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# Codecov configuration to make it a bit less noisy | ||
coverage: | ||
status: | ||
patch: false | ||
project: | ||
default: | ||
threshold: 50% | ||
comment: | ||
layout: "header" | ||
require_changes: false | ||
branches: null | ||
behavior: default | ||
flags: null | ||
paths: null |
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openfe_gromacs/_version.py export-subst |
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# How to contribute | ||
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We welcome contributions from external contributors, and this document | ||
describes how to merge code changes into this openfe_gromacs. | ||
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## Getting Started | ||
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* Make sure you have a [GitHub account](https://github.com/signup/free). | ||
* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub. | ||
* On your local machine, | ||
[clone](https://help.github.com/articles/cloning-a-repository/) your fork of | ||
the repository. | ||
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## Making Changes | ||
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* Add some really awesome code to your local fork. It's usually a [good | ||
idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/) | ||
to make changes on a | ||
[branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) | ||
with the branch name relating to the feature you are going to add. | ||
* When you are ready for others to examine and comment on your new feature, | ||
navigate to your fork of openfe_gromacs on GitHub and open a [pull | ||
request](https://help.github.com/articles/using-pull-requests/) (PR). Note that | ||
after you launch a PR from one of your fork's branches, all | ||
subsequent commits to that branch will be added to the open pull request | ||
automatically. Each commit added to the PR will be validated for | ||
mergability, compilation and test suite compliance; the results of these tests | ||
will be visible on the PR page. | ||
* If you're providing a new feature, you must add test cases and documentation. | ||
* When the code is ready to go, make sure you run the test suite using pytest. | ||
* When you're ready to be considered for merging, check the "Ready to go" | ||
box on the PR page to let the openfe_gromacs devs know that the changes are complete. | ||
The code will not be merged until this box is checked, the continuous | ||
integration returns checkmarks, | ||
and multiple core developers give "Approved" reviews. | ||
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# Additional Resources | ||
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* [General GitHub documentation](https://help.github.com/) | ||
* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/) | ||
* [A guide to contributing to software packages](http://www.contribution-guide.org) | ||
* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR) |
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## Description | ||
Provide a brief description of the PR's purpose here. | ||
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## Todos | ||
Notable points that this PR has either accomplished or will accomplish. | ||
- [ ] TODO 1 | ||
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## Questions | ||
- [ ] Question1 | ||
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## Status | ||
- [ ] Ready to go |
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name: CI | ||
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on: | ||
# GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | ||
# The cookiecutter uses the "--initial-branch" flag when it runs git-init | ||
push: | ||
branches: | ||
- "main" | ||
pull_request: | ||
branches: | ||
- "main" | ||
schedule: | ||
# Weekly tests run on main by default: | ||
# Scheduled workflows run on the latest commit on the default or base branch. | ||
# (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | ||
- cron: "0 0 * * 0" | ||
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jobs: | ||
test: | ||
name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | ||
runs-on: ${{ matrix.os }} | ||
strategy: | ||
matrix: | ||
os: [macOS-latest, ubuntu-latest, windows-latest] | ||
python-version: [3.9, "3.10", "3.11"] | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
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- name: Additional info about the build | ||
shell: bash | ||
run: | | ||
uname -a | ||
df -h | ||
ulimit -a | ||
# More info on options: https://github.com/marketplace/actions/provision-with-micromamba | ||
- uses: mamba-org/provision-with-micromamba@main | ||
with: | ||
environment-file: devtools/conda-envs/test_env.yaml | ||
environment-name: test | ||
channels: conda-forge,defaults | ||
extra-specs: | | ||
python=${{ matrix.python-version }} | ||
- name: Install package | ||
# conda setup requires this special shell | ||
shell: bash -l {0} | ||
run: | | ||
python -m pip install . --no-deps | ||
micromamba list | ||
- name: Run tests | ||
# conda setup requires this special shell | ||
shell: bash -l {0} | ||
run: | | ||
pytest -v --cov=openfe_gromacs --cov-report=xml --color=yes openfe_gromacs/tests/ | ||
- name: CodeCov | ||
uses: codecov/codecov-action@v3 | ||
if: ${{ github.event != 'schedule' }} # Don't upload results on scheduled runs | ||
with: | ||
file: ./coverage.xml | ||
flags: unittests | ||
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} |
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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
env/ | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
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# 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 | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
.pytest_cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
.hypothesis/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
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# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
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# Scrapy stuff: | ||
.scrapy | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# PyBuilder | ||
target/ | ||
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# Jupyter Notebook | ||
.ipynb_checkpoints | ||
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# pyenv | ||
.python-version | ||
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# celery beat schedule file | ||
celerybeat-schedule | ||
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# SageMath parsed files | ||
*.sage.py | ||
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# dotenv | ||
.env | ||
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# virtualenv | ||
.venv | ||
venv/ | ||
ENV/ | ||
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# Spyder project settings | ||
.spyderproject | ||
.spyproject | ||
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# Rope project settings | ||
.ropeproject | ||
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# mkdocs documentation | ||
/site | ||
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# mypy | ||
.mypy_cache/ | ||
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# profraw files from LLVM? Unclear exactly what triggers this | ||
# There are reports this comes from LLVM profiling, but also Xcode 9. | ||
*profraw | ||
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# In-tree generated files | ||
*/_version.py | ||
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# Created by https://www.toptal.com/developers/gitignore/api/osx,windows,linux | ||
# Edit at https://www.toptal.com/developers/gitignore?templates=osx,windows,linux | ||
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### Linux ### | ||
*~ | ||
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# temporary files which can be created if a process still has a handle open of a deleted file | ||
.fuse_hidden* | ||
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# KDE directory preferences | ||
.directory | ||
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# Linux trash folder which might appear on any partition or disk | ||
.Trash-* | ||
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# .nfs files are created when an open file is removed but is still being accessed | ||
.nfs* | ||
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### OSX ### | ||
# General | ||
.DS_Store | ||
.AppleDouble | ||
.LSOverride | ||
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# Icon must end with two \r | ||
Icon | ||
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|
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# Thumbnails | ||
._* | ||
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# Files that might appear in the root of a volume | ||
.DocumentRevisions-V100 | ||
.fseventsd | ||
.Spotlight-V100 | ||
.TemporaryItems | ||
.Trashes | ||
.VolumeIcon.icns | ||
.com.apple.timemachine.donotpresent | ||
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# Directories potentially created on remote AFP share | ||
.AppleDB | ||
.AppleDesktop | ||
Network Trash Folder | ||
Temporary Items | ||
.apdisk | ||
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### Windows ### | ||
# Windows thumbnail cache files | ||
Thumbs.db | ||
Thumbs.db:encryptable | ||
ehthumbs.db | ||
ehthumbs_vista.db | ||
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# Dump file | ||
*.stackdump | ||
|
||
# Folder config file | ||
[Dd]esktop.ini | ||
|
||
# Recycle Bin used on file shares | ||
$RECYCLE.BIN/ | ||
|
||
# Windows Installer files | ||
*.cab | ||
*.msi | ||
*.msix | ||
*.msm | ||
*.msp | ||
|
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# Windows shortcuts | ||
*.lnk | ||
|
||
# End of https://www.toptal.com/developers/gitignore/api/osx,windows,linux |
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ci: | ||
autoupdate_schedule: "quarterly" | ||
repos: | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v4.4.0 | ||
hooks: | ||
- id: check-yaml | ||
- id: debug-statements | ||
- id: end-of-file-fixer | ||
- id: trailing-whitespace | ||
- id: check-builtin-literals | ||
- id: check-executables-have-shebangs | ||
- id: check-json | ||
- repo: https://github.com/psf/black | ||
rev: 22.12.0 | ||
hooks: | ||
- id: black | ||
files: ^openfe_gromacs | ||
- repo: https://github.com/PyCQA/isort | ||
rev: 5.12.0 | ||
hooks: | ||
- id: isort | ||
files: ^openfe_gromacs | ||
- repo: https://github.com/PyCQA/flake8 | ||
rev: 6.0.0 | ||
hooks: | ||
- id: flake8 | ||
files: ^openfe_gromacs | ||
additional_dependencies: [Flake8-pyproject] | ||
- repo: https://github.com/asottile/pyupgrade | ||
rev: 'v3.3.1' | ||
hooks: | ||
- id: pyupgrade | ||
args: | ||
- --py39-plus |
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