[med-svn] [python-biom-format] 05/11: Provide documentation in separate arch-independent package.
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Sat Mar 5 18:16:15 UTC 2016
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a commit to branch master
in repository python-biom-format.
commit 3940c67f27fe881b66b62ce321d4c4729c062f67
Author: Ghislain Antony Vaillant <ghisvail at gmail.com>
Date: Sat Mar 5 15:49:48 2016 +0000
Provide documentation in separate arch-independent package.
---
debian/clean | 2 ++
debian/control | 34 ++++++++++++++++++++--
debian/install | 1 -
debian/linktrees | 4 ---
debian/manpages | 2 +-
.../{doc-base => python-biom-format-doc.doc-base} | 4 +--
debian/python-biom-format-doc.docs | 1 +
.../{examples => python-biom-format-doc.examples} | 0
debian/rules | 14 ++++++---
9 files changed, 48 insertions(+), 14 deletions(-)
diff --git a/debian/clean b/debian/clean
index 9321e3c..3e5e0b9 100644
--- a/debian/clean
+++ b/debian/clean
@@ -1 +1,3 @@
biom/_*.c
+build/html
+build/man
diff --git a/debian/control b/debian/control
index 20500af..69d03a0 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,6 @@ Testsuite: autopkgtest
Priority: optional
Build-Depends: debhelper (>= 9),
dh-python,
- dh-linktree,
cython,
python-dev,
python-numpy,
@@ -17,9 +16,9 @@ Build-Depends: debhelper (>= 9),
python-cogent,
python-future,
python-nose,
- python-sphinx,
python-setuptools,
bash-completion
+Build-Depends-Indep: python-sphinx
Standards-Version: 3.9.7
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-biom-format.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/python-biom-format.git
@@ -36,6 +35,7 @@ Depends: ${python:Depends},
python-scipy,
python-h5py,
pyqi
+Suggests: python-biom-format-doc
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
@@ -56,3 +56,33 @@ Description: Biological Observation Matrix (BIOM) format
observations in this case again might correspond to SEED subsystems, and
the counts would correspond to the number of times each subsystem is
observed in each genome.
+ .
+ This package provides the BIOM format library for the Python 2 interpreter.
+
+Package: python-biom-format-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+ ${sphinxdoc:Depends}
+Description: documentation for BIOM format
+ The BIOM file format (canonically pronounced biome) is designed to be a
+ general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth
+ Microbiome Project and is a Genomics Standards Consortium candidate
+ project.
+ .
+ The BIOM format is designed for general use in broad areas of
+ comparative -omics. For example, in marker-gene surveys, the primary use
+ of this format is to represent OTU tables: the observations in this case
+ are OTUs and the matrix contains counts corresponding to the number of
+ times each OTU is observed in each sample. With respect to metagenome
+ data, this format would be used to represent metagenome tables: the
+ observations in this case might correspond to SEED subsystems, and the
+ matrix would contain counts corresponding to the number of times each
+ subsystem is observed in each metagenome. Similarly, with respect to
+ genome data, this format may be used to represent a set of genomes: the
+ observations in this case again might correspond to SEED subsystems, and
+ the counts would correspond to the number of times each subsystem is
+ observed in each genome.
+ .
+ This package provides the documentation for the BIOM format Python package.
diff --git a/debian/install b/debian/install
deleted file mode 100644
index 00ba084..0000000
--- a/debian/install
+++ /dev/null
@@ -1 +0,0 @@
-doc/_build/singlehtml/* usr/share/doc/python-biom-format/html
diff --git a/debian/linktrees b/debian/linktrees
deleted file mode 100644
index 3201bf7..0000000
--- a/debian/linktrees
+++ /dev/null
@@ -1,4 +0,0 @@
-replace usr/share/sphinx/themes/basic/static/doctools.js usr/share/doc/python-biom-format/html/_static/doctools.js
-replace usr/share/sphinx/themes/basic/static/jquery.js usr/share/doc/python-biom-format/html/_static/jquery.js
-replace usr/share/sphinx/themes/basic/static/underscore.js usr/share/doc/python-biom-format/html/_static/underscore.js
-replace usr/share/sphinx/themes/basic/static/websupport.js usr/share/doc/python-biom-format/html/_static/websupport.js
diff --git a/debian/manpages b/debian/manpages
index 7a234a3..b19f8c8 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1 +1 @@
-doc/_build/man/*
+build/man/*
diff --git a/debian/doc-base b/debian/python-biom-format-doc.doc-base
similarity index 82%
rename from debian/doc-base
rename to debian/python-biom-format-doc.doc-base
index 949daae..2b49f50 100644
--- a/debian/doc-base
+++ b/debian/python-biom-format-doc.doc-base
@@ -10,5 +10,5 @@ Abstract: Biological Observation Matrix (BIOM) format
Section: Science/Biology
Format: html
-Index: /usr/share/doc/python-biom-format/html/index.html
-Files: /usr/share/doc/python-biom-format/html/
+Index: /usr/share/doc/python-biom-format-doc/html/index.html
+Files: /usr/share/doc/python-biom-format-doc/html/
diff --git a/debian/python-biom-format-doc.docs b/debian/python-biom-format-doc.docs
new file mode 100644
index 0000000..6d28621
--- /dev/null
+++ b/debian/python-biom-format-doc.docs
@@ -0,0 +1 @@
+build/html
diff --git a/debian/examples b/debian/python-biom-format-doc.examples
similarity index 100%
rename from debian/examples
rename to debian/python-biom-format-doc.examples
diff --git a/debian/rules b/debian/rules
index 3ad99cd..4f737bb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,12 +11,14 @@ export PYBUILD_NAME=biom-format
export PYBUILD_BEFORE_TEST=cp -r {dir}/examples {dir}/tests {build_dir}
%:
- dh $@ --with python2 --buildsystem=pybuild --with linktree
+ dh $@ --with python2 --buildsystem=pybuild
-override_dh_auto_build:
+override_dh_auto_build-arch:
USE_CYTHON=true dh_auto_build
- PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc doc/_build/singlehtml
- PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc doc/_build/man
+
+override_dh_auto_build-indep:
+ PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
+ PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
override_dh_auto_clean:
rm -rf build/tests
@@ -33,3 +35,7 @@ override_dh_install:
# All *.py scripts simply say
# "This script no longer exists. ..."
rm -f $(bindir)/*.py
+
+override_dh_installdocs-indep:
+ dh_installdocs --indep
+ dh_sphinxdoc --indep
--
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