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.cru...@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.cru...@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 You're receiving this email because of your account on salsa.debian.org.
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