[med-svn] [Git][med-team/python-cogent][master] 5 commits: Revert "TODO: Add python3-jupyter-sphinx from build depends again"
Emmanuel Arias (@eamanu)
gitlab at salsa.debian.org
Thu Jun 27 01:49:01 BST 2024
Emmanuel Arias pushed to branch master at Debian Med / python-cogent
Commits:
c4bc0414 by Emmanuel Arias at 2024-06-26T16:21:56-03:00
Revert "TODO: Add python3-jupyter-sphinx from build depends again"
This reverts commit 892eb2e7ebfd6b1b66a4a3e0319d471999ff96ec.
- - - - -
03c64403 by Emmanuel Arias at 2024-06-26T16:42:26-03:00
d/control: Add ${sphinxdoc:Depends} as Depends in python-cogent-doc package.
* d/control: Add ${sphinxdoc:Depends} as Depends in python-cogent-doc
package.
- d/rules: Add --with sphinxdoc.
- - - - -
db08e466 by Emmanuel Arias at 2024-06-26T20:38:27-03:00
d/control: Add libjs-requirejs as build dependency. Also add as Depends in the python-cogent-doc package.
* d/control: Add libjs-requirejs as build dependency. Also add as Depends in
the python-cogent-doc package.
- d/rules: add override_dh_sphinxdoc to replace external link to
require.min.js to use installed lib and avoid privacy leak.
- - - - -
a9707159 by Emmanuel Arias at 2024-06-26T20:39:43-03:00
d/control: Bump Standards-Version to 4.7.0 (from 4.6.2; no further changes needed).
- - - - -
dd570a2a by Emmanuel Arias at 2024-06-26T21:26:33-03:00
prepare for upload
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/remove-jupyter-sphinx.patch
- debian/patches/series
- debian/patches/sphinx.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-python-cogent (2024.5.7a1+dfsg-1.1) UNRELEASED; urgency=medium
+python-cogent (2024.5.7a1+dfsg-1) unstable; urgency=medium
[ Ananthu C V ]
* Team upload
@@ -7,14 +7,23 @@ python-cogent (2024.5.7a1+dfsg-1.1) UNRELEASED; urgency=medium
* Add python3-stevedore build dependency and apply wrap-and-sort
* Use execute_after syntax over override in d/rules where possible
- [ Emmanuel Arias ]
- * TODO: Add python3-jupyter-sphinx from build depends again
-
[ Andreas Tille ]
* debian/control:
- Build-Depends: architecture-is-64-bit, architecture-is-little-endian
- Architecture: any
+ [ Emmanuel Arias ]
+ * d/control: Add ${sphinxdoc:Depends} as Depends in python-cogent-doc
+ package.
+ - d/rules: Add --with sphinxdoc.
+ * d/control: Add libjs-requirejs as build dependency. Also add as Depends in
+ the python-cogent-doc package.
+ - d/rules: add override_dh_sphinxdoc to replace external link to
+ require.min.js to use installed lib and avoid privacy leak.
+ - wrap-and-sort.
+ * d/control: Bump Standards-Version to 4.7.0 (from 4.6.2; no further changes
+ needed).
+
-- Emmanuel Arias <eamanu at debian.org> Wed, 26 Jun 2024 01:24:50 -0300
python-cogent (2023.12.15a1+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,22 +1,22 @@
Source: python-cogent
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: cython3,
+Build-Depends: architecture-is-64-bit,
+ architecture-is-little-endian,
+ cython3,
debhelper-compat (= 13),
dh-sequence-python3,
- architecture-is-64-bit,
- architecture-is-little-endian,
flit,
+ libjs-requirejs,
pandoc,
pybuild-plugin-pyproject,
python3-all-dev,
python3-chardet,
python3-isort,
- python3-jupyter-sphinx,
python3-jupyter-sphinx-theme,
python3-jupyterlab-server,
python3-matplotlib,
@@ -40,8 +40,8 @@ Build-Depends: cython3,
python3-stevedore,
python3-tinydb,
python3-tqdm,
- python3-typing-extensions <!nocheck>
-Standards-Version: 4.6.2
+ python3-typing-extensions <!nocheck>,
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/python-cogent
Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git
Homepage: https://github.com/cogent3/cogent3
@@ -58,10 +58,11 @@ Depends: python3-matplotlib,
python3-tqdm,
${misc:Depends},
${python3:Depends},
- ${shlibs:Depends}
-Recommends: dialign, ncbi-blast+-legacy
-Suggests: python-cogent-doc
-Provides: python-cogent
+ ${shlibs:Depends},
+Recommends: dialign,
+ ncbi-blast+-legacy,
+Suggests: python-cogent-doc,
+Provides: python-cogent,
Description: framework for genomic biology
PyCogent is a software library for genomic biology. It is a fully
integrated and thoroughly tested framework for:
@@ -78,8 +79,12 @@ Package: python-cogent-doc
Architecture: all
Multi-Arch: foreign
Section: doc
-Depends: libjs-jquery, libjs-underscore, ${misc:Depends}
-Suggests: python3-cogent3 (= ${binary:Version})
+Depends: libjs-jquery,
+ libjs-requirejs,
+ libjs-underscore,
+ ${misc:Depends},
+ ${sphinxdoc:Depends},
+Suggests: python3-cogent3 (= ${binary:Version}),
Description: docs for python3-cogent3
PyCogent is a software library for genomic biology.
.
=====================================
debian/patches/remove-jupyter-sphinx.patch
=====================================
@@ -0,0 +1,22 @@
+Description: Remove jupyter-sphinx from pyproject.toml
+Author: Nilesh Patra <nilesh at debian.org>
+Forwarded: not-needed
+Last-Update: 2024-06-26
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -64,7 +64,6 @@
+ "ipykernel",
+ "ipython",
+ "ipywidgets",
+- "jupyter-sphinx",
+ "jupyter_client",
+ "jupyterlab",
+ "jupytext",
+@@ -92,7 +91,6 @@
+ "ipython",
+ "ipywidgets",
+ "isort==5.13.2",
+- "jupyter-sphinx",
+ "jupyter_client",
+ "jupyterlab",
+ "jupytext",
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,5 @@
sphinx.patch
fix_interpreter.patch
+remove-jupyter-sphinx.patch
ignore_tests_accessing_network.patch
skip-parallel-tests-on-single-cpu-systems.patch
=====================================
debian/patches/sphinx.patch
=====================================
@@ -5,12 +5,18 @@ Forwarded: not-needed
--- a/doc/conf.py
+++ b/doc/conf.py
-@@ -29,7 +29,7 @@
+@@ -27,11 +27,11 @@ release = today.strftime("%Y.%m.%d")
+ # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
extensions = [
- "jupyter_sphinx",
+- "jupyter_sphinx",
++# "jupyter_sphinx",
"nbsphinx",
- "numpydoc",
-+ # "numpydoc",
++# "numpydoc",
"sphinx.ext.autodoc",
- "sphinx.ext.autosummary",
+- "sphinx.ext.autosummary",
++# "sphinx.ext.autosummary",
"sphinx.ext.doctest",
+ "sphinx.ext.githubpages",
+ "sphinx.ext.mathjax",
=====================================
debian/rules
=====================================
@@ -17,7 +17,7 @@ endif
include /usr/share/dpkg/default.mk
%:
- dh $@ --buildsystem=pybuild
+ dh $@ --with sphinxdoc --buildsystem=pybuild
override_dh_clean:
#These files are rebuilt on-the-fly
@@ -39,6 +39,10 @@ ifeq (,$(filter $(DEB_HOST_ARCH), armel mipsel))
rm -rf doc/_build/html/_images/math/
endif
+override_dh_sphinxdoc:
+ dh_sphinxdoc
+ sed -i 's%https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js%file:///usr/share/javascript/requirejs/require.min.js%' `find $(CURDIR)/debian/python-cogent-doc/usr/share/doc/python-cogent-doc/html/ -type f -name "*.html"`
+
execute_after_dh_shlibdeps:
dh_numpy3
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/d787b323522b18087b6c849050bf5ece3b9b6e13...dd570a2aa7fefe08b207f269af94d30f45fdeb3c
--
This project does not include diff previews in email notifications.
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/d787b323522b18087b6c849050bf5ece3b9b6e13...dd570a2aa7fefe08b207f269af94d30f45fdeb3c
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240627/2b704e57/attachment-0001.htm>
More information about the debian-med-commit
mailing list