[med-svn] r11982 - trunk/packages/python-biom-format/trunk/debian
Andreas Tille
tille at alioth.debian.org
Fri Aug 3 14:08:13 UTC 2012
Author: tille
Date: 2012-08-03 14:08:13 +0000 (Fri, 03 Aug 2012)
New Revision: 11982
Added:
trunk/packages/python-biom-format/trunk/debian/biom_validator.1
trunk/packages/python-biom-format/trunk/debian/convert_biom.1
trunk/packages/python-biom-format/trunk/debian/create-manpages
trunk/packages/python-biom-format/trunk/debian/manpages
Modified:
trunk/packages/python-biom-format/trunk/debian/changelog
trunk/packages/python-biom-format/trunk/debian/control
trunk/packages/python-biom-format/trunk/debian/rules
Log:
Decide to go with statically created man pages and provide the script to do so because proper creation with help2man would need some extra build-depends extra for this purpose which migh uselessly stress some auto-builders.
Added: trunk/packages/python-biom-format/trunk/debian/biom_validator.1
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/biom_validator.1 (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/biom_validator.1 2012-08-03 14:08:13 UTC (rev 11982)
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
+.TH BIOM_VALIDATOR "1" "August 2012" "biom_validator 1.0.0" "User Commands"
+.SH NAME
+biom_validator \- Test a biom file for adherence to the format specification
+.SH SYNOPSIS
+.B biom_validator
+[\fIoptions\fR] \fI{-i/--biom_fp BIOM_FP}\fR
+.SH DESCRIPTION
+[] indicates optional input (order unimportant)
+{} indicates required input (order unimportant)
+.PP
+Test a biom file for adherence to the format specification. This specification is defined at http://www.qiime.org/...
+.PP
+Example usage:
+Print help message and exit
+.IP
+biom_validator \fB\-h\fR
+.PP
+Validate the my_data.biom file.
+.IP
+biom_validator \fB\-i\fR my_data.biom
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Print information during execution \fB\-\-\fR useful for
+debugging [default: False]
+.TP
+\fB\-f\fR FORMAT_VERSION, \fB\-\-format\-version\fR=\fIFORMAT_VERSION\fR
+The specific format string, defaults to [default:
+Biological Observation Matrix 1.0.0]
+.IP
+REQUIRED options:
+.IP
+The following options must be provided under all circumstances.
+.TP
+\fB\-i\fR BIOM_FP, \fB\-\-biom_fp\fR=\fIBIOM_FP\fR
+the BIological Observation Matrix filepath to validate
+[REQUIRED]
Modified: trunk/packages/python-biom-format/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/changelog 2012-08-03 09:26:02 UTC (rev 11981)
+++ trunk/packages/python-biom-format/trunk/debian/changelog 2012-08-03 14:08:13 UTC (rev 11982)
@@ -1,4 +1,4 @@
-python-biom-format (1.0.0-1) UNRELEASED; urgency=low
+python-biom-format (1.0.0-1) unstable; urgency=low
* Initial release (Closes: #682242)
Modified: trunk/packages/python-biom-format/trunk/debian/control
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/control 2012-08-03 09:26:02 UTC (rev 11981)
+++ trunk/packages/python-biom-format/trunk/debian/control 2012-08-03 14:08:13 UTC (rev 11982)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6), python-numpy, cython, help2man
+Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6), python-numpy, cython
Standards-Version: 3.9.3
Homepage: http://biom-format.org/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biom-format/trunk/
@@ -12,7 +12,8 @@
Package: python-biom-format
Architecture: any
-Depends: ${shlibs:Depends}, ${python:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${python:Depends}, ${misc:Depends},
+ python-dateutil, python-cogent
Description: Biological Observation Matrix (BIOM) format
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation
Added: trunk/packages/python-biom-format/trunk/debian/convert_biom.1
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/convert_biom.1 (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/convert_biom.1 2012-08-03 14:08:13 UTC (rev 11982)
@@ -0,0 +1,68 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
+.TH CONVERT_BIOM "1" "August 2012" "convert_biom 1.0.0c" "User Commands"
+.SH NAME
+convert_biom \- Script to convert biom formatted files
+.SH SYNOPSIS
+.B Detailed
+\fIusage examples can be found here: http://biom-format.org/documentation/biom_conversion.html\fR
+.SH DESCRIPTION
+Script to convert biom formatted files.
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.IP
+Required Options:
+.TP
+\fB\-i\fR INPUT_FP, \fB\-\-input_fp\fR=\fIINPUT_FP\fR
+the input filepath
+.TP
+\fB\-o\fR OUTPUT_FP, \fB\-\-output_fp\fR=\fIOUTPUT_FP\fR
+the output filepath
+.IP
+Optional Options:
+.TP
+\fB\-t\fR BIOM_TYPE, \fB\-\-biom_type\fR=\fIBIOM_TYPE\fR
+Type of biom file to write (dense or sparse)
+whenpassed a classic table [default: sparse]
+.TP
+\fB\-b\fR, \fB\-\-biom_to_classic_table\fR
+Convert biom file to classictable file [default:
+convert classic table file to biom file]
+.TP
+\fB\-\-sparse_biom_to_dense_biom\fR
+Convert sparse biom file to a dense biom file
+[default: convert classic table file to biom file]
+.TP
+\fB\-\-dense_biom_to_sparse_biom\fR
+Convert dense biom file to a sparse biom file
+[default: convert classic table file to biom file]
+.TP
+\fB\-m\fR SAMPLE_MAPPING_FP, \fB\-\-sample_mapping_fp\fR=\fISAMPLE_MAPPING_FP\fR
+The mapping filepath (will add sample metadata to biom
+file, if provided) [default: none]
+.TP
+\fB\-\-observation_mapping_fp\fR=\fIOBSERVATION_MAPPING_FP\fR
+The mapping filepath (will add observation metadata to
+biom file, if provided) [default: none]
+.TP
+\fB\-\-header_key\fR=\fIHEADER_KEY\fR
+Pull this key from observation metadata within a biom
+file when writing a classic table [default: no
+observation metadata will be written]
+.TP
+\fB\-\-output_metadata_id\fR=\fIOUTPUT_METADATA_ID\fR
+Name for the observation metadata column when writing
+a biom file as a classic table [default: same name as
+in biom\-formatted table]
+.TP
+\fB\-\-process_obs_metadata\fR=\fIPROCESS_OBS_METADATA\fR
+Process metadata associated with observations
+(taxonomy,naive,sc_separated) when converting from a
+classic table [default: naive]
+.TP
+\fB\-\-biom_table_type\fR=\fIBIOM_TABLE_TYPE\fR
+The biom table type to get converted into
Added: trunk/packages/python-biom-format/trunk/debian/create-manpages
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/create-manpages (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/create-manpages 2012-08-03 14:08:13 UTC (rev 11982)
@@ -0,0 +1,37 @@
+#!/bin/sh
+# Create manpages using help2man
+# When calling help2man at package build time this would require
+# the following Build-Depends:
+
+HELP2MANDEPENDS="help2man python-dateutil python-cogent"
+
+# Specifically the last one does not come really cheap on slow
+# architectures - so we build the manpages statically here
+
+missingdepends=`dpkg -l ${HELP2MANDEPENDS} | \
+ grep -v -e "^ii" -e "^|" -e "^++" -e "^ " -e "^..[^[:space:]]" | \
+ sed 's/^[a-z][a-z][[:space:]]\+\([^[:space:]]\+\)[[:space:]]\+.*/\1/'`
+if [ "$missingdepends" != "" ] ; then \
+ echo "Please install the following packages to rebuild the upstream source tarball:"
+ echo $missingdepends
+ exit 1
+fi
+
+mandir=`dirname $0`
+bindir=`dirname ${mandir}`/scripts
+codedir=`dirname ${mandir}`/python-code
+version=`dpkg-parsechangelog -l${mandir}/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- `
+
+mkdir -p ${mandir}
+# later we will strip .py extension - so we need to rename the scripts here as well
+ln -s ${bindir}/biom_validator.py biom_validator
+help2man --no-info --name='Test a biom file for adherence to the format specification' \
+ --version-string="${version}" \
+ biom_validator > ${mandir}/biom_validator.1
+rm biom_validator
+
+ln -s ${bindir}/convert_biom.py convert_biom
+PYTHONPATH=${codedir} \
+help2man --no-info --name='Script to convert biom formatted files' \
+ convert_biom > ${mandir}/convert_biom.1
+rm convert_biom
Property changes on: trunk/packages/python-biom-format/trunk/debian/create-manpages
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/python-biom-format/trunk/debian/manpages
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/manpages (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/manpages 2012-08-03 14:08:13 UTC (rev 11982)
@@ -0,0 +1 @@
+debian/*.1
Modified: trunk/packages/python-biom-format/trunk/debian/rules
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/rules 2012-08-03 09:26:02 UTC (rev 11981)
+++ trunk/packages/python-biom-format/trunk/debian/rules 2012-08-03 14:08:13 UTC (rev 11982)
@@ -20,6 +20,9 @@
cp -a python-code/support-code/_sparsemat.cpp debian/cythonized-files
echo "$(UVER)" >| debian/cythonized-files/VERSION
+manpages:
+ debian/create-manpages
+
override_dh_auto_clean:
dh_auto_clean
rm -rf python-code/support-code/_sparsemat.cpp
@@ -28,13 +31,6 @@
dh_install
# remove language extension
rename 's/\.py$$//;' $(bindir)/*
- # try to create man pages whereever possible
- mkdir -p $(mandir)
- help2man --no-info --name='Test a biom file for adherence to the format specification' \
- --version-string="$(version)" \
- $(bindir)/biom_validator > $(mandir)/biom_validator.1
- help2man --no-info --name='Script to convert biom formatted files' \
- $(bindir)/convert_biom > $(mandir)/convert_biom.1
get-orig-source:
. debian/get-orig-source
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