Merge pull request #3 from biowdl/release_0.2.0

Release 0.2.0

.github/PULL_REQUEST_TEMPLATE.md

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+
+### Checklist
+- [ ] Pull request details were added to CHANGELOG.rst

.github/release_checklist.md

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+Release checklist
+- [ ] Check outstanding issues on JIRA and Github
+- [ ] Create a release branch 
+  - [ ] Set version to a stable number.
+  - [ ] Change current development version in `CHANGELOG.rst` to stable version.
+- [ ] Merge the release branch into `master`
+- [ ] Create a test pypi package from the master branch. ([Instructions.](
+https://packaging.python.org/tutorials/packaging-projects/#generating-distribution-archives
+))
+- [ ] Install the packages from the test pypi repository to see if they work.
+- [ ] Created an annotated tag with the stable version number. Include changes 
+from `CHANGELOG.rst`.
+- [ ] Push tag to remote.
+- [ ] Push tested packages to pypi
+- [ ] merge `master` branch back into `develop`.
+- [ ] Add updated version number to develop

.gitignore

@@ -1 +1,104 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
 venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

.travis.yml

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+language: python
+install:
+  - pip install tox
+dist: xenial
+python: 3.5  # Use the oldest supported version of python as default.
+script:
+    - tox -e $TOX_ENV
+matrix:
+  include:
+    - env: TOX_ENV=lint
+    - env: TOX_ENV=py35
+      install:
+        - pip install codecov
+        - pip install tox
+      after_success:
+        - codecov -v  # -v to make sure coverage upload works.
+    - env: TOX_ENV=py36
+      python: 3.6
+    - env: TOX_ENV=py37
+      python: 3.7
+    - env: TOX_ENV=py38
+      python: 3.8

CHANGELOG.rst

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+==========
+Changelog
+==========
+
+.. Newest changes should be on top.
+
+.. NOTE: This document is user facing. Please word the changes in such a way
+.. that users understand how the changes affect the new version.
+
+0.2.0
+---------------
++ Make a package from the prepull_singularity script.
+
+0.1.0
+---------------
+Initial release of the prepull-singularity script.

LICENSE

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+MIT License
+
+Copyright (c) 2019 Leiden University Medical Center
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

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+prepull-singularity
+===================
+Application to populate the singularity cache. Useful for HPC clusters where
+multiple nodes may pull to the same cache at the same time if images are not
+yet present.
+
+Installation
+-------------
+prepull-singularity is tested on python 3.5, 3.6, 3.7 and 3.8. It can be
+installed with:
+
+``pip install prepull-singularity``
+
+How to run
+----------
+
+1. Make a YAML file listing the images to be pulled.
+
+.. code-block:: yaml
+
+    alpine: "alpine:latest"
+    debian: "debian:stretch-slim"
+
+2. Run the program ``prepull-singularity images.yml``
+
+Usage
+-----
+
+.. code-block:: text
+
+    usage: prepull-singularity [-h] [-a MAX_ATTEMPTS] [-p PREFIX]
+                               [--stop-on-failure] [--show-output-on-failure]
+                               [--show-output-on-success]
+                               [--singularity-exe SINGULARITY_EXE] [--use-digest]
+                               input
+
+    Pull images from listed in a YAML file, so they get cached and can be run
+    without pulling later.
+
+    positional arguments:
+      input                 A YAML file listing the images to be pulled, either as
+                            a map or list.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -a MAX_ATTEMPTS, --max-attempts MAX_ATTEMPTS
+                            Maximum number of times to attempt pulling each image;
+                            defaults to 3.
+      -p PREFIX, --prefix PREFIX
+                            Prefix for the image url; defaults to 'docker://'.
+      --stop-on-failure     Stop when pulling an image fails; by default all
+                            images will be attempted to be pull even if one fails.
+      --show-output-on-failure
+                            Print the stderr and stdout when pulling an image
+                            fails.
+      --show-output-on-success
+                            Print the stderr and stdout when pulling an image
+                            succeeds.
+      --singularity-exe SINGULARITY_EXE
+                            The command for running singularity; defaults to
+                            'singularity'
+      --use-digest          Retrieve the image digestes from dockerhub or quay.io
+                            and use those (instead of the tags) to pull the
+                            images. Only usable with docker images.

mypy.ini

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+[mypy]
+# This ignores a lot of errors that are a huge headache to fix.
+ignore_missing_imports = True

setup.cfg

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+[metadata]
+license_file=LICENSE

setup.py

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+# Copyright (c) 2019 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from pathlib import Path
+
+from setuptools import find_packages, setup
+
+LONG_DESCRIPTION = Path("README.rst").read_text()
+
+setup(
+    name="prepull-singularity",
+    version="0.2.0",
+    description="A tool for pulling singularity images in HPC environments.",
+    author="Leiden University Medical Center",
+    author_email="sasc@lumc.nl",
+    long_description=LONG_DESCRIPTION,
+    long_description_content_type="text/x-rst",
+    license="MIT",
+    keywords="singularity pull prepull hpc image container",
+    zip_safe=False,
+    packages=find_packages('src'),
+    package_dir={'': 'src'},
+    url="https://github.com/biowdl/prepull-singularity",
+    classifiers=[
+        "Programming Language :: Python :: 3 :: Only",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.5",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "License :: OSI Approved :: MIT License",
+    ],
+    python_requires=">=3.5",  # Because of type annotation
+    install_requires=[
+        "pyyaml",
+        "requests"
+    ],
+    entry_points={"console_scripts": [
+        "prepull-singularity = prepull_singularity:main"]}
+)