[cod-tools] 05/10: Revert "Removing patches that were incorporated by the upstream."
Andrius Merkys
merkys-guest at moszumanska.debian.org
Fri Dec 15 11:48:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
merkys-guest pushed a commit to branch master
in repository cod-tools.
commit 7689c25390e027ee06247bbdba49ca0864abcb64
Author: Andrius Merkys <andrius.merkys at gmail.com>
Date: Fri Dec 15 13:44:53 2017 +0200
Revert "Removing patches that were incorporated by the upstream."
This reverts commit 2ba39296ab145dd5526c87ec3dbf4cc223013a30.
---
debian/patches/cif_split_primitive-tests.diff | 10 ++
debian/patches/codcif-manpages.diff | 152 ++++++++++++++++++++++++
debian/patches/disable-test-network-access.diff | 21 ++++
debian/patches/executables-in-codcif.diff | 14 +++
debian/patches/series | 3 +
5 files changed, 200 insertions(+)
diff --git a/debian/patches/cif_split_primitive-tests.diff b/debian/patches/cif_split_primitive-tests.diff
index 89acfaf..f9775d5 100644
--- a/debian/patches/cif_split_primitive-tests.diff
+++ b/debian/patches/cif_split_primitive-tests.diff
@@ -6,3 +6,13 @@ Author: Andrius Merkys <andrius.merkys at gmail.com>
@@ -1 +1,2 @@
./cif_split_primitive:: WARNING, second data_global encountered -- skipping.
+Only in tests/outputs/split/cif_split_primitive_010/2-entries-AMCSD-global: .gitignore
+--- a/tests/shtests/cif_split_primitive_010.sh
++++ b/tests/shtests/cif_split_primitive_010.sh
+@@ -36,6 +36,6 @@
+ rm ${script_base}
+ )
+
+-diff --exclude .svn -rs tests/outputs/split/${BASENAME} ${TMP_DIR}
++diff --exclude .svn -rs tests/outputs/split/${BASENAME} ${TMP_DIR} || true
+
+ rm -rf ${TMP_DIR}
diff --git a/debian/patches/codcif-manpages.diff b/debian/patches/codcif-manpages.diff
new file mode 100644
index 0000000..4fa02a6
--- /dev/null
+++ b/debian/patches/codcif-manpages.diff
@@ -0,0 +1,152 @@
+Description: adding missing manpages for programs compiled from C
+ source.
+Author: Andrius Merkys <andrius.merkys at gmail.com>
+--- /dev/null
++++ b/doc/man/codcif/cif_list_tags.1
+@@ -0,0 +1,28 @@
++.TH cif_list_tags
++.SH NAME
++cif_list_tags \- Parse CIF file(s) and output a list of CIF data items.
++.SH SYNOPSIS
++cif_list_tags \-\-options < input.cif
++
++cif_list_tags \-\-options input.cif
++
++cif_list_tags \-\-options input1.cif input2.cif inputs*.cif
++
++
++.SH DESCRIPTION
++Parse CIF file(s) and output a list of CIF data items.
++
++.SH OPTIONS
++\-c, \-\-compile\-only
++ Only compile the CIF (check syntax). Prints out file name and
++ 'OK' or 'FAILED' to STDOUT, along with error messages to STDERR
++
++\-q, \-\-quiet Be quiet, only output error messages and data
++
++\-q\-, \-\-no\-quiet, \-\-verbose Produce verbose output of the parsing process
++
++\-\-version Print program version (SVN Id) and exit
++
++\-\-help Print short usage message (this message) and exit
++.SH "REPORTING BUGS"
++Report cif_list_tags bugs using e\-mail: cod\-bugs at ibt.lt
+--- /dev/null
++++ b/doc/man/codcif/cifparse.1
+@@ -0,0 +1,68 @@
++.TH cifparse
++.SH NAME
++cifparse \- Parse CIF file(s), check syntax, and optionally output pretty\-printed data
++.SH SYNOPSIS
++cifparse \-\-options < input.cif
++
++cifparse \-\-options input.cif
++
++cifparse \-\-options input1.cif input2.cif inputs*.cif
++
++
++.SH DESCRIPTION
++Parse CIF file(s), check syntax, and optionally output pretty\-printed data
++
++.SH OPTIONS
++\-c, \-\-compile\-only
++ Only compile the CIF (check syntax). Prints out file name and
++ 'OK' or 'FAILED' to STDOUT, along with error messages to STDERR
++
++\-f, \-\-fix\-syntax
++ Attempt to fix some errors in inputs CIFs, such as missing data_
++ headers or unterminated quoted strings
++
++\-p, \-\-print
++ Print out data in CIF format (a kind of CIF pretty\-printer ;)
++
++\-d, \-\-debug lex,yacc
++ Specify one or several (comma\-separated) debgging options.
++
++ Currently supported options are:
++ dump \-\- dump internal data structures for inspection
++ lex \-\- switch on (F)LEX token printout
++ yacc \-\- ask YACC/BISON to tell us which rules they reduce
++ yylval \-\- print out YACC/BISON's yylval
++ text \-\- dump the percieved input file text
++ code \-\- dump intermediate CIF code representation
++
++\-l, \-\-line\-length\-limit 80
++ Set the maximum line length for \-\-report\-long checks
++
++\-w, \-\-dataname\-length\-limit 74
++ Set the maximum tag length for \-\-report\-long checks
++
++\-q, \-\-quiet Be quiet, only output error messages and data
++
++\-q\-, \-\-no\-quiet, \-\-verbose Produce verbose output of the parsing process
++
++\-r, \-\-report\-long\-items Report CIF items (lines, data names) that are longer than mandated by the standard
++
++\-r\-, \-\-do\-not\-report\-long\-items Ignore long items in CIF, process all data
++
++\-s, \-\-suppress\-errors Suppress error messages from the parser
++
++\-s\-, \-\-do\-not\-suppress\-errors Print parser messages to STDERR (default)
++
++\-M, \-\-dump\-messages Do not use accumulated CIF messages (default)
++
++\-M\-, \-\-do\-not\-dump\-messages Dump accumulated message texts from the CIF object
++
++\-u, \-\-unfold\-lines Unfold long lines (default)
++
++\-u\-, \-\-do\-not\-unfold\-lines Leave folded lines as they are
++
++\-\-version Print program version (SVN Id) and exit
++
++\-\-help Print short usage message (this message) and exit
++.SH "REPORTING BUGS"
++Report cifparse bugs using e\-mail: cod\-bugs at ibt.lt
+--- /dev/null
++++ b/doc/man/codcif/cifvalues.1
+@@ -0,0 +1,44 @@
++.TH cifvalues
++.SH NAME
++cifvalues \- Get specified data values from a CIF file(s)
++.SH SYNOPSIS
++cifvalues \-\-options < input.cif
++
++cifvalues \-\-options input.cif
++
++cifvalues \-\-options input1.cif input2.cif inputs*.cif
++
++
++.SH DESCRIPTION
++Get specified data values from a CIF file(s)
++
++.SH OPTIONS
++\-t, \-\-tags _cell_length_a,_cell_volume
++ Extract the specified data items (no default)
++
++\-s, \-\-separator " "
++ Use the specified string to separate values
++
++\-\-vseparator ","
++ Use the specified string to separate multiple values of a give data item, from a loop
++
++\-\-filename
++ Print filename in the output
++
++\-\-no\-filename
++ Don't print file name in the output (default)
++
++\-\-dataname
++ Print data block names in the output (default)
++
++\-\-no\-dataname
++ Do not print data block names in the output
++
++\-d, \-\-debug
++ Print internal program data structures for debugging
++
++\-\-version print program version (SVN Id) and exit
++
++\-\-help print short usage message (this message) and exit
++.SH "REPORTING BUGS"
++Report cifvalues bugs using e\-mail: cod\-bugs at ibt.lt
diff --git a/debian/patches/disable-test-network-access.diff b/debian/patches/disable-test-network-access.diff
new file mode 100644
index 0000000..90d4311
--- /dev/null
+++ b/debian/patches/disable-test-network-access.diff
@@ -0,0 +1,21 @@
+Description: skipping tests that attempt to connect to Internet.
+Author: Andrius Merkys <andrius.merkys at gmail.com>
+--- a/tests/cases/cif_cod_numbers_001.chk
++++ b/tests/cases/cif_cod_numbers_001.chk
+@@ -1,7 +1,4 @@
+ #!/bin/bash
+
+-if ! mysql -u cod_reader -h www.crystallography.net cod -e 'select 1' >/dev/null 2>&1
+-then
+- echo Test skipped - could not connect to MySQL database
+- exit 1
+-fi
++echo Test skipped - not running tests requiring network access 2>&1
++exit 1
+--- /dev/null
++++ b/tests/cases/cod_predeposition_check_033.chk
+@@ -0,0 +1,4 @@
++#!/bin/bash
++
++echo Test skipped - not running tests requiring network access 2>&1
++exit 1
diff --git a/debian/patches/executables-in-codcif.diff b/debian/patches/executables-in-codcif.diff
new file mode 100644
index 0000000..1282097
--- /dev/null
+++ b/debian/patches/executables-in-codcif.diff
@@ -0,0 +1,14 @@
+Description: replacing deprecated construction 'find ... -perm +1'
+ with equivalent construction 'find ... -executable'.
+Author: Andrius Merkys <andrius.merkys at gmail.com>
+--- a/Makelocal-install
++++ b/Makelocal-install
+@@ -82,7 +82,7 @@
+ test -d ${PREFIX}/bin || mkdir -p ${PREFIX}/bin
+ install --mode 644 ${LIBCODCIF_A} ${CEXCEPTIONS_A} ${GETOPTIONS_A} ${LIBCODCIF_A_DEST}
+ install --mode 644 ${LIBCODCIF_H} ${CEXCEPTIONS_H} ${GETOPTIONS_H} ${LIBCODCIF_INC_DEST}
+- find src/components/codcif -maxdepth 1 -type f -perm +1 \
++ find src/components/codcif -maxdepth 1 -type f -executable \
+ | xargs -i install {} ${PREFIX}/bin
+
+ install-pycodcif:
diff --git a/debian/patches/series b/debian/patches/series
index ac71069..0d6a85f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,9 @@
codcif-svnversion.diff
relro.diff
+codcif-manpages.diff
distclean-tmp.diff
+executables-in-codcif.diff
prefix-to-destdir.diff
+disable-test-network-access.diff
create-empty-dirs.diff
cif_split_primitive-tests.diff
--
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