[med-svn] [Git][med-team/galaxy-lib][master] 2 commits: drop python2 package
Michael R. Crusoe
gitlab at salsa.debian.org
Sun Mar 10 10:07:28 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / galaxy-lib
Commits:
5fb26896 by Michael R. Crusoe at 2019-03-10T07:40:47Z
drop python2 package
- - - - -
802344d6 by Michael R. Crusoe at 2019-03-10T10:05:28Z
run tests, ship docs
- - - - -
7 changed files:
- debian/control
- + debian/doc-base
- debian/python3-galaxy-lib.docs → debian/docs
- + debian/patches/remove_badges
- + debian/patches/repro
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -7,41 +7,30 @@ Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper (>= 12~),
dh-python,
- python-all,
- python-docutils,
- python-setuptools,
- python-six (>= 1.9.0),
- python-yaml,
python3-all,
python3-docutils,
python3-setuptools,
python3-six (>= 1.9.0),
- python3-yaml
+ python3-yaml,
+ python3-markupsafe,
+ python3-packaging,
+ python3-boltons,
+ python3-unittest2,
+ python3-nose,
+ python3-sphinx,
+ python3-recommonmark,
+ python3-sphinx-rtd-theme
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/galaxy-lib
Vcs-Git: https://salsa.debian.org/med-team/galaxy-lib.git
Homepage: https://github.com/galaxyproject/galaxy-lib
-Package: python-galaxy-lib
-Architecture: all
-Depends: ${misc:Depends},
- ${python:Depends}
-Recommends: ${python:Recommends}
-Suggests: ${python:Suggests}
-Description: Subset of Galaxy workflow platform's core code base - Python 2.X
- A small subset of the Galaxy project for reuse outside the core.
- The Galaxy software framework enables researchers without informatics
- expertise to perform computational analyses through the web. A user interacts
- with Galaxy through the web by uploading and analyzing the data. Galaxy
- interacts with underlying computational infrastructure (servers that run the
- analyses and disks that store the data) without exposing it to the user.
- .
- This is the Python 2.x version.
-
Package: python3-galaxy-lib
Architecture: all
Depends: ${misc:Depends},
- ${python3:Depends}
+ ${python3:Depends},
+ ${sphinxdoc:Depends}
+Built-Using: ${sphinxdoc:Built-Using}
Recommends: ${python3:Recommends}
Suggests: ${python3:Suggests}
Description: Subset of Galaxy core code base designed to be used
=====================================
debian/doc-base
=====================================
@@ -0,0 +1,11 @@
+Document: galaxy-lib
+Title: Galaxy-Lib Documentation
+Author: Galaxy Project and Community
+Abstract: A small subset of the Galaxy project for reuse outside the core. This
+ subset has minimal dependencies and should be Python 3 compatible.
+Section: Programming/Python
+
+Format: html
+Index: /usr/share/doc/python3-galaxy-lib/html/index.html
+Files: /usr/share/doc/python3-galaxy-lib/html/*
+
=====================================
debian/python3-galaxy-lib.docs → debian/docs
=====================================
@@ -1 +1,2 @@
README.rst
+build/html
=====================================
debian/patches/remove_badges
=====================================
@@ -0,0 +1,20 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Respect user privacy and don't include remote images
+Forwarded: not applicable
+--- galaxy-lib.orig/README.rst
++++ galaxy-lib/README.rst
+@@ -1,14 +1,3 @@
+-
+-.. image:: https://readthedocs.org/projects/galaxy-lib/badge/?version=latest
+- :target: http://galaxy-lib.readthedocs.io/en/latest/?badge=latest
+- :alt: Documentation Status
+-
+-.. image:: https://badge.fury.io/py/galaxy-lib.svg
+- :target: https://pypi.python.org/pypi/galaxy-lib/
+-
+-.. image:: https://travis-ci.org/galaxyproject/galaxy-lib.png?branch=master
+- :target: https://travis-ci.org/galaxyproject/galaxy-lib
+-
+ Overview
+ --------
+
=====================================
debian/patches/repro
=====================================
@@ -0,0 +1,35 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: keep environment variables out of generated docs
+--- galaxy-lib.orig/galaxy/tools/verify/test_data.py
++++ galaxy-lib/galaxy/tools/verify/test_data.py
+@@ -28,7 +28,9 @@
+
+ class TestDataResolver(object):
+
+- def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ):
++ def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=None):
++ if environ is None:
++ environ = os.environ
+ if file_dirs is None:
+ file_dirs = environ.get(env_var, None)
+ if file_dirs is None:
+--- galaxy-lib.orig/galaxy/util/__init__.py
++++ galaxy-lib/galaxy/util/__init__.py
+@@ -1527,7 +1527,7 @@
+ return os.path.abspath(galaxy_root_path)
+
+
+-def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root_path):
++def config_directories_from_setting(directories_setting, galaxy_root=None):
+ """
+ Parse the ``directories_setting`` into a list of relative or absolute
+ filesystem paths that will be searched to discover plugins.
+@@ -1541,6 +1541,8 @@
+ :rtype: list of strings
+ :returns: list of filesystem paths
+ """
++ if galaxy_root is None:
++ galaxy_root = galaxy_root_path
+ directories = []
+ if not directories_setting:
+ return directories
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,2 @@
+repro
+remove_badges
=====================================
debian/rules
=====================================
@@ -1,7 +1,14 @@
#! /usr/bin/make -f
export PYBUILD_NAME=galaxy-lib
-export PYBUILD_DISABLE=test
export PYBUILD_AFTER_INSTALL_python2=rm -rf {destdir}/usr/bin/
%:
- dh $@ --with python2,python3 --buildsystem=pybuild
+ dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+
+override_dh_auto_build:
+ dh_auto_build
+ PYTHONPATH=. http_proxy='http://127.0.0.1:9/' python3 -m sphinx -N -E -bhtml docs build/html
+
+override_dh_auto_install:
+ dh_auto_install
+ rm -Rf debian/python3-galaxy-lib/usr/bin # remove later if users request them
View it on GitLab: https://salsa.debian.org/med-team/galaxy-lib/compare/ca0abb70c85b96fda6634f8dfd8a27d1fc0403ac...802344d6c9869f015bab0740aa1b73d8c0f40096
--
View it on GitLab: https://salsa.debian.org/med-team/galaxy-lib/compare/ca0abb70c85b96fda6634f8dfd8a27d1fc0403ac...802344d6c9869f015bab0740aa1b73d8c0f40096
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