[med-svn] [Git][med-team/emperor][master] Build the documentation
Liubov Chuprikova
gitlab at salsa.debian.org
Fri Jul 19 08:20:23 BST 2019
Liubov Chuprikova pushed to branch master at Debian Med / emperor
Commits:
c524c24a by Liubov Chuprikova at 2019-07-19T07:20:13Z
Build the documentation
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/correct_jsdoc_arguments.patch
- + debian/patches/do_not_use_custom_numpydoc.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,6 +1,7 @@
emperor (1.0.0-beta.19+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes #<bug>)
+ TODO: add doc/source/sphinxext/numpydoc to Files-Exclude
-- Liubov Chuprikova <chuprikovalv at gmail.com> Wed, 17 Jul 2019 18:19:24 +0300
=====================================
debian/control
=====================================
@@ -1,10 +1,25 @@
Source: emperor
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Kerim Ölçer <kerimlcr at gmail.com>,
- Afif Elghraoui <afif at debian.org>
+ Afif Elghraoui <afif at debian.org>,
+ Liubov Chuprikova <chuprikovalv at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10), dh-python, python-all, python-setuptools, python3-all, python3-setuptools
+Build-Depends: debhelper (>= 12~),
+ dh-python,
+ python-all,
+ python-setuptools,
+ python3-all,
+ python3-setuptools,
+ python3-sphinx,
+ python3-sphinx-bootstrap-theme,
+ python3-numpydoc,
+ python3-numpy,
+ python3-pandas,
+ python3-skbio,
+ python3-future,
+ python3-click,
+ jsdoc-toolkit
Standards-Version: 4.4.0
Homepage: https://biocore.github.io/emperor/
Vcs-Browser: https://salsa.debian.org/med-team/emperor
@@ -12,7 +27,14 @@ Vcs-Git: https://salsa.debian.org/med-team/emperor.git
Package: python-emperor
Architecture: all
-Depends: ${python:Depends}, ${misc:Depends}, python-numpy, python-scipy, python-click, python-pandas, python-jinja2, python-future
+Depends: ${python:Depends},
+ ${misc:Depends},
+ python-numpy,
+ python-scipy,
+ python-click,
+ python-pandas,
+ python-jinja2,
+ python-future
Suggests: python-emperor-doc
Description: visualizing high-throughput microbial community data
Emperor is an interactive next generation tool for the analysis,
@@ -29,7 +51,14 @@ Description: visualizing high-throughput microbial community data
Package: python3-emperor
Architecture: all
-Depends: ${python3:Depends}, ${misc:Depends}, python3-numpy, python3-scipy, python3-click, python3-pandas, python3-jinja2, python3-future
+Depends: ${python3:Depends},
+ ${misc:Depends},
+ python3-numpy,
+ python3-scipy,
+ python3-click,
+ python3-pandas,
+ python3-jinja2,
+ python3-future
Suggests: python-emperor-doc
Description: visualizing high-throughput microbial community data
Emperor is an interactive next generation tool for the analysis,
@@ -47,7 +76,8 @@ Description: visualizing high-throughput microbial community data
Package: python-emperor-doc
Architecture: all
Section: doc
-Depends: ${sphinxdoc:Depends}, ${misc:Depends}
+Depends: ${sphinxdoc:Depends},
+ ${misc:Depends}
Description: visualizing high-throughput microbial community data
Emperor is an interactive next generation tool for the analysis,
visualization and understanding of high throughput microbial
=====================================
debian/patches/correct_jsdoc_arguments.patch
=====================================
@@ -0,0 +1,11 @@
+--- a/doc/Makefile
++++ b/doc/Makefile
+@@ -54,7 +54,7 @@
+
+ html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+- jsdoc ../emperor/support_files/js/ -d $(BUILDDIR)/jsdoc -c jsdoc-config.json
++ jsdoc ../emperor/support_files/js/ -d=$(BUILDDIR)/jsdoc -c=jsdoc-config.json
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
=====================================
debian/patches/do_not_use_custom_numpydoc.patch
=====================================
@@ -0,0 +1,11 @@
+--- a/doc/source/conf.py
++++ b/doc/source/conf.py
+@@ -23,7 +23,7 @@
+ # If extensions (or modules to document with autodoc) are in another directory,
+ # add these directories to sys.path here. If the directory is relative to the
+ # documentation root, use os.path.abspath to make it absolute, like shown here.
+-sys.path.insert(0, os.path.abspath('sphinxext/numpydoc/'))
++#sys.path.insert(0, os.path.abspath('sphinxext/numpydoc/'))
+
+ # -- Options for autosummary ----------------------------------------------
+ autosummary_generate = glob.glob('*.rst') + glob.glob('source/*.rst')
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,2 @@
+do_not_use_custom_numpydoc.patch
+correct_jsdoc_arguments.patch
=====================================
debian/rules
=====================================
@@ -5,15 +5,10 @@
export PYBUILD_NAME=emperor
-%:
- dh $@ --with python2,python3 --buildsystem=pybuild
-
+export PYBUILD_AFTER_BUILD_python3=python{version} setup.py develop --install-dir {build_dir}; \
+ cp -r {dir}/doc {build_dir}; cd {build_dir}/doc; make html
-# If you need to rebuild the Sphinx documentation
-# Add spinxdoc to the dh --with line
-#override_dh_auto_build:
-# dh_auto_build
-# PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml docs/ build/html # HTML generator
-# PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman docs/ build/man # Manpage generator
+%:
+ dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
override_dh_auto_test:
View it on GitLab: https://salsa.debian.org/med-team/emperor/commit/c524c24a3752b4718b010584390efc53e04329a7
--
View it on GitLab: https://salsa.debian.org/med-team/emperor/commit/c524c24a3752b4718b010584390efc53e04329a7
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