Commit c524c24a authored by Liubov Chuprikova's avatar Liubov Chuprikova
Browse files

Build the documentation

parent c79f0764

debian/changelog

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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@gmail.com>  Wed, 17 Jul 2019 18:19:24 +0300

debian/control

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Source: emperor

Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

Uploaders: Kerim Ölçer <kerimlcr@gmail.com>,

           Afif Elghraoui <afif@debian.org>

           Afif Elghraoui <afif@debian.org>,

           Liubov Chuprikova <chuprikovalv@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 → 100644
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--- 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 → 100644
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--- 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

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do_not_use_custom_numpydoc.patch

correct_jsdoc_arguments.patch