debian/changelog | 27 +
debian/clean | 17 +
debian/compat | 1 +
debian/control | 156 +
debian/copyright | 55 +
debian/libapophenia0-dev.install | 4 +
debian/libapophenia0.install | 1 +
debian/libapophenia0.symbols | 339 ++
debian/patches/debianization-adhoc.patch | 30 +
...ianization-bug-597187_757967-mysql_config.patch | 17 +
debian/patches/debianization-documentation.patch | 29 +
debian/patches/debianization-help2man.patch | 54 +
debian/patches/debianization.patch | 103 +
debian/patches/series | 10 +
debian/patches/upstream-C2help2man.patch | 157 +
debian/patches/upstream-doxygen-typo.patch | 86 +
.../patches/upstream-error-format_security.patch | 25 +
.../upstream-rationalization-autotools.patch | 4269 ++++++++++++++++++++
.../upstream-rationalization-version_script.patch | 360 ++
debian/repack | 110 +
debian/rules | 16 +
debian/source/format | 1 +
debian/source/include-binaries | 1 +
debian/source/lintian-overrides | 1 +
debian/source/options | 2 +
debian/watch | 4 +
34 files changed, 5979 insertions(+)
diff --git a/debian/adhoc/examples/build.sh b/debian/adhoc/examples/build.sh
new file mode 100755
index 0000000..bbe2c1a
--- /dev/null
+++ b/debian/adhoc/examples/build.sh
@@ -0,0 +1,78 @@
+#! /bin/sh
+# /usr/share/doc/apophenia-doc/examples/build.sh
+#
+# ad hoc script for building the example sources distributed
+# within the debian package apophenia-doc.
+#
+# Recommended usage:
+# create a dedicated folder somewhere in your HOME directory;
+# link all the files in /usr/share/doc/apophenia-doc/examples in the dedicated folder;
+# launch this script in the dedicated folder;
+# to cleanup, if not yet done, create a link clean.sh to this script, and run this link.
+#
+# written for Debian by Jerome Benoit <calculus at rezozer.net>
+# copyright: 2014 Jerome Benoit <calculus at rezozer.net>
+# distributed under the terms and conditions of GPL version 2 or later
+#
+
+CC="gcc -std=c99 $(pkg-config apophenia --cflags --libs)"
+
+listof_zsource=$(find . -maxdepth 1 -regextype posix-egrep -regex '.*\.c(\.gz|\.bz2|\.xz)?' -printf '%f\n')
+
+for zsource in $listof_zsource ; do
+ executable=${zsource%%.*}
+ for extension in gz bz2 xz ; do
+ if [ -f ${zsource}.${extension} ]; then
+ rm -rf ${zsource}
+ fi
+ done
+ if [ -f ${executable}.o ]; then
+ rm -f ${executable}.o
+ fi
+ if [ -x ${executable} ]; then
+ rm -f ${executable}
+ fi
+done
+
+if [ "${0##*/}" = "clean.sh" ]; then exit 0 ; fi
+
+listof_zsource=$(find . -maxdepth 1 -regextype posix-egrep -regex '.*\.c(\.gz|\.bz2|\.xz)?' -printf '%f\n')
+
+for zsource in $listof_zsource ; do
+ zextension=${zsource##*.}
+ executable=${zsource%%.*}
+ printf "%-35s -> %-25s\n" ${zsource} ${executable}
+ case ${zextension} in
+ gz)
+ source=${zsource%.*}
+ zcat ${zsource} > ${source}
+ ;;
+ bz2)
+ source=${zsource%.*}
+ bzcat ${zsource} > ${source}
+ ;;
+ xz)
+ source=${zsource%.*}
+ xzcat ${zsource} > ${source}
+ ;;
+ *)
+ source=${zsource}
+ ;;
+ esac
+ extension=${source#*.}
+ case ${extension} in
+ c)
+ $CC -o ${executable} ${source}
+ ;;
+ *)
+ ;;
+ esac
+ if [ "${source}" != "${zsource}" ]; then
+ rm -f ${source}
+ fi
+ rm -f ${executable}.o
+done
+
+exit 0
+##
+## eos
diff --git a/debian/adhoc/images/structs.png b/debian/adhoc/images/structs.png
new file mode 100644
index 0000000..d2e246c
Binary files /dev/null and b/debian/adhoc/images/structs.png differ
diff --git a/debian/apophenia-bin.install b/debian/apophenia-bin.install
new file mode 100644
index 0000000..1df36c6
--- /dev/null
+++ b/debian/apophenia-bin.install
@@ -0,0 +1 @@
+usr/bin/*
diff --git a/debian/apophenia-bin.manpages b/debian/apophenia-bin.manpages
new file mode 100644
index 0000000..4450a71
--- /dev/null
+++ b/debian/apophenia-bin.manpages
@@ -0,0 +1 @@
+debian/tmp/usr/share/man/man1/*.1
diff --git a/debian/apophenia-doc.doc-base b/debian/apophenia-doc.doc-base
new file mode 100644
index 0000000..def2e2a
--- /dev/null
+++ b/debian/apophenia-doc.doc-base
@@ -0,0 +1,17 @@
+Document: apophenia
+Title: Apophenia
+Author: Ben Klemens
+Abstract:
+ The Apophenia Statistical C Library is an open source C library for working
+ with data sets and statistical models. It provides functions on the same level
+ as those of the typical stats packages (such as OLS, probit, or singular value
+ decomposition) but gives the user more flexibility to be creative in model-building.
+ Apophenia is meant to scale well, to comfortably work with gigabyte data sets,
+ million-step simulations, or computationally-intensive agent-based models.
+ The source code is distributed under the GNU General Public License version 2 (GPL2)
+ with two modifications.
+Section: Science/Mathematics
+
+Format: HTML
+Index: /usr/share/doc/apophenia-doc/html/index.html
+Files: /usr/share/doc/apophenia-doc/html/*.html
diff --git a/debian/apophenia-doc.docs b/debian/apophenia-doc.docs
new file mode 100644
index 0000000..a8ae8ed
--- /dev/null
+++ b/debian/apophenia-doc.docs
@@ -0,0 +1 @@
+docs/html
diff --git a/debian/apophenia-doc.examples b/debian/apophenia-doc.examples
new file mode 100644
index 0000000..2976de4
--- /dev/null
+++ b/debian/apophenia-doc.examples
@@ -0,0 +1,4 @@
+debian/adhoc/examples/build.sh
+eg/*.c
+tests/data
+tests/faith.data
diff --git a/debian/apophenia-doc.links b/debian/apophenia-doc.links
new file mode 100644
index 0000000..5685f23
--- /dev/null
+++ b/debian/apophenia-doc.links
@@ -0,0 +1,2 @@
+usr/share/doc/apophenia-doc/examples/build.sh usr/share/doc/apophenia-doc/examples/clean.sh
+usr/share/doc/apophenia-doc/examples usr/share/doc/apophenia-doc/eg
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..086f327
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,27 @@
+apophenia (0.999a+ds-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #755493).
+ * Debianization:
+ - debian/copyright in DEP-5 format;
+ - debian/control:
+ - debhelper build-dep to >= 9;
+ - Standards Version 3.9.5;
+ - Vcs-* headers.
+ - debian/source, format 3.0 (quilt);
+ - debian/patches/ patches in DEP-3 format;
+ - debian/watch file;
+ - debian/repack, repack script to clean up and gain weight;
+ - debian/rules:
+ - autoreconf-iguration;
+ - full and minal dh integration;
+ - get-orig-source uscan based target which downloads the currently
+ packaged upstream tarball and repacks it;
+ - default target which basically queries package status with uscan
+ -- output in DEHS format;
+ - gpg-signature check support, neutralize;
+ - ad hoc script to build/clean the upstream source examples, provide.
+ * Fixes, enhancements, request for a better autotools machinery support
+ (more rational, passing the `make distcheck' test, explicit gnulib support)
+ and bug reports has been submitted to the upstream maintainer.
+
+ -- Jerome Benoit <calculus at rezozer.net> Fri, 15 Aug 2014 08:46:42 +0000
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..9121a54
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,17 @@
+cmd/apop_db_to_crosstab.1
+cmd/apop_plot_query.1
+cmd/apop_text_to_db.1
+tests/ff.db
+tests/runs.db
+tests/td.db
+tests/draws-k
+tests/draws-k2
+tests/draws-mvN
+tests/draws-N
+tests/draws-std_multinormal
+tests/draws-std_normal
+tests/the_data.txt
+tests/print_test.out
+tests/xxx
+docs/model_doc.h
+docs/missing_model_parts
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..8bb7a5d
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,156 @@
+Source: apophenia
+Section: math
+Priority: extra
+Maintainer: Debian Science Maintainers <debian-science-maintainers at lists.alioth.debian.org>
+Uploaders: Jerome Benoit <calculus at rezozer.net>
+Build-Depends:
+ debhelper (>= 9),
+ autotools-dev, autoconf-archive, dh-autoreconf, libtool,
+ pkg-config, help2man,
+ zlib1g-dev, libmysqlclient-dev, libsqlite3-dev, libgsl0-dev,
+ bc, sqlite3,
+ doxygen, texlive-latex-recommended, texlive-fonts-recommended, ghostscript,
+ rdfind, symlinks
+Standards-Version: 3.9.5
+Homepage: http://apophenia.info/
+Vcs-Git: git://anonscm.debian.org/debian-science/packages/apophenia.git
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-science/packages/apophenia.git
+
+Package: libapophenia0
+Provides: libapophenia
+Section: libs
+Architecture: any
+Pre-Depends: ${misc:Pre-Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: libapophenia
+Suggests: apophenia-doc (= ${binary:Version})
+Multi-Arch: same
+Description: Apophenia Statistical C Library -- library package
+ The Apophenia Statistical C Library is an open source C library for
+ working with data sets and statistical models. It provides functions
+ on the same level as those of the typical stats packages (such as OLS,
+ probit, or singular value decomposition) but gives the user more
+ flexibility to be creative in model-building.
+ .
+ Apophenia is meant to scale well, to comfortably work with gigabyte
+ data sets, million-step simulations, or computationally-intensive
+ agent-based models.
+ .
+ Apophenia builds upon the GNU Scientific and SQLite libraries,
+ MySQL/mariaDB is also supported. The core functions are written
+ in C, but experience has shown them to be easy to bind in Python,
+ Julia, Perl, Ruby, etc. The source code is distributed under the
+ GNU General Public License version 2 (GPL2) with two modifications.
+ .
+ This package provides the shared libraries required to run programs
+ compiled against the Apophenia Statistical C Library. To compile your
+ own programs you also need to install the libapophenia0-dev package.
+
+Package: libapophenia0-dev
+Provides: libapophenia-dev
+Section: libdevel
+Architecture: any
+Depends: libapophenia0 (= ${binary:Version}), ${misc:Depends}
+Conflicts: libapophenia-dev
+Suggests: pkg-config
+Multi-Arch: same
+Description: Apophenia Statistical C Library -- development package
+ The Apophenia Statistical C Library is an open source C library for
+ working with data sets and statistical models. It provides functions
+ on the same level as those of the typical stats packages (such as OLS,
+ probit, or singular value decomposition) but gives the user more
+ flexibility to be creative in model-building.
+ .
+ Apophenia is meant to scale well, to comfortably work with gigabyte
+ data sets, million-step simulations, or computationally-intensive
+ agent-based models.
+ .
+ Apophenia builds upon the GNU Scientific and SQLite libraries,
+ MySQL/mariaDB is also supported. The core functions are written
+ in C, but experience has shown them to be easy to bind in Python,
+ Julia, Perl, Ruby, etc. The source code is distributed under the
+ GNU General Public License version 2 (GPL2) with two modifications.
+ .
+ This package contains the header files, static libraries and symbolic
+ links that developers using the Apophenia Statistical C Library will
+ need.
+
+Package: apophenia-bin
+Architecture: any
+Depends: libapophenia0 (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}
+Suggests: sqlite3
+Multi-Arch: foreign
+Description: Apophenia Statistical C Library -- binary package
+ The Apophenia Statistical C Library is an open source C library for
+ working with data sets and statistical models. It provides functions
+ on the same level as those of the typical stats packages (such as OLS,
+ probit, or singular value decomposition) but gives the user more
+ flexibility to be creative in model-building.
+ .
+ Apophenia is meant to scale well, to comfortably work with gigabyte
+ data sets, million-step simulations, or computationally-intensive
+ agent-based models.
+ .
+ Apophenia builds upon the GNU Scientific and SQLite libraries,
+ MySQL/mariaDB is also supported. The core functions are written
+ in C, but experience has shown them to be easy to bind in Python,
+ Julia, Perl, Ruby, etc. The source code is distributed under the
+ GNU General Public License version 2 (GPL2) with two modifications.
+ .
+ This package provides several command line utility examples.
+
+Package: libapophenia0-dbg
+Provides: libapophenia-dbg
+Section: debug
+Architecture: any
+Depends: libapophenia0 (= ${binary:Version}), ${misc:Depends}
+Conflicts: libapophenia-dbg
+Multi-Arch: same
+Description: Apophenia Statistical C Library -- debug symbols package
+ The Apophenia Statistical C Library is an open source C library for
+ working with data sets and statistical models. It provides functions
+ on the same level as those of the typical stats packages (such as OLS,
+ probit, or singular value decomposition) but gives the user more
+ flexibility to be creative in model-building.
+ .
+ Apophenia is meant to scale well, to comfortably work with gigabyte
+ data sets, million-step simulations, or computationally-intensive
+ agent-based models.
+ .
+ Apophenia builds upon the GNU Scientific and SQLite libraries,
+ MySQL/mariaDB is also supported. The core functions are written
+ in C, but experience has shown them to be easy to bind in Python,
+ Julia, Perl, Ruby, etc. The source code is distributed under the
+ GNU General Public License version 2 (GPL2) with two modifications.
+ .
+ This package provides the debugging symbols for the libraries from
+ the libapophenia0-dev package.
+
+Package: apophenia-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests:
+ libapophenia0 (= ${binary:Version}), libapophenia0-dev (= ${binary:Version}),
+# pdf-viewer,
+ www-browser,
+ gsl-doc-pdf, gsl-ref-html
+Description: Apophenia Statistical C Library -- reference manual
+ The Apophenia Statistical C Library is an open source C library for
+ working with data sets and statistical models. It provides functions
+ on the same level as those of the typical stats packages (such as OLS,
+ probit, or singular value decomposition) but gives the user more
+ flexibility to be creative in model-building.
+ .
+ Apophenia is meant to scale well, to comfortably work with gigabyte
+ data sets, million-step simulations, or computationally-intensive
+ agent-based models.
+ .
+ Apophenia builds upon the GNU Scientific and SQLite libraries,
+ MySQL/mariaDB is also supported. The core functions are written
+ in C, but experience has shown them to be easy to bind in Python,
+ Julia, Perl, Ruby, etc. The source code is distributed under the
+ GNU General Public License version 2 (GPL2) with two modifications.
+ .
+ This package provides the reference manual for the Apophenia
+ Statistical C Library; it also contains examples.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4e28d27
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,55 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0
+Upstream-Name: apophenia
+Upstream-Contact: Ben Klemens <fluffmail at f-m.fm>
+Source: http://apophenia.info/
+X-Source: https://neunhoef.github.io/io/
+X-Source-Downloaded-From: https://github.com/b-k/apophenia/releases
+X-Upstream-Vcs: git clone https://github.com/b-k/apophenia.git
+X-Upstream-Bugs: https://github.com/b-k/apophenia/issues
+Comment:
+ The upstream source tarball is repacked to drop off the regenarated
+ material, mainly autotools related, to gain substantial weight.
+
+Files: *
+Copyright: 2005-2014 Ben Klemens <fluffmail at f-m.fm>
+License: GPL-2 with two modifications
+
+Files: debian/*
+Copyright:
+ 2014 Jerome Benoit <calculus at rezozer.net>
+License: GPL-2+
+
+License: GPL-2 with two modifications
+ This software is licensed under the GNU GPL v2, with two modifications,
+ as follows:
+ .
+ --An application hosted on a server and remotely operated by users, such
+ as a web application or database server, is understood to be distribution
+ of the software, and therefore all GPL v2 clauses regarding distribution
+ apply. For example, a web application must include a link for downloading
+ the application source code.
+ .
+ --You are explicitly granted permission to link this software to other
+ code licensed under other licenses, such as GPL v3 or the BSD license.
+ Linking to a differently-licensed code base does not free this code (or
+ the combination) of the stipulations of the GPLv2 plus the above clause.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/libapophenia0-dev.install b/debian/libapophenia0-dev.install
new file mode 100644
index 0000000..0e6cd1d
--- /dev/null
+++ b/debian/libapophenia0-dev.install
@@ -0,0 +1,4 @@
+usr/lib/*/libapophenia.so
+usr/lib/*/libapophenia.a
+usr/lib/*/pkgconfig/*
+usr/include/*
diff --git a/debian/libapophenia0.install b/debian/libapophenia0.install
new file mode 100644
index 0000000..5e3ff8c
--- /dev/null
+++ b/debian/libapophenia0.install
@@ -0,0 +1 @@
+usr/lib/*/libapophenia.so.*
diff --git a/debian/libapophenia0.symbols b/debian/libapophenia0.symbols
new file mode 100644
index 0000000..7ab0e56
--- /dev/null
+++ b/debian/libapophenia0.symbols
@@ -0,0 +1,339 @@
+libapophenia.so.0 libapophenia0 #MINVER#
+ LIBAPOPHENIA_0.0.0 at LIBAPOPHENIA_0.0.0 0.999
+ apop_anova_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_arms_draw at LIBAPOPHENIA_0.0.0 0.999
+ apop_arms_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_arms_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_arms_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_array_to_vector_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_bernoulli at LIBAPOPHENIA_0.0.0 0.999
+ apop_beta at LIBAPOPHENIA_0.0.0 0.999
+ apop_beta_from_mean_var at LIBAPOPHENIA_0.0.0 0.999
+ apop_binomial at LIBAPOPHENIA_0.0.0 0.999
+ apop_bootstrap_cov_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_cdf at LIBAPOPHENIA_0.0.0 0.999
+ apop_cdf_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_cdf_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_cdf_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_composition at LIBAPOPHENIA_0.0.0 0.999
+ apop_composition_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_composition_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_composition_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_coordinate_transform at LIBAPOPHENIA_0.0.0 0.999
+ apop_crosstab_to_db at LIBAPOPHENIA_0.0.0 0.999
+ apop_ct_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_ct_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_ct_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_add_named_elmt at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_add_names_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_add_page at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_alloc_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_calloc_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_correlation at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_covariance at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_fill_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_free_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_get_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_get_factor_names_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_get_page_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_listwise_delete_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_memcpy at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_pack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_pmf_compress at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_print_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_prune_columns_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_ptr_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_rank_compress at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_rank_expand at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_rm_columns at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_rm_page_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_rm_rows_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_set_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_set_row at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_show at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_sort_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_split at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_stack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_summarize at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_to_bins_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_to_db at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_to_dummies_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_to_factors_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_transpose_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_data_unpack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_db_close_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_db_open at LIBAPOPHENIA_0.0.0 0.999
+ apop_db_paired_t_test at LIBAPOPHENIA_0.0.0 0.999
+ apop_db_t_test at LIBAPOPHENIA_0.0.0 0.999
+ apop_db_to_crosstab at LIBAPOPHENIA_0.0.0 0.999
+ apop_dconstrain at LIBAPOPHENIA_0.0.0 0.999
+ apop_dconstrain_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_dconstrain_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_dconstrain_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_det_and_inv at LIBAPOPHENIA_0.0.0 0.999
+ apop_dirichlet at LIBAPOPHENIA_0.0.0 0.999
+ apop_dot_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_draw at LIBAPOPHENIA_0.0.0 0.999
+ apop_estimate at LIBAPOPHENIA_0.0.0 0.999
+ apop_estimate_coefficient_of_determination at LIBAPOPHENIA_0.0.0 0.999
+ apop_estimate_parameter_tests at LIBAPOPHENIA_0.0.0 0.999
+ apop_estimate_restart_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_exponential at LIBAPOPHENIA_0.0.0 0.999
+ apop_f_test_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_gamma at LIBAPOPHENIA_0.0.0 0.999
+ apop_generalized_harmonic at LIBAPOPHENIA_0.0.0 0.999
+ apop_histograms_test_goodness_of_fit at LIBAPOPHENIA_0.0.0 0.999
+ apop_improper_uniform at LIBAPOPHENIA_0.0.0 0.999
+ apop_iv at LIBAPOPHENIA_0.0.0 0.999
+ apop_jackknife_cov at LIBAPOPHENIA_0.0.0 0.999
+ apop_kernel_density at LIBAPOPHENIA_0.0.0 0.999
+ apop_kernel_density_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_kernel_density_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_kernel_density_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_kl_divergence_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_linear_constraint_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_lm_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_lm_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_lm_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_loess at LIBAPOPHENIA_0.0.0 0.999
+ apop_loess_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_loess_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_loess_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_log_likelihood at LIBAPOPHENIA_0.0.0 0.999
+ apop_logit at LIBAPOPHENIA_0.0.0 0.999
+ apop_lognormal at LIBAPOPHENIA_0.0.0 0.999
+ apop_map_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_map_sum_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_apply at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_apply_all at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_determinant at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_inverse at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_is_positive_semidefinite_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_map at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_map_all at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_map_all_sum at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_map_sum at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_mean at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_mean_and_var at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_normalize at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_pca_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_print_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_realloc at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_rm_columns at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_show at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_stack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_sum at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_to_data at LIBAPOPHENIA_0.0.0 0.999
+ apop_matrix_to_positive_semidefinite at LIBAPOPHENIA_0.0.0 0.999
+ apop_maximum_likelihood at LIBAPOPHENIA_0.0.0 0.999
+ apop_mcmc_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_mcmc_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_mcmc_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_mixture at LIBAPOPHENIA_0.0.0 0.999
+ apop_mixture_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_mixture_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_mixture_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_ml_impute at LIBAPOPHENIA_0.0.0 0.999
+ apop_mle_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_mle_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_mle_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_clear at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_draws_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_fix_params at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_fix_params_get_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_hessian_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_metropolis_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_mixture_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_numerical_covariance_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_print at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_print_type_check at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_set_parameters_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_show at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_stack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_model_to_pmf_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_multinomial at LIBAPOPHENIA_0.0.0 0.999
+ apop_multivariate_gamma at LIBAPOPHENIA_0.0.0 0.999
+ apop_multivariate_lngamma at LIBAPOPHENIA_0.0.0 0.999
+ apop_multivariate_normal at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_add at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_alloc at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_find at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_print at LIBAPOPHENIA_0.0.0 0.999
+ apop_name_stack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_normal at LIBAPOPHENIA_0.0.0 0.999
+ apop_numerical_gradient_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_ols at LIBAPOPHENIA_0.0.0 0.999
+ apop_opts at LIBAPOPHENIA_0.0.0 0.999
+ apop_p at LIBAPOPHENIA_0.0.0 0.999
+ apop_paired_t_test at LIBAPOPHENIA_0.0.0 0.999
+ apop_parameter_model at LIBAPOPHENIA_0.0.0 0.999
+ apop_parameter_model_type_check at LIBAPOPHENIA_0.0.0 0.999
+ apop_parts_wanted_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_parts_wanted_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_parts_wanted_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_plot_histogram_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_plot_lattice_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_plot_line_and_scatter_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_plot_qq_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_plot_triangle_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_pm_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_pm_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_pm_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_pmf at LIBAPOPHENIA_0.0.0 0.999
+ apop_pmf_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_pmf_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_pmf_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_poisson at LIBAPOPHENIA_0.0.0 0.999
+ apop_predict at LIBAPOPHENIA_0.0.0 0.999
+ apop_predict_type_check at LIBAPOPHENIA_0.0.0 0.999
+ apop_prep at LIBAPOPHENIA_0.0.0 0.999
+ apop_probit at LIBAPOPHENIA_0.0.0 0.999
+ apop_query at LIBAPOPHENIA_0.0.0 0.999
+ apop_query_to_data at LIBAPOPHENIA_0.0.0 0.999
+ apop_query_to_float at LIBAPOPHENIA_0.0.0 0.999
+ apop_query_to_matrix at LIBAPOPHENIA_0.0.0 0.999
+ apop_query_to_mixed_data at LIBAPOPHENIA_0.0.0 0.999
+ apop_query_to_text at LIBAPOPHENIA_0.0.0 0.999
+ apop_query_to_vector at LIBAPOPHENIA_0.0.0 0.999
+ apop_rake_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_regex_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_rng_GHgB3 at LIBAPOPHENIA_0.0.0 0.999
+ apop_rng_alloc at LIBAPOPHENIA_0.0.0 0.999
+ apop_rng_get_thread_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_score at LIBAPOPHENIA_0.0.0 0.999
+ apop_score_type_check at LIBAPOPHENIA_0.0.0 0.999
+ apop_settings_copy_group at LIBAPOPHENIA_0.0.0 0.999
+ apop_settings_get_grp at LIBAPOPHENIA_0.0.0 0.999
+ apop_settings_group_alloc at LIBAPOPHENIA_0.0.0 0.999
+ apop_settings_group_alloc_wm at LIBAPOPHENIA_0.0.0 0.999
+ apop_settings_remove_group at LIBAPOPHENIA_0.0.0 0.999
+ apop_stack at LIBAPOPHENIA_0.0.0 0.999
+ apop_stack_settings_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_stack_settings_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_stack_settings_init at LIBAPOPHENIA_0.0.0 0.999
+ apop_system at LIBAPOPHENIA_0.0.0 0.999
+ apop_t_distribution at LIBAPOPHENIA_0.0.0 0.999
+ apop_t_test at LIBAPOPHENIA_0.0.0 0.999
+ apop_table_exists_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_test_anova_independence at LIBAPOPHENIA_0.0.0 0.999
+ apop_test_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_test_fisher_exact at LIBAPOPHENIA_0.0.0 0.999
+ apop_test_kolmogorov at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_add at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_alloc at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_fill_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_free at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_paste_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_to_data_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_to_db_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_text_unique_elements at LIBAPOPHENIA_0.0.0 0.999
+ apop_uniform at LIBAPOPHENIA_0.0.0 0.999
+ apop_update_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_update_type_check at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_apply at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_bounded_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_copy at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_correlation at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_cov_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_distance_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_exp at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_fill_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_kurtosis at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_kurtosis_pop_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_log10 at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_log at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_map at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_map_sum at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_mean_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_moving_average at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_normalize_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_percentiles_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_print_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_realloc at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_show at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_skew at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_skew_pop_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_stack_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_sum at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_to_data at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_to_matrix_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_unique_elements at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_var_base at LIBAPOPHENIA_0.0.0 0.999
+ apop_vector_var_m at LIBAPOPHENIA_0.0.0 0.999
+ apop_vtable_add at LIBAPOPHENIA_0.0.0 0.999
+ apop_vtable_drop at LIBAPOPHENIA_0.0.0 0.999
+ apop_vtable_get at LIBAPOPHENIA_0.0.0 0.999
+ apop_yule at LIBAPOPHENIA_0.0.0 0.999
+ apop_zipf at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_anova at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_array_to_vector at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_bootstrap_cov at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_alloc at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_calloc at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_get at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_get_factor_names at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_get_page at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_listwise_delete at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_pack at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_print at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_ptr at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_rm_page at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_rm_rows at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_set at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_sort at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_stack at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_to_bins at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_to_dummies at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_to_factors at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_transpose at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_data_unpack at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_db_close at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_dot at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_estimate_restart at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_f_test at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_kl_divergence at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_linear_constraint at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_map at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_map_sum at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_matrix_is_positive_semidefinite at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_matrix_pca at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_matrix_print at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_matrix_stack at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_model_draws at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_model_hessian at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_model_metropolis at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_model_numerical_covariance at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_model_to_pmf at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_name_stack at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_numerical_gradient at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_plot_histogram at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_plot_lattice at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_plot_line_and_scatter at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_plot_qq at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_plot_triangle at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_rake at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_regex at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_table_exists at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_test at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_text_paste at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_text_to_data at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_text_to_db at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_update at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_bounded at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_cov at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_distance at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_kurtosis_pop at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_mean at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_normalize at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_percentiles at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_print at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_skew_pop at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_stack at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_to_matrix at LIBAPOPHENIA_0.0.0 0.999
+ variadic_apop_vector_var at LIBAPOPHENIA_0.0.0 0.999
diff --git a/debian/patches/debianization-adhoc.patch b/debian/patches/debianization-adhoc.patch
new file mode 100644
index 0000000..90db1df
--- /dev/null
+++ b/debian/patches/debianization-adhoc.patch
@@ -0,0 +1,30 @@
+Description: debianization -- ad hoc
+ Meant to address Debian Policy requirements through ad hoc approaches:
+ a PNG image that must be present in the source tarball is imported
+ and incorporated as is as Debian material; this regrettable oversight
+ has been reported to the upstream maintainer.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- a/docs/Makefile.am
++++ b/docs/Makefile.am
+@@ -31,6 +31,7 @@
+ doc: documentation.h model_doc.h $(apophenia_IMAGES) $(apophenia_JS)
+ doxygen doxygen.conf
+ cp $(apophenia_IMAGES) $(apophenia_JS) html/
++ cp $(top_srcdir)/debian/adhoc/images/structs.png html/
+ sed -i -f edit_outline.sed html/index.html html/outline.html
+ sed -i -f edit_globals.sed html/globals.html
+ sed -i -f edit_group.sed html/group__models.html
+--- a/docs/documentation.h
++++ b/docs/documentation.h
+@@ -2419,7 +2419,7 @@
+ which will be useful to you if only because it lists some of the functions that act on
+ GSL vectors and matrices that are useful (in fact, essential) but out of the scope of the Apophenia documentation.
+
+-\image html http://apophenia.info/structs.png
++\image html structs.png
+ \image latex structs.png
+
+
diff --git a/debian/patches/debianization-bug-597187_757967-mysql_config.patch b/debian/patches/debianization-bug-597187_757967-mysql_config.patch
new file mode 100644
index 0000000..f0e9010
--- /dev/null
+++ b/debian/patches/debianization-bug-597187_757967-mysql_config.patch
@@ -0,0 +1,17 @@
+Description: debianization -- workaround around bugs
+ Meant to workaround bugs #597187 and #757967
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-12
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,6 +68,8 @@
+ ## Debian package version
+ DEB_PKG_VERSION=$(dpkg-parsechangelog | sed -n -e '/^Version:/s/Version: //p')
+ AC_SUBST(DEB_PKG_VERSION)
++## work around for bugs #597187 and #757967
++MYSQL_CFLAGS=$(echo "${MYSQL_CFLAGS}" | sed -e 's/-DNDEBUG//' -e 's/-g//' -e 's/-fno-strict-aliasing//' -e 's/[ ]*$//')
+
+ AC_CONFIG_FILES([
+ apophenia.pc
diff --git a/debian/patches/debianization-documentation.patch b/debian/patches/debianization-documentation.patch
new file mode 100644
index 0000000..17a07db
--- /dev/null
+++ b/debian/patches/debianization-documentation.patch
@@ -0,0 +1,29 @@
+Description: debianization -- documentation
+ Address Debian Policy requirements for documentation.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- a/docs/head.html
++++ b/docs/head.html
+@@ -2,13 +2,7 @@
+ <html> <head>
+ <title>Apophenia: a library for scientific computing</title>
+
+-<!-- Google is watching. -->
+-<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
+-</script>
+-<script type="text/javascript">
+-_uacct = "UA-134313-2";
+-urchinTracker();
+-</script>
++<!-- Google is no more watching. -->
+
+
+ <link rel="stylesheet" href="typical.css" type="text/css" >
+--- a/docs/foot.html
++++ b/docs/foot.html
+@@ -1,2 +1,2 @@
+ <p><p>
+-<div class="tiny">Autogenerated by doxygen on $date.</div></body></html>
++<div class="tiny">Autogenerated by doxygen on $date (Debian $projectnumber).</div></body></html>
diff --git a/debian/patches/debianization-help2man.patch b/debian/patches/debianization-help2man.patch
new file mode 100644
index 0000000..2564b73
--- /dev/null
+++ b/debian/patches/debianization-help2man.patch
@@ -0,0 +1,54 @@
+Description: debianization -- help2man
+ Generate help2man man pages for the command line utilities.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-12
+
+--- a/cmd/Makefile.am
++++ b/cmd/Makefile.am
+@@ -8,7 +8,35 @@
+ -I $(top_srcdir) \
+ $(GSL_CFLAGS)
+
++man_MANS = \
++ apop_text_to_db.1 \
++ apop_db_to_crosstab.1 \
++ apop_plot_query.1
++
+ LDADD = \
+ $(top_builddir)/libapophenia.la \
+ $(GSL_LIBS)
+
++AM_H2MFLAGS = \
++ --manual="Apophenia" \
++ --version-string="$(PACKAGE_VERSION)" \
++ --source="Apophenia (Debian $(DEB_PKG_VERSION))" \
++ --libtool \
++ --no-info
++
++%.1: %
++ $(HELP2MAN) \
++ -s 1 \
++ $(AM_H2MFLAGS) \
++ -I $(top_srcdir)/debian/man/$(subst nauty-,,$*).h2m \
++ -n $(if $($(subst -,_,$*)_DESCRIPTION), $($(subst -,_,$*)_DESCRIPTION), "manual page for $*") \
++ -o $@ \
++ $(top_builddir)/cmd/$<
++
++## short descriptions inspired from the header of the C source files
++apop_text_to_db_DESCRIPTION = "command line utility to convert a text file into a database table"
++apop_db_to_crosstab_DESCRIPTION = "command line utility to convert a three-column table to a crosstab"
++apop_plot_query_DESCRIPTION = "command line utility to take in a query and put out a Gnuplot table file"
++
++CLEANFILES = \
++ $(man_MANS)
+--- a/configure.ac
++++ b/configure.ac
+@@ -22,6 +22,7 @@
+ gl_LD_VERSION_SCRIPT
+
+ # Checks for programs.
++AC_PATH_PROG([HELP2MAN],[help2man])
+ AC_PROG_CC
+ AC_PROG_CC_C99
+
diff --git a/debian/patches/debianization.patch b/debian/patches/debianization.patch
new file mode 100644
index 0000000..5791f3c
--- /dev/null
+++ b/debian/patches/debianization.patch
@@ -0,0 +1,103 @@
+Description: debianization
+ Meant to maintain a minimal debian/rules, to fix warnings,
+ to address Debian specific stuff in general.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- a/docs/Makefile.am
++++ b/docs/Makefile.am
+@@ -3,6 +3,8 @@
+
+ default:
+
++all: html
++
+ ## adhoc
+ html man: doc
+
+@@ -33,6 +35,8 @@
+ sed -i -f edit_globals.sed html/globals.html
+ sed -i -f edit_group.sed html/group__models.html
+ sed -i -f edit_width.sed html/*.html
++ rdfind -outputname /dev/null -makesymlinks true html
++ symlinks -r -c -s -v html
+
+ doc-clean:
+ -rm -rf html latex man
+@@ -56,3 +60,12 @@
+ typical.css \
+ documentation.h
+
++
++if MAINTAINER_MODE
++
++DISTCLEANFILES = $(MAINTAINERCLEANFILES)
++
++distclean-local: doc-clean
++
++endif
++
+--- a/docs/doxygen.conf.in
++++ b/docs/doxygen.conf.in
+@@ -32,7 +32,7 @@
+ # This could be handy for archiving the generated documentation or
+ # if some version control system is used.
+
+-PROJECT_NUMBER =
++PROJECT_NUMBER = "@DEB_PKG_VERSION@"
+
+ # Using the PROJECT_BRIEF tag one can provide an optional one line description
+ # for a project that appears at the top of each page and should give viewer
+@@ -687,7 +687,7 @@
+ # Note that relative paths are relative to the directory from which doxygen is
+ # run.
+
+-EXCLUDE =
++EXCLUDE = @abs_top_srcdir@/debian
+
+ # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+ # directories that are symbolic links (a Unix file system feature) are excluded
+@@ -1216,7 +1216,7 @@
+ # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+ # generate Latex output.
+
+-GENERATE_LATEX = YES
++GENERATE_LATEX = NO
+
+ # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+ # If a relative path is entered the value of OUTPUT_DIRECTORY will be
+@@ -1357,7 +1357,7 @@
+ # If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+ # generate man pages
+
+-GENERATE_MAN = YES
++GENERATE_MAN = NO
+
+ # The MAN_OUTPUT tag is used to specify where the man pages will be put.
+ # If a relative path is entered the value of OUTPUT_DIRECTORY will be
+--- a/configure.ac
++++ b/configure.ac
+@@ -63,6 +63,11 @@
+ AC_PATH_PROGS([SQLITE3],[sqlite3],[/usr/bin/sqlite3])
+
+
++# Debian stuff
++## Debian package version
++DEB_PKG_VERSION=$(dpkg-parsechangelog | sed -n -e '/^Version:/s/Version: //p')
++AC_SUBST(DEB_PKG_VERSION)
++
+ AC_CONFIG_FILES([
+ apophenia.pc
+ Makefile
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -5,7 +5,7 @@
+ dist-bzip2 \
+ dist-zip
+
+-AM_CFLAGS = -g -Wall -O3
++AM_CFLAGS = -O3
+
+ ## Library versioning (C:R:A == current:revision:age)
+ LIBAPOPHENIA_LT_VERSION = 0:0:0
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..956fef8
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,10 @@
+upstream-rationalization-version_script.patch
+upstream-doxygen-typo.patch
+upstream-rationalization-autotools.patch
+upstream-error-format_security.patch
+upstream-C2help2man.patch
+debianization.patch
+debianization-help2man.patch
+debianization-documentation.patch
+debianization-bug-597187_757967-mysql_config.patch
+debianization-adhoc.patch
diff --git a/debian/patches/upstream-C2help2man.patch b/debian/patches/upstream-C2help2man.patch
new file mode 100644
index 0000000..8f89508
--- /dev/null
+++ b/debian/patches/upstream-C2help2man.patch
@@ -0,0 +1,157 @@
+Description: format usages and helps
+ Attempt to format and harmonize helps of the wrapper programs
+ wrt UN*X customs in view to employ help2man to generate manpages.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-14
+
+--- a/cmd/apop_plot_query.c
++++ b/cmd/apop_plot_query.c
+@@ -1,5 +1,5 @@
+ /** \file
+- Command line utility to take in a query and put out a Gnuplottable file.
++ Command line utility to take in a query and put out a Gnuplot table file.
+
+ Copyright (c) 2006--2007 by Ben Klemens. Licensed under the modified GNU GPL v2; see COPYING and COPYING2. */
+
+@@ -64,21 +64,24 @@
+ }
+
+ int main(int argc, char **argv){
+- char c, *q = NULL,
++ char c, *q = NULL,
+ *d = NULL,
+ *outfile = NULL;
+ int sf = 0,
+ no_plot = 0;
+
+- const char* msg= "%s [opts] dbname query\n\n"
++ const char* msg= "Usage: %s [opts] dbname query\n"
++"\n"
+ "Runs a query, and pipes the output directly to gnuplot. Use -f to dump to stdout or a file.\n"
+-"-d\tdatabase to use\t\t\t\t\tmandatory \n"
+-"-q\tquery to run\t\t\t\t\tmandatory (or use -Q)\n"
+-"-Q\tfile from which to read the query\t\t\n"
+-"-n\tno plot: just run the query and display results to stdout\t\t\n"
+-"-t\tplot type (points, bars, ...)\t\t\tdefault=\"lines\"\n"
+-"-H\tplot histogram with this many bins (e.g., -H100). To let the system auto-select bin sizes, use -H0 .\n"
+-"-f\tfile to dump to. If -f- then use stdout.\tdefault=pipe to Gnuplot\n";
++" -d\tdatabase to use (mandatory)\n"
++" -q\tquery to run (mandatory or use -Q)\n"
++" -Q\tfile from which to read the query\t\t\n"
++" -n\tno plot: just run the query and display results to stdout\t\t\n"
++" -t\tplot type (points, bars, ...) (default: \"lines\")\n"
++" -H\tplot histogram with this many bins (e.g., -H100) (to let the system auto-select bin sizes, use -H0)\n"
++" -f\tfile to dump to. If -f- then use stdout (default: pipe to Gnuplot)\n"
++" -h\tdisplay this help and exit\n"
++"\n";
+
+ Apop_stopif(argc<2, return 1, 0, msg, argv[0]);
+ while ((c = getopt (argc, argv, "ad:f:hH:nQ:q:st:-")) != -1)
+@@ -88,7 +91,7 @@
+ } else if (c=='H'){
+ histoplotting = 1;
+ histobins = atoi(optarg);
+- }
++ }
+ else if (c=='h'||c=='-') {
+ printf(msg, argv[0]);
+ return 0;
+@@ -104,7 +107,7 @@
+ q = argv[optind+1];
+ } else if (optind == argc-1)
+ q = argv[optind];
+-
++
+ Apop_stopif(!q, return 1, 0, "I need a query specified with -q.\n");
+
+ if (!plot_type) plot_type = strdup("lines");
+--- a/cmd/apop_db_to_crosstab.c
++++ b/cmd/apop_db_to_crosstab.c
+@@ -8,16 +8,17 @@
+
+ int main(int argc, char **argv){
+ char c, verbose=0;
+- char const *msg="%s [opts] dbname table_name rows columns data\n\n"
+- "A command-line wrapper for the apop_db_to_crosstab function.\n"
+- "See Apophenia's online documentation for that function for details and tricks.\n"
+- "-d\tdelimiter\t\tdefault=<tab>\n"
+- "-v\tverbose: prints status info on stderr\n"
+- "-v -v\textra verbose: also print queries executed on stderr\n";
++ char const *msg="Usage: %s [opts] dbname table_name rows columns data\n"
++"\n"
++"A command-line wrapper for the apop_db_to_crosstab function.\n"
++"See Apophenia's online documentation for that function for details and tricks.\n"
++" -d\tdelimiter (default: <tab>)\n"
++" -v\tverbose: prints status info on stderr\n"
++" -v -v\tvery verbose: also print queries executed on stderr\n"
++" -h\tdisplay this help and exit\n"
++"\n";
+
+- Apop_stopif(argc<5, return 1, 0, msg, argv[0]);
+-
+- apop_opts.verbose=0; //so don't print queries until -v -v.
++ apop_opts.verbose=0; //so don't print queries until -v -v.
+
+ while ((c = getopt (argc, argv, "d:f:hv-")) != -1)
+ if (c=='d') strcpy(apop_opts.output_delimiter,optarg);
+@@ -33,6 +34,6 @@
+ argv[optind], argv[optind +1], argv[optind+2], argv[optind+3], argv[optind+4]);
+ }
+ apop_db_open(argv[optind]);
+- apop_data *m = apop_db_to_crosstab(argv[optind +1], argv[optind+2], argv[optind+3], argv[optind+4]);
++ apop_data *m = apop_db_to_crosstab(argv[optind +1], argv[optind+2], argv[optind+3], argv[optind+4]);
+ apop_data_print(m);
+ }
+--- a/cmd/apop_text_to_db.c
++++ b/cmd/apop_text_to_db.c
+@@ -25,28 +25,29 @@
+ tab_exists_check = 0;
+ char **field_names = NULL;
+
+- Asprintf(&msg, "%s [-d delimiters] text_file table_name dbname\n"
+- "e.g.: %s -d\",|\" infile.txt a_table info.db\n"
++ Asprintf(&msg, "Usage: %s [-d delimiters] text_file table_name dbname\n"
++"\n"
+ "If the input text file name is a single dash, -, then read from STDIN.\n"
+ "Input must be plain ASCII or UTF-8.\n"
+-"-d\t\tThe single-character delimiters to use, e.g., -d \" ,\" or -d \"\\t\" (which you \n"
+-"\t\t\twill almost certainly have to write as -d \"\\\\t\"). Default: \"|,\\t\", meaning \n"
+-"\t\t\tthat any of a pipe, comma, or tab will delimit separate entries\n"
+-"-nc\t\tData does not include column names\n"
+-"-n regex\t\tCase-insensitive regular expression indicating Null values. Default: NaN \n"
+-"-m\t\tUse a mysql database (default: SQLite)\n"
+-"-f\t\tfixed width field ends: -f\"3,8,12,17\" (first char is one, not zero)\n"
+-"-u\t\tmysql username\n"
+-"-p\t\tmysql password\n"
+-"-r\t\tData includes row names\n"
+-"-v\t\tVerbose\n"
+-"-N\t\tA comma-separated list of column names: -N\"apple,banana,carrot,durian\"\n"
+-"-en\t\tIf table exists, do nothing; exit.\n"
+-"-ed\t\tIf table exists, retain the table, delete all data, refill with the new data (i.e., call 'delete * from your_table').\n"
+-"-eo\t\tIf table exists, overwrite the table from scratch; deleting the previous table entirely.\n"
+-"-ea\t\tIf table exists, append new data to the existing table.\n"
+-"-h\t\tPrint this help\n\n"
+-, argv[0], argv[0]);
++" -d\t\tthe single-character delimiters to use, e.g., -d \" ,\" or -d \"\\t\" (which you \n"
++ " \t\t\twill almost certainly have to write as -d \"\\\\t\") (default: \"|,\\t\", meaning \n"
++ " \t\t\tthat any of a pipe, comma, or tab will delimit separate entries)\n"
++" -nc\t\tdata does not include column names\n"
++" -n regex\t\tcase-insensitive regular expression indicating Null values (default: NaN)\n"
++" -m\t\tuse a MySQL database (default: SQLite)\n"
++" -f\t\tfixed width field ends: -f\"3,8,12,17\" (first char is one, not zero)\n"
++" -u\t\tmysql username\n"
++" -p\t\tmysql password\n"
++" -r\t\tdata includes row names\n"
++" -v\t\tverbosity\n"
++" -N\t\ta comma-separated list of column names: -N\"apple,banana,carrot,durian\"\n"
++" -en\t\tif table exists, do nothing and exit\n"
++" -ed\t\tif table exists, retain the table, delete all data, refill with the new data (i.e., call 'delete * from your_table')\n"
++" -eo\t\tif table exists, overwrite the table from scratch (deleting the previous table entirely)\n"
++" -ea\t\tif table exists, append new data to the existing table\n"
++" -h\t\tdisplay this help and exit\n"
++"\n"
++, argv[0]);
+ int * field_list = NULL;
+ char if_exists = 'n';
+
diff --git a/debian/patches/upstream-doxygen-typo.patch b/debian/patches/upstream-doxygen-typo.patch
new file mode 100644
index 0000000..f92b143
--- /dev/null
+++ b/debian/patches/upstream-doxygen-typo.patch
@@ -0,0 +1,86 @@
+Description: Typographic correction in Doxygen comments
+ Meant to be reported to the upstream maintainer.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- a/apop_sort.c
++++ b/apop_sort.c
+@@ -137,7 +137,7 @@
+
+ A few examples:
+
+-\include "../tests/sort_example.c"
++\include sort_example.c
+
+ \li This function uses the \ref designated syntax for inputs.
+ */
+--- a/docs/documentation.h
++++ b/docs/documentation.h
+@@ -24,24 +24,23 @@
+ \li t-tests, F-tests, et cetera
+ \li Several optimization methods available for your own new models
+ \li It does <em>not</em> re-implement basic matrix operations or build yet another database
+-engine. Instead, it builds upon the excellent <a href="http://sources.redhat.com/gsl/">GNU
++engine. Instead, it builds upon the excellent <a href="https://www.gnu.org/software/gsl/">GNU
+ Scientific</a> and <a href="http://www.sqlite.org/">SQLite</a> libraries. MySQL/mariaDB is also supported.
+
+ For the full list, click the <a href="globals.html">index</a> link from the header.
+
+-<h5><a href="https://github.com/b-k/Apophenia/archive/pkg.zip">Download Apophenia here</a>.</h5>
++<h5><a href="https://github.com/b-k/apophenia/archive/pkg.zip">Download Apophenia here</a>.</h5>
+
+ Most users will just want to download the latest packaged version linked from the <a
+-href="https://github.com/b-k/Apophenia/archive/pkg.zip">Download
+-Apophenia here</a> header.
++href="https://github.com/b-k/apophenia/archive/pkg.zip">Download Apophenia here</a> header.
+
+ Those who would like to work on a cutting-edge copy of the source code
+ can get the latest version by cutting and pasting the following onto
+ the command line. If you follow this route, be sure to read the development README in the
+-<tt>Apophenia</tt> directory this command will create.
++<tt>apophenia</tt> directory this command will create.
+
+ \code
+-git clone https://github.com/b-k/Apophenia.git
++git clone https://github.com/b-k/apophenia.git
+ \endcode
+
+ <!--git clone git://apophenia.git.sourceforge.net/gitroot/apophenia/apophenia
+@@ -66,7 +65,7 @@
+ Algebraic System of Statistical Models</em></a> (PDF) discusses some of the theoretical
+ structures underlying the library.
+
+-There is a <a href="https://github.com/b-k/Apophenia/wiki">wiki</a> with some convenience
++There is a <a href="https://github.com/b-k/apophenia/wiki">wiki</a> with some convenience
+ functions, tips, and so on.
+
+ <h5>Notable features</h5>
+@@ -133,7 +132,7 @@
+ wrapper</a> which you could expand upon.
+
+ If you're interested, <a href="mailto:fluffmail at f-m.fm">write to the maintainer</a> (Ben Klemens), or join the
+-<a href="https://github.com/b-k/Apophenia">GitHub</a> project.
++<a href="https://github.com/b-k/apophenia">GitHub</a> project.
+ */
+
+ /** \page eg Some examples
+@@ -182,15 +181,15 @@
+ sudo apt-get install make gcc libgsl0-dev libsqlite3-dev
+ \endcode
+
+-or
++or
+
+ \code
+ sudo yum install make gcc gsl-devel libsqlite3x-devel
+ \endcode
+
+-\li <a href="https://github.com/b-k/Apophenia/archive/pkg.zip">Download Apophenia here</a>.
++\li <a href="https://github.com/b-k/apophenia/archive/pkg.zip">Download Apophenia here</a>.
+
+-\li Once you have the library downloaded, compile it using
++\li Once you have the library downloaded, compile it using
+
+ \code
+ tar xvzf apop*tgz && cd apophenia-0.999
diff --git a/debian/patches/upstream-error-format_security.patch b/debian/patches/upstream-error-format_security.patch
new file mode 100644
index 0000000..4d2c90f
--- /dev/null
+++ b/debian/patches/upstream-error-format_security.patch
@@ -0,0 +1,25 @@
+Description: silence format-security gcc warnings
+ Silence format-security wanings as emmitted by GGC;
+ this brute force but localized silencing has been
+ sumitted to the upstream maintainer.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- a/tests/error_test.c
++++ b/tests/error_test.c
+@@ -16,10 +16,13 @@
+ */
+ char errorbuff[10000];
+
+-void check_log(char*fn_to_check, char*msg){
++void check_log(char *fn_to_check, char *msg){
+ #ifdef HAVE_FMEMOPEN
+ fflush(NULL);
++#pragma GCC diagnostic push
++#pragma GCC diagnostic warning "-Wformat-security"
+ Apop_stopif (!apop_regex(errorbuff, fn_to_check), abort(), 0, msg);
++#pragma GCC diagnostic pop
+ #endif
+ }
+
diff --git a/debian/patches/upstream-rationalization-autotools.patch b/debian/patches/upstream-rationalization-autotools.patch
new file mode 100644
index 0000000..8244a5e
--- /dev/null
+++ b/debian/patches/upstream-rationalization-autotools.patch
@@ -0,0 +1,4269 @@
+Description: rationalization -- autotools machinery
+ In order to ease future maintenance on both side, the upstream
+ autotools machinery is revisited with respect to general Linux
+ customs (read non Debian centric customs) and the original scheme.
+ Discusion has been initiated with the upstrema maintainer to step
+ further.
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,85 +1,103 @@
+-AM_CFLAGS = -g -Wall -O3 $(SQLITE_CFLAGS) $(MYSQL_CFLAGS) $(OPENMP_CFLAGS)
+-AM_LDFLAGS = $(SQLITE_LDFLAGS) $(OPENMP_CFLAGS) $(MYSQL_LDFLAGS)
+-CC = $(PTHREAD_CC)
+-ACLOCAL_AMFLAGS=-I m4
++ACLOCAL_AMFLAGS = -I m4
+
+-lib_LTLIBRARIES = libapophenia.la
+-libapophenia_la_SOURCES = \
+- apop_arms.c apop_asst.c apop_bootstrap.c apop_conversions.c \
+- apop_data.c apop_db.c apop_fexact.c apop_hist.c \
+- apop_linear_algebra.c apop_linear_constraint.c apop_mapply.c \
+- apop_mcmc.c apop_missing_data.c apop_mle.c apop_model.c \
+- apop_name.c apop_output.c apop_rake.c \
+- apop_regression.c apop_settings.c apop_smoothing.c apop_sort.c \
+- apop_stats.c apop_tests.c apop_update.c apop_vtables.c \
+- asprintf.c \
+- transform/apop_dcompose.c \
+- transform/apop_dconstrain.c transform/apop_fix_params.c \
+- transform/apop_coordinate_transform.c \
+- transform/apop_mixture.c transform/apop_stack.c \
+- model/apop_bernoulli.c model/apop_beta.c \
+- model/apop_dirichlet.c \
+- model/apop_exponential.c model/apop_gamma.c \
+- model/apop_histogram.c model/apop_loess.c \
+- model/apop_multinomial.c model/apop_multivariate_normal.c \
+- model/apop_normal.c model/apop_ols.c \
+- model/apop_pmf.c model/apop_poisson.c \
+- model/apop_probit.c model/apop_t.c \
+- model/apop_uniform.c model/apop_wishart.c \
+- model/apop_yule.c model/apop_zipf.c
++AUTOMAKE_OPTIONS = \
++ dist-xz \
++ dist-bzip2 \
++ dist-zip
+
+-include_HEADERS = apop.h
++AM_CFLAGS = -g -Wall -O3
+
+-pkgconfig_DATA= apophenia.pc
+-pkgconfigdir = `pkg-config --variable pc_path pkg-config | cut -f1 -d:`
++## Library versioning (C:R:A == current:revision:age)
++LIBAPOPHENIA_LT_VERSION = 0:0:0
++
++SUBDIRS = transform model . cmd tests docs eg
+
+-SUBDIRS=. tests
+
+-#The programs
+-bin_PROGRAMS = apop_text_to_db apop_db_to_crosstab apop_plot_query
+-apop_text_to_db_SOURCES = cmd/apop_text_to_db.c
+-apop_db_to_crosstab_SOURCES = cmd/apop_db_to_crosstab.c
+-apop_plot_query_SOURCES = cmd/apop_plot_query.c
++include_HEADERS = apop.h
+
+-apop_text_to_db_LDADD = libapophenia.la
+-apop_db_to_crosstab_LDADD = libapophenia.la
+-apop_plot_query_LDADD = libapophenia.la
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA= apophenia.pc
+
+-VPATH= @srcdir@
++lib_LTLIBRARIES = libapophenia.la
+
+-EXTRA_DIST = docs/doxyconfig $(srcdir)/docs/*.png $(srcdir)/docs/*.gif \
+- $(srcdir)/docs/*.js \
+- docs/edit_group $(srcdir)/docs/*.html docs/typical.css \
+- docs/make_model_doc.awk docs/documentation.h rpm.spec \
+- eg apop_db_mysql.c apop_db_sqlite.c \
+- apop_internal.h COPYING2 apophenia.pc
++libapophenia_la_LD_VERSION_SCRIPT=
++if HAVE_LD_VERSION_SCRIPT
++libapophenia_la_LD_VERSION_SCRIPT+= -Wl,--version-script=$(top_srcdir)/apophenia.map
++endif
++
++SUBLIBS = \
++ libapopkernel.la \
++ transform/libapoptransform.la \
++ model/libapopmodel.la
++
++libapophenia_la_SOURCES = \
++ asprintf.c
+
+-DISTCLEANFILES = apophenia.pc* apophenia-uninstalled.pc apophenia-uninstalled.sh tests/*dat* tests/printing_sample 1
++noinst_LTLIBRARIES = libapopkernel.la
+
+-%.c: %.m4.c
+- m4 -P prep_variadics.m4 $< > $@
++noinst_HEADERS = apop_internal.h
+
+-%.h: %.m4.h
+- m4 -P prep_variadics.m4 $< > $@
++libapopkernel_la_SOURCES = \
++ apop_arms.c \
++ apop_asst.c \
++ apop_bootstrap.c \
++ apop_conversions.c \
++ apop_data.c \
++ apop_db.c \
++ apop_fexact.c \
++ apop_hist.c \
++ apop_linear_algebra.c \
++ apop_linear_constraint.c \
++ apop_mapply.c \
++ apop_mcmc.c \
++ apop_missing_data.c \
++ apop_mle.c apop_model.c \
++ apop_name.c \
++ apop_output.c \
++ apop_rake.c \
++ apop_regression.c \
++ apop_settings.c \
++ apop_smoothing.c \
++ apop_sort.c \
++ apop_stats.c \
++ apop_tests.c \
++ apop_update.c \
++ apop_vtables.c
++
++apop_db_INCLUDES = \
++ apop_db_mysql.c \
++ apop_db_sqlite.c
++
++apop_db.c: $(apop_db_INCLUDES)
++
++libapopkernel_la_CFLAGS = \
++ $(PTHREAD_CFLAGS) \
++ $(OPENMP_CFLAGS) \
++ $(MYSQL_CFLAGS) \
++ $(SQLITE3_CFLAGS) \
++ $(GSL_CFLAGS)
++
++libapophenia_la_LDFLAGS = \
++ -version-info $(LIBAPOPHENIA_LT_VERSION) \
++ $(libapophenia_la_LD_VERSION_SCRIPT)
++
++libapophenia_la_LIBADD = \
++ $(SUBLIBS) \
++ $(MYSQL_LDFLAGS) \
++ $(SQLITE3_LDFLAGS) \
++ $(GSL_LIBS) \
++ $(PTHREAD_LIBS) \
++ $(LIBM)
++
++EXTRA_DIST = \
++ COPYING2 \
++ rpm.spec \
++ apophenia.pc.in \
++ apophenia.map
+
+-#The Doxygen documentation, which you'll have to call yourself (via make doc).
++EXTRA_DIST += \
++ $(apop_db_INCLUDES)
+
++## compatibility
+ doc:
+- -rm tests/apophenia/*h
+- cat model/*.c transform/*.c | awk -f docs/make_model_doc.awk > docs/model_doc.h
+- doxygen docs/doxyconfig
+- cp docs/flake.gif docs/search.gif docs/right.png docs/down.png html/
+- @sed -i -e 's|Outlineheader \([^ ]*\)\(.*\)</p>|<h2><a class="anchor" name="\1"><div class="trigger" onClick="showBranch('\''\1d'\'');swapFolder('\''\1f'\'')"><img src="right.png" border="0" id="\1f" alt="pip">\2</div></a></h2><div class="branch" id="\1d">|' \
+--e 's|endofdiv</p>|</div>|' \
+--e 's|ALLBUTTON|<span class="trigger" onClick="showAll();"<a>Expand all </a></span> \| <span class="trigger" onClick="closeAll();"<a>Collapse all </a></span>|' html/index.html html/outline.html
+- @sed -i -e '/index_x/s/- x -/ /' -e '/index_a/s/- a -/ /' -e '/Here is a list of all/d' -e '/<span>[a-z]<\/span><\/a><\/li>/d' html/globals.html
+- @sed -i -e '/div class="contents"/aSee also the <a class="el" href="group__models.html">models</a> and <a class="el" href="group__settings.html">settings</a> pages.' html/globals.html
+- @sed -i 's|<td width="100%"></td>||g' html/*html
+- @sed -i -f docs/edit_group html/group__models.html
+- cp docs/*js html/
+- sudo cp man/man3/* /usr/share/man/man3/
+-
+-install-data-local:
+- @echo
+- @echo "OK. If you'd like to generate documentation via Doxygen, run make doc; to test, run make check."
+- @echo
++ -$(MAKE) -C docs doc
+--- a/tests/Makefile.am
++++ b/tests/Makefile.am
+@@ -1,20 +1,83 @@
+-check_PROGRAMS= db_tests distribution_tests error_test nist_tests rake_test sort_example test_apop update_via_rng \
+-../eg/apop_map_row ../eg/binning ../eg/dconstrain ../eg/draw_to_db ../eg/db_fns ../eg/dot_products \
+-../eg/fake_logit ../eg/fix_params ../eg/hills2 ../eg/iv ../eg/jacobian ../eg/ks_tests ../eg/normalizations \
+-../eg/parameterization ../eg/pmf_test ../eg/simple_subsets ../eg/some_cdfs ../eg/stack_models \
+-../eg/test_distances ../eg/test_fisher ../eg/test_harmonic ../eg/test_kl_divergence \
+-../eg/test_pruning ../eg/test_ranks ../eg/test_regex ../eg/test_updating
+-
+-TESTS=utilities_test $(check_PROGRAMS)
+-
+-LDADD=../libapophenia.la
+-AM_CFLAGS = -DTesting $(CFLAGS) -DDatadir=\"$(srcdir)/\" -I$(srcdir) -I$(srcdir)/..
+-
+-EXTRA_DIST = utilities_test Readme data numacc4.dat pontius.dat amash_vote_analysis.csv faith.data test_data test_data2 \
+- data-mixed test_data_nans wampler1.dat printing_sample test_data_fixed_width sort_tests.c
+-
+-
+-AM_TESTS_ENVIRONMENT = for i in $(EXTRA_DIST); do \
+- if [ ! -e $$i ]; then \
+- cp $(srcdir)/$$i .; \
+- fi; done;
++check_PROGRAMS= \
++ db_tests \
++ distribution_tests \
++ error_test \
++ nist_tests \
++ rake_test \
++ sort_example \
++ test_apop \
++ update_via_rng \
++ $(top_builddir)/eg/apop_map_row \
++ $(top_builddir)/eg/binning \
++ $(top_builddir)/eg/dconstrain \
++ $(top_builddir)/eg/draw_to_db \
++ $(top_builddir)/eg/db_fns \
++ $(top_builddir)/eg/dot_products \
++ $(top_builddir)/eg/fake_logit \
++ $(top_builddir)/eg/fix_params \
++ $(top_builddir)/eg/hills2 \
++ $(top_builddir)/eg/iv \
++ $(top_builddir)/eg/jacobian \
++ $(top_builddir)/eg/ks_tests \
++ $(top_builddir)/eg/normalizations \
++ $(top_builddir)/eg/parameterization \
++ $(top_builddir)/eg/pmf_test \
++ $(top_builddir)/eg/simple_subsets \
++ $(top_builddir)/eg/some_cdfs \
++ $(top_builddir)/eg/stack_models \
++ $(top_builddir)/eg/test_distances \
++ $(top_builddir)/eg/test_fisher \
++ $(top_builddir)/eg/test_harmonic \
++ $(top_builddir)/eg/test_kl_divergence \
++ $(top_builddir)/eg/test_pruning \
++ $(top_builddir)/eg/test_ranks \
++ $(top_builddir)/eg/test_regex \
++ $(top_builddir)/eg/test_updating
++
++TESTS = \
++ utilities_test \
++ $(check_PROGRAMS)
++
++AM_CFLAGS = \
++ -DTesting \
++ -DDatadir=\"$(top_srcdir)/tests/\" \
++ -I$(top_srcdir)/tests \
++ -I$(top_srcdir) \
++ $(GSL_CFLAGS)
++
++AM_LDFLAGS = \
++ $(top_builddir)/libapophenia.la \
++ $(GSL_LIBS)
++
++DATA_DIST = \
++ data \
++ data-mixed \
++ printing_sample \
++ test_data \
++ test_data2 \
++ test_data_nans\
++ test_data_fixed_width \
++ amash_vote_analysis.csv \
++ numacc4.dat \
++ pontius.dat \
++ wampler1.dat \
++ faith.data \
++ sort_tests.c
++
++EXTRA_DIST = \
++ Readme \
++ $(DATA_DIST)
++
++CLEANFILES = \
++ ff.db \
++ runs.db \
++ td.db \
++ draws-k \
++ draws-k2 \
++ draws-mvN \
++ draws-N \
++ draws-std_multinormal \
++ draws-std_normal \
++ the_data.txt \
++ print_test.out \
++ xxx
+--- a/configure.ac
++++ b/configure.ac
+@@ -3,39 +3,41 @@
+ m4_define([m4_apop_version], [m4_esyscmd_s(date +%Y%m%d)]) #will switch to this soon.
+
+ AC_PREREQ(2.60)
+-AC_INIT([apophenia], [0.999], [fluffmail at f-m.fm])
++AC_INIT([apophenia], [0.999a], [fluffmail at f-m.fm])
+ AM_SILENT_RULES([yes])
+ AC_CONFIG_SRCDIR([apop_arms.c])
+ AC_CONFIG_HEADER([config.h])
+ AC_CONFIG_MACRO_DIR([m4])
++AC_CONFIG_AUX_DIR([build-aux])
+ AM_INIT_AUTOMAKE
++AM_MAINTAINER_MODE
+
+ # The normal /usr/local default confused too many people
+-AC_PREFIX_DEFAULT([/usr])
++##AC_PREFIX_DEFAULT([/usr])
+
+-# Windows:
++# libtool:
+ LT_INIT
+
++# check linker script support
++gl_LD_VERSION_SCRIPT
++
+ # Checks for programs.
+ AC_PROG_CC
+ AC_PROG_CC_C99
+
++ACX_PTHREAD
++AC_OPENMP
++
+ # Checks for libraries.
+-AC_CHECK_LIB([m],[cos])
+-AC_CHECK_LIB([gslcblas],[cblas_dgemm])
+-AC_CHECK_LIB([gsl],[gsl_blas_dgemm])
+-#AC_CHECK_LIB([mysqlclient], [mysql_query], , , [-L/usr/lib/mysql -lz])
+-AC_CHECK_LIB([sqlite3], [sqlite3_exec])
+-
+-AC_CHECK_HEADER([gsl/gsl_matrix.h], , [AC_MSG_ERROR(
+- [Couldn't find the GSL header files (I searched for <gsl/gsl_matrix.h> on the include path). \
+-If you are using a package manager, don't forget to install the libgsl-devel package, as well as \
+-libgsl itself (and the same for SQLite3).])])
+-
+-AC_CHECK_HEADER([sqlite3.h], , [AC_MSG_ERROR(
+- [Couldn't find the SQLite3 header file, sqlite3.h, on the include path. \
+-If you are using a package manager, don't forget to install the libsqlite3-devel \
+-package, as well as libsqlite3 itself.])])
++## math library
++LT_LIB_M
++## GNU Scientific Library (GSL)
++AX_PATH_GSL([1.16.0],[],[AC_MSG_ERROR(could not find required version of GSL)])
++## DataBase system libraries
++#### MySQL library
++AX_LIB_MYSQL
++#### SQLite3 library
++AX_LIB_SQLITE3
+
+ # Checks for header files.
+ AC_FUNC_ALLOCA
+@@ -56,48 +58,27 @@
+ AC_FUNC_STRTOD
+ AC_CHECK_FUNCS([floor memset pow regcomp sqrt strcasecmp asprintf])
+
+-#Check for database systems, then export results to automake
+-AX_LIB_MYSQL
+-AX_LIB_SQLITE3
+-AM_CONDITIONAL([HAVE_MYSQL], [test x$HAVE_MYSQL = xtrue])
+-
+-
+-PACKAGE_NAME=apophenia
+-
+-ACX_PTHREAD
+-AC_OPENMP
+-
+-AC_CONFIG_FILES([Makefile tests/Makefile apophenia.pc])
++# Checks for tests tools
++AC_PATH_PROGS([BC],[bc],[/usr/bin/bc])
++AC_PATH_PROGS([SQLITE3],[sqlite3],[/usr/bin/sqlite3])
++
++
++AC_CONFIG_FILES([
++ apophenia.pc
++ Makefile
++ transform/Makefile
++ model/Makefile
++ cmd/Makefile
++ tests/utilities_test
++ tests/Makefile
++ docs/doxygen.conf
++ docs/Makefile
++ eg/Makefile
++ ],
++ [
++ chmod a+x tests/utilities_test
++ ])
+ AC_OUTPUT
+
+-echo \
+-"-----------------------------------------------------------
+-
+-Thanks for trying ${PACKAGE_NAME} v.${PACKAGE_VERSION}.
+-
+-Root for the install: '${prefix}'.
+- Compiler: '${CC} ${CFLAGS} ${CPPFLAGS}'
+-"
+-echo $mysql_message
+-
+-echo \
+-"
+-Now type 'make @<:@<target>@:>@'
+- where the optional <target> is:
+- all - build all binaries
+- check - test the installation
+- install - install everything [e.g., sudo make install]
+- doc - generate documentation via doxygen
+-
+-------------------------------------------------------------"
+-
+-#mySQL claims these vars as its own.
+-sed '$a\
+-\#undef PACKAGE \
+-\#undef PACKAGE_BUGREPORT \
+-\#undef PACKAGE_NAME \
+-\#undef PACKAGE_STRING \
+-\#undef PACKAGE_TARNAME \
+-\#undef PACKAGE_VERSION \
+-\#undef VERSION' < config.h > conftmp
+-mv conftmp config.h
++##
++## eof
+--- /dev/null
++++ b/docs/Makefile.am
+@@ -0,0 +1,58 @@
++
++#The Doxygen documentation, which you'll have to call yourself (via make doc).
++
++default:
++
++## adhoc
++html man: doc
++
++apophenia_CSOURCES = \
++ $(wildcard $(top_srcdir)/model/*.c) \
++ $(wildcard $(top_srcdir)/transform/*.c)
++
++apophenia_IMAGES = \
++ flake.gif \
++ search.gif \
++ right.png \
++ down.png
++
++apophenia_IMAGES_EXTRA = \
++ triangle.png \
++ model.png
++
++apophenia_JS = \
++ tree.js
++
++model_doc.h: $(apophenia_CSOURCES)
++ cat $^ | awk -f make_model_doc.awk > $@
++
++doc: documentation.h model_doc.h $(apophenia_IMAGES) $(apophenia_JS)
++ doxygen doxygen.conf
++ cp $(apophenia_IMAGES) $(apophenia_JS) html/
++ sed -i -f edit_outline.sed html/index.html html/outline.html
++ sed -i -f edit_globals.sed html/globals.html
++ sed -i -f edit_group.sed html/group__models.html
++ sed -i -f edit_width.sed html/*.html
++
++doc-clean:
++ -rm -rf html latex man
++
++CLEANFILES = \
++ missing_model_parts
++
++MAINTAINERCLEANFILES = \
++ model_doc.h \
++ doxygen.log
++
++maintainer-clean-local: doc-clean
++
++EXTRA_DIST = \
++ make_model_doc.awk \
++ $(apophenia_IMAGES) \
++ $(apophenia_IMAGES_EXTRA) \
++ $(apophenia_JS) \
++ edit_outline.sed edit_globals.sed edit_group.sed edit_width.sed \
++ apop_data_fig.html head.html foot.html \
++ typical.css \
++ documentation.h
++
+--- a/docs/edit_group
++++ /dev/null
+@@ -1,18 +0,0 @@
+-s/Enumeration Type Documentation/Model Documentation/
+-s/<h2>Enumerations/<h2>Models/
+-/<h2>Models/,/<h2>Functions/{
+- s/[{}]//
+- s/<br\/>$//
+- s/<li>enum/<li>apop_model/
+- s/.*>(Overview|Name|Input_format|Estimate_results|Predict|RNG|CDF|Exampe|Settings)_x[0-9].*x_//
+-}
+-s/<b>Enumerator: <\/b>//
+-s/<td class="memname">enum <a class="el"/<td class="memname">apop_model <a class="el"/
+-s/_x[0-9]*x_//g
+-s/model_specific/Methods are Default or Model-specific/g
+-s/[eE]stimate_results/Post-estimate/g
+-s/[iI]nput_format/Input format/g
+-s/[pP]arameter_format/Parameter format/g
+-#delete all between the two markers, but not the second marker
+-/name="enum-members"/,/name="func-members"/{/name="func-members"/!d}
+-/<div class="summary">/,/\#func-members/d
+--- /dev/null
++++ b/docs/edit_group.sed
+@@ -0,0 +1,18 @@
++s/Enumeration Type Documentation/Model Documentation/
++s/<h2>Enumerations/<h2>Models/
++/<h2>Models/,/<h2>Functions/{
++ s/[{}]//
++ s/<br\/>$//
++ s/<li>enum/<li>apop_model/
++ s/.*>(Overview|Name|Input_format|Estimate_results|Predict|RNG|CDF|Exampe|Settings)_x[0-9].*x_//
++}
++s/<b>Enumerator: <\/b>//
++s/<td class="memname">enum <a class="el"/<td class="memname">apop_model <a class="el"/
++s/_x[0-9]*x_//g
++s/model_specific/Methods are Default or Model-specific/g
++s/[eE]stimate_results/Post-estimate/g
++s/[iI]nput_format/Input format/g
++s/[pP]arameter_format/Parameter format/g
++#delete all between the two markers, but not the second marker
++/name="enum-members"/,/name="func-members"/{/name="func-members"/!d}
++/<div class="summary">/,/\#func-members/d
+--- /dev/null
++++ b/docs/edit_width.sed
+@@ -0,0 +1 @@
++s|<td width="100%"></td>||g
+--- a/docs/doxyconfig
++++ /dev/null
+@@ -1,1350 +0,0 @@
+-# Doxyfile 1.5.5
+-
+-# This file describes the settings to be used by the documentation system
+-# doxygen (www.doxygen.org) for a project
+-#
+-# All text after a hash (#) is considered a comment and will be ignored
+-# The format is:
+-# TAG = value [value, ...]
+-# For lists items can also be appended using:
+-# TAG += value [value, ...]
+-# Values that contain spaces should be placed between quotes (" ")
+-
+-#---------------------------------------------------------------------------
+-# Project related configuration options
+-#---------------------------------------------------------------------------
+-
+-# This tag specifies the encoding used for all characters in the config file
+-# that follow. The default is UTF-8 which is also the encoding used for all
+-# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+-# iconv built into libc) for the transcoding. See
+-# http://www.gnu.org/software/libiconv for the list of possible encodings.
+-
+-DOXYFILE_ENCODING = UTF-8
+-
+-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+-# by quotes) that should identify the project.
+-
+-PROJECT_NAME = Apophenia
+-
+-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+-# This could be handy for archiving the generated documentation or
+-# if some version control system is used.
+-
+-PROJECT_NUMBER =
+-
+-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+-# base path where the generated documentation will be put.
+-# If a relative path is entered, it will be relative to the location
+-# where doxygen was started. If left blank the current directory will be used.
+-
+-OUTPUT_DIRECTORY =
+-
+-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+-# 4096 sub-directories (in 2 levels) under the output directory of each output
+-# format and will distribute the generated files over these directories.
+-# Enabling this option can be useful when feeding doxygen a huge amount of
+-# source files, where putting all generated files in the same directory would
+-# otherwise cause performance problems for the file system.
+-
+-CREATE_SUBDIRS = NO
+-
+-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+-# documentation generated by doxygen is written. Doxygen will use this
+-# information to generate all constant output in the proper language.
+-# The default language is English, other supported languages are:
+-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+-# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek,
+-# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages),
+-# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish,
+-# Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish,
+-# and Ukrainian.
+-
+-OUTPUT_LANGUAGE = English
+-
+-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+-# include brief member descriptions after the members that are listed in
+-# the file and class documentation (similar to JavaDoc).
+-# Set to NO to disable this.
+-
+-BRIEF_MEMBER_DESC = YES
+-
+-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+-# the brief description of a member or function before the detailed description.
+-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+-# brief descriptions will be completely suppressed.
+-
+-REPEAT_BRIEF = YES
+-
+-# This tag implements a quasi-intelligent brief description abbreviator
+-# that is used to form the text in various listings. Each string
+-# in this list, if found as the leading text of the brief description, will be
+-# stripped from the text and the result after processing the whole list, is
+-# used as the annotated text. Otherwise, the brief description is used as-is.
+-# If left blank, the following values are used ("$name" is automatically
+-# replaced with the name of the entity): "The $name class" "The $name widget"
+-# "The $name file" "is" "provides" "specifies" "contains"
+-# "represents" "a" "an" "the"
+-
+-ABBREVIATE_BRIEF =
+-
+-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+-# Doxygen will generate a detailed section even if there is only a brief
+-# description.
+-
+-ALWAYS_DETAILED_SEC = NO
+-
+-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+-# inherited members of a class in the documentation of that class as if those
+-# members were ordinary class members. Constructors, destructors and assignment
+-# operators of the base classes will not be shown.
+-
+-INLINE_INHERITED_MEMB = NO
+-
+-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+-# path before files name in the file list and in the header files. If set
+-# to NO the shortest path that makes the file name unique will be used.
+-
+-FULL_PATH_NAMES = YES
+-
+-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+-# can be used to strip a user-defined part of the path. Stripping is
+-# only done if one of the specified strings matches the left-hand part of
+-# the path. The tag can be used to show relative paths in the file list.
+-# If left blank the directory from which doxygen is run is used as the
+-# path to strip.
+-
+-STRIP_FROM_PATH =
+-
+-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+-# the path mentioned in the documentation of a class, which tells
+-# the reader which header file to include in order to use a class.
+-# If left blank only the name of the header file containing the class
+-# definition is used. Otherwise one should specify the include paths that
+-# are normally passed to the compiler using the -I flag.
+-
+-STRIP_FROM_INC_PATH =
+-
+-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+-# (but less readable) file names. This can be useful is your file systems
+-# doesn't support long names like on DOS, Mac, or CD-ROM.
+-
+-SHORT_NAMES = NO
+-
+-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+-# will interpret the first line (until the first dot) of a JavaDoc-style
+-# comment as the brief description. If set to NO, the JavaDoc
+-# comments will behave just like regular Qt-style comments
+-# (thus requiring an explicit @brief command for a brief description.)
+-
+-JAVADOC_AUTOBRIEF = NO
+-
+-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+-# interpret the first line (until the first dot) of a Qt-style
+-# comment as the brief description. If set to NO, the comments
+-# will behave just like regular Qt-style comments (thus requiring
+-# an explicit \brief command for a brief description.)
+-
+-QT_AUTOBRIEF = NO
+-
+-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+-# comments) as a brief description. This used to be the default behaviour.
+-# The new default is to treat a multi-line C++ comment block as a detailed
+-# description. Set this tag to YES if you prefer the old behaviour instead.
+-
+-MULTILINE_CPP_IS_BRIEF = NO
+-
+-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+-# member inherits the documentation from any documented member that it
+-# re-implements.
+-
+-INHERIT_DOCS = YES
+-
+-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+-# a new page for each member. If set to NO, the documentation of a member will
+-# be part of the file/class/namespace that contains it.
+-
+-SEPARATE_MEMBER_PAGES = NO
+-
+-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+-# Doxygen uses this value to replace tabs by spaces in code fragments.
+-
+-TAB_SIZE = 5
+-
+-# This tag can be used to specify a number of aliases that acts
+-# as commands in the documentation. An alias has the form "name=value".
+-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+-# put the command \sideeffect (or @sideeffect) in the documentation, which
+-# will result in a user-defined paragraph with heading "Side Effects:".
+-# You can put \n's in the value part of an alias to insert newlines.
+-
+-ALIASES =
+-
+-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+-# sources only. Doxygen will then generate output that is more tailored for C.
+-# For instance, some of the names that are used will be different. The list
+-# of all members will be omitted, etc.
+-
+-OPTIMIZE_OUTPUT_FOR_C = YES
+-
+-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+-# sources only. Doxygen will then generate output that is more tailored for
+-# Java. For instance, namespaces will be presented as packages, qualified
+-# scopes will look different, etc.
+-
+-OPTIMIZE_OUTPUT_JAVA = NO
+-
+-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+-# sources only. Doxygen will then generate output that is more tailored for
+-# Fortran.
+-
+-OPTIMIZE_FOR_FORTRAN = NO
+-
+-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+-# sources. Doxygen will then generate output that is tailored for
+-# VHDL.
+-
+-OPTIMIZE_OUTPUT_VHDL = NO
+-
+-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+-# to include (a tag file for) the STL sources as input, then you should
+-# set this tag to YES in order to let doxygen match functions declarations and
+-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+-# func(std::string) {}). This also make the inheritance and collaboration
+-# diagrams that involve STL classes more complete and accurate.
+-
+-BUILTIN_STL_SUPPORT = NO
+-
+-# If you use Microsoft's C++/CLI language, you should set this option to YES to
+-# enable parsing support.
+-
+-CPP_CLI_SUPPORT = NO
+-
+-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+-# Doxygen will parse them like normal C++ but will assume all classes use public
+-# instead of private inheritance when no explicit protection keyword is present.
+-
+-SIP_SUPPORT = NO
+-
+-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+-# tag is set to YES, then doxygen will reuse the documentation of the first
+-# member in the group (if any) for the other members of the group. By default
+-# all members of a group must be documented explicitly.
+-
+-DISTRIBUTE_GROUP_DOC = NO
+-
+-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+-# the same type (for instance a group of public functions) to be put as a
+-# subgroup of that type (e.g. under the Public Functions section). Set it to
+-# NO to prevent subgrouping. Alternatively, this can be done per class using
+-# the \nosubgrouping command.
+-
+-SUBGROUPING = YES
+-
+-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+-# is documented as struct, union, or enum with the name of the typedef. So
+-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+-# with name TypeT. When disabled the typedef will appear as a member of a file,
+-# namespace, or class. And the struct will be named TypeS. This can typically
+-# be useful for C code in case the coding convention dictates that all compound
+-# types are typedef'ed and only the typedef is referenced, never the tag name.
+-
+-TYPEDEF_HIDES_STRUCT = NO
+-
+-#---------------------------------------------------------------------------
+-# Build related configuration options
+-#---------------------------------------------------------------------------
+-
+-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+-# documentation are documented, even if no documentation was available.
+-# Private class members and static file members will be hidden unless
+-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+-
+-EXTRACT_ALL = NO
+-
+-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+-# will be included in the documentation.
+-
+-EXTRACT_PRIVATE = NO
+-
+-# If the EXTRACT_STATIC tag is set to YES all static members of a file
+-# will be included in the documentation.
+-
+-EXTRACT_STATIC = NO
+-
+-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+-# defined locally in source files will be included in the documentation.
+-# If set to NO only classes defined in header files are included.
+-
+-EXTRACT_LOCAL_CLASSES = YES
+-
+-# This flag is only useful for Objective-C code. When set to YES local
+-# methods, which are defined in the implementation section but not in
+-# the interface are included in the documentation.
+-# If set to NO (the default) only methods in the interface are included.
+-
+-EXTRACT_LOCAL_METHODS = NO
+-
+-# If this flag is set to YES, the members of anonymous namespaces will be
+-# extracted and appear in the documentation as a namespace called
+-# 'anonymous_namespace{file}', where file will be replaced with the base
+-# name of the file that contains the anonymous namespace. By default
+-# anonymous namespace are hidden.
+-
+-EXTRACT_ANON_NSPACES = NO
+-
+-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+-# undocumented members of documented classes, files or namespaces.
+-# If set to NO (the default) these members will be included in the
+-# various overviews, but no documentation section is generated.
+-# This option has no effect if EXTRACT_ALL is enabled.
+-
+-HIDE_UNDOC_MEMBERS = NO
+-
+-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+-# undocumented classes that are normally visible in the class hierarchy.
+-# If set to NO (the default) these classes will be included in the various
+-# overviews. This option has no effect if EXTRACT_ALL is enabled.
+-
+-HIDE_UNDOC_CLASSES = NO
+-
+-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+-# friend (class|struct|union) declarations.
+-# If set to NO (the default) these declarations will be included in the
+-# documentation.
+-
+-HIDE_FRIEND_COMPOUNDS = NO
+-
+-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+-# documentation blocks found inside the body of a function.
+-# If set to NO (the default) these blocks will be appended to the
+-# function's detailed documentation block.
+-
+-HIDE_IN_BODY_DOCS = NO
+-
+-# The INTERNAL_DOCS tag determines if documentation
+-# that is typed after a \internal command is included. If the tag is set
+-# to NO (the default) then the documentation will be excluded.
+-# Set it to YES to include the internal documentation.
+-
+-INTERNAL_DOCS = NO
+-
+-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+-# file names in lower-case letters. If set to YES upper-case letters are also
+-# allowed. This is useful if you have classes or files whose names only differ
+-# in case and if your file system supports case sensitive file names. Windows
+-# and Mac users are advised to set this option to NO.
+-
+-CASE_SENSE_NAMES = YES
+-
+-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+-# will show members with their full class and namespace scopes in the
+-# documentation. If set to YES the scope will be hidden.
+-
+-HIDE_SCOPE_NAMES = NO
+-
+-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+-# will put a list of the files that are included by a file in the documentation
+-# of that file.
+-
+-SHOW_INCLUDE_FILES = NO
+-
+-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+-# is inserted in the documentation for inline members.
+-
+-INLINE_INFO = YES
+-
+-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+-# will sort the (detailed) documentation of file and class members
+-# alphabetically by member name. If set to NO the members will appear in
+-# declaration order.
+-
+-SORT_MEMBER_DOCS = YES
+-
+-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+-# brief documentation of file, namespace and class members alphabetically
+-# by member name. If set to NO (the default) the members will appear in
+-# declaration order.
+-
+-SORT_BRIEF_DOCS = NO
+-
+-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+-# hierarchy of group names into alphabetical order. If set to NO (the default)
+-# the group names will appear in their defined order.
+-
+-SORT_GROUP_NAMES = NO
+-
+-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+-# sorted by fully-qualified names, including namespaces. If set to
+-# NO (the default), the class list will be sorted only by class name,
+-# not including the namespace part.
+-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+-# Note: This option applies only to the class list, not to the
+-# alphabetical list.
+-
+-SORT_BY_SCOPE_NAME = NO
+-
+-# The GENERATE_TODOLIST tag can be used to enable (YES) or
+-# disable (NO) the todo list. This list is created by putting \todo
+-# commands in the documentation.
+-
+-GENERATE_TODOLIST = YES
+-
+-# The GENERATE_TESTLIST tag can be used to enable (YES) or
+-# disable (NO) the test list. This list is created by putting \test
+-# commands in the documentation.
+-
+-GENERATE_TESTLIST = YES
+-
+-# The GENERATE_BUGLIST tag can be used to enable (YES) or
+-# disable (NO) the bug list. This list is created by putting \bug
+-# commands in the documentation.
+-
+-GENERATE_BUGLIST = YES
+-
+-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+-# disable (NO) the deprecated list. This list is created by putting
+-# \deprecated commands in the documentation.
+-
+-GENERATE_DEPRECATEDLIST= YES
+-
+-# The ENABLED_SECTIONS tag can be used to enable conditional
+-# documentation sections, marked by \if sectionname ... \endif.
+-
+-ENABLED_SECTIONS =
+-
+-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+-# the initial value of a variable or define consists of for it to appear in
+-# the documentation. If the initializer consists of more lines than specified
+-# here it will be hidden. Use a value of 0 to hide initializers completely.
+-# The appearance of the initializer of individual variables and defines in the
+-# documentation can be controlled using \showinitializer or \hideinitializer
+-# command in the documentation regardless of this setting.
+-
+-MAX_INITIALIZER_LINES = 30
+-
+-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+-# at the bottom of the documentation of classes and structs. If set to YES the
+-# list will mention the files that were used to generate the documentation.
+-
+-SHOW_USED_FILES = NO
+-
+-# If the sources in your project are distributed over multiple directories
+-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+-# in the documentation. The default is NO.
+-
+-SHOW_DIRECTORIES = NO
+-
+-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+-# doxygen should invoke to get the current version for each file (typically from
+-# the version control system). Doxygen will invoke the program by executing (via
+-# popen()) the command <command> <input-file>, where <command> is the value of
+-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+-# provided by doxygen. Whatever the program writes to standard output
+-# is used as the file version. See the manual for examples.
+-
+-FILE_VERSION_FILTER =
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to warning and progress messages
+-#---------------------------------------------------------------------------
+-
+-# The QUIET tag can be used to turn on/off the messages that are generated
+-# by doxygen. Possible values are YES and NO. If left blank NO is used.
+-
+-QUIET = YES
+-
+-# The WARNINGS tag can be used to turn on/off the warning messages that are
+-# generated by doxygen. Possible values are YES and NO. If left blank
+-# NO is used.
+-
+-WARNINGS = YES
+-
+-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+-# automatically be disabled.
+-
+-WARN_IF_UNDOCUMENTED = NO
+-
+-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+-# potential errors in the documentation, such as not documenting some
+-# parameters in a documented function, or documenting parameters that
+-# don't exist or using markup commands wrongly.
+-
+-WARN_IF_DOC_ERROR = YES
+-
+-# This WARN_NO_PARAMDOC option can be abled to get warnings for
+-# functions that are documented, but have no documentation for their parameters
+-# or return value. If set to NO (the default) doxygen will only warn about
+-# wrong or incomplete parameter documentation, but not about the absence of
+-# documentation.
+-
+-WARN_NO_PARAMDOC = NO
+-
+-# The WARN_FORMAT tag determines the format of the warning messages that
+-# doxygen can produce. The string should contain the $file, $line, and $text
+-# tags, which will be replaced by the file and line number from which the
+-# warning originated and the warning text. Optionally the format may contain
+-# $version, which will be replaced by the version of the file (if it could
+-# be obtained via FILE_VERSION_FILTER)
+-
+-WARN_FORMAT = "$file:$line: $text"
+-
+-# The WARN_LOGFILE tag can be used to specify a file to which warning
+-# and error messages should be written. If left blank the output is written
+-# to stderr.
+-
+-WARN_LOGFILE =
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the input files
+-#---------------------------------------------------------------------------
+-
+-# The INPUT tag can be used to specify the files and/or directories that contain
+-# documented source files. You may enter file names like "myfile.cpp" or
+-# directories like "/usr/src/myproject". Separate the files or directories
+-# with spaces.
+-
+-INPUT =
+-
+-# This tag can be used to specify the character encoding of the source files
+-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+-# also the default input encoding. Doxygen uses libiconv (or the iconv built
+-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+-# the list of possible encodings.
+-
+-INPUT_ENCODING = UTF-8
+-
+-# If the value of the INPUT tag contains directories, you can use the
+-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+-# and *.h) to filter out the source-files in the directories. If left
+-# blank the following patterns are tested:
+-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
+-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+-
+-FILE_PATTERNS =
+-
+-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+-# should be searched for input files as well. Possible values are YES and NO.
+-# If left blank NO is used.
+-
+-RECURSIVE = YES
+-
+-# The EXCLUDE tag can be used to specify files and/or directories that should
+-# excluded from the INPUT source files. This way you can easily exclude a
+-# subdirectory from a directory tree whose root is specified with the INPUT tag.
+-
+-EXCLUDE =
+-
+-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+-# directories that are symbolic links (a Unix filesystem feature) are excluded
+-# from the input.
+-
+-EXCLUDE_SYMLINKS = NO
+-
+-# If the value of the INPUT tag contains directories, you can use the
+-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+-# certain files from those directories. Note that the wildcards are matched
+-# against the file with absolute path, so to exclude all test directories
+-# for example use the pattern */test/*
+-
+-EXCLUDE_PATTERNS =
+-
+-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+-# (namespaces, classes, functions, etc.) that should be excluded from the
+-# output. The symbol name can be a fully qualified name, a word, or if the
+-# wildcard * is used, a substring. Examples: ANamespace, AClass,
+-# AClass::ANamespace, ANamespace::*Test
+-
+-EXCLUDE_SYMBOLS =
+-
+-# The EXAMPLE_PATH tag can be used to specify one or more files or
+-# directories that contain example code fragments that are included (see
+-# the \include command).
+-
+-#see recursive below
+-EXAMPLE_PATH = .
+-
+-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+-# and *.h) to filter out the source-files in the directories. If left
+-# blank all files are included.
+-
+-EXAMPLE_PATTERNS =
+-
+-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+-# searched for input files to be used with the \include or \dontinclude
+-# commands irrespective of the value of the RECURSIVE tag.
+-# Possible values are YES and NO. If left blank NO is used.
+-
+-EXAMPLE_RECURSIVE = YES
+-
+-# The IMAGE_PATH tag can be used to specify one or more files or
+-# directories that contain image that are included in the documentation (see
+-# the \image command).
+-
+-IMAGE_PATH = docs/
+-
+-# The INPUT_FILTER tag can be used to specify a program that doxygen should
+-# invoke to filter for each input file. Doxygen will invoke the filter program
+-# by executing (via popen()) the command <filter> <input-file>, where <filter>
+-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+-# input file. Doxygen will then use the output that the filter program writes
+-# to standard output. If FILTER_PATTERNS is specified, this tag will be
+-# ignored.
+-
+-INPUT_FILTER =
+-
+-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+-# basis. Doxygen will compare the file name with each pattern and apply the
+-# filter if there is a match. The filters are a list of the form:
+-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
+-# is applied to all files.
+-
+-FILTER_PATTERNS =
+-
+-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+-# INPUT_FILTER) will be used to filter the input files when producing source
+-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+-
+-FILTER_SOURCE_FILES = NO
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to source browsing
+-#---------------------------------------------------------------------------
+-
+-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+-# be generated. Documented entities will be cross-referenced with these sources.
+-# Note: To get rid of all source code in the generated output, make sure also
+-# VERBATIM_HEADERS is set to NO.
+-
+-SOURCE_BROWSER = NO
+-
+-# Setting the INLINE_SOURCES tag to YES will include the body
+-# of functions and classes directly in the documentation.
+-
+-INLINE_SOURCES = NO
+-
+-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+-# doxygen to hide any special comment blocks from generated source code
+-# fragments. Normal C and C++ comments will always remain visible.
+-
+-STRIP_CODE_COMMENTS = YES
+-
+-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
+-# then for each documented function all documented
+-# functions referencing it will be listed.
+-
+-REFERENCED_BY_RELATION = NO
+-
+-# If the REFERENCES_RELATION tag is set to YES (the default)
+-# then for each documented function all documented entities
+-# called/used by that function will be listed.
+-
+-REFERENCES_RELATION = NO
+-
+-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+-# link to the source code. Otherwise they will link to the documentstion.
+-
+-REFERENCES_LINK_SOURCE = YES
+-
+-# If the USE_HTAGS tag is set to YES then the references to source code
+-# will point to the HTML generated by the htags(1) tool instead of doxygen
+-# built-in source browser. The htags tool is part of GNU's global source
+-# tagging system (see http://www.gnu.org/software/global/global.html). You
+-# will need version 4.8.6 or higher.
+-
+-USE_HTAGS = NO
+-
+-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+-# will generate a verbatim copy of the header file for each class for
+-# which an include is specified. Set to NO to disable this.
+-
+-VERBATIM_HEADERS = YES
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the alphabetical class index
+-#---------------------------------------------------------------------------
+-
+-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+-# of all compounds will be generated. Enable this if the project
+-# contains a lot of classes, structs, unions or interfaces.
+-
+-ALPHABETICAL_INDEX = YES
+-
+-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+-# in which this list will be split (can be a number in the range [1..20])
+-
+-COLS_IN_ALPHA_INDEX = 3
+-
+-# In case all classes in a project start with a common prefix, all
+-# classes will be put under the same header in the alphabetical index.
+-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+-# should be ignored while generating the index headers.
+-
+-#IGNORE_PREFIX = apop_
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the HTML output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+-# generate HTML output.
+-
+-GENERATE_HTML = YES
+-
+-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+-# put in front of it. If left blank `html' will be used as the default path.
+-
+-HTML_OUTPUT = html
+-
+-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+-# doxygen will generate files with .html extension.
+-
+-HTML_FILE_EXTENSION = .html
+-
+-# The HTML_HEADER tag can be used to specify a personal HTML header for
+-# each generated HTML page. If it is left blank doxygen will generate a
+-# standard header.
+-
+-HTML_HEADER = docs/head.html
+-
+-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+-# each generated HTML page. If it is left blank doxygen will generate a
+-# standard footer.
+-
+-HTML_FOOTER = docs/foot.html
+-
+-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+-# style sheet that is used by each HTML page. It can be used to
+-# fine-tune the look of the HTML output. If the tag is left blank doxygen
+-# will generate a default style sheet. Note that doxygen will try to copy
+-# the style sheet file to the HTML output directory, so don't put your own
+-# stylesheet in the HTML output directory as well, or it will be erased!
+-
+-HTML_STYLESHEET = docs/typical.css
+-
+-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+-# files or namespaces will be aligned in HTML using tables. If set to
+-# NO a bullet list will be used.
+-
+-HTML_ALIGN_MEMBERS = NO
+-
+-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+-# will be generated that can be used as input for tools like the
+-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+-# of the generated HTML documentation.
+-
+-GENERATE_HTMLHELP = NO
+-
+-# If the GENERATE_DOCSET tag is set to YES, additional index files
+-# will be generated that can be used as input for Apple's Xcode 3
+-# integrated development environment, introduced with OSX 10.5 (Leopard).
+-# To create a documentation set, doxygen will generate a Makefile in the
+-# HTML output directory. Running make will produce the docset in that
+-# directory and running "make install" will install the docset in
+-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+-# it at startup.
+-
+-GENERATE_DOCSET = NO
+-
+-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+-# feed. A documentation feed provides an umbrella under which multiple
+-# documentation sets from a single provider (such as a company or product suite)
+-# can be grouped.
+-
+-DOCSET_FEEDNAME = "Doxygen generated docs"
+-
+-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+-# should uniquely identify the documentation set bundle. This should be a
+-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+-# will append .docset to the name.
+-
+-DOCSET_BUNDLE_ID = org.doxygen.Project
+-
+-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+-# documentation will contain sections that can be hidden and shown after the
+-# page has loaded. For this to work a browser that supports
+-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+-
+-HTML_DYNAMIC_SECTIONS = NO
+-
+-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+-# be used to specify the file name of the resulting .chm file. You
+-# can add a path in front of the file if the result should not be
+-# written to the html output directory.
+-
+-CHM_FILE =
+-
+-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+-# be used to specify the location (absolute path including file name) of
+-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+-# the HTML help compiler on the generated index.hhp.
+-
+-HHC_LOCATION =
+-
+-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+-# controls if a separate .chi index file is generated (YES) or that
+-# it should be included in the master .chm file (NO).
+-
+-GENERATE_CHI = NO
+-
+-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+-# controls whether a binary table of contents is generated (YES) or a
+-# normal table of contents (NO) in the .chm file.
+-
+-BINARY_TOC = NO
+-
+-# The TOC_EXPAND flag can be set to YES to add extra items for group members
+-# to the contents of the HTML help documentation and to the tree view.
+-
+-TOC_EXPAND = NO
+-
+-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+-# top of each HTML page. The value NO (the default) enables the index and
+-# the value YES disables it.
+-
+-DISABLE_INDEX = YES
+-
+-# This tag can be used to set the number of enum values (range [1..20])
+-# that doxygen will group on one line in the generated HTML documentation.
+-
+-ENUM_VALUES_PER_LINE = 4
+-
+-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
+-# generated containing a tree-like index structure (just like the one that
+-# is generated for HTML Help). For this to work a browser that supports
+-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
+-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
+-# probably better off using the HTML help feature.
+-
+-GENERATE_TREEVIEW = NO
+-
+-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+-# used to set the initial width (in pixels) of the frame in which the tree
+-# is shown.
+-
+-TREEVIEW_WIDTH = 250
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the LaTeX output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+-# generate Latex output.
+-
+-GENERATE_LATEX = YES
+-
+-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+-# put in front of it. If left blank `latex' will be used as the default path.
+-
+-LATEX_OUTPUT = latex
+-
+-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+-# invoked. If left blank `latex' will be used as the default command name.
+-
+-LATEX_CMD_NAME = latex
+-
+-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+-# generate index for LaTeX. If left blank `makeindex' will be used as the
+-# default command name.
+-
+-MAKEINDEX_CMD_NAME = makeindex
+-
+-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+-# LaTeX documents. This may be useful for small projects and may help to
+-# save some trees in general.
+-
+-COMPACT_LATEX = NO
+-
+-# The PAPER_TYPE tag can be used to set the paper type that is used
+-# by the printer. Possible values are: a4, a4wide, letter, legal and
+-# executive. If left blank a4wide will be used.
+-
+-PAPER_TYPE = a4wide
+-
+-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+-# packages that should be included in the LaTeX output.
+-
+-EXTRA_PACKAGES =
+-
+-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+-# the generated latex document. The header should contain everything until
+-# the first chapter. If it is left blank doxygen will generate a
+-# standard header. Notice: only use this tag if you know what you are doing!
+-
+-LATEX_HEADER =
+-
+-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+-# contain links (just like the HTML output) instead of page references
+-# This makes the output suitable for online browsing using a pdf viewer.
+-
+-PDF_HYPERLINKS = YES
+-
+-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+-# plain latex in the generated Makefile. Set this option to YES to get a
+-# higher quality PDF documentation.
+-
+-USE_PDFLATEX = NO
+-
+-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+-# command to the generated LaTeX files. This will instruct LaTeX to keep
+-# running if errors occur, instead of asking the user for help.
+-# This option is also used when generating formulas in HTML.
+-
+-LATEX_BATCHMODE = NO
+-
+-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+-# include the index chapters (such as File Index, Compound Index, etc.)
+-# in the output.
+-
+-LATEX_HIDE_INDICES = NO
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the RTF output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+-# The RTF output is optimized for Word 97 and may not look very pretty with
+-# other RTF readers or editors.
+-
+-GENERATE_RTF = NO
+-
+-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+-# put in front of it. If left blank `rtf' will be used as the default path.
+-
+-RTF_OUTPUT = rtf
+-
+-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+-# RTF documents. This may be useful for small projects and may help to
+-# save some trees in general.
+-
+-COMPACT_RTF = NO
+-
+-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+-# will contain hyperlink fields. The RTF file will
+-# contain links (just like the HTML output) instead of page references.
+-# This makes the output suitable for online browsing using WORD or other
+-# programs which support those fields.
+-# Note: wordpad (write) and others do not support links.
+-
+-RTF_HYPERLINKS = NO
+-
+-# Load stylesheet definitions from file. Syntax is similar to doxygen's
+-# config file, i.e. a series of assignments. You only have to provide
+-# replacements, missing definitions are set to their default value.
+-
+-RTF_STYLESHEET_FILE =
+-
+-# Set optional variables used in the generation of an rtf document.
+-# Syntax is similar to doxygen's config file.
+-
+-RTF_EXTENSIONS_FILE =
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the man page output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+-# generate man pages
+-
+-GENERATE_MAN = YES
+-
+-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+-# put in front of it. If left blank `man' will be used as the default path.
+-
+-MAN_OUTPUT = man
+-
+-# The MAN_EXTENSION tag determines the extension that is added to
+-# the generated man pages (default is the subroutine's section .3)
+-
+-MAN_EXTENSION = .3
+-
+-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+-# then it will generate one additional man file for each entity
+-# documented in the real man page(s). These additional files
+-# only source the real man page, but without them the man command
+-# would be unable to find the correct page. The default is NO.
+-
+-MAN_LINKS = YES
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the XML output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_XML tag is set to YES Doxygen will
+-# generate an XML file that captures the structure of
+-# the code including all documentation.
+-
+-GENERATE_XML = NO
+-
+-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+-# put in front of it. If left blank `xml' will be used as the default path.
+-
+-XML_OUTPUT = xml
+-
+-# The XML_SCHEMA tag can be used to specify an XML schema,
+-# which can be used by a validating XML parser to check the
+-# syntax of the XML files.
+-
+-XML_SCHEMA =
+-
+-# The XML_DTD tag can be used to specify an XML DTD,
+-# which can be used by a validating XML parser to check the
+-# syntax of the XML files.
+-
+-XML_DTD =
+-
+-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+-# dump the program listings (including syntax highlighting
+-# and cross-referencing information) to the XML output. Note that
+-# enabling this will significantly increase the size of the XML output.
+-
+-XML_PROGRAMLISTING = YES
+-
+-#---------------------------------------------------------------------------
+-# configuration options for the AutoGen Definitions output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+-# generate an AutoGen Definitions (see autogen.sf.net) file
+-# that captures the structure of the code including all
+-# documentation. Note that this feature is still experimental
+-# and incomplete at the moment.
+-
+-GENERATE_AUTOGEN_DEF = NO
+-
+-#---------------------------------------------------------------------------
+-# configuration options related to the Perl module output
+-#---------------------------------------------------------------------------
+-
+-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+-# generate a Perl module file that captures the structure of
+-# the code including all documentation. Note that this
+-# feature is still experimental and incomplete at the
+-# moment.
+-
+-GENERATE_PERLMOD = NO
+-
+-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+-# to generate PDF and DVI output from the Perl module output.
+-
+-PERLMOD_LATEX = NO
+-
+-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+-# nicely formatted so it can be parsed by a human reader. This is useful
+-# if you want to understand what is going on. On the other hand, if this
+-# tag is set to NO the size of the Perl module output will be much smaller
+-# and Perl will parse it just the same.
+-
+-PERLMOD_PRETTY = YES
+-
+-# The names of the make variables in the generated doxyrules.make file
+-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+-# This is useful so different doxyrules.make files included by the same
+-# Makefile don't overwrite each other's variables.
+-
+-PERLMOD_MAKEVAR_PREFIX =
+-
+-#---------------------------------------------------------------------------
+-# Configuration options related to the preprocessor
+-#---------------------------------------------------------------------------
+-
+-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+-# evaluate all C-preprocessor directives found in the sources and include
+-# files.
+-
+-ENABLE_PREPROCESSING = YES
+-
+-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+-# names in the source code. If set to NO (the default) only conditional
+-# compilation will be performed. Macro expansion can be done in a controlled
+-# way by setting EXPAND_ONLY_PREDEF to YES.
+-
+-MACRO_EXPANSION = NO
+-
+-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+-# then the macro expansion is limited to the macros specified with the
+-# PREDEFINED and EXPAND_AS_DEFINED tags.
+-
+-EXPAND_ONLY_PREDEF = NO
+-
+-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+-# in the INCLUDE_PATH (see below) will be search if a #include is found.
+-
+-SEARCH_INCLUDES = YES
+-
+-# The INCLUDE_PATH tag can be used to specify one or more directories that
+-# contain include files that are not input files but should be processed by
+-# the preprocessor.
+-
+-INCLUDE_PATH =
+-
+-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+-# patterns (like *.h and *.hpp) to filter out the header-files in the
+-# directories. If left blank, the patterns specified with FILE_PATTERNS will
+-# be used.
+-
+-INCLUDE_FILE_PATTERNS =
+-
+-# The PREDEFINED tag can be used to specify one or more macro names that
+-# are defined before the preprocessor is started (similar to the -D option of
+-# gcc). The argument of the tag is a list of macros of the form: name
+-# or name=definition (no spaces). If the definition and the = are
+-# omitted =1 is assumed. To prevent a macro definition from being
+-# undefined via #undef or recursively expanded use the := operator
+-# instead of the = operator.
+-
+-PREDEFINED = APOP_NO_VARIADIC
+-
+-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+-# this tag can be used to specify a list of macro names that should be expanded.
+-# The macro definition that is found in the sources will be used.
+-# Use the PREDEFINED tag if you want to use a different macro definition.
+-
+-EXPAND_AS_DEFINED =
+-
+-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+-# doxygen's preprocessor will remove all function-like macros that are alone
+-# on a line, have an all uppercase name, and do not end with a semicolon. Such
+-# function macros are typically used for boiler-plate code, and will confuse
+-# the parser if not removed.
+-
+-SKIP_FUNCTION_MACROS = NO
+-
+-#---------------------------------------------------------------------------
+-# Configuration::additions related to external references
+-#---------------------------------------------------------------------------
+-
+-# The TAGFILES option can be used to specify one or more tagfiles.
+-# Optionally an initial location of the external documentation
+-# can be added for each tagfile. The format of a tag file without
+-# this location is as follows:
+-# TAGFILES = file1 file2 ...
+-# Adding location for the tag files is done as follows:
+-# TAGFILES = file1=loc1 "file2 = loc2" ...
+-# where "loc1" and "loc2" can be relative or absolute paths or
+-# URLs. If a location is present for each tag, the installdox tool
+-# does not have to be run to correct the links.
+-# Note that each tag file must have a unique name
+-# (where the name does NOT include the path)
+-# If a tag file is not located in the directory in which doxygen
+-# is run, you must also specify the path to the tagfile here.
+-
+-TAGFILES =
+-
+-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+-# a tag file that is based on the input files it reads.
+-
+-GENERATE_TAGFILE =
+-
+-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+-# in the class index. If set to NO only the inherited external classes
+-# will be listed.
+-
+-ALLEXTERNALS = NO
+-
+-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+-# in the modules index. If set to NO, only the current project's groups will
+-# be listed.
+-
+-EXTERNAL_GROUPS = YES
+-
+-# The PERL_PATH should be the absolute path and name of the perl script
+-# interpreter (i.e. the result of `which perl').
+-
+-PERL_PATH = /usr/bin/perl
+-
+-#---------------------------------------------------------------------------
+-# Configuration options related to the dot tool
+-#---------------------------------------------------------------------------
+-
+-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+-# or super classes. Setting the tag to NO turns the diagrams off. Note that
+-# this option is superseded by the HAVE_DOT option below. This is only a
+-# fallback. It is recommended to install and use dot, since it yields more
+-# powerful graphs.
+-
+-CLASS_DIAGRAMS = NO
+-
+-# You can define message sequence charts within doxygen comments using the \msc
+-# command. Doxygen will then run the mscgen tool (see
+-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+-# the mscgen tool resides. If left empty the tool is assumed to be found in the
+-# default search path.
+-
+-MSCGEN_PATH =
+-
+-# If set to YES, the inheritance and collaboration graphs will hide
+-# inheritance and usage relations if the target is undocumented
+-# or is not a class.
+-
+-HIDE_UNDOC_RELATIONS = YES
+-
+-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+-# available from the path. This tool is part of Graphviz, a graph visualization
+-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+-# have no effect if this option is set to NO (the default)
+-
+-HAVE_DOT = NO
+-
+-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+-# will generate a graph for each documented class showing the direct and
+-# indirect inheritance relations. Setting this tag to YES will force the
+-# the CLASS_DIAGRAMS tag to NO.
+-
+-CLASS_GRAPH = NO
+-
+-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+-# will generate a graph for each documented class showing the direct and
+-# indirect implementation dependencies (inheritance, containment, and
+-# class references variables) of the class with other documented classes.
+-
+-COLLABORATION_GRAPH = NO
+-
+-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+-# will generate a graph for groups, showing the direct groups dependencies
+-
+-GROUP_GRAPHS = YES
+-
+-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+-# collaboration diagrams in a style similar to the OMG's Unified Modeling
+-# Language.
+-
+-UML_LOOK = NO
+-
+-# If set to YES, the inheritance and collaboration graphs will show the
+-# relations between templates and their instances.
+-
+-TEMPLATE_RELATIONS = NO
+-
+-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+-# tags are set to YES then doxygen will generate a graph for each documented
+-# file showing the direct and indirect include dependencies of the file with
+-# other documented files.
+-
+-INCLUDE_GRAPH = NO
+-
+-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+-# documented header file showing the documented files that directly or
+-# indirectly include this file.
+-
+-INCLUDED_BY_GRAPH = NO
+-
+-# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+-# doxygen will generate a call dependency graph for every global function
+-# or class method. Note that enabling this option will significantly increase
+-# the time of a run. So in most cases it will be better to enable call graphs
+-# for selected functions only using the \callgraph command.
+-
+-CALL_GRAPH = NO
+-
+-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+-# doxygen will generate a caller dependency graph for every global function
+-# or class method. Note that enabling this option will significantly increase
+-# the time of a run. So in most cases it will be better to enable caller
+-# graphs for selected functions only using the \callergraph command.
+-
+-CALLER_GRAPH = NO
+-
+-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+-# will graphical hierarchy of all classes instead of a textual one.
+-
+-GRAPHICAL_HIERARCHY = YES
+-
+-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+-# then doxygen will show the dependencies a directory has on other directories
+-# in a graphical way. The dependency relations are determined by the #include
+-# relations between the files in the directories.
+-
+-DIRECTORY_GRAPH = YES
+-
+-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+-# generated by dot. Possible values are png, jpg, or gif
+-# If left blank png will be used.
+-
+-DOT_IMAGE_FORMAT = png
+-
+-# The tag DOT_PATH can be used to specify the path where the dot tool can be
+-# found. If left blank, it is assumed the dot tool can be found in the path.
+-
+-DOT_PATH =
+-
+-# The DOTFILE_DIRS tag can be used to specify one or more directories that
+-# contain dot files that are included in the documentation (see the
+-# \dotfile command).
+-
+-DOTFILE_DIRS =
+-
+-# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+-# nodes that will be shown in the graph. If the number of nodes in a graph
+-# becomes larger than this value, doxygen will truncate the graph, which is
+-# visualized by representing a node as a red box. Note that doxygen if the
+-# number of direct children of the root node in a graph is already larger than
+-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+-
+-DOT_GRAPH_MAX_NODES = 50
+-
+-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+-# graphs generated by dot. A depth value of 3 means that only nodes reachable
+-# from the root by following a path via at most 3 edges will be shown. Nodes
+-# that lay further from the root node will be omitted. Note that setting this
+-# option to 1 or 2 may greatly reduce the computation time needed for large
+-# code bases. Also note that the size of a graph can be further restricted by
+-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+-
+-MAX_DOT_GRAPH_DEPTH = 0
+-
+-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+-# background. This is enabled by default, which results in a transparent
+-# background. Warning: Depending on the platform used, enabling this option
+-# may lead to badly anti-aliased labels on the edges of a graph (i.e. they
+-# become hard to read).
+-
+-DOT_TRANSPARENT = YES
+-
+-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+-# files in one run (i.e. multiple -o and -T options on the command line). This
+-# makes dot run faster, but since only newer versions of dot (>1.8.10)
+-# support this, this feature is disabled by default.
+-
+-DOT_MULTI_TARGETS = NO
+-
+-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+-# generate a legend page explaining the meaning of the various boxes and
+-# arrows in the dot generated graphs.
+-
+-GENERATE_LEGEND = YES
+-
+-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+-# remove the intermediate dot files that are used to generate
+-# the various graphs.
+-
+-DOT_CLEANUP = YES
+-
+-#---------------------------------------------------------------------------
+-# Configuration::additions related to the search engine
+-#---------------------------------------------------------------------------
+-
+-# The SEARCHENGINE tag specifies whether or not a search engine should be
+-# used. If set to NO the values of all tags below this one will be ignored.
+-
+-SEARCHENGINE = NO
+--- /dev/null
++++ b/docs/edit_globals.sed
+@@ -0,0 +1,5 @@
++/index_x/s/- x -/ /
++/index_a/s/- a -/ /
++/Here is a list of all/d
++/<span>[a-z]<\/span><\/a><\/li>/d
++/div class="contents"/aSee also the <a class="el" href="group__models.html">models</a> and <a class="el" href="group__settings.html">settings</a> pages.
+--- /dev/null
++++ b/docs/edit_outline.sed
+@@ -0,0 +1,3 @@
++s|Outlineheader \([^ ]*\)\(.*\)</p>|<h2><a class="anchor" name="\1"><div class="trigger" onClick="showBranch('\1d');swapFolder('\1f')"><img src="right.png" border="0" id="\1f" alt="pip">\2</div></a></h2><div class="branch" id="\1d">|
++s|endofdiv</p>|</div>|
++s|ALLBUTTON|<span class="trigger" onClick="showAll();"<a>Expand all </a></span> \| <span class="trigger" onClick="closeAll();"<a>Collapse all </a></span>|
+--- /dev/null
++++ b/docs/doxygen.conf.in
+@@ -0,0 +1,1792 @@
++# Doxyfile 1.8.1.2
++
++# This file describes the settings to be used by the documentation system
++# doxygen (www.doxygen.org) for a project.
++#
++# All text after a hash (#) is considered a comment and will be ignored.
++# The format is:
++# TAG = value [value, ...]
++# For lists items can also be appended using:
++# TAG += value [value, ...]
++# Values that contain spaces should be placed between quotes (" ").
++
++#---------------------------------------------------------------------------
++# Project related configuration options
++#---------------------------------------------------------------------------
++
++# This tag specifies the encoding used for all characters in the config file
++# that follow. The default is UTF-8 which is also the encoding used for all
++# text before the first occurrence of this tag. Doxygen uses libiconv (or the
++# iconv built into libc) for the transcoding. See
++# http://www.gnu.org/software/libiconv for the list of possible encodings.
++
++DOXYFILE_ENCODING = UTF-8
++
++# The PROJECT_NAME tag is a single word (or sequence of words) that should
++# identify the project. Note that if you do not use Doxywizard you need
++# to put quotes around the project name if it contains spaces.
++
++PROJECT_NAME = Apophenia
++
++# The PROJECT_NUMBER tag can be used to enter a project or revision number.
++# This could be handy for archiving the generated documentation or
++# if some version control system is used.
++
++PROJECT_NUMBER =
++
++# Using the PROJECT_BRIEF tag one can provide an optional one line description
++# for a project that appears at the top of each page and should give viewer
++# a quick idea about the purpose of the project. Keep the description short.
++
++PROJECT_BRIEF =
++
++# With the PROJECT_LOGO tag one can specify an logo or icon that is
++# included in the documentation. The maximum height of the logo should not
++# exceed 55 pixels and the maximum width should not exceed 200 pixels.
++# Doxygen will copy the logo to the output directory.
++
++PROJECT_LOGO =
++
++# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
++# base path where the generated documentation will be put.
++# If a relative path is entered, it will be relative to the location
++# where doxygen was started. If left blank the current directory will be used.
++
++OUTPUT_DIRECTORY =
++
++# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
++# 4096 sub-directories (in 2 levels) under the output directory of each output
++# format and will distribute the generated files over these directories.
++# Enabling this option can be useful when feeding doxygen a huge amount of
++# source files, where putting all generated files in the same directory would
++# otherwise cause performance problems for the file system.
++
++CREATE_SUBDIRS = NO
++
++# The OUTPUT_LANGUAGE tag is used to specify the language in which all
++# documentation generated by doxygen is written. Doxygen will use this
++# information to generate all constant output in the proper language.
++# The default language is English, other supported languages are:
++# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
++# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
++# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
++# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
++# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
++# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
++
++OUTPUT_LANGUAGE = English
++
++# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
++# include brief member descriptions after the members that are listed in
++# the file and class documentation (similar to JavaDoc).
++# Set to NO to disable this.
++
++BRIEF_MEMBER_DESC = YES
++
++# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
++# the brief description of a member or function before the detailed description.
++# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
++# brief descriptions will be completely suppressed.
++
++REPEAT_BRIEF = YES
++
++# This tag implements a quasi-intelligent brief description abbreviator
++# that is used to form the text in various listings. Each string
++# in this list, if found as the leading text of the brief description, will be
++# stripped from the text and the result after processing the whole list, is
++# used as the annotated text. Otherwise, the brief description is used as-is.
++# If left blank, the following values are used ("$name" is automatically
++# replaced with the name of the entity): "The $name class" "The $name widget"
++# "The $name file" "is" "provides" "specifies" "contains"
++# "represents" "a" "an" "the"
++
++ABBREVIATE_BRIEF =
++
++# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
++# Doxygen will generate a detailed section even if there is only a brief
++# description.
++
++ALWAYS_DETAILED_SEC = NO
++
++# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
++# inherited members of a class in the documentation of that class as if those
++# members were ordinary class members. Constructors, destructors and assignment
++# operators of the base classes will not be shown.
++
++INLINE_INHERITED_MEMB = NO
++
++# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
++# path before files name in the file list and in the header files. If set
++# to NO the shortest path that makes the file name unique will be used.
++
++FULL_PATH_NAMES = NO
++
++# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
++# can be used to strip a user-defined part of the path. Stripping is
++# only done if one of the specified strings matches the left-hand part of
++# the path. The tag can be used to show relative paths in the file list.
++# If left blank the directory from which doxygen is run is used as the
++# path to strip.
++
++STRIP_FROM_PATH =
++
++# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
++# the path mentioned in the documentation of a class, which tells
++# the reader which header file to include in order to use a class.
++# If left blank only the name of the header file containing the class
++# definition is used. Otherwise one should specify the include paths that
++# are normally passed to the compiler using the -I flag.
++
++STRIP_FROM_INC_PATH =
++
++# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
++# (but less readable) file names. This can be useful if your file system
++# doesn't support long names like on DOS, Mac, or CD-ROM.
++
++SHORT_NAMES = NO
++
++# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
++# will interpret the first line (until the first dot) of a JavaDoc-style
++# comment as the brief description. If set to NO, the JavaDoc
++# comments will behave just like regular Qt-style comments
++# (thus requiring an explicit @brief command for a brief description.)
++
++JAVADOC_AUTOBRIEF = NO
++
++# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
++# interpret the first line (until the first dot) of a Qt-style
++# comment as the brief description. If set to NO, the comments
++# will behave just like regular Qt-style comments (thus requiring
++# an explicit \brief command for a brief description.)
++
++QT_AUTOBRIEF = NO
++
++# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
++# treat a multi-line C++ special comment block (i.e. a block of //! or ///
++# comments) as a brief description. This used to be the default behaviour.
++# The new default is to treat a multi-line C++ comment block as a detailed
++# description. Set this tag to YES if you prefer the old behaviour instead.
++
++MULTILINE_CPP_IS_BRIEF = NO
++
++# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
++# member inherits the documentation from any documented member that it
++# re-implements.
++
++INHERIT_DOCS = YES
++
++# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
++# a new page for each member. If set to NO, the documentation of a member will
++# be part of the file/class/namespace that contains it.
++
++SEPARATE_MEMBER_PAGES = NO
++
++# The TAB_SIZE tag can be used to set the number of spaces in a tab.
++# Doxygen uses this value to replace tabs by spaces in code fragments.
++
++TAB_SIZE = 5
++
++# This tag can be used to specify a number of aliases that acts
++# as commands in the documentation. An alias has the form "name=value".
++# For example adding "sideeffect=\par Side Effects:\n" will allow you to
++# put the command \sideeffect (or @sideeffect) in the documentation, which
++# will result in a user-defined paragraph with heading "Side Effects:".
++# You can put \n's in the value part of an alias to insert newlines.
++
++ALIASES =
++
++# This tag can be used to specify a number of word-keyword mappings (TCL only).
++# A mapping has the form "name=value". For example adding
++# "class=itcl::class" will allow you to use the command class in the
++# itcl::class meaning.
++
++TCL_SUBST =
++
++# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
++# sources only. Doxygen will then generate output that is more tailored for C.
++# For instance, some of the names that are used will be different. The list
++# of all members will be omitted, etc.
++
++OPTIMIZE_OUTPUT_FOR_C = YES
++
++# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
++# sources only. Doxygen will then generate output that is more tailored for
++# Java. For instance, namespaces will be presented as packages, qualified
++# scopes will look different, etc.
++
++OPTIMIZE_OUTPUT_JAVA = NO
++
++# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
++# sources only. Doxygen will then generate output that is more tailored for
++# Fortran.
++
++OPTIMIZE_FOR_FORTRAN = NO
++
++# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
++# sources. Doxygen will then generate output that is tailored for
++# VHDL.
++
++OPTIMIZE_OUTPUT_VHDL = NO
++
++# Doxygen selects the parser to use depending on the extension of the files it
++# parses. With this tag you can assign which parser to use for a given extension.
++# Doxygen has a built-in mapping, but you can override or extend it using this
++# tag. The format is ext=language, where ext is a file extension, and language
++# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
++# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
++# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
++# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
++# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
++
++EXTENSION_MAPPING =
++
++# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
++# comments according to the Markdown format, which allows for more readable
++# documentation. See http://daringfireball.net/projects/markdown/ for details.
++# The output of markdown processing is further processed by doxygen, so you
++# can mix doxygen, HTML, and XML commands with Markdown formatting.
++# Disable only in case of backward compatibilities issues.
++
++MARKDOWN_SUPPORT = YES
++
++# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
++# to include (a tag file for) the STL sources as input, then you should
++# set this tag to YES in order to let doxygen match functions declarations and
++# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
++# func(std::string) {}). This also makes the inheritance and collaboration
++# diagrams that involve STL classes more complete and accurate.
++
++BUILTIN_STL_SUPPORT = NO
++
++# If you use Microsoft's C++/CLI language, you should set this option to YES to
++# enable parsing support.
++
++CPP_CLI_SUPPORT = NO
++
++# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
++# Doxygen will parse them like normal C++ but will assume all classes use public
++# instead of private inheritance when no explicit protection keyword is present.
++
++SIP_SUPPORT = NO
++
++# For Microsoft's IDL there are propget and propput attributes to indicate getter
++# and setter methods for a property. Setting this option to YES (the default)
++# will make doxygen replace the get and set methods by a property in the
++# documentation. This will only work if the methods are indeed getting or
++# setting a simple type. If this is not the case, or you want to show the
++# methods anyway, you should set this option to NO.
++
++IDL_PROPERTY_SUPPORT = YES
++
++# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
++# tag is set to YES, then doxygen will reuse the documentation of the first
++# member in the group (if any) for the other members of the group. By default
++# all members of a group must be documented explicitly.
++
++DISTRIBUTE_GROUP_DOC = NO
++
++# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
++# the same type (for instance a group of public functions) to be put as a
++# subgroup of that type (e.g. under the Public Functions section). Set it to
++# NO to prevent subgrouping. Alternatively, this can be done per class using
++# the \nosubgrouping command.
++
++SUBGROUPING = YES
++
++# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
++# unions are shown inside the group in which they are included (e.g. using
++# @ingroup) instead of on a separate page (for HTML and Man pages) or
++# section (for LaTeX and RTF).
++
++INLINE_GROUPED_CLASSES = NO
++
++# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
++# unions with only public data fields will be shown inline in the documentation
++# of the scope in which they are defined (i.e. file, namespace, or group
++# documentation), provided this scope is documented. If set to NO (the default),
++# structs, classes, and unions are shown on a separate page (for HTML and Man
++# pages) or section (for LaTeX and RTF).
++
++INLINE_SIMPLE_STRUCTS = NO
++
++# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
++# is documented as struct, union, or enum with the name of the typedef. So
++# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
++# with name TypeT. When disabled the typedef will appear as a member of a file,
++# namespace, or class. And the struct will be named TypeS. This can typically
++# be useful for C code in case the coding convention dictates that all compound
++# types are typedef'ed and only the typedef is referenced, never the tag name.
++
++TYPEDEF_HIDES_STRUCT = NO
++
++# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
++# determine which symbols to keep in memory and which to flush to disk.
++# When the cache is full, less often used symbols will be written to disk.
++# For small to medium size projects (<1000 input files) the default value is
++# probably good enough. For larger projects a too small cache size can cause
++# doxygen to be busy swapping symbols to and from disk most of the time
++# causing a significant performance penalty.
++# If the system has enough physical memory increasing the cache will improve the
++# performance by keeping more symbols in memory. Note that the value works on
++# a logarithmic scale so increasing the size by one will roughly double the
++# memory usage. The cache size is given by this formula:
++# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
++# corresponding to a cache size of 2^16 = 65536 symbols.
++
++SYMBOL_CACHE_SIZE = 0
++
++# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
++# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
++# their name and scope. Since this can be an expensive process and often the
++# same symbol appear multiple times in the code, doxygen keeps a cache of
++# pre-resolved symbols. If the cache is too small doxygen will become slower.
++# If the cache is too large, memory is wasted. The cache size is given by this
++# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
++# corresponding to a cache size of 2^16 = 65536 symbols.
++
++LOOKUP_CACHE_SIZE = 0
++
++#---------------------------------------------------------------------------
++# Build related configuration options
++#---------------------------------------------------------------------------
++
++# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
++# documentation are documented, even if no documentation was available.
++# Private class members and static file members will be hidden unless
++# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
++
++EXTRACT_ALL = NO
++
++# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
++# will be included in the documentation.
++
++EXTRACT_PRIVATE = NO
++
++# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
++
++EXTRACT_PACKAGE = NO
++
++# If the EXTRACT_STATIC tag is set to YES all static members of a file
++# will be included in the documentation.
++
++EXTRACT_STATIC = NO
++
++# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
++# defined locally in source files will be included in the documentation.
++# If set to NO only classes defined in header files are included.
++
++EXTRACT_LOCAL_CLASSES = YES
++
++# This flag is only useful for Objective-C code. When set to YES local
++# methods, which are defined in the implementation section but not in
++# the interface are included in the documentation.
++# If set to NO (the default) only methods in the interface are included.
++
++EXTRACT_LOCAL_METHODS = NO
++
++# If this flag is set to YES, the members of anonymous namespaces will be
++# extracted and appear in the documentation as a namespace called
++# 'anonymous_namespace{file}', where file will be replaced with the base
++# name of the file that contains the anonymous namespace. By default
++# anonymous namespaces are hidden.
++
++EXTRACT_ANON_NSPACES = NO
++
++# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
++# undocumented members of documented classes, files or namespaces.
++# If set to NO (the default) these members will be included in the
++# various overviews, but no documentation section is generated.
++# This option has no effect if EXTRACT_ALL is enabled.
++
++HIDE_UNDOC_MEMBERS = NO
++
++# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
++# undocumented classes that are normally visible in the class hierarchy.
++# If set to NO (the default) these classes will be included in the various
++# overviews. This option has no effect if EXTRACT_ALL is enabled.
++
++HIDE_UNDOC_CLASSES = NO
++
++# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
++# friend (class|struct|union) declarations.
++# If set to NO (the default) these declarations will be included in the
++# documentation.
++
++HIDE_FRIEND_COMPOUNDS = NO
++
++# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
++# documentation blocks found inside the body of a function.
++# If set to NO (the default) these blocks will be appended to the
++# function's detailed documentation block.
++
++HIDE_IN_BODY_DOCS = NO
++
++# The INTERNAL_DOCS tag determines if documentation
++# that is typed after a \internal command is included. If the tag is set
++# to NO (the default) then the documentation will be excluded.
++# Set it to YES to include the internal documentation.
++
++INTERNAL_DOCS = NO
++
++# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
++# file names in lower-case letters. If set to YES upper-case letters are also
++# allowed. This is useful if you have classes or files whose names only differ
++# in case and if your file system supports case sensitive file names. Windows
++# and Mac users are advised to set this option to NO.
++
++CASE_SENSE_NAMES = YES
++
++# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
++# will show members with their full class and namespace scopes in the
++# documentation. If set to YES the scope will be hidden.
++
++HIDE_SCOPE_NAMES = NO
++
++# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
++# will put a list of the files that are included by a file in the documentation
++# of that file.
++
++SHOW_INCLUDE_FILES = NO
++
++# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
++# will list include files with double quotes in the documentation
++# rather than with sharp brackets.
++
++FORCE_LOCAL_INCLUDES = NO
++
++# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
++# is inserted in the documentation for inline members.
++
++INLINE_INFO = YES
++
++# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
++# will sort the (detailed) documentation of file and class members
++# alphabetically by member name. If set to NO the members will appear in
++# declaration order.
++
++SORT_MEMBER_DOCS = YES
++
++# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
++# brief documentation of file, namespace and class members alphabetically
++# by member name. If set to NO (the default) the members will appear in
++# declaration order.
++
++SORT_BRIEF_DOCS = NO
++
++# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
++# will sort the (brief and detailed) documentation of class members so that
++# constructors and destructors are listed first. If set to NO (the default)
++# the constructors will appear in the respective orders defined by
++# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
++# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
++# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
++
++SORT_MEMBERS_CTORS_1ST = NO
++
++# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
++# hierarchy of group names into alphabetical order. If set to NO (the default)
++# the group names will appear in their defined order.
++
++SORT_GROUP_NAMES = NO
++
++# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
++# sorted by fully-qualified names, including namespaces. If set to
++# NO (the default), the class list will be sorted only by class name,
++# not including the namespace part.
++# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
++# Note: This option applies only to the class list, not to the
++# alphabetical list.
++
++SORT_BY_SCOPE_NAME = NO
++
++# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
++# do proper type resolution of all parameters of a function it will reject a
++# match between the prototype and the implementation of a member function even
++# if there is only one candidate or it is obvious which candidate to choose
++# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
++# will still accept a match between prototype and implementation in such cases.
++
++STRICT_PROTO_MATCHING = NO
++
++# The GENERATE_TODOLIST tag can be used to enable (YES) or
++# disable (NO) the todo list. This list is created by putting \todo
++# commands in the documentation.
++
++GENERATE_TODOLIST = YES
++
++# The GENERATE_TESTLIST tag can be used to enable (YES) or
++# disable (NO) the test list. This list is created by putting \test
++# commands in the documentation.
++
++GENERATE_TESTLIST = YES
++
++# The GENERATE_BUGLIST tag can be used to enable (YES) or
++# disable (NO) the bug list. This list is created by putting \bug
++# commands in the documentation.
++
++GENERATE_BUGLIST = YES
++
++# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
++# disable (NO) the deprecated list. This list is created by putting
++# \deprecated commands in the documentation.
++
++GENERATE_DEPRECATEDLIST= YES
++
++# The ENABLED_SECTIONS tag can be used to enable conditional
++# documentation sections, marked by \if sectionname ... \endif.
++
++ENABLED_SECTIONS =
++
++# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
++# the initial value of a variable or macro consists of for it to appear in
++# the documentation. If the initializer consists of more lines than specified
++# here it will be hidden. Use a value of 0 to hide initializers completely.
++# The appearance of the initializer of individual variables and macros in the
++# documentation can be controlled using \showinitializer or \hideinitializer
++# command in the documentation regardless of this setting.
++
++MAX_INITIALIZER_LINES = 30
++
++# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
++# at the bottom of the documentation of classes and structs. If set to YES the
++# list will mention the files that were used to generate the documentation.
++
++SHOW_USED_FILES = NO
++
++# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
++# This will remove the Files entry from the Quick Index and from the
++# Folder Tree View (if specified). The default is YES.
++
++SHOW_FILES = YES
++
++# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
++# Namespaces page.
++# This will remove the Namespaces entry from the Quick Index
++# and from the Folder Tree View (if specified). The default is YES.
++
++SHOW_NAMESPACES = YES
++
++# The FILE_VERSION_FILTER tag can be used to specify a program or script that
++# doxygen should invoke to get the current version for each file (typically from
++# the version control system). Doxygen will invoke the program by executing (via
++# popen()) the command <command> <input-file>, where <command> is the value of
++# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
++# provided by doxygen. Whatever the program writes to standard output
++# is used as the file version. See the manual for examples.
++
++FILE_VERSION_FILTER =
++
++# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
++# by doxygen. The layout file controls the global structure of the generated
++# output files in an output format independent way. To create the layout file
++# that represents doxygen's defaults, run doxygen with the -l option.
++# You can optionally specify a file name after the option, if omitted
++# DoxygenLayout.xml will be used as the name of the layout file.
++
++LAYOUT_FILE =
++
++# The CITE_BIB_FILES tag can be used to specify one or more bib files
++# containing the references data. This must be a list of .bib files. The
++# .bib extension is automatically appended if omitted. Using this command
++# requires the bibtex tool to be installed. See also
++# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
++# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
++# feature you need bibtex and perl available in the search path.
++
++CITE_BIB_FILES =
++
++#---------------------------------------------------------------------------
++# configuration options related to warning and progress messages
++#---------------------------------------------------------------------------
++
++# The QUIET tag can be used to turn on/off the messages that are generated
++# by doxygen. Possible values are YES and NO. If left blank NO is used.
++
++QUIET = YES
++
++# The WARNINGS tag can be used to turn on/off the warning messages that are
++# generated by doxygen. Possible values are YES and NO. If left blank
++# NO is used.
++
++WARNINGS = YES
++
++# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
++# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
++# automatically be disabled.
++
++WARN_IF_UNDOCUMENTED = NO
++
++# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
++# potential errors in the documentation, such as not documenting some
++# parameters in a documented function, or documenting parameters that
++# don't exist or using markup commands wrongly.
++
++WARN_IF_DOC_ERROR = YES
++
++# The WARN_NO_PARAMDOC option can be enabled to get warnings for
++# functions that are documented, but have no documentation for their parameters
++# or return value. If set to NO (the default) doxygen will only warn about
++# wrong or incomplete parameter documentation, but not about the absence of
++# documentation.
++
++WARN_NO_PARAMDOC = NO
++
++# The WARN_FORMAT tag determines the format of the warning messages that
++# doxygen can produce. The string should contain the $file, $line, and $text
++# tags, which will be replaced by the file and line number from which the
++# warning originated and the warning text. Optionally the format may contain
++# $version, which will be replaced by the version of the file (if it could
++# be obtained via FILE_VERSION_FILTER)
++
++WARN_FORMAT = "$file:$line: $text"
++
++# The WARN_LOGFILE tag can be used to specify a file to which warning
++# and error messages should be written. If left blank the output is written
++# to stderr.
++
++WARN_LOGFILE = doxygen.log
++
++#---------------------------------------------------------------------------
++# configuration options related to the input files
++#---------------------------------------------------------------------------
++
++# The INPUT tag can be used to specify the files and/or directories that contain
++# documented source files. You may enter file names like "myfile.cpp" or
++# directories like "/usr/src/myproject". Separate the files or directories
++# with spaces.
++
++INPUT = @abs_top_srcdir@
++
++# This tag can be used to specify the character encoding of the source files
++# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
++# also the default input encoding. Doxygen uses libiconv (or the iconv built
++# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
++# the list of possible encodings.
++
++INPUT_ENCODING = UTF-8
++
++# If the value of the INPUT tag contains directories, you can use the
++# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
++# and *.h) to filter out the source-files in the directories. If left
++# blank the following patterns are tested:
++# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
++# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
++# *.f90 *.f *.for *.vhd *.vhdl
++
++FILE_PATTERNS =
++
++# The RECURSIVE tag can be used to turn specify whether or not subdirectories
++# should be searched for input files as well. Possible values are YES and NO.
++# If left blank NO is used.
++
++RECURSIVE = YES
++
++# The EXCLUDE tag can be used to specify files and/or directories that should be
++# excluded from the INPUT source files. This way you can easily exclude a
++# subdirectory from a directory tree whose root is specified with the INPUT tag.
++# Note that relative paths are relative to the directory from which doxygen is
++# run.
++
++EXCLUDE =
++
++# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
++# directories that are symbolic links (a Unix file system feature) are excluded
++# from the input.
++
++EXCLUDE_SYMLINKS = NO
++
++# If the value of the INPUT tag contains directories, you can use the
++# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
++# certain files from those directories. Note that the wildcards are matched
++# against the file with absolute path, so to exclude all test directories
++# for example use the pattern */test/*
++
++EXCLUDE_PATTERNS =
++
++# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
++# (namespaces, classes, functions, etc.) that should be excluded from the
++# output. The symbol name can be a fully qualified name, a word, or if the
++# wildcard * is used, a substring. Examples: ANamespace, AClass,
++# AClass::ANamespace, ANamespace::*Test
++
++EXCLUDE_SYMBOLS =
++
++# The EXAMPLE_PATH tag can be used to specify one or more files or
++# directories that contain example code fragments that are included (see
++# the \include command).
++
++EXAMPLE_PATH = @abs_top_srcdir@
++
++# If the value of the EXAMPLE_PATH tag contains directories, you can use the
++# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
++# and *.h) to filter out the source-files in the directories. If left
++# blank all files are included.
++
++EXAMPLE_PATTERNS =
++
++# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
++# searched for input files to be used with the \include or \dontinclude
++# commands irrespective of the value of the RECURSIVE tag.
++# Possible values are YES and NO. If left blank NO is used.
++
++EXAMPLE_RECURSIVE = YES
++
++# The IMAGE_PATH tag can be used to specify one or more files or
++# directories that contain image that are included in the documentation (see
++# the \image command).
++
++IMAGE_PATH = .
++
++# The INPUT_FILTER tag can be used to specify a program that doxygen should
++# invoke to filter for each input file. Doxygen will invoke the filter program
++# by executing (via popen()) the command <filter> <input-file>, where <filter>
++# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
++# input file. Doxygen will then use the output that the filter program writes
++# to standard output.
++# If FILTER_PATTERNS is specified, this tag will be
++# ignored.
++
++INPUT_FILTER =
++
++# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
++# basis.
++# Doxygen will compare the file name with each pattern and apply the
++# filter if there is a match.
++# The filters are a list of the form:
++# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
++# info on how filters are used. If FILTER_PATTERNS is empty or if
++# non of the patterns match the file name, INPUT_FILTER is applied.
++
++FILTER_PATTERNS =
++
++# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
++# INPUT_FILTER) will be used to filter the input files when producing source
++# files to browse (i.e. when SOURCE_BROWSER is set to YES).
++
++FILTER_SOURCE_FILES = NO
++
++# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
++# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
++# and it is also possible to disable source filtering for a specific pattern
++# using *.ext= (so without naming a filter). This option only has effect when
++# FILTER_SOURCE_FILES is enabled.
++
++FILTER_SOURCE_PATTERNS =
++
++#---------------------------------------------------------------------------
++# configuration options related to source browsing
++#---------------------------------------------------------------------------
++
++# If the SOURCE_BROWSER tag is set to YES then a list of source files will
++# be generated. Documented entities will be cross-referenced with these sources.
++# Note: To get rid of all source code in the generated output, make sure also
++# VERBATIM_HEADERS is set to NO.
++
++SOURCE_BROWSER = NO
++
++# Setting the INLINE_SOURCES tag to YES will include the body
++# of functions and classes directly in the documentation.
++
++INLINE_SOURCES = NO
++
++# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
++# doxygen to hide any special comment blocks from generated source code
++# fragments. Normal C, C++ and Fortran comments will always remain visible.
++
++STRIP_CODE_COMMENTS = YES
++
++# If the REFERENCED_BY_RELATION tag is set to YES
++# then for each documented function all documented
++# functions referencing it will be listed.
++
++REFERENCED_BY_RELATION = NO
++
++# If the REFERENCES_RELATION tag is set to YES
++# then for each documented function all documented entities
++# called/used by that function will be listed.
++
++REFERENCES_RELATION = NO
++
++# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
++# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
++# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
++# link to the source code.
++# Otherwise they will link to the documentation.
++
++REFERENCES_LINK_SOURCE = YES
++
++# If the USE_HTAGS tag is set to YES then the references to source code
++# will point to the HTML generated by the htags(1) tool instead of doxygen
++# built-in source browser. The htags tool is part of GNU's global source
++# tagging system (see http://www.gnu.org/software/global/global.html). You
++# will need version 4.8.6 or higher.
++
++USE_HTAGS = NO
++
++# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
++# will generate a verbatim copy of the header file for each class for
++# which an include is specified. Set to NO to disable this.
++
++VERBATIM_HEADERS = YES
++
++#---------------------------------------------------------------------------
++# configuration options related to the alphabetical class index
++#---------------------------------------------------------------------------
++
++# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
++# of all compounds will be generated. Enable this if the project
++# contains a lot of classes, structs, unions or interfaces.
++
++ALPHABETICAL_INDEX = YES
++
++# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
++# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
++# in which this list will be split (can be a number in the range [1..20])
++
++COLS_IN_ALPHA_INDEX = 3
++
++# In case all classes in a project start with a common prefix, all
++# classes will be put under the same header in the alphabetical index.
++# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
++# should be ignored while generating the index headers.
++
++IGNORE_PREFIX =
++
++#---------------------------------------------------------------------------
++# configuration options related to the HTML output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
++# generate HTML output.
++
++GENERATE_HTML = YES
++
++# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
++# If a relative path is entered the value of OUTPUT_DIRECTORY will be
++# put in front of it. If left blank `html' will be used as the default path.
++
++HTML_OUTPUT = html
++
++# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
++# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
++# doxygen will generate files with .html extension.
++
++HTML_FILE_EXTENSION = .html
++
++# The HTML_HEADER tag can be used to specify a personal HTML header for
++# each generated HTML page. If it is left blank doxygen will generate a
++# standard header. Note that when using a custom header you are responsible
++# for the proper inclusion of any scripts and style sheets that doxygen
++# needs, which is dependent on the configuration options used.
++# It is advised to generate a default header using "doxygen -w html
++# header.html footer.html stylesheet.css YourConfigFile" and then modify
++# that header. Note that the header is subject to change so you typically
++# have to redo this when upgrading to a newer version of doxygen or when
++# changing the value of configuration settings such as GENERATE_TREEVIEW!
++
++HTML_HEADER = head.html
++
++# The HTML_FOOTER tag can be used to specify a personal HTML footer for
++# each generated HTML page. If it is left blank doxygen will generate a
++# standard footer.
++
++HTML_FOOTER = foot.html
++
++# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
++# style sheet that is used by each HTML page. It can be used to
++# fine-tune the look of the HTML output. If the tag is left blank doxygen
++# will generate a default style sheet. Note that doxygen will try to copy
++# the style sheet file to the HTML output directory, so don't put your own
++# style sheet in the HTML output directory as well, or it will be erased!
++
++HTML_STYLESHEET = typical.css
++
++# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
++# other source files which should be copied to the HTML output directory. Note
++# that these files will be copied to the base HTML output directory. Use the
++# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
++# files. In the HTML_STYLESHEET file, use the file name only. Also note that
++# the files will be copied as-is; there are no commands or markers available.
++
++HTML_EXTRA_FILES =
++
++# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
++# Doxygen will adjust the colors in the style sheet and background images
++# according to this color. Hue is specified as an angle on a colorwheel,
++# see http://en.wikipedia.org/wiki/Hue for more information.
++# For instance the value 0 represents red, 60 is yellow, 120 is green,
++# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
++# The allowed range is 0 to 359.
++
++HTML_COLORSTYLE_HUE = 220
++
++# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
++# the colors in the HTML output. For a value of 0 the output will use
++# grayscales only. A value of 255 will produce the most vivid colors.
++
++HTML_COLORSTYLE_SAT = 100
++
++# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
++# the luminance component of the colors in the HTML output. Values below
++# 100 gradually make the output lighter, whereas values above 100 make
++# the output darker. The value divided by 100 is the actual gamma applied,
++# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
++# and 100 does not change the gamma.
++
++HTML_COLORSTYLE_GAMMA = 80
++
++# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
++# page will contain the date and time when the page was generated. Setting
++# this to NO can help when comparing the output of multiple runs.
++
++HTML_TIMESTAMP = YES
++
++# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
++# documentation will contain sections that can be hidden and shown after the
++# page has loaded.
++
++HTML_DYNAMIC_SECTIONS = NO
++
++# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
++# entries shown in the various tree structured indices initially; the user
++# can expand and collapse entries dynamically later on. Doxygen will expand
++# the tree to such a level that at most the specified number of entries are
++# visible (unless a fully collapsed tree already exceeds this amount).
++# So setting the number of entries 1 will produce a full collapsed tree by
++# default. 0 is a special value representing an infinite number of entries
++# and will result in a full expanded tree by default.
++
++HTML_INDEX_NUM_ENTRIES = 100
++
++# If the GENERATE_DOCSET tag is set to YES, additional index files
++# will be generated that can be used as input for Apple's Xcode 3
++# integrated development environment, introduced with OSX 10.5 (Leopard).
++# To create a documentation set, doxygen will generate a Makefile in the
++# HTML output directory. Running make will produce the docset in that
++# directory and running "make install" will install the docset in
++# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
++# it at startup.
++# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
++# for more information.
++
++GENERATE_DOCSET = NO
++
++# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
++# feed. A documentation feed provides an umbrella under which multiple
++# documentation sets from a single provider (such as a company or product suite)
++# can be grouped.
++
++DOCSET_FEEDNAME = "Doxygen generated docs"
++
++# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
++# should uniquely identify the documentation set bundle. This should be a
++# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
++# will append .docset to the name.
++
++DOCSET_BUNDLE_ID = org.doxygen.Project
++
++# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
++# the documentation publisher. This should be a reverse domain-name style
++# string, e.g. com.mycompany.MyDocSet.documentation.
++
++DOCSET_PUBLISHER_ID = org.doxygen.Publisher
++
++# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
++
++DOCSET_PUBLISHER_NAME = Publisher
++
++# If the GENERATE_HTMLHELP tag is set to YES, additional index files
++# will be generated that can be used as input for tools like the
++# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
++# of the generated HTML documentation.
++
++GENERATE_HTMLHELP = NO
++
++# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
++# be used to specify the file name of the resulting .chm file. You
++# can add a path in front of the file if the result should not be
++# written to the html output directory.
++
++CHM_FILE =
++
++# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
++# be used to specify the location (absolute path including file name) of
++# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
++# the HTML help compiler on the generated index.hhp.
++
++HHC_LOCATION =
++
++# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
++# controls if a separate .chi index file is generated (YES) or that
++# it should be included in the master .chm file (NO).
++
++GENERATE_CHI = NO
++
++# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
++# is used to encode HtmlHelp index (hhk), content (hhc) and project file
++# content.
++
++CHM_INDEX_ENCODING =
++
++# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
++# controls whether a binary table of contents is generated (YES) or a
++# normal table of contents (NO) in the .chm file.
++
++BINARY_TOC = NO
++
++# The TOC_EXPAND flag can be set to YES to add extra items for group members
++# to the contents of the HTML help documentation and to the tree view.
++
++TOC_EXPAND = NO
++
++# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
++# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
++# that can be used as input for Qt's qhelpgenerator to generate a
++# Qt Compressed Help (.qch) of the generated HTML documentation.
++
++GENERATE_QHP = NO
++
++# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
++# be used to specify the file name of the resulting .qch file.
++# The path specified is relative to the HTML output folder.
++
++QCH_FILE =
++
++# The QHP_NAMESPACE tag specifies the namespace to use when generating
++# Qt Help Project output. For more information please see
++# http://doc.trolltech.com/qthelpproject.html#namespace
++
++QHP_NAMESPACE = org.doxygen.Project
++
++# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
++# Qt Help Project output. For more information please see
++# http://doc.trolltech.com/qthelpproject.html#virtual-folders
++
++QHP_VIRTUAL_FOLDER = doc
++
++# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
++# add. For more information please see
++# http://doc.trolltech.com/qthelpproject.html#custom-filters
++
++QHP_CUST_FILTER_NAME =
++
++# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
++# custom filter to add. For more information please see
++# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
++# Qt Help Project / Custom Filters</a>.
++
++QHP_CUST_FILTER_ATTRS =
++
++# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
++# project's
++# filter section matches.
++# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
++# Qt Help Project / Filter Attributes</a>.
++
++QHP_SECT_FILTER_ATTRS =
++
++# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
++# be used to specify the location of Qt's qhelpgenerator.
++# If non-empty doxygen will try to run qhelpgenerator on the generated
++# .qhp file.
++
++QHG_LOCATION =
++
++# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
++# will be generated, which together with the HTML files, form an Eclipse help
++# plugin. To install this plugin and make it available under the help contents
++# menu in Eclipse, the contents of the directory containing the HTML and XML
++# files needs to be copied into the plugins directory of eclipse. The name of
++# the directory within the plugins directory should be the same as
++# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
++# the help appears.
++
++GENERATE_ECLIPSEHELP = NO
++
++# A unique identifier for the eclipse help plugin. When installing the plugin
++# the directory name containing the HTML and XML files should also have
++# this name.
++
++ECLIPSE_DOC_ID = org.doxygen.Project
++
++# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
++# at top of each HTML page. The value NO (the default) enables the index and
++# the value YES disables it. Since the tabs have the same information as the
++# navigation tree you can set this option to NO if you already set
++# GENERATE_TREEVIEW to YES.
++
++DISABLE_INDEX = YES
++
++# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
++# structure should be generated to display hierarchical information.
++# If the tag value is set to YES, a side panel will be generated
++# containing a tree-like index structure (just like the one that
++# is generated for HTML Help). For this to work a browser that supports
++# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
++# Windows users are probably better off using the HTML help feature.
++# Since the tree basically has the same information as the tab index you
++# could consider to set DISABLE_INDEX to NO when enabling this option.
++
++GENERATE_TREEVIEW = NO
++
++# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
++# (range [0,1..20]) that doxygen will group on one line in the generated HTML
++# documentation. Note that a value of 0 will completely suppress the enum
++# values from appearing in the overview section.
++
++ENUM_VALUES_PER_LINE = 4
++
++# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
++# used to set the initial width (in pixels) of the frame in which the tree
++# is shown.
++
++TREEVIEW_WIDTH = 250
++
++# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
++# links to external symbols imported via tag files in a separate window.
++
++EXT_LINKS_IN_WINDOW = NO
++
++# Use this tag to change the font size of Latex formulas included
++# as images in the HTML documentation. The default is 10. Note that
++# when you change the font size after a successful doxygen run you need
++# to manually remove any form_*.png images from the HTML output directory
++# to force them to be regenerated.
++
++FORMULA_FONTSIZE = 10
++
++# Use the FORMULA_TRANPARENT tag to determine whether or not the images
++# generated for formulas are transparent PNGs. Transparent PNGs are
++# not supported properly for IE 6.0, but are supported on all modern browsers.
++# Note that when changing this option you need to delete any form_*.png files
++# in the HTML output before the changes have effect.
++
++FORMULA_TRANSPARENT = YES
++
++# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
++# (see http://www.mathjax.org) which uses client side Javascript for the
++# rendering instead of using prerendered bitmaps. Use this if you do not
++# have LaTeX installed or if you want to formulas look prettier in the HTML
++# output. When enabled you may also need to install MathJax separately and
++# configure the path to it using the MATHJAX_RELPATH option.
++
++USE_MATHJAX = NO
++
++# When MathJax is enabled you need to specify the location relative to the
++# HTML output directory using the MATHJAX_RELPATH option. The destination
++# directory should contain the MathJax.js script. For instance, if the mathjax
++# directory is located at the same level as the HTML output directory, then
++# MATHJAX_RELPATH should be ../mathjax. The default value points to
++# the MathJax Content Delivery Network so you can quickly see the result without
++# installing MathJax.
++# However, it is strongly recommended to install a local
++# copy of MathJax from http://www.mathjax.org before deployment.
++
++MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
++
++# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
++# names that should be enabled during MathJax rendering.
++
++MATHJAX_EXTENSIONS =
++
++# When the SEARCHENGINE tag is enabled doxygen will generate a search box
++# for the HTML output. The underlying search engine uses javascript
++# and DHTML and should work on any modern browser. Note that when using
++# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
++# (GENERATE_DOCSET) there is already a search function so this one should
++# typically be disabled. For large projects the javascript based search engine
++# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
++
++SEARCHENGINE = NO
++
++# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
++# implemented using a PHP enabled web server instead of at the web client
++# using Javascript. Doxygen will generate the search PHP script and index
++# file to put on the web server. The advantage of the server
++# based approach is that it scales better to large projects and allows
++# full text search. The disadvantages are that it is more difficult to setup
++# and does not have live searching capabilities.
++
++SERVER_BASED_SEARCH = NO
++
++#---------------------------------------------------------------------------
++# configuration options related to the LaTeX output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
++# generate Latex output.
++
++GENERATE_LATEX = YES
++
++# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
++# If a relative path is entered the value of OUTPUT_DIRECTORY will be
++# put in front of it. If left blank `latex' will be used as the default path.
++
++LATEX_OUTPUT = latex
++
++# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
++# invoked. If left blank `latex' will be used as the default command name.
++# Note that when enabling USE_PDFLATEX this option is only used for
++# generating bitmaps for formulas in the HTML output, but not in the
++# Makefile that is written to the output directory.
++
++LATEX_CMD_NAME = latex
++
++# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
++# generate index for LaTeX. If left blank `makeindex' will be used as the
++# default command name.
++
++MAKEINDEX_CMD_NAME = makeindex
++
++# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
++# LaTeX documents. This may be useful for small projects and may help to
++# save some trees in general.
++
++COMPACT_LATEX = NO
++
++# The PAPER_TYPE tag can be used to set the paper type that is used
++# by the printer. Possible values are: a4, letter, legal and
++# executive. If left blank a4wide will be used.
++
++PAPER_TYPE = a4wide
++
++# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
++# packages that should be included in the LaTeX output.
++
++EXTRA_PACKAGES =
++
++# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
++# the generated latex document. The header should contain everything until
++# the first chapter. If it is left blank doxygen will generate a
++# standard header. Notice: only use this tag if you know what you are doing!
++
++LATEX_HEADER =
++
++# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
++# the generated latex document. The footer should contain everything after
++# the last chapter. If it is left blank doxygen will generate a
++# standard footer. Notice: only use this tag if you know what you are doing!
++
++LATEX_FOOTER =
++
++# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
++# is prepared for conversion to pdf (using ps2pdf). The pdf file will
++# contain links (just like the HTML output) instead of page references
++# This makes the output suitable for online browsing using a pdf viewer.
++
++PDF_HYPERLINKS = YES
++
++# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
++# plain latex in the generated Makefile. Set this option to YES to get a
++# higher quality PDF documentation.
++
++USE_PDFLATEX = NO
++
++# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
++# command to the generated LaTeX files. This will instruct LaTeX to keep
++# running if errors occur, instead of asking the user for help.
++# This option is also used when generating formulas in HTML.
++
++LATEX_BATCHMODE = NO
++
++# If LATEX_HIDE_INDICES is set to YES then doxygen will not
++# include the index chapters (such as File Index, Compound Index, etc.)
++# in the output.
++
++LATEX_HIDE_INDICES = NO
++
++# If LATEX_SOURCE_CODE is set to YES then doxygen will include
++# source code with syntax highlighting in the LaTeX output.
++# Note that which sources are shown also depends on other settings
++# such as SOURCE_BROWSER.
++
++LATEX_SOURCE_CODE = NO
++
++# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
++# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
++# http://en.wikipedia.org/wiki/BibTeX for more info.
++
++LATEX_BIB_STYLE = plain
++
++#---------------------------------------------------------------------------
++# configuration options related to the RTF output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
++# The RTF output is optimized for Word 97 and may not look very pretty with
++# other RTF readers or editors.
++
++GENERATE_RTF = NO
++
++# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
++# If a relative path is entered the value of OUTPUT_DIRECTORY will be
++# put in front of it. If left blank `rtf' will be used as the default path.
++
++RTF_OUTPUT = rtf
++
++# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
++# RTF documents. This may be useful for small projects and may help to
++# save some trees in general.
++
++COMPACT_RTF = NO
++
++# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
++# will contain hyperlink fields. The RTF file will
++# contain links (just like the HTML output) instead of page references.
++# This makes the output suitable for online browsing using WORD or other
++# programs which support those fields.
++# Note: wordpad (write) and others do not support links.
++
++RTF_HYPERLINKS = NO
++
++# Load style sheet definitions from file. Syntax is similar to doxygen's
++# config file, i.e. a series of assignments. You only have to provide
++# replacements, missing definitions are set to their default value.
++
++RTF_STYLESHEET_FILE =
++
++# Set optional variables used in the generation of an rtf document.
++# Syntax is similar to doxygen's config file.
++
++RTF_EXTENSIONS_FILE =
++
++#---------------------------------------------------------------------------
++# configuration options related to the man page output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
++# generate man pages
++
++GENERATE_MAN = YES
++
++# The MAN_OUTPUT tag is used to specify where the man pages will be put.
++# If a relative path is entered the value of OUTPUT_DIRECTORY will be
++# put in front of it. If left blank `man' will be used as the default path.
++
++MAN_OUTPUT = man
++
++# The MAN_EXTENSION tag determines the extension that is added to
++# the generated man pages (default is the subroutine's section .3)
++
++MAN_EXTENSION = .3
++
++# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
++# then it will generate one additional man file for each entity
++# documented in the real man page(s). These additional files
++# only source the real man page, but without them the man command
++# would be unable to find the correct page. The default is NO.
++
++MAN_LINKS = YES
++
++#---------------------------------------------------------------------------
++# configuration options related to the XML output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_XML tag is set to YES Doxygen will
++# generate an XML file that captures the structure of
++# the code including all documentation.
++
++GENERATE_XML = NO
++
++# The XML_OUTPUT tag is used to specify where the XML pages will be put.
++# If a relative path is entered the value of OUTPUT_DIRECTORY will be
++# put in front of it. If left blank `xml' will be used as the default path.
++
++XML_OUTPUT = xml
++
++# The XML_SCHEMA tag can be used to specify an XML schema,
++# which can be used by a validating XML parser to check the
++# syntax of the XML files.
++
++XML_SCHEMA =
++
++# The XML_DTD tag can be used to specify an XML DTD,
++# which can be used by a validating XML parser to check the
++# syntax of the XML files.
++
++XML_DTD =
++
++# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
++# dump the program listings (including syntax highlighting
++# and cross-referencing information) to the XML output. Note that
++# enabling this will significantly increase the size of the XML output.
++
++XML_PROGRAMLISTING = YES
++
++#---------------------------------------------------------------------------
++# configuration options for the AutoGen Definitions output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
++# generate an AutoGen Definitions (see autogen.sf.net) file
++# that captures the structure of the code including all
++# documentation. Note that this feature is still experimental
++# and incomplete at the moment.
++
++GENERATE_AUTOGEN_DEF = NO
++
++#---------------------------------------------------------------------------
++# configuration options related to the Perl module output
++#---------------------------------------------------------------------------
++
++# If the GENERATE_PERLMOD tag is set to YES Doxygen will
++# generate a Perl module file that captures the structure of
++# the code including all documentation. Note that this
++# feature is still experimental and incomplete at the
++# moment.
++
++GENERATE_PERLMOD = NO
++
++# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
++# the necessary Makefile rules, Perl scripts and LaTeX code to be able
++# to generate PDF and DVI output from the Perl module output.
++
++PERLMOD_LATEX = NO
++
++# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
++# nicely formatted so it can be parsed by a human reader.
++# This is useful
++# if you want to understand what is going on.
++# On the other hand, if this
++# tag is set to NO the size of the Perl module output will be much smaller
++# and Perl will parse it just the same.
++
++PERLMOD_PRETTY = YES
++
++# The names of the make variables in the generated doxyrules.make file
++# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
++# This is useful so different doxyrules.make files included by the same
++# Makefile don't overwrite each other's variables.
++
++PERLMOD_MAKEVAR_PREFIX =
++
++#---------------------------------------------------------------------------
++# Configuration options related to the preprocessor
++#---------------------------------------------------------------------------
++
++# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
++# evaluate all C-preprocessor directives found in the sources and include
++# files.
++
++ENABLE_PREPROCESSING = YES
++
++# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
++# names in the source code. If set to NO (the default) only conditional
++# compilation will be performed. Macro expansion can be done in a controlled
++# way by setting EXPAND_ONLY_PREDEF to YES.
++
++MACRO_EXPANSION = NO
++
++# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
++# then the macro expansion is limited to the macros specified with the
++# PREDEFINED and EXPAND_AS_DEFINED tags.
++
++EXPAND_ONLY_PREDEF = NO
++
++# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
++# pointed to by INCLUDE_PATH will be searched when a #include is found.
++
++SEARCH_INCLUDES = YES
++
++# The INCLUDE_PATH tag can be used to specify one or more directories that
++# contain include files that are not input files but should be processed by
++# the preprocessor.
++
++INCLUDE_PATH =
++
++# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
++# patterns (like *.h and *.hpp) to filter out the header-files in the
++# directories. If left blank, the patterns specified with FILE_PATTERNS will
++# be used.
++
++INCLUDE_FILE_PATTERNS =
++
++# The PREDEFINED tag can be used to specify one or more macro names that
++# are defined before the preprocessor is started (similar to the -D option of
++# gcc). The argument of the tag is a list of macros of the form: name
++# or name=definition (no spaces). If the definition and the = are
++# omitted =1 is assumed. To prevent a macro definition from being
++# undefined via #undef or recursively expanded use the := operator
++# instead of the = operator.
++
++PREDEFINED = APOP_NO_VARIADIC
++
++# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
++# this tag can be used to specify a list of macro names that should be expanded.
++# The macro definition that is found in the sources will be used.
++# Use the PREDEFINED tag if you want to use a different macro definition that
++# overrules the definition found in the source code.
++
++EXPAND_AS_DEFINED =
++
++# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
++# doxygen's preprocessor will remove all references to function-like macros
++# that are alone on a line, have an all uppercase name, and do not end with a
++# semicolon, because these will confuse the parser if not removed.
++
++SKIP_FUNCTION_MACROS = NO
++
++#---------------------------------------------------------------------------
++# Configuration::additions related to external references
++#---------------------------------------------------------------------------
++
++# The TAGFILES option can be used to specify one or more tagfiles. For each
++# tag file the location of the external documentation should be added. The
++# format of a tag file without this location is as follows:
++#
++# TAGFILES = file1 file2 ...
++# Adding location for the tag files is done as follows:
++#
++# TAGFILES = file1=loc1 "file2 = loc2" ...
++# where "loc1" and "loc2" can be relative or absolute paths
++# or URLs. Note that each tag file must have a unique name (where the name does
++# NOT include the path). If a tag file is not located in the directory in which
++# doxygen is run, you must also specify the path to the tagfile here.
++
++TAGFILES =
++
++# When a file name is specified after GENERATE_TAGFILE, doxygen will create
++# a tag file that is based on the input files it reads.
++
++GENERATE_TAGFILE =
++
++# If the ALLEXTERNALS tag is set to YES all external classes will be listed
++# in the class index. If set to NO only the inherited external classes
++# will be listed.
++
++ALLEXTERNALS = NO
++
++# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
++# in the modules index. If set to NO, only the current project's groups will
++# be listed.
++
++EXTERNAL_GROUPS = YES
++
++# The PERL_PATH should be the absolute path and name of the perl script
++# interpreter (i.e. the result of `which perl').
++
++PERL_PATH = /usr/bin/perl
++
++#---------------------------------------------------------------------------
++# Configuration options related to the dot tool
++#---------------------------------------------------------------------------
++
++# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
++# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
++# or super classes. Setting the tag to NO turns the diagrams off. Note that
++# this option also works with HAVE_DOT disabled, but it is recommended to
++# install and use dot, since it yields more powerful graphs.
++
++CLASS_DIAGRAMS = NO
++
++# You can define message sequence charts within doxygen comments using the \msc
++# command. Doxygen will then run the mscgen tool (see
++# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
++# documentation. The MSCGEN_PATH tag allows you to specify the directory where
++# the mscgen tool resides. If left empty the tool is assumed to be found in the
++# default search path.
++
++MSCGEN_PATH =
++
++# If set to YES, the inheritance and collaboration graphs will hide
++# inheritance and usage relations if the target is undocumented
++# or is not a class.
++
++HIDE_UNDOC_RELATIONS = YES
++
++# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
++# available from the path. This tool is part of Graphviz, a graph visualization
++# toolkit from AT&T and Lucent Bell Labs. The other options in this section
++# have no effect if this option is set to NO (the default)
++
++HAVE_DOT = NO
++
++# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
++# allowed to run in parallel. When set to 0 (the default) doxygen will
++# base this on the number of processors available in the system. You can set it
++# explicitly to a value larger than 0 to get control over the balance
++# between CPU load and processing speed.
++
++DOT_NUM_THREADS = 0
++
++# By default doxygen will use the Helvetica font for all dot files that
++# doxygen generates. When you want a differently looking font you can specify
++# the font name using DOT_FONTNAME. You need to make sure dot is able to find
++# the font, which can be done by putting it in a standard location or by setting
++# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
++# directory containing the font.
++
++DOT_FONTNAME = Helvetica
++
++# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
++# The default size is 10pt.
++
++DOT_FONTSIZE = 10
++
++# By default doxygen will tell dot to use the Helvetica font.
++# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
++# set the path where dot can find it.
++
++DOT_FONTPATH =
++
++# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
++# will generate a graph for each documented class showing the direct and
++# indirect inheritance relations. Setting this tag to YES will force the
++# CLASS_DIAGRAMS tag to NO.
++
++CLASS_GRAPH = NO
++
++# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
++# will generate a graph for each documented class showing the direct and
++# indirect implementation dependencies (inheritance, containment, and
++# class references variables) of the class with other documented classes.
++
++COLLABORATION_GRAPH = NO
++
++# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
++# will generate a graph for groups, showing the direct groups dependencies
++
++GROUP_GRAPHS = YES
++
++# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
++# collaboration diagrams in a style similar to the OMG's Unified Modeling
++# Language.
++
++UML_LOOK = NO
++
++# If the UML_LOOK tag is enabled, the fields and methods are shown inside
++# the class node. If there are many fields or methods and many nodes the
++# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
++# threshold limits the number of items for each type to make the size more
++# managable. Set this to 0 for no limit. Note that the threshold may be
++# exceeded by 50% before the limit is enforced.
++
++UML_LIMIT_NUM_FIELDS = 10
++
++# If set to YES, the inheritance and collaboration graphs will show the
++# relations between templates and their instances.
++
++TEMPLATE_RELATIONS = NO
++
++# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
++# tags are set to YES then doxygen will generate a graph for each documented
++# file showing the direct and indirect include dependencies of the file with
++# other documented files.
++
++INCLUDE_GRAPH = NO
++
++# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
++# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
++# documented header file showing the documented files that directly or
++# indirectly include this file.
++
++INCLUDED_BY_GRAPH = NO
++
++# If the CALL_GRAPH and HAVE_DOT options are set to YES then
++# doxygen will generate a call dependency graph for every global function
++# or class method. Note that enabling this option will significantly increase
++# the time of a run. So in most cases it will be better to enable call graphs
++# for selected functions only using the \callgraph command.
++
++CALL_GRAPH = NO
++
++# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
++# doxygen will generate a caller dependency graph for every global function
++# or class method. Note that enabling this option will significantly increase
++# the time of a run. So in most cases it will be better to enable caller
++# graphs for selected functions only using the \callergraph command.
++
++CALLER_GRAPH = NO
++
++# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
++# will generate a graphical hierarchy of all classes instead of a textual one.
++
++GRAPHICAL_HIERARCHY = YES
++
++# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
++# then doxygen will show the dependencies a directory has on other directories
++# in a graphical way. The dependency relations are determined by the #include
++# relations between the files in the directories.
++
++DIRECTORY_GRAPH = YES
++
++# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
++# generated by dot. Possible values are svg, png, jpg, or gif.
++# If left blank png will be used. If you choose svg you need to set
++# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
++# visible in IE 9+ (other browsers do not have this requirement).
++
++DOT_IMAGE_FORMAT = png
++
++# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
++# enable generation of interactive SVG images that allow zooming and panning.
++# Note that this requires a modern browser other than Internet Explorer.
++# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
++# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
++# visible. Older versions of IE do not have SVG support.
++
++INTERACTIVE_SVG = NO
++
++# The tag DOT_PATH can be used to specify the path where the dot tool can be
++# found. If left blank, it is assumed the dot tool can be found in the path.
++
++DOT_PATH =
++
++# The DOTFILE_DIRS tag can be used to specify one or more directories that
++# contain dot files that are included in the documentation (see the
++# \dotfile command).
++
++DOTFILE_DIRS =
++
++# The MSCFILE_DIRS tag can be used to specify one or more directories that
++# contain msc files that are included in the documentation (see the
++# \mscfile command).
++
++MSCFILE_DIRS =
++
++# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
++# nodes that will be shown in the graph. If the number of nodes in a graph
++# becomes larger than this value, doxygen will truncate the graph, which is
++# visualized by representing a node as a red box. Note that doxygen if the
++# number of direct children of the root node in a graph is already larger than
++# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
++# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
++
++DOT_GRAPH_MAX_NODES = 50
++
++# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
++# graphs generated by dot. A depth value of 3 means that only nodes reachable
++# from the root by following a path via at most 3 edges will be shown. Nodes
++# that lay further from the root node will be omitted. Note that setting this
++# option to 1 or 2 may greatly reduce the computation time needed for large
++# code bases. Also note that the size of a graph can be further restricted by
++# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
++
++MAX_DOT_GRAPH_DEPTH = 0
++
++# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
++# background. This is disabled by default, because dot on Windows does not
++# seem to support this out of the box. Warning: Depending on the platform used,
++# enabling this option may lead to badly anti-aliased labels on the edges of
++# a graph (i.e. they become hard to read).
++
++DOT_TRANSPARENT = YES
++
++# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
++# files in one run (i.e. multiple -o and -T options on the command line). This
++# makes dot run faster, but since only newer versions of dot (>1.8.10)
++# support this, this feature is disabled by default.
++
++DOT_MULTI_TARGETS = NO
++
++# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
++# generate a legend page explaining the meaning of the various boxes and
++# arrows in the dot generated graphs.
++
++GENERATE_LEGEND = YES
++
++# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
++# remove the intermediate dot files that are used to generate
++# the various graphs.
++
++DOT_CLEANUP = YES
+--- a/apophenia.pc.in
++++ b/apophenia.pc.in
+@@ -6,6 +6,10 @@
+
+ Name: Apophenia
+ Description: The Apophenia library
++URL: http://apophenia.info/
++Requires: gsl
++Requires.private: sqlite3
+ Version: @VERSION@
+-Libs: -L at libdir@ -lapophenia @LIBS@
+-Cflags: @CFLAGS@
++Cflags: @MYSQL_CFLAGS@
++Libs: -L${libdir} -lapophenia
++Libs.private: @MYSQL_LDFLAGS@
+--- /dev/null
++++ b/cmd/Makefile.am
+@@ -0,0 +1,14 @@
++#The programs
++bin_PROGRAMS = \
++ apop_text_to_db \
++ apop_db_to_crosstab \
++ apop_plot_query
++
++AM_CFLAGS = \
++ -I $(top_srcdir) \
++ $(GSL_CFLAGS)
++
++LDADD = \
++ $(top_builddir)/libapophenia.la \
++ $(GSL_LIBS)
++
+--- a/tests/utilities_test
++++ /dev/null
+@@ -1,52 +0,0 @@
+-Diff(){
+-return `echo 'out=0
+- if (('"$1 - $2"')^2 < 1/1000) out=1
+- print out' | bc -l`
+-}
+-
+-read_faith(){
+- rm -f ff.db
+- if ! apop_text_to_db faith.data faith ff.db ;
+- then return 1;
+- elif ! sed '1,/id/d' faith.data | apop_text_to_db -N"number,len,delay" - faith2 ff.db
+- then return 2;
+- elif Diff `apop_plot_query -n ff.db "select avg(eruptions) - avg(len)
+- from faith, faith2 where id==number" | sed '/avg/d'` 0
+- then return 3;
+- else return 0;
+- fi
+-}
+-
+-crosstab(){
+- if [ ! `apop_db_to_crosstab -eo ff.db "faith group by round(eruptions), waiting" waiting 'round(eruptions)' 'count(id)'|sed -n '/70/p' | cut -f 4` \
+- -eq `sqlite3 ff.db "select count(*) from faith where round(eruptions)=4 and waiting=70"` ]
+- then echo crosstabbing failed.; return 1;
+- elif [ ! `apop_db_to_crosstab -d'|' ff.db "faith group by round(eruptions), waiting" waiting 'round(eruptions)' 'count(id)'|sed -n '/70/p' | cut -d'|' -f 4` \
+- -eq `sqlite3 ff.db "select count(*) from faith where round(eruptions)=4 and waiting=70"` ]
+- then echo crosstabbing with nonstandard delimiter failed.; return 2;
+- else
+- return 0;
+- fi
+-}
+-
+-fixed_read(){
+- apop_text_to_db -ed -f "3,6" -nc test_data_fixed_width td td.db
+- apop_text_to_db -ea -f "3,6" -nc test_data_fixed_width td td.db
+- if Diff $(sqlite3 td.db "select col_2 from td where rowid=4") 2.71828
+- then return 1
+- else return 0
+- fi
+-}
+-
+-#Hard to find where Autoconf put the binaries we're testing.
+-export PATH=..:.:$PATH
+-
+-( #one big subshell, so exits don't kill the parent shell.
+-if [ ! `echo 123 | bc` ];
+- then echo "Missing POSIX-standard bc; exiting without running tests."; exit 0; #not a fail.
+-elif ! read_faith
+- then echo apop_text_to_db test failed with code $?.; exit 1;
+-elif ! fixed_read
+- then echo read of fixed data failed with code $?.; exit 2;
+-fi
+-)
+--- /dev/null
++++ b/tests/utilities_test.in
+@@ -0,0 +1,61 @@
++#!/bin/sh
++
++APOP_DATA_DIR=@abs_top_srcdir@/tests
++APOP_CMD_DIR=@top_builddir@/cmd
++
++BC=@BC@
++SQLITE3=@SQLITE3@
++
++APOP_PLOT_QUERY=${APOP_CMD_DIR}/apop_plot_query
++APOP_TEXT_TO_DB=${APOP_CMD_DIR}/apop_text_to_db
++APOP_DB_TO_CROSSTAB=${APOP_CMD_DIR}/apop_db_to_crosstab
++
++Diff(){
++return `echo 'out=0
++ if (('"$1 - $2"')^2 < 1/1000) out=1
++ print out' | bc -l`
++}
++
++read_faith(){
++ rm -f ff.db
++ if ! $APOP_TEXT_TO_DB ${APOP_DATA_DIR}/faith.data faith ff.db ;
++ then return 1;
++ elif ! sed '1,/id/d' ${APOP_DATA_DIR}/faith.data | $APOP_TEXT_TO_DB -N"number,len,delay" - faith2 ff.db
++ then return 2;
++ elif Diff `$APOP_PLOT_QUERY -n ff.db "select avg(eruptions) - avg(len)
++ from faith, faith2 where id==number" | sed '/avg/d'` 0
++ then return 3;
++ else return 0;
++ fi
++}
++
++crosstab(){
++ if [ ! `$APOP_DB_TO_CROSSTAB -eo ff.db "faith group by round(eruptions), waiting" waiting 'round(eruptions)' 'count(id)'|sed -n '/70/p' | cut -f 4` \
++ -eq `$SQLITE3 ff.db "select count(*) from faith where round(eruptions)=4 and waiting=70"` ]
++ then echo crosstabbing failed.; return 1;
++ elif [ ! `$APOP_DB_TO_CROSSTAB -d'|' ff.db "faith group by round(eruptions), waiting" waiting 'round(eruptions)' 'count(id)'|sed -n '/70/p' | cut -d'|' -f 4` \
++ -eq `$SQLITE3 ff.db "select count(*) from faith where round(eruptions)=4 and waiting=70"` ]
++ then echo crosstabbing with nonstandard delimiter failed.; return 2;
++ else
++ return 0;
++ fi
++}
++
++fixed_read(){
++ $APOP_TEXT_TO_DB -ed -f "3,6" -nc ${APOP_DATA_DIR}/test_data_fixed_width td td.db
++ $APOP_TEXT_TO_DB -ea -f "3,6" -nc ${APOP_DATA_DIR}/test_data_fixed_width td td.db
++ if Diff $($SQLITE3 td.db "select col_2 from td where rowid=4") 2.71828
++ then return 1
++ else return 0
++ fi
++}
++
++( #one big subshell, so exits don't kill the parent shell.
++if [ ! `echo 123 | $BC` ];
++ then echo "Missing POSIX-standard bc; exiting without running tests."; exit 0; #not a fail.
++elif ! read_faith
++ then echo "$APOP_TEXT_TO_DB test failed with code $?."; exit 1;
++elif ! fixed_read
++ then echo "read of fixed data failed with code $?."; exit 2;
++fi
++)
+--- /dev/null
++++ b/transform/Makefile.am
+@@ -0,0 +1,17 @@
++
++noinst_LTLIBRARIES = libapoptransform.la
++
++libapoptransform_la_SOURCES = \
++ apop_dcompose.c \
++ apop_dconstrain.c\
++ apop_fix_params.c \
++ apop_coordinate_transform.c \
++ apop_mixture.c \
++ apop_stack.c
++
++libapoptransform_la_CFLAGS = \
++ -I $(top_srcdir) \
++ $(PTHREAD_CFLAGS) \
++ $(OPENMP_CFLAGS) \
++ $(SQLITE3_CFLAGS) \
++ $(GSL_CFLAGS)
+--- /dev/null
++++ b/model/Makefile.am
+@@ -0,0 +1,30 @@
++
++noinst_LTLIBRARIES = libapopmodel.la
++
++libapopmodel_la_SOURCES = \
++ apop_bernoulli.c \
++ apop_beta.c \
++ apop_dirichlet.c \
++ apop_exponential.c \
++ apop_gamma.c \
++ apop_histogram.c \
++ apop_loess.c \
++ apop_multinomial.c \
++ apop_multivariate_normal.c \
++ apop_normal.c \
++ apop_ols.c \
++ apop_pmf.c \
++ apop_poisson.c \
++ apop_probit.c \
++ apop_t.c \
++ apop_uniform.c \
++ apop_wishart.c \
++ apop_yule.c \
++ apop_zipf.c
++
++libapopmodel_la_CFLAGS = \
++ -I $(top_srcdir) \
++ $(PTHREAD_CFLAGS) \
++ $(OPENMP_CFLAGS) \
++ $(SQLITE3_CFLAGS) \
++ $(GSL_CFLAGS)
+--- /dev/null
++++ b/eg/Makefile.am
+@@ -0,0 +1,39 @@
++
++EXTRA_DIST = \
++ apop_map_row.c \
++ banana.c \
++ binning.c \
++ db_fns.c \
++ dconstrain.c \
++ dot_products.c \
++ draw_some_normals.c \
++ draw_to_db.c \
++ faithful.c \
++ fake_logit.c \
++ fix_params.c \
++ hills2.c \
++ iv.c \
++ jacobian.c \
++ kernel.c \
++ ks_tests.c \
++ ls_tables.c \
++ normalizations.c \
++ ols2.c \
++ ols.c \
++ parameterization.c \
++ pmf_test.c \
++ scatter.c \
++ simple_subsets.c \
++ some_cdfs.c \
++ sql_to_html.c \
++ stack_models.c \
++ t_test_by_rows.c \
++ test_distances.c \
++ test_fisher.c \
++ test_harmonic.c \
++ test_kl_divergence.c \
++ test_pruning.c \
++ test_ranks.c \
++ test_regex.c \
++ test_updating.c \
++ text_demo.c
+--- a/tests/db_tests.c
++++ b/tests/db_tests.c
+@@ -18,6 +18,12 @@
+ export APOP_DB_ENGINE=mysql
+ */
+
++#ifdef Datadir
++#define DATADIR Datadir
++#else
++#define DATADIR "."
++#endif
++
+ #include <apop.h>
+ #include <unistd.h>
+ int verbose = 1;
+@@ -27,7 +33,7 @@
+ void test_data_to_db() {
+ int i, j;
+ if (!apop_table_exists("snps"))
+- apop_text_to_db("data-mixed", "snps");
++ apop_text_to_db( DATADIR "/" "data-mixed" , "snps");
+ apop_data *d = apop_query_to_mixed_data("tvttmmmt", "select * from snps");
+ apop_data_print(d, "snps2", .output_type='d');
+ apop_data *d2 = apop_query_to_mixed_data("vmmmtttt", "select * from snps2");
+@@ -71,11 +77,11 @@
+ apop_db_open(NULL);
+ if (!apop_table_exists("d")){
+ apop_data *field_params = apop_text_alloc(NULL,2,2);
+- apop_text_fill(field_params,
++ apop_text_fill(field_params,
+ "[ab][ab]", "numeric",
+ ".*", apop_opts.db_engine =='s' ? "character": "varchar(20)"
+ );
+- apop_text_to_db("data-mixed", "d", 0, 1, NULL, .field_params=field_params);
++ apop_text_to_db( DATADIR "/" "data-mixed" , "d", 0, 1, NULL, .field_params=field_params);
+ }
+ apop_data *d = apop_query_to_mixed_data ("tmttmmmt", "select * from d");
+ int b_allele_col = apop_name_find(d->names, "b_allele", 't');
+@@ -145,7 +151,7 @@
+ apop_table_exists("nandata", 'd');
+ apop_table_exists("fw", 'd');
+ apop_table_exists("fww", 'd');
+- apop_text_to_db("test_data_nans", "nandata");
++ apop_text_to_db( DATADIR "/" "test_data_nans" , "nandata");
+ strcpy(apop_opts.db_name_column, "head");
+ apop_opts.nan_string = "nan";
+ apop_data *d = apop_query_to_data("select * from nandata");
+@@ -157,7 +163,7 @@
+ assert(!apop_data_get(d2, .rowname="fourth", .colname="b"));
+ apop_data_free(d2);
+ apop_opts.nan_string = "NaN";
+-
++
+ //while we're here, test querying just names & no data.
+ apop_data *justnames = apop_query_to_data("select head from nandata");
+ assert(justnames->names->rowct == 4);
+@@ -165,12 +171,12 @@
+ apop_data_free(justnames);
+
+ //Oh, and let's test fixed-width inputs.
+- apop_text_to_db("test_data_fixed_width", .tabname="fw", .has_col_names='n', .field_ends=(int[]){3,6});
++ apop_text_to_db( DATADIR "/" "test_data_fixed_width" , .tabname="fw", .has_col_names='n', .field_ends=(int[]){3,6});
+ assert(apop_query_to_float("select col_2 from fw")==3.14159);
+ apop_data *t=apop_query_to_text("select col_1 from fw");
+ assert(!strcmp(*t->text[0], "A#C"));
+ assert(!strcmp(*t->text[1], " BC"));
+- apop_text_to_db("test_data_fixed_width", .tabname="fww", .field_names=(char*[]){"number", "text", "foat"}, .field_ends=(int[]){3,6});
++ apop_text_to_db( DATADIR "/" "test_data_fixed_width" , .tabname="fww", .field_names=(char*[]){"number", "text", "foat"}, .field_ends=(int[]){3,6});
+ assert(apop_query_to_float("select number from fww where number<0")==-21);
+ assert(apop_query_to_float("select foat from fww where text=' BC'")==2.71828);
+ unlink("nantest");
+@@ -216,7 +222,7 @@
+ strcpy(apop_opts.output_delimiter, "\t");
+ apop_vector_print(d->weights, .output_type='p', .output_pipe=f);
+ fclose(f);
+- int has_diffs = apop_system("diff -b printing_sample %s", outfile);
++ int has_diffs = apop_system( "diff -b %s/printing_sample %s", DATADIR, outfile);
+ assert(!has_diffs);
+ //apop_system("rm %s", outfile);
+ unlink(outfile);
+@@ -226,7 +232,7 @@
+ void test_crosstabbing() {
+ apop_db_close(); //gotta test it somewhere
+ if (!apop_table_exists("snps"))
+- apop_text_to_db("data-mixed", "snps", 0, 1);
++ apop_text_to_db( DATADIR "/" "data-mixed" , "snps", 0, 1);
+ apop_table_exists("snp_ct", 'd');
+ apop_query("create table snp_ct as "
+ " select a_allele, b_allele, count(*) as ct "
+--- a/tests/test_apop.c
++++ b/tests/test_apop.c
+@@ -26,6 +26,12 @@
+ room for better numeric precision; we all know this without reminders from the
+ post-install tests. */
+
++#ifdef Datadir
++#define DATADIR Datadir
++#else
++#define DATADIR "."
++#endif
++
+ #define _GNU_SOURCE
+ #include <apop.h>
+ #include <unistd.h>
+@@ -570,7 +576,7 @@
+
+ void test_summarize(){
+ apop_table_exists("td", 'd');
+- apop_text_to_db("test_data", .has_row_names= 0,1, .tabname = "td");
++ apop_text_to_db( DATADIR "/" "test_data" , .has_row_names= 0,1, .tabname = "td");
+ gsl_matrix *m = apop_query_to_matrix("select * from td");
+ apop_data *s = apop_data_summarize(apop_matrix_to_data(m));
+ gsl_matrix_free(m);
+@@ -583,8 +589,8 @@
+ }
+
+ void test_dot(){
+-apop_data *d1 = apop_text_to_data(.text_file="test_data2",0,1); // 55 x 2
+-apop_data *d2 = apop_text_to_data("test_data2"); // 55 x 2
++apop_data *d1 = apop_text_to_data(.text_file= DATADIR "/" "test_data2" ,0,1); // 55 x 2
++apop_data *d2 = apop_text_to_data( DATADIR "/" "test_data2" ); // 55 x 2
+ apop_data *d3 = apop_dot(d1, d2, .form2='t');
+ gsl_vector v1 = gsl_matrix_row(d1->matrix, 0).vector;
+ apop_data *dv = apop_vector_to_data(&v1); // 2 x 1
+@@ -951,7 +957,7 @@
+ }
+
+ void dummies_and_factors(){
+- apop_text_to_db("data-mixed", "genes");
++ apop_text_to_db( DATADIR "/" "data-mixed" , "genes");
+ apop_data *d = apop_query_to_mixed_data("mmmt", "select aa, bb, 1, a_allele from genes");
+ apop_data *dum = apop_data_to_dummies(d, 0, 't', 0);
+ check_for_dummies(d, dum, 0);
+@@ -983,7 +989,7 @@
+ }
+
+ void test_transpose(){
+- apop_data *t = apop_text_to_data("test_data", 0, 1);
++ apop_data *t = apop_text_to_data( DATADIR "/" "test_data" , 0, 1);
+ apop_data *tt = apop_data_transpose(t, .inplace='n');
+ assert(apop_data_get(tt, 0, 3) == 9);
+ assert(apop_data_get(tt, 1, 0) == 4);
+@@ -1331,12 +1337,6 @@
+ if (verbose) printf("\nPASS. ");}
+
+ int main(int argc, char **argv){
+- char *srcdir = getenv("srcdir");
+- if (srcdir){ //if defined, this is probably via an automake rule.
+- char buf[10000];
+- if (strcmp(srcdir, ".") && strcmp(srcdir, getcwd(buf, 10000)))
+- apop_system("cp %s/*dat* %s/printing_sample .", srcdir, srcdir); //needed for make distcheck. No-op in many cases.
+- }
+ int slow_tests = 0;
+ apop_opts.thread_count = 2;
+ char c, opts[] = "sqt:";
+@@ -1349,7 +1349,7 @@
+
+ //set up some global or common variables
+ gsl_rng *r = apop_rng_alloc(8);
+- apop_data *d = apop_text_to_data("test_data2",0,1);
++ apop_data *d = apop_text_to_data( DATADIR "/" "test_data2" ,0,1);
+ apop_model *an_ols_model = apop_model_copy(apop_ols);
+ Apop_model_add_group(an_ols_model, apop_lm, .want_expected_value= 1);
+ apop_model *e = apop_estimate(d, an_ols_model);
+--- a/eg/simple_subsets.c
++++ b/eg/simple_subsets.c
+@@ -1,8 +1,14 @@
+ #include <apop.h>
+
++#ifdef Datadir
++#define DATAFILE Datadir "/" "data"
++#else
++#define DATAFILE "data"
++#endif
++
+ int main(){
+- apop_table_exists("data", 'd');
+- apop_data *d = apop_text_to_data("data");
++ apop_table_exists( DATAFILE , 'd');
++ apop_data *d = apop_text_to_data( DATAFILE );
+
+ //tally row zero of the data set's matrix by viewing it as a vector:
+ gsl_vector *one_row = Apop_rv(d, 0);
+--- a/tests/nist_tests.c
++++ b/tests/nist_tests.c
+@@ -2,6 +2,12 @@
+ Notice that I use various levels of tolerance, so this gives you an idea
+ of the relative accuracies of various operations. */
+
++#ifdef Datadir
++#define DATADIR Datadir
++#else
++#define DATADIR "."
++#endif
++
+ #include <apop.h>
+ #include <unistd.h>
+
+@@ -12,7 +18,7 @@
+ #define Diff(L, R, eps) Apop_stopif(isnan(L-R) || fabs((L)-(R))>(eps), abort(), 0, "%g is too different from %g (abitrary limit=%g).", (double)(L), (double)(R), eps);
+
+ void pontius(){
+- apop_text_to_db("pontius.dat","pont", .delimiters=" ");
++ apop_text_to_db( DATADIR "/" "pontius.dat" ,"pont", .delimiters=" ");
+ apop_data *d = apop_query_to_data("select y, x, pow(x,2) as p from pont");
+ apop_model *est = apop_estimate(d, apop_ols);
+
+@@ -28,7 +34,7 @@
+ }
+
+ void wampler1(){
+- apop_text_to_db("wampler1.dat","w1", .delimiters=" ");
++ apop_text_to_db( DATADIR "/" "wampler1.dat" ,"w1", .delimiters=" ");
+ apop_data *d = apop_query_to_data("select y, x, pow(x,2) as p2, \
+ pow(x,3) as p3, pow(x,4) as p4, pow(x,5) as p5 from w1");
+ apop_model *est = apop_estimate(d, apop_ols);
+@@ -41,7 +47,7 @@
+ }
+
+ void numacc4(){
+- apop_data *d = apop_text_to_data("numacc4.dat");
++ apop_data *d = apop_text_to_data( DATADIR "/" "numacc4.dat" );
+ gsl_vector *v = Apop_cv(d, 0);
+ Diff(apop_vector_mean(v), 10000000.2, 1e-5);
+ Diff(apop_vector_var(v)*(v->size -1)/v->size, 0.01, TOL3);
+@@ -50,8 +56,6 @@
+ }
+
+ int main(){
+- chdir(Datadir); //Datadir is defined via autoconf.
+-
+ pontius();
+ wampler1();
+ numacc4();
+--- /dev/null
++++ b/m4/ld-version-script.m4
+@@ -0,0 +1,53 @@
++# ld-version-script.m4 serial 3
++dnl Copyright (C) 2008-2014 Free Software Foundation, Inc.
++dnl This file is free software; the Free Software Foundation
++dnl gives unlimited permission to copy and/or distribute it,
++dnl with or without modifications, as long as this notice is preserved.
++
++dnl From Simon Josefsson
++
++# FIXME: The test below returns a false positive for mingw
++# cross-compiles, 'local:' statements does not reduce number of
++# exported symbols in a DLL. Use --disable-ld-version-script to work
++# around the problem.
++
++# gl_LD_VERSION_SCRIPT
++# --------------------
++# Check if LD supports linker scripts, and define automake conditional
++# HAVE_LD_VERSION_SCRIPT if so.
++AC_DEFUN([gl_LD_VERSION_SCRIPT],
++[
++ AC_ARG_ENABLE([ld-version-script],
++ AS_HELP_STRING([--enable-ld-version-script],
++ [enable linker version script (default is enabled when possible)]),
++ [have_ld_version_script=$enableval], [])
++ if test -z "$have_ld_version_script"; then
++ AC_MSG_CHECKING([if LD -Wl,--version-script works])
++ save_LDFLAGS="$LDFLAGS"
++ LDFLAGS="$LDFLAGS -Wl,--version-script=conftest.map"
++ cat > conftest.map <<EOF
++foo
++EOF
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
++ [accepts_syntax_errors=yes], [accepts_syntax_errors=no])
++ if test "$accepts_syntax_errors" = no; then
++ cat > conftest.map <<EOF
++VERS_1 {
++ global: sym;
++};
++
++VERS_2 {
++ global: sym;
++} VERS_1;
++EOF
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
++ [have_ld_version_script=yes], [have_ld_version_script=no])
++ else
++ have_ld_version_script=no
++ fi
++ rm -f conftest.map
++ LDFLAGS="$save_LDFLAGS"
++ AC_MSG_RESULT($have_ld_version_script)
++ fi
++ AM_CONDITIONAL(HAVE_LD_VERSION_SCRIPT, test "$have_ld_version_script" = "yes")
++])
+--- a/tests/sort_example.c
++++ b/tests/sort_example.c
+@@ -1,19 +1,20 @@
++#ifdef Datadir
++#define DATADIR Datadir
++#else
++#define DATADIR "."
++#endif
++
+ #include <apop.h>
+ #include <unistd.h>
+ #ifdef Testing
+ #include "sort_tests.c" //For Apophenia's test suite, some tedious checks that the sorts worked
+ #endif
+
+-#ifndef Datadir //In the test suite, this is defined via Automake
+-#define Datadir "."
+-#endif
+-
+ //get_distance is for the sort-by-Euclidian distance example below.
+ double get_distance(gsl_vector *v) {return apop_vector_distance(v);}
+
+ int main(){
+- chdir(Datadir); //Datadir is defined via autoconf.
+- apop_text_to_db("amash_vote_analysis.csv", .tabname="amash_vote_analysis");
++ apop_text_to_db( DATADIR "/" "amash_vote_analysis.csv" , .tabname="amash_vote_analysis");
+ apop_data *d = apop_query_to_mixed_data("mntmtm", "select 1,id,party,contribs/1000.0,vote,ideology from amash_vote_analysis ");
+
+ //use the default order of columns for sorting
+@@ -48,7 +49,7 @@
+
+ //take each row of the matrix as a vector; store the Euclidian distance to the origin in the vector;
+ //sort in descending order.
+- apop_data *rowvectors = apop_text_to_data("test_data");
++ apop_data *rowvectors = apop_text_to_data( DATADIR "/" "test_data" );
+ apop_map(rowvectors, .fn_v=get_distance, .part='r', .inplace='y');
+ apop_data *arow = apop_data_copy(Apop_r(rowvectors, 0));
+ arow->matrix=NULL; //sort only by the distance vector
diff --git a/debian/patches/upstream-rationalization-version_script.patch b/debian/patches/upstream-rationalization-version_script.patch
new file mode 100644
index 0000000..c0309ff
--- /dev/null
+++ b/debian/patches/upstream-rationalization-version_script.patch
@@ -0,0 +1,360 @@
+Description: rationalization -- version script
+ Provides a version script [1] for the shipped library.
+ The map was basically generated from the (unique) header apop.h with
+ the help of cproto as follows:
+ $ cproto -X 1 -f 0 apop.h | sed -e '/^\/\*/d' | tr -d '*()' | rev | cut -d ' ' -f1 | rev ;
+ The version script, along the script to generate it, has been submitted to
+ the upstream maintainer.
+ [1] https://www.gnu.org/software/gnulib/manual/html_node/LD-Version-Scripts.html
+Origin: debian
+Author: Jerome Benoit <calculus at rezozer.net>
+Last-Update: 2014-08-11
+
+--- /dev/null
++++ b/apophenia.map
+@@ -0,0 +1,345 @@
++LIBAPOPHENIA_0.0.0 {
++global:
++apop_opts;
++apop_name_alloc;
++apop_name_add;
++apop_name_free;
++apop_name_print;
++apop_name_stack_base;
++variadic_apop_name_stack;
++apop_name_copy;
++apop_name_find;
++apop_data_add_names_base;
++apop_data_free_base;
++apop_matrix_to_data;
++apop_vector_to_data;
++apop_data_alloc_base;
++variadic_apop_data_alloc;
++apop_data_calloc_base;
++variadic_apop_data_calloc;
++apop_data_stack_base;
++variadic_apop_data_stack;
++apop_data_split;
++apop_data_copy;
++apop_data_rm_columns;
++apop_data_memcpy;
++apop_data_ptr_base;
++variadic_apop_data_ptr;
++apop_data_get_base;
++variadic_apop_data_get;
++apop_data_set_base;
++variadic_apop_data_set;
++apop_data_add_named_elmt;
++apop_text_add;
++apop_text_alloc;
++apop_text_free;
++apop_data_transpose_base;
++variadic_apop_data_transpose;
++apop_matrix_realloc;
++apop_vector_realloc;
++apop_data_prune_columns_base;
++apop_data_get_page_base;
++variadic_apop_data_get_page;
++apop_data_add_page;
++apop_data_rm_page_base;
++variadic_apop_data_rm_page;
++apop_data_rm_rows_base;
++variadic_apop_data_rm_rows;
++apop_model_draws_base;
++variadic_apop_model_draws;
++apop_vector_copy;
++apop_vector_to_matrix_base;
++variadic_apop_vector_to_matrix;
++apop_matrix_copy;
++apop_db_to_crosstab;
++apop_array_to_vector_base;
++variadic_apop_array_to_vector;
++apop_text_to_data_base;
++variadic_apop_text_to_data;
++apop_text_to_db_base;
++variadic_apop_text_to_db;
++apop_data_rank_expand;
++apop_data_rank_compress;
++apop_crosstab_to_db;
++apop_data_pack_base;
++variadic_apop_data_pack;
++apop_data_unpack_base;
++variadic_apop_data_unpack;
++apop_data_fill_base;
++apop_vector_fill_base;
++apop_text_fill_base;
++apop_data_set_row;
++apop_beta;
++apop_bernoulli;
++apop_binomial;
++apop_chi_squared;
++apop_dirichlet;
++apop_exponential;
++apop_f_distribution;
++apop_gamma;
++apop_improper_uniform;
++apop_iv;
++apop_kernel_density;
++apop_loess;
++apop_logit;
++apop_lognormal;
++apop_multinomial;
++apop_multivariate_normal;
++apop_normal;
++apop_ols;
++apop_pmf;
++apop_poisson;
++apop_probit;
++apop_t_distribution;
++apop_uniform;
++apop_wls;
++apop_yule;
++apop_zipf;
++apop_coordinate_transform;
++apop_composition;
++apop_dconstrain;
++apop_mixture;
++apop_stack;
++apop_model_free;
++apop_model_print;
++apop_model_show;
++apop_model_copy;
++apop_model_clear;
++apop_estimate;
++apop_score;
++apop_log_likelihood;
++apop_p;
++apop_cdf;
++apop_draw;
++apop_prep;
++apop_parameter_model;
++apop_predict;
++apop_beta_from_mean_var;
++apop_model_set_parameters_base;
++apop_model_mixture_base;
++apop_model_stack_base;
++apop_map_base;
++variadic_apop_map;
++apop_map_sum_base;
++variadic_apop_map_sum;
++apop_matrix_map;
++apop_vector_map;
++apop_matrix_apply;
++apop_vector_apply;
++apop_matrix_map_all;
++apop_matrix_apply_all;
++apop_vector_map_sum;
++apop_matrix_map_sum;
++apop_matrix_map_all_sum;
++apop_plot_line_and_scatter_base;
++variadic_apop_plot_line_and_scatter;
++apop_plot_histogram_base;
++variadic_apop_plot_histogram;
++apop_plot_lattice_base;
++variadic_apop_plot_lattice;
++apop_plot_qq_base;
++variadic_apop_plot_qq;
++apop_plot_triangle_base;
++variadic_apop_plot_triangle;
++apop_matrix_print_base;
++variadic_apop_matrix_print;
++apop_vector_print_base;
++variadic_apop_vector_print;
++apop_data_print_base;
++variadic_apop_data_print;
++apop_matrix_show;
++apop_vector_show;
++apop_data_show;
++apop_vector_mean_base;
++variadic_apop_vector_mean;
++apop_vector_var_base;
++variadic_apop_vector_var;
++apop_vector_skew_pop_base;
++variadic_apop_vector_skew_pop;
++apop_vector_kurtosis_pop_base;
++variadic_apop_vector_kurtosis_pop;
++apop_vector_cov_base;
++variadic_apop_vector_cov;
++apop_vector_distance_base;
++variadic_apop_vector_distance;
++apop_vector_normalize_base;
++variadic_apop_vector_normalize;
++apop_matrix_normalize;
++apop_data_covariance;
++apop_data_correlation;
++apop_matrix_sum;
++apop_matrix_mean;
++apop_matrix_mean_and_var;
++apop_data_summarize;
++apop_test_fisher_exact;
++apop_matrix_is_positive_semidefinite_base;
++variadic_apop_matrix_is_positive_semidefinite;
++apop_matrix_to_positive_semidefinite;
++apop_multivariate_gamma;
++apop_multivariate_lngamma;
++apop_t_test;
++apop_paired_t_test;
++apop_anova_base;
++variadic_apop_anova;
++apop_f_test_base;
++variadic_apop_f_test;
++apop_text_unique_elements;
++apop_vector_unique_elements;
++apop_data_to_factors_base;
++variadic_apop_data_to_factors;
++apop_data_get_factor_names_base;
++variadic_apop_data_get_factor_names;
++apop_data_to_dummies_base;
++variadic_apop_data_to_dummies;
++apop_kl_divergence_base;
++variadic_apop_kl_divergence;
++apop_estimate_coefficient_of_determination;
++apop_estimate_parameter_tests;
++apop_jackknife_cov;
++apop_bootstrap_cov_base;
++variadic_apop_bootstrap_cov;
++apop_rng_alloc;
++apop_rng_GHgB3;
++apop_rng_get_thread_base;
++apop_arms_draw;
++apop_numerical_gradient_base;
++variadic_apop_numerical_gradient;
++apop_model_hessian_base;
++variadic_apop_model_hessian;
++apop_model_numerical_covariance_base;
++variadic_apop_model_numerical_covariance;
++apop_maximum_likelihood;
++apop_estimate_restart_base;
++variadic_apop_estimate_restart;
++apop_linear_constraint_base;
++variadic_apop_linear_constraint;
++apop_model_fix_params;
++apop_model_fix_params_get_base;
++apop_vtable_add;
++apop_vtable_get;
++apop_vtable_drop;
++apop_update_type_check;
++apop_score_type_check;
++apop_parameter_model_type_check;
++apop_predict_type_check;
++apop_model_print_type_check;
++apop_generalized_harmonic;
++apop_test_anova_independence;
++apop_regex_base;
++variadic_apop_regex;
++apop_system;
++apop_vector_moving_average;
++apop_histograms_test_goodness_of_fit;
++apop_test_kolmogorov;
++apop_data_pmf_compress;
++apop_data_to_bins_base;
++variadic_apop_data_to_bins;
++apop_model_to_pmf_base;
++variadic_apop_model_to_pmf;
++apop_text_paste_base;
++variadic_apop_text_paste;
++apop_data_listwise_delete_base;
++variadic_apop_data_listwise_delete;
++apop_ml_impute;
++apop_model_metropolis_base;
++variadic_apop_model_metropolis;
++apop_update_base;
++variadic_apop_update;
++apop_test_base;
++variadic_apop_test;
++apop_vector_percentiles_base;
++variadic_apop_vector_percentiles;
++apop_data_sort_base;
++variadic_apop_data_sort;
++apop_rake_base;
++variadic_apop_rake;
++apop_det_and_inv;
++apop_dot_base;
++variadic_apop_dot;
++apop_vector_bounded_base;
++variadic_apop_vector_bounded;
++apop_matrix_inverse;
++apop_matrix_determinant;
++apop_matrix_pca_base;
++variadic_apop_matrix_pca;
++apop_vector_stack_base;
++variadic_apop_vector_stack;
++apop_matrix_stack_base;
++variadic_apop_matrix_stack;
++apop_matrix_rm_columns;
++apop_vector_log;
++apop_vector_log10;
++apop_vector_exp;
++apop_vector_sum;
++apop_vector_var_m;
++apop_vector_correlation;
++apop_vector_kurtosis;
++apop_vector_skew;
++apop_table_exists_base;
++variadic_apop_table_exists;
++apop_db_open;
++apop_db_close_base;
++variadic_apop_db_close;
++apop_query;
++apop_query_to_matrix;
++apop_query_to_text;
++apop_query_to_data;
++apop_query_to_mixed_data;
++apop_query_to_vector;
++apop_query_to_float;
++apop_data_to_db;
++apop_db_t_test;
++apop_db_paired_t_test;
++apop_settings_get_grp;
++apop_settings_remove_group;
++apop_settings_copy_group;
++apop_settings_group_alloc;
++apop_settings_group_alloc_wm;
++apop_ct_settings_init;
++apop_ct_settings_copy;
++apop_ct_settings_free;
++apop_lm_settings_init;
++apop_lm_settings_copy;
++apop_lm_settings_free;
++apop_pm_settings_init;
++apop_pm_settings_copy;
++apop_pm_settings_free;
++apop_pmf_settings_init;
++apop_pmf_settings_copy;
++apop_pmf_settings_free;
++apop_mle_settings_init;
++apop_mle_settings_copy;
++apop_mle_settings_free;
++apop_cdf_settings_init;
++apop_cdf_settings_copy;
++apop_cdf_settings_free;
++apop_arms_settings_init;
++apop_arms_settings_copy;
++apop_arms_settings_free;
++apop_mcmc_settings_init;
++apop_mcmc_settings_copy;
++apop_mcmc_settings_free;
++apop_loess_settings_init;
++apop_loess_settings_copy;
++apop_loess_settings_free;
++apop_stack_settings_init;
++apop_stack_settings_copy;
++apop_stack_settings_free;
++apop_mixture_settings_init;
++apop_mixture_settings_copy;
++apop_mixture_settings_free;
++apop_dconstrain_settings_init;
++apop_dconstrain_settings_copy;
++apop_dconstrain_settings_free;
++apop_composition_settings_init;
++apop_composition_settings_copy;
++apop_composition_settings_free;
++apop_parts_wanted_settings_init;
++apop_parts_wanted_settings_copy;
++apop_parts_wanted_settings_free;
++apop_kernel_density_settings_init;
++apop_kernel_density_settings_copy;
++apop_kernel_density_settings_free;
++
++local: *;
++};
diff --git a/debian/repack b/debian/repack
new file mode 100755
index 0000000..2f0a902
--- /dev/null
+++ b/debian/repack
@@ -0,0 +1,110 @@
+#!/bin/sh
+
+PACKAGE_NAME=apophenia
+
+set -e
+set -u
+
+usage() {
+ echo "Usage: repack --upstream-version <ver> <downloaded file>"
+ exit 1
+ }
+
+if [ "$#" != "3" ]; then
+ usage
+fi
+if [ "$1" != "--upstream-version" ]; then
+ usage
+fi
+if [ ! -f "$3" ]; then
+ if [ -n "$3" ]; then
+ echo "$3 doesn't exist"
+ fi
+ usage
+fi
+UPSTREAM_VERSION="$2"
+UPSTREAM_TARBALLZZ="$3"
+
+DEBIAN_SUFFIX="+ds"
+
+DEBIAN_UVERSION=${UPSTREAM_VERSION}${DEBIAN_SUFFIX}
+DEBIAN_ROOTFOLDERNAME="${PACKAGE_NAME}-${DEBIAN_UVERSION}.orig"
+DEBIAN_TARBALLXZ="$(dirname $UPSTREAM_TARBALLZZ)/${PACKAGE_NAME}_${DEBIAN_UVERSION}.orig.tar.xz"
+
+REPACK_TMPDIR=`mktemp -d ./repackXXXXXX`
+REPACK_TMPDIR=$(readlink -f "$REPACK_TMPDIR")
+trap "/bin/rm -rf \"$REPACK_TMPDIR\"" QUIT INT EXIT
+
+message() {
+ echo
+ echo "-- -- $1"
+ echo
+ }
+
+message "Repackaging $UPSTREAM_TARBALLZZ"
+
+UPSTREAM_ROOTFOLDER="${REPACK_TMPDIR}/unpacked"
+mkdir "${UPSTREAM_ROOTFOLDER}"
+tar -C "${UPSTREAM_ROOTFOLDER}" -xf "${UPSTREAM_TARBALLZZ}" || unzip -d "${UPSTREAM_ROOTFOLDER}" "${UPSTREAM_TARBALLZZ}"
+if [ `ls -1 "${UPSTREAM_ROOTFOLDER}" | wc -l` -eq 1 ]; then
+ UPSTREAM_ROOTFOLDER="${UPSTREAM_ROOTFOLDER}/`ls -1 "${UPSTREAM_ROOTFOLDER}"`"
+fi
+
+DEBIAN_ROOTFOLDER="${REPACK_TMPDIR}/${DEBIAN_ROOTFOLDERNAME}"
+## repack
+set -f
+REPACK_WORKING_FOLDER=$(pwd)
+cd "${UPSTREAM_ROOTFOLDER}"
+
+####. "${REPACK_WORKING_FOLDER}/debian/repack.local"
+## wipe out
+## clean up
+rm --verbose --force apophenia.pc
+##
+rm --verbose --force m4/lt~obsolete.m4
+rm --verbose --force m4/ltsugar.m4
+rm --verbose --force m4/ltoptions.m4
+rm --verbose --force m4/ltversion.m4
+rm --verbose --force m4/libtool.m4
+rm --verbose --force tests/Makefile.in
+rm --verbose --force tests/Makefile
+rm --verbose --force acinclude.m4
+rm --verbose --force aclocal.m4
+rm --verbose --force config.h.in
+rm --verbose --force Makefile.in
+rm --verbose --force test-driver
+rm --verbose --force depcomp
+rm --verbose --force install-sh
+rm --verbose --force ltmain.sh
+rm --verbose --force missing
+rm --verbose --force config.sub
+rm --verbose --force config.guess
+rm --verbose --force configure
+#:
+
+cd ${REPACK_WORKING_FOLDER}
+set +f
+## end
+mv "${UPSTREAM_ROOTFOLDER}" "${DEBIAN_ROOTFOLDER}"
+
+REPACK_TARBALL="${REPACK_TMPDIR}/repacked.tar"
+REPACK_TARBALLXZ="${REPACK_TARBALL}.xz"
+( cd "${REPACK_TMPDIR}" && \
+ find -L "${DEBIAN_ROOTFOLDERNAME}" -xdev -type f -o -type d -print | sort | \
+ tar -T- --owner=root --group=root --mode=a+rX --create --file "${REPACK_TARBALL}" \
+ )
+xz -9e < "${REPACK_TARBALL}" > "${REPACK_TARBALLXZ}"
+mv "${REPACK_TARBALLXZ}" "${DEBIAN_TARBALLXZ}"
+
+message "Testing ${DEBIAN_TARBALLXZ}"
+
+xz --verbose --test "${DEBIAN_TARBALLXZ}"
+
+message "Printing information about ${DEBIAN_TARBALLXZ}"
+
+xz --verbose --list "${DEBIAN_TARBALLXZ}"
+
+message "Quitting"
+
+##
+## eos
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..131a82e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+default:
+ @uscan --no-conf --dehs --report || true
+
+%:
+ dh $@ --with autoreconf
+
+override_dh_auto_configure:
+ dh_auto_configure -- --enable-maintainer-mode
+
+override_dh_strip:
+ dh_strip --dbg-package=libapophenia0-dbg
+
+get-orig-source:
+ uscan --no-conf --download-current-version --verbose
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..f598275
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/adhoc/images/structs.png
diff --git a/debian/source/lintian-overrides b/debian/source/lintian-overrides
new file mode 100644
index 0000000..8b06cb1
--- /dev/null
+++ b/debian/source/lintian-overrides
@@ -0,0 +1 @@
+debian-watch-may-check-gpg-signature
diff --git a/debian/source/options b/debian/source/options
new file mode 100644
index 0000000..22a4de9
--- /dev/null
+++ b/debian/source/options
@@ -0,0 +1,2 @@
+compression = xz
+compression-level = 9
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..133f64d
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+opts=dversionmangle=s/\+ds//,filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/apophenia-$1\.tar\.gz/ \
+https://github.com/b-k/Apophenia/tags .*/v?(\d\S*)\.tar\.gz \
+debian sh debian/repack
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/apophenia.git
More information about the debian-science-commits
mailing list