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.ci/autopep8.sh 0 → 100755
View file @ 28dfc8fd
autopep8 -i -r --select E201,E202,E11,E101,E127,E129,E22,E301,E302,E303,E304,E306,E711,W291,W292,W293,W391 ./galaxy
.ci/flake8_docstrings_include_list.txt 0 → 100644
View file @ 28dfc8fd
galaxy/jobs/metrics
galaxy/exceptions
.ci/flake8_wrapper_docstrings.sh 0 → 100755
View file @ 28dfc8fd
#!/bin/bash
set -e
flake8 `paste .ci/flake8_docstrings_include_list.txt`
.coveragerc 0 → 100644
View file @ 28dfc8fd
# .coveragerc to control coverage.py
[run]
branch = True
include = galaxy/*
[report]
# Regexes for lines to exclude from consideration
exclude_lines =
if __name__ == .__main__.:
ignore_errors = True
[html]
directory = htmlcov/
.editorconfig 0 → 100644
View file @ 28dfc8fd
# http://editorconfig.org
root = true
[*]
indent_style = space
indent_size = 4
trim_trailing_whitespace = true
insert_final_newline = true
charset = utf-8
end_of_line = lf
[*.bat]
indent_style = tab
end_of_line = crlf
[LICENSE]
insert_final_newline = false
[Makefile]
indent_style = tab
\ No newline at end of file
.gitignore 0 → 100644
View file @ 28dfc8fd
*.py[cod]
# C extensions
*.so
# Packages
.eggs
*.egg
*.egg-info
dist
build
eggs
parts
bin
var
sdist
develop-eggs
.installed.cfg
lib
lib64
# Installer logs
pip-log.txt
# Unit test / coverage reports
.coverage
.tox
nosetests.xml
htmlcov
# Translations
*.mo
# Mr Developer
.mr.developer.cfg
.project
.pydevproject
# Complexity
output/*.html
output/*/index.html
# Sphinx
docs/_build
.venv
# Download of involucro
involucro
# Bioconda recipes for auto update.
bioconda-recipes/
\ No newline at end of file
.travis.yml 0 → 100644
View file @ 28dfc8fd
language: python
sudo: false
python: 2.7
env:
- TOX_ENV=py27-lint
- TOX_ENV=py34-lint
- TOX_ENV=py27-lint-readme
- TOX_ENV=py27
- TOX_ENV=py34
- TOX_ENV=py27-lint-docstring-include-list
install:
# Setup git to allow git operations.
- git config --global user.name "Travis Test User"
- git config --global user.email "galaxy_test@galaxyproject.org"
- pip install tox coveralls
script: tox -e $TOX_ENV
after_success:
- coveralls
HISTORY.rst
View file @ 28dfc8fd
......@@ -5,6 +5,34 @@ History
.. to_doc
---------------------
18.9.1 (2018-09-15)
---------------------
* More work improving channel handling for mulled containers.
---------------------
18.9.0 (2018-09-14)
---------------------
* Update Conda channel order (thanks to @bgruening).
* Bring in the latest Galaxy changes and add Galaxy XSD to the project.
* Various cwltool fixes (thanks to @nsoranzo).
---------------------
18.5.15 (2018-09-12)
---------------------
* More tweaks to CWL tool loading to support newer versions of cwltool.
---------------------
18.5.14 (2018-09-12)
---------------------
* Improved tool linting and reporting thanks to @natefoo and @nsoranzo.
* Add support for newer cwltool thanks to @nsoranzo.
* Improved mulled building thanks to @pcm32.
---------------------
18.5.13 (2018-05-23)
---------------------
......
Makefile 0 → 100644
View file @ 28dfc8fd
# Default tests run with make test and make quick-tests
NOSE_TESTS?=--exclude galaxy/util/dictobj.py,galaxy/util/jstree.py tests galaxy
# Default environment for make tox
ENV?=py27
# Extra arguments supplied to tox command
ARGS?=
# Location of virtualenv used for development.
VENV?=.venv
# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
# TODO: add this upstream as a remote if it doesn't already exist.
UPSTREAM?=galaxyproject
SOURCE_DIR?=galaxy
BUILD_SCRIPTS_DIR=scripts
VERSION?=$(shell python $(BUILD_SCRIPTS_DIR)/print_version_for_release.py $(SOURCE_DIR))
DOC_URL?=https://galaxy-lib.readthedocs.org
PROJECT_URL?=https://github.com/galaxyproject/galaxy-lib
PROJECT_NAME?=galaxy-lib
TEST_DIR?=tests
.PHONY: clean-pyc clean-build docs clean
help:
@echo "clean - remove all build, test, coverage and Python artifacts"
@echo "clean-build - remove build artifacts"
@echo "clean-pyc - remove Python file artifacts"
@echo "clean-test - remove test and coverage artifacts"
@echo "setup-venv - setup a development virutalenv in current directory."
@echo "lint - check style using tox and flake8 for Python 2 and Python 3"
@echo "lint-readme - check README formatting for PyPI"
@echo "flake8 - check style using flake8 for current Python (faster than lint)"
@echo "test - run tests with the default Python (faster than tox)"
@echo "quick-test - run quickest tests with the default Python"
@echo "coverage - check code coverage quickly with the default Python"
@echo "docs - generate Sphinx HTML documentation, including API docs"
@echo "open-docs - generate Sphinx HTML documentation and open in browser"
@echo "open-rtd - open docs on readthedocs.org"
@echo "open-project - open project on github"
@echo "release - package, review, and upload a release"
@echo "dist - package"
@echo "setup-git-hook-lint - setup precommit hook for linting project"
@echo "setup-git-hook-lint-and-test - setup precommit hook for linting and testing project"
@echo "update-extern - update external artifacts copied locally"
clean: clean-build clean-pyc clean-test
clean-build:
rm -fr build/
rm -fr dist/
rm -fr *.egg-info
clean-pyc:
find . -name '*.pyc' -exec rm -f {} +
find . -name '*.pyo' -exec rm -f {} +
find . -name '*~' -exec rm -f {} +
find . -name '__pycache__' -exec rm -fr {} +
clean-test:
rm -fr .tox/
rm -f .coverage
rm -fr htmlcov/
setup-venv:
if [ ! -d $(VENV) ]; then virtualenv $(VENV); exit; fi;
$(IN_VENV) pip install -r requirements.txt && pip install -r dev-requirements.txt
setup-git-hook-lint:
cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint .git/hooks/pre-commit
setup-git-hook-lint-and-test:
cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint-and-test .git/hooks/pre-commit
flake8:
$(IN_VENV) flake8 --max-complexity 15 $(SOURCE_DIR) $(TEST_DIR)
lint:
$(IN_VENV) tox -e py27-lint && tox -e py34-lint
lint-readme:
$(IN_VENV) python setup.py check -r -s
test:
$(IN_VENV) nosetests $(NOSE_TESTS)
tox:
$(IN_VENV) tox -e $(ENV) -- $(ARGS)
coverage:
coverage run --source $(SOURCE_DIR) setup.py $(TEST_DIR)
coverage report -m
coverage html
open htmlcov/index.html || xdg-open htmlcov/index.html
docs:
$(IN_VENV) sphinx-apidoc -f -o docs/ galaxy
$(IN_VENV) $(MAKE) -C docs clean
$(IN_VENV) $(MAKE) -C docs html
_open-docs:
open docs/_build/html/index.html || xdg-open docs/_build/html/index.html
open-docs: docs _open-docs
open-rtd: docs
open $(DOC_URL) || xdg-open $(PROJECT_URL)
open-project:
open $(PROJECT_URL) || xdg-open $(PROJECT_URL)
dist: clean
$(IN_VENV) python setup.py sdist bdist_egg bdist_wheel
ls -l dist
release-test-artifacts: dist
$(IN_VENV) twine upload -r test dist/*
open https://testpypi.python.org/pypi/$(PROJECT_NAME) || xdg-open https://testpypi.python.org/pypi/$(PROJECT_NAME)
release-aritfacts: release-test-artifacts
@while [ -z "$$CONTINUE" ]; do \
read -r -p "Have you executed release-test and reviewed results? [y/N]: " CONTINUE; \
done ; \
[ $$CONTINUE = "y" ] || [ $$CONTINUE = "Y" ] || (echo "Exiting."; exit 1;)
@echo "Releasing"
$(IN_VENV) twine upload dist/*
commit-version:
$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/commit_version.py $(SOURCE_DIR) $(VERSION)
new-version:
$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/new_version.py $(SOURCE_DIR) $(VERSION) 2
release-local: commit-version release-aritfacts new-version
push-release:
git push $(UPSTREAM) master
git push --tags $(UPSTREAM)
release: release-local push-release
add-history:
$(IN_VENV) python scripts/bootstrap_history.py $(ITEM)
PKG-INFO deleted 100644 → 0
View file @ 7810804a
Metadata-Version: 1.1
Name: galaxy-lib
Version: 18.5.13
Summary: Subset of Galaxy (http://galaxyproject.org/) core code base designed to be used a library.
Home-page: https://github.com/galaxyproject/galaxy-lib
Author: Galaxy Project and Community
Author-email: jmchilton@gmail.com
License: AFL
Description-Content-Type: UNKNOWN
Description:
.. 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
--------
A small subset of the Galaxy_ project for reuse outside the core. This subset has minimal dependencies and should be Python 3 compatible.
* Free software: Academic Free License version 3.0
* Documentation: https://galaxy-lib.readthedocs.org.
* Code: https://github.com/galaxyproject/galaxy-lib
.. _Galaxy: http://galaxyproject.org/
.. _GitHub: https://github.com/
.. _Docker: https://www.docker.com/
.. _Homebrew: http://brew.sh/
.. _linuxbrew: https://github.com/Homebrew/linuxbrew
.. _Vagrant: https://www.vagrantup.com/
.. _Travis CI: http://travis-ci.org/
.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
.. _Common Workfow Language: http://common-workflow-language.github.io
History
-------
.. to_doc
---------------------
18.5.13 (2018-05-23)
---------------------
* Small updates to test parsing to support Galaxy workflow testing.
---------------------
18.5.12 (2018-05-22)
---------------------
* Update test data processing to allow URIs in Galaxy workflow tests.
---------------------
18.5.11 (2018-05-16)
---------------------
* Parse CWL SoftwareRequirements to Galaxy requirements (required to fix various Planemo functionality
for CWL tools).
---------------------
18.5.10 (2018-05-10)
---------------------
* Docker logging API fix for Planemo.
---------------------
18.5.9 (2018-05-07)
---------------------
* Update CWL linting to target CWL 1.0.
---------------------
18.5.8 (2018-05-06)
---------------------
* Better error handling for Conda searching (thanks to @bgruening).
* Update against the latest Galaxy codebase.
* Add Galaxy tool linting to ensure versions are PEP 440 compliant (thanks to @davebx).
---------------------
18.5.7 (2018-03-12)
---------------------
* More tool testing client fixes, this time for ephemeris.
---------------------
18.5.6 (2018-03-12)
---------------------
* Bring in the latest Galaxy dev branch - includes code cleanup and many Python 3 fixes from
@nsoranzo as well as client code for executing tool tests against external Galaxy instances.
* Extend tool testing client from Galaxy's dev branch with even more data collection for compatiblity
with Planemo.
---------------------
18.5.5 (2018-03-06)
---------------------
* Fix mulled to use shlex.quote to escape single quotes in test command
(thanks to @mbargull).
* Make markupsafe a dependency since it is import unconditionally in galaxy.tools.toolbox
(thanks to @mbargull).
* Python 3 fix for assertion testing.
---------------------
18.5.4 (2018-03-01)
---------------------
* Make conda image for mulled builds configurable via an environment variable
(thanks to @mbargull).
---------------------
18.5.3 (2018-02-28)
---------------------
* Fix path module for import on Windows for Pulsar.
---------------------
18.5.2 (2018-02-28)
---------------------
* Various fixes for library usage mostly related to Conda (with help from @nsoranzo).
---------------------
18.5.1 (2018-02-26)
---------------------
* Redo last release - pushed to PyPI without actually including the desired fix.
---------------------
18.5.0 (2018-02-26)
---------------------
* Another Python 3 fix for Planemo.
* Fix galaxy-lib version - this has actually been tracking the 18.05 release of Galaxy for the last two releases.
---------------------
18.1.0 (2018-02-26)
---------------------
* More Python 3 fixes for Planemo thanks to @nsoranzo.
* Bring in the latest Galaxy development branch.
---------------------
17.9.12 (2018-02-22)
---------------------
* Python 3 fix for Planemo thanks to @nsoranzo.
* Fix bad merge of miniconda update for mulled work.
---------------------
17.9.11 (2018-02-22)
---------------------
* Update to the latest Galaxy dev just prior to the branch of 18.01.
* Python 3 fixes.
---------------------
17.9.10 (2017-11-23)
---------------------
* Added docs for using mulled-build with your own quay.io account
(thanks to @jerowe).
* Catch errors in Conda search if nothing is found (preventing planemo-monitor
from functioning properly) (thanks to @bgruening).
* Make multi-requirement container building via mulled more stable
(thanks to @bgruening).
---------------------
17.9.9 (2017-09-27)
---------------------
* Bring in latest updates from the 17.09 branch of Galaxy - including updating the default target Conda version and fixes for module resolution.
---------------------
17.9.8 (2017-09-26)
---------------------
* Bring in updated CWL utilities from the upstream work on CWL integration.
---------------------
17.9.7 (2017-09-19)
---------------------
* Bring in updated CWL utilities from the upstream work on CWL integration.
---------------------
17.9.6 (2017-09-15)
---------------------
* Remove ``command`` lint check that is no longer valid.
---------------------
17.9.5 (2017-09-06)
---------------------
* Bring in updated CWL utilities from the upstream work on CWL integration.
---------------------
17.9.4 (2017-09-06)
---------------------
* Bring in various Galaxy updates including numerous Conda fixes and changes (thanks to @nsoranzo).
* Improved error handling when parsing tool reStructuredText (thanks to @erasche).
* Updated CWL utilities.
---------------------
17.9.3 (2017-06-27)
---------------------
* Bug fix in from_dict parsing of tool dependency specs.
---------------------
17.9.2 (2017-06-22)
---------------------
* Sync with mulled enhancements and fixes from Galaxy's development branch.
---------------------
17.9.1 (2017-06-17)
---------------------
* Various small Singularity fixes and enhancements.
---------------------
17.9.0 (2017-06-11)
---------------------
* Bring in latest Galaxy dev changes.
* Implement support for building Singularity mulled containers.
* Implement mulled version 2 package hashing.
* Fix default namespace for mulled operations from mulled to biocontainers.
---------------------
17.5.11 (2017-05-31)
---------------------
* Fix HISTORY.rst formatting to properly render release on PyPI.
* Fix bug in new offline Conda search function introduced in 17.5.10.
---------------------
17.5.10 (2017-05-30)
---------------------
* Always clean up build directory in mulled commands (thanks to @johanneskoester).
* Expose offline mode in Conda search utility (for repeated fast searches).
* When publishing mulled containers - use quay.io API to publish them as public.
* Add explicit option ``--check-published`` to ``mulled-build-*``.
* Fix auto-installation of Involucro on first attempt.
* Handle explicit tags in ``mulled-build-files`` and add an implicit tag of ``0`` if none found.
* Fix tab parsing in ``mulled-build-files``.
---------------------
17.5.9 (2017-05-16)
---------------------
* Make mulled-search to search biocontainers instead of mulled repository by default
(thanks to @tom-tan).
* Allow setting a new base image with mulled-build.
---------------------
17.5.8 (2017-04-23)
---------------------
* Fix mulled image cleanup. #55.
---------------------
17.5.7 (2017-03-15)
---------------------
* Updates to CWL library functionality for several months worth of CWL tool updates.
* Allow finding tools by a URI-like strings (e.g. ``file://``, ``http://``, ``dockstore://``).
* Bring in latest Galaxy updates.
---------------------
17.5.6 (2017-03-01)
---------------------
* Expanded options for mulled CLI tools and library functionality.
Fixes #49.
---------------------
17.5.5 (2017-02-26)
---------------------
* Fix bug in 17.5.4 where under certain conditions conda-build would attempt to be setup
with the conda --use-local flag - which is not allowed.
---------------------
17.5.4 (2017-02-26)
---------------------
* Fix local builds Conda support to reflect conda-build is required.
* Fix default target path for miniconda installs.
---------------------
17.5.3 (2017-02-24)
---------------------
* Update against the latest Galaxy dev branch changes.
* Update Conda utilities to allow using locally built packages.
---------------------
17.5.2 (2017-02-21)
---------------------
* Conda utility enhancements to fix a Planemo bug.
---------------------
17.5.1 (2017-02-21)
---------------------
* Various improvements to Galaxy tool linting.
---------------------
17.5.0 (2017-02-16)
---------------------
* Bring in the last of the Galaxy dev changes.
* Allow Conda installs to target global Conda config (for Planemo)
---------------------
17.1.2 (2017-01-23)
---------------------
* Bring in the last of the Galaxy dev changes before branch of release_17.01.
* Improvements to mulled testing thanks to @mvdbeek.
---------------------
17.1.1 (2016-12-14)
---------------------
* Revert changes to shell command execution in Galaxy that had unintended consequences for Planemo.
---------------------
17.1.0 (2016-12-12)
---------------------
* Improved mulled logging thanks to @bgruening.
* Bring in the latest Galaxy dev changes.
---------------------
16.10.10 (2016-10-24)
---------------------
* Fix mulled package data fetching for Mac OS X (thanks to @dannon).
---------------------
16.10.9 (2016-10-21)
---------------------
* Small fixes including to reflect mulled name on quay.io changed to biocontainers.
---------------------
16.10.8 (2016-10-10)
---------------------
* More mulled enhancements and bug fixes thanks to @bgruening and @daler.
---------------------
16.10.7 (2016-10-08)
---------------------
* More mulled enhancements and bug fixes thanks to @bgruening.
* Fix bioconda support by adding conda-forge to list of default channels.
---------------------
16.10.6 (2016-10-07)
---------------------
* More mulled enhancements thanks to @bgruening.
---------------------
16.10.5 (2016-10-04)
---------------------
* Some docstring cleanup and minor tweaks to Conda support for downstream planemo mulled work.
---------------------
16.10.4 (2016-10-03)
---------------------
* More mulled fixes and enhancements.
---------------------
16.10.3 (2016-10-02)
---------------------
* Small mulled and Conda related fix and enhancements.
---------------------
16.10.2 (2016-09-30)
---------------------
* Fix setup.py for features in 16.10.1.
---------------------
16.10.1 (2016-09-29)
---------------------
* Updates for recents changes to Galaxy and initial mulled scripts and container resolver.
---------------------
16.10.0 (2016-08-31)
---------------------
* Updates for recent changes to Galaxy.
---------------------
16.7.10 (2016-08-04)
---------------------
* Updates for recent change to Galaxy.
---------------------
16.7.9 (2016-06-13)
---------------------
* Updates for recent changes to Galaxy and cwltool.
---------------------
16.7.8 (2016-06-05)
---------------------
* Updates to include Galaxy library for verifying test outputs
and the latest dev changes to Galaxy.
---------------------
16.7.7 (2016-05-23)
---------------------
* Fixes to CWL and Docker libraries for Planemo.
---------------------
16.7.6 (2016-05-11)
---------------------
* Fixes to cwl processing for Planemo.
---------------------
16.7.5 (2016-05-11)
---------------------
* Updates to cwl processing for Planemo.
---------------------
16.7.4 (2016-05-10)
---------------------
* Updates to cwl processing for Planemo.
---------------------
16.7.3 (2016-05-07)
---------------------
* Updates to cwltool_deps for Planemo.
---------------------
16.7.2 (2016-05-06)
---------------------
* Updates to tool parsing and linting for Planemo.
---------------------
16.7.1 (2016-05-02)
---------------------
* Update against the latest development branch of Galaxy.
---------------------
16.7.0 (2016-04-21)
---------------------
* Update against the latest development branch of Galaxy.
---------------------
16.4.1 (2016-04-08)
---------------------
* Update against the latest development branch of Galaxy.
---------------------
16.4.0 (2016-02-15)
---------------------
* Update against the latest development branch of Galaxy.
---------------------
16.1.9 (2016-01-14)
---------------------
* Fix a bug in the source distribution of galaxy-lib.
---------------------
16.1.8 (2016-01-12)
---------------------
* Update against Galaxy's release_16.01 branch.
---------------------
16.1.7 (2016-01-03)
---------------------
* Update against Galaxy's dev branch - including conda updates,
dependency resolution changes, and toolbox updates.
---------------------
16.1.6 (2015-12-28)
---------------------
* Additional fixes to setup.py and updates for recent changes to
Galaxy's dev branch.
---------------------
16.1.5 (2015-12-22)
---------------------
* Fix another bug that was preventing dependency resolution from
working in Pulsar.
---------------------
16.1.4 (2015-12-22)
---------------------
* Another setup.py fix for job metrics module.
---------------------
16.1.3 (2015-12-22)
---------------------
* Python 3 fixes and updates for recent Galaxy dev commits.
---------------------
16.1.2 (2015-12-21)
---------------------
* Fix for missing galaxy.tools.parser package in setup.py.
* Fix LICENSE in repository.
---------------------
16.1.1 (2015-12-20)
---------------------
* Fix small issues with dependencies, naming, and versioning with first release.
---------------------
16.1.0 (2015-12-20)
---------------------
* Setup project.
.. _bioblend: https://github.com/galaxyproject/bioblend/
.. _XSD: http://www.w3schools.com/schema/
.. _lxml: http://lxml.de/
.. _xmllint: http://xmlsoft.org/xmllint.html
.. _nose: https://nose.readthedocs.org/en/latest/
Keywords: galaxy
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: Academic Free License (AFL)
Classifier: Operating System :: POSIX
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Code Generators
Classifier: Topic :: Software Development :: Testing
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
debian/changelog
View file @ 28dfc8fd
galaxy-lib (18.5.13-1) unstable; urgency=low
galaxy-lib (18.9.1-1) UNRELEASED; urgency=medium
* New upstream version.
* Another upload (Closes: #890061).
* Added two names to debian/copyright
* Added myself to uploaders, mentioned team management
* Initial Debianization (Closes: #890061).
-- Steffen Moeller <moeller@debian.org> Wed, 13 Jun 2018 23:00:11 +0200
galaxy-lib (17.9.10-1) UNRELEASED; urgency=low
* Initial Debianization.
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 10 Feb 2018 16:37:00 +0000
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 08 Dec 2018 21:20:38 +0100
debian/control
View file @ 28dfc8fd
......@@ -3,8 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
Steffen Moeller <moeller@debian.org>
Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
dh-python,
python-all,
python-docutils,
......@@ -16,7 +17,7 @@ Build-Depends: debhelper (>= 10),
python3-setuptools,
python3-six (>= 1.9.0),
python3-yaml
Standards-Version: 4.1.4
Standards-Version: 4.2.1
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
......
debian/watch
View file @ 28dfc8fd
# try also https://pypi.debian.net/galaxy-lib/watch
version=3
version=4
opts=uversionmangle=s/(rc|a|b|c)/~$1/ \
https://pypi.debian.net/galaxy-lib/galaxy-lib-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
https://github.com/galaxyproject/galaxy-lib/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
dev-requirements.txt 0 → 100644
View file @ 28dfc8fd
# For testing
tox
nose
coverage
#Building Docs
sphinx
sphinx_rtd_theme
recommonmark
# Used to check readme.
readme
# For Python 2.6 tests
unittest2
# Used for code checking.
pyflakes
flake8
# For release
wheel
twine
docs/.planemo.yml 0 → 100644
View file @ 28dfc8fd
## Specify a default galaxy_root for test and server commands here.
#galaxy_root: /home/user/galaxy
## Specify github credentials for publishing gists links (e.g. with
## the share_test command).
#github:
# username: <username>
# password: <password>
sheds:
# For each Tool Shed you wish to target enter the API key
# or both email and password.
toolshed:
key: "<TODO>"
#email: "<TODO>"
#password: "<TODO>"
testtoolshed:
key: "<TODO>"
#email: "<TODO>"
#password: "<TODO>"
local:
key: "<TODO>"
#email: "<TODO>"
#password: "<TODO>"
custom_shed:
key: "<TODO>"
url: "http://customurl/"
#email: "<TODO>"
#password: "<TODO>"
docs/Makefile 0 → 100644
View file @ 28dfc8fd
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
clean:
rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/complexity.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/complexity.qhc"
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/complexity"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/complexity"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
\ No newline at end of file
docs/conduct.rst 0 → 100644
View file @ 28dfc8fd
.. include:: ../CODE_OF_CONDUCT.rst
docs/conf.py 0 → 100644
View file @ 28dfc8fd
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# complexity documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 9 22:26:36 2013.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys
import os
# 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('.'))
# Get the project root dir, which is the parent dir of this
cwd = os.getcwd()
project_root = os.path.dirname(cwd)
# Insert the project root dir as the first element in the PYTHONPATH.
# This lets us ensure that the source package is imported, and that its
# version is used.
sys.path.insert(0, project_root)
from recommonmark.parser import CommonMarkParser
import sphinx_rtd_theme
source_parsers = {
'.md': CommonMarkParser,
}
import galaxy as project_module
# -- General configuration ---------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = ['.rst', '.md']
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'galaxy-lib'
copyright = u'2015'
# The version info for the project you're documenting, acts as replacement
# for |version| and |release|, also used in various other places throughout
# the built documents.
#
# The short X.Y version.
version = project_module.__version__
# The full version, including alpha/beta/rc tags.
release = project_module.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to
# some non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built
# documents.
#keep_warnings = False
# -- Options for HTML output -------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = "sphinx_rtd_theme"
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# Theme options are theme-specific and customize the look and feel of a
# theme further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as
# html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the
# top of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon
# of the docs. This file should be a Windows icon file (.ico) being
# 16x16 or 32x32 pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets)
# here, relative to this directory. They are copied after the builtin
# static files, so a file named "default.css" will overwrite the builtin
# "default.css".
html_static_path = ['_static']
# If not '', a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names
# to template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer.
# Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer.
# Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages
# will contain a <link> tag referring to it. The value of this option
# must be the base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'planemodoc'
# -- Options for LaTeX output ------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass
# [howto/manual]).
latex_documents = [
('index', 'galaxy-lib.tex',
u'Galaxy-lib Documentation',
u'Galaxy Project and Community', 'manual'),
]
# The name of an image file (relative to this directory) to place at
# the top of the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings
# are parts, not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output ------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'galaxy-lib',
u'Galaxy-lib Documentation',
[u'Galaxy Project and Community'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output ----------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'galaxy-lib',
u'Galaxy-Lib Documentation',
u'Galaxy Project and Community',
'galaxy-lib',
'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
docs/contributing.rst 0 → 100644
View file @ 28dfc8fd
.. include:: ../CONTRIBUTING.rst
\ No newline at end of file