[voronota] 01/03: Moving missing manpages to a patch, somewhy not working yet.

Andrius Merkys merkys-guest at moszumanska.debian.org
Wed Oct 18 08:48:15 UTC 2017 

This is an automated email from the git hooks/post-receive script.

merkys-guest pushed a commit to branch master
in repository voronota.

commit f58ac5b78808fdb6c9df6c3df6d7f480e2a1aff8
Author: Andrius Merkys <andrius.merkys at gmail.com>
Date:   Wed Oct 18 11:42:39 2017 +0300

    Moving missing manpages to a patch, somewhy not working yet.
---
 debian/patches/manfiles.diff | 224 +++++++++++++++++++++++++++++++++++++++++++
 debian/patches/series        |   1 +
 debian/rules                 |  15 ---
 3 files changed, 225 insertions(+), 15 deletions(-)

diff --git a/debian/patches/manfiles.diff b/debian/patches/manfiles.diff
new file mode 100644
index 0000000..130af1a
--- /dev/null
+++ b/debian/patches/manfiles.diff
@@ -0,0 +1,224 @@
+--- /dev/null
++++ b/voronota-cadscore.man
+@@ -0,0 +1,72 @@
++.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
++.TH VORONOTA-CADSCORE "1" "October 2017" "voronota-cadscore 1.18.1877" "User Commands"
++.SH NAME
++voronota-cadscore \- manual page for voronota-cadscore 1.18.1877
++.SH DESCRIPTION
++\&'voronota\-cadscore' script is an implementation of CAD\-score method using Voronota.
++.SS "Basic options:"
++.TP
++\fB\-\-input\-target\fR | \fB\-t\fR
++string   *  input target structure file in PDB format
++.TP
++\fB\-\-input\-model\fR | \fB\-m\fR
++string   *  input model structure file in PDB format
++.TP
++\fB\-\-input\-filter\-query\fR
++string      input atoms filtering query parameters
++.TP
++\fB\-\-output\-residue\-scores\fR
++string      output text file with residue scores
++.TP
++\fB\-\-output\-residue\-scores\-pdb\-t\fR
++string      output target PDB file with residue scores as B\-factors
++.TP
++\fB\-\-output\-residue\-scores\-pdb\-m\fR
++string      output model PDB file with residue scores as B\-factors
++.TP
++\fB\-\-smoothing\-window\fR
++number      residue scores smoothing window size, default is 0
++.TP
++\fB\-\-contacts\-query\fR
++string      contacts query parameters
++.TP
++\fB\-\-contacts\-query\-inter\-chain\fR
++flag to consider only inter\-chain contacts
++.TP
++\fB\-\-contacts\-query\-by\-code\fR
++string      contacts query code, possible codes are AA, AS, SS, AM, MM, MS
++.TP
++\fB\-\-use\-all\-query\-codes\fR
++flag to output global scores for all query codes, one line per code
++.TP
++\fB\-\-cache\-dir\fR
++string      path to cache directory
++.TP
++\fB\-\-output\-header\fR
++flag to output header before result line
++.TP
++\fB\-\-help\fR | \fB\-h\fR
++flag to display help message and exit
++.SS "Advanced options:"
++.TP
++\fB\-\-ignore\-residue\-names\fR
++flag to consider just residue numbers and ignore residue names
++.TP
++\fB\-\-enable\-site\-based\-scoring\fR
++falg to enable site\-based scoring
++.TP
++\fB\-\-multiple\-models\fR
++flag to handle multiple models in PDB file
++.TP
++\fB\-\-remap\-chains\fR
++flag to automatically rearrange chain names for higher scores
++.TP
++\fB\-\-remap\-chains\-output\fR
++string      output file with chain names rearrangement
++.TP
++\fB\-\-old\-regime\fR
++flag to calculate areas as in pre\-Voronota CAD\-score
++.SS "Standard output (one line):"
++.IP
++{target file path} {model file path} {query code} {number of residues} {global score} {target total area} {corresponding model total area}
++[ {site\-based number of residues} {site\-based global score} {site\-based target total area} {corresponding site\-based model total area} ]
+--- /dev/null
++++ b/voronota-contacts.man
+@@ -0,0 +1,45 @@
++.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
++.TH VORONOTA-CONTACTS "1" "October 2017" "voronota-contacts 1.18.1877" "User Commands"
++.SH NAME
++voronota-contacts \- manual page for voronota-contacts 1.18.1877
++.SH DESCRIPTION
++\&'voronota\-contacts' script provides a way for calculating and querying interatomic contacts
++with just one command (without the need to construct a pipeline from 'voronota' calls).
++.SS "Basic options:"
++.TP
++\fB\-\-input\fR | \fB\-i\fR
++string   *  input structure file in PDB format
++.TP
++\fB\-\-input\-filter\-query\fR
++string      input atoms filtering query parameters
++.TP
++\fB\-\-contacts\-query\fR
++string      contacts query parameters
++.TP
++\fB\-\-contacts\-query\-additional\fR
++string      additional contacts query parameters
++.TP
++\fB\-\-cache\-dir\fR
++string      path to cache directory
++.TP
++\fB\-\-sum\-at\-end\fR
++flag to print sum of areas as the last line in output
++.TP
++\fB\-\-help\fR | \fB\-h\fR
++flag to display help message and exit
++.SS "Advanced options:"
++.TP
++\fB\-\-output\-drawing\fR
++string      output file with drawing script for PyMol
++.TP
++\fB\-\-drawing\-parameters\fR
++string      drawing parameters
++.TP
++\fB\-\-wireframe\-drawing\fR
++flag to draw wireframe representation of contacts
++.TP
++\fB\-\-multiple\-models\fR
++flag to handle multiple models in PDB file
++.SS "Standard output (multiple lines):"
++.IP
++{contacting atom} {contacting atom} {contact area} {distance between atoms centers} {tags} {adjunct values}
+--- /dev/null
++++ b/voronota-volumes.man
+@@ -0,0 +1,36 @@
++.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
++.TH VORONOTA-VOLUMES "1" "October 2017" "voronota-volumes 1.18.1877" "User Commands"
++.SH NAME
++voronota-volumes \- manual page for voronota-volumes 1.18.1877
++.SH DESCRIPTION
++\&'voronota\-volumes' script provides a way for calculating and querying atomic volumes
++with just one command (without the need to construct a pipeline from 'voronota' calls).
++.SS "Basic options:"
++.TP
++\fB\-\-input\fR | \fB\-i\fR
++string   *  input structure file in PDB format
++.TP
++\fB\-\-input\-filter\-query\fR
++string      input atoms filtering query parameters
++.TP
++\fB\-\-cache\-dir\fR
++string      path to cache directory
++.TP
++\fB\-\-sum\-at\-end\fR
++flag to print sum of areas as the last line in output
++.TP
++\fB\-\-help\fR | \fB\-h\fR
++flag to display help message and exit
++.SS "Advanced options:"
++.TP
++\fB\-\-atoms\-query\fR
++string      atoms query parameters
++.TP
++\fB\-\-per\-residue\fR
++flag to output per\-residue results
++.TP
++\fB\-\-multiple\-models\fR
++flag to handle multiple models in PDB file
++.SS "Standard output (multiple lines):"
++.IP
++{name} {volume}
+--- /dev/null
++++ b/voronota-voromqa.man
+@@ -0,0 +1,59 @@
++.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
++.TH VORONOTA-VOROMQA "1" "October 2017" "voronota-voromqa 1.18.1877" "User Commands"
++.SH NAME
++voronota-voromqa \- manual page for voronota-voromqa 1.18.1877
++.SH DESCRIPTION
++\&'voronota\-voromqa' script is an implementation of VoroMQA method using Voronota.
++.SS "Basic options:"
++.TP
++\fB\-\-input\fR | \fB\-i\fR
++string   *  input structure file in PDB format
++.TP
++\fB\-\-input\-filter\-query\fR
++string      input atoms filtering query parameters
++.TP
++\fB\-\-output\-atom\-scores\fR
++string      output text file with atom scores
++.TP
++\fB\-\-output\-atom\-scores\-pdb\fR
++string      output PDB file with atom scores as B\-factors
++.TP
++\fB\-\-output\-residue\-scores\fR
++string      output text file with residue scores
++.TP
++\fB\-\-output\-residue\-scores\-pdb\fR
++string      output PDB file with residue scores as B\-factors
++.TP
++\fB\-\-output\-residue\-scores\-plot\fR
++string      output PNG image file with residue scores plot, requires R
++.TP
++\fB\-\-help\fR | \fB\-h\fR
++flag to display help message and exit
++.SS "Advanced options:"
++.TP
++\fB\-\-cache\-dir\fR
++string      path to cache directory
++.TP
++\fB\-\-smoothing\-window\fR
++number      residue scores smoothing window size, default is 5
++.TP
++\fB\-\-atoms\-query\fR
++string      atoms query parameters to define selection
++.TP
++\fB\-\-contacts\-query\fR
++string      contacts query parameters to define selection
++.TP
++\fB\-\-output\-selected\-scores\fR
++string      output text file with selected atom scores
++.TP
++\fB\-\-reference\-sequence\fR
++string      sequence file or string for residue renumbering
++.TP
++\fB\-\-output\-sequence\-alignment\fR
++string      output text file with sequence alignment
++.TP
++\fB\-\-multiple\-models\fR
++flag to handle multiple models in PDB file
++.SS "Standard output (one line):"
++.IP
++{input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c8d7729
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+manfiles.diff
diff --git a/debian/rules b/debian/rules
index 4d2663a..17715d9 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,24 +13,9 @@
 # package maintainers to append LDFLAGS
 #export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
 
-GENERATED_MAN_FILES = voronota.1 voronota-cadscore.1 \
-	voronota-contacts.1 voronota-volumes.1 voronota-voromqa.1
-MAN_FILES = ${GENERATED_MAN_FILES} # voronota.man
-
-DEB_UPSTREAM_VERSION=$(shell dpkg-parsechangelog | sed -rne 's,^Version: ([^-]+).*,\1,p')
-
 %:
 	dh $@  --with autotools_dev
 
-override_dh_installman: ${MAN_FILES}
-	dh_installman $+
-
-%.1: %
-	help2man ./$* --no-discard-stderr --no-info --version-string ${DEB_UPSTREAM_VERSION} --help-option '-h' > $@
-
-clean:
-	rm -f ${GENERATED_MAN_FILES}
-
 # dh_make generated override targets
 # This is example for Cmake (See https://bugs.debian.org/641051 )
 #override_dh_auto_configure:

-- 
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