generated from rosalindfranklininstitute/python-template
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
0 parents
commit 610bfe0
Showing
12 changed files
with
865 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,48 @@ | ||
# This workflow will install Python dependencies, run tests and lint with a variety of Python versions | ||
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | ||
|
||
name: Python package | ||
|
||
on: | ||
push: | ||
branches: [ "main" ] | ||
pull_request: | ||
branches: [ "main" ] | ||
|
||
# Allows you to run this workflow manually from the Actions tab | ||
workflow_dispatch: | ||
|
||
jobs: | ||
build: | ||
|
||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
python-version: ["3.8", "3.9", "3.10", "3.11"] | ||
|
||
steps: | ||
- uses: actions/checkout@v3 | ||
- name: Set up Python ${{ matrix.python-version }} | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
python -m pip install flake8 black pytest pytest-cov | ||
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | ||
- name: Install package | ||
run: | | ||
python -m pip install -e . | ||
- name: Run black --check | ||
run: black --check src tests | ||
- name: Lint with flake8 | ||
run: | | ||
# stop the build if there are Python syntax errors or undefined names | ||
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
- name: Test with pytest | ||
run: | | ||
pytest |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,166 @@ | ||
# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
|
||
# C extensions | ||
*.so | ||
|
||
# Distribution / packaging | ||
.Python | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
share/python-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/ | ||
.nox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
*.py,cover | ||
.hypothesis/ | ||
.pytest_cache/ | ||
cover/ | ||
|
||
# Translations | ||
*.mo | ||
*.pot | ||
|
||
# Django stuff: | ||
*.log | ||
local_settings.py | ||
db.sqlite3 | ||
db.sqlite3-journal | ||
|
||
# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
|
||
# Scrapy stuff: | ||
.scrapy | ||
|
||
# Sphinx documentation | ||
docs/_build/ | ||
|
||
# PyBuilder | ||
.pybuilder/ | ||
target/ | ||
|
||
# Jupyter Notebook | ||
.ipynb_checkpoints | ||
|
||
# IPython | ||
profile_default/ | ||
ipython_config.py | ||
|
||
# pyenv | ||
# For a library or package, you might want to ignore these files since the code is | ||
# intended to run in multiple environments; otherwise, check them in: | ||
# .python-version | ||
|
||
# pipenv | ||
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. | ||
# However, in case of collaboration, if having platform-specific dependencies or dependencies | ||
# having no cross-platform support, pipenv may install dependencies that don't work, or not | ||
# install all needed dependencies. | ||
#Pipfile.lock | ||
|
||
# poetry | ||
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. | ||
# This is especially recommended for binary packages to ensure reproducibility, and is more | ||
# commonly ignored for libraries. | ||
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control | ||
#poetry.lock | ||
|
||
# pdm | ||
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. | ||
#pdm.lock | ||
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it | ||
# in version control. | ||
# https://pdm.fming.dev/#use-with-ide | ||
.pdm.toml | ||
|
||
# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm | ||
__pypackages__/ | ||
|
||
# Celery stuff | ||
celerybeat-schedule | ||
celerybeat.pid | ||
|
||
# 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/ | ||
.dmypy.json | ||
dmypy.json | ||
|
||
# Pyre type checker | ||
.pyre/ | ||
|
||
# pytype static type analyzer | ||
.pytype/ | ||
|
||
# Cython debug symbols | ||
cython_debug/ | ||
|
||
# PyCharm | ||
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can | ||
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore | ||
# and can be added to the global gitignore or merged into this file. For a more nuclear | ||
# option (not recommended) you can uncomment the following to ignore the entire idea folder. | ||
#.idea/ | ||
|
||
# Ignore ctags | ||
tags | ||
|
||
# Ignore setuptools-scm version file | ||
_version.py |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,43 @@ | ||
repos: | ||
- repo: https://github.com/ambv/black | ||
rev: 23.10.1 | ||
hooks: | ||
- id: black | ||
args: [--safe] | ||
language_version: python3 | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v2.1.0 | ||
hooks: | ||
- id: check-added-large-files | ||
- id: trailing-whitespace | ||
- id: end-of-file-fixer | ||
- id: debug-statements | ||
- id: name-tests-test | ||
- id: requirements-txt-fixer | ||
- id: flake8 | ||
args: ['--max-line-length=88', '--select=W291,W292,W293,F401'] | ||
language_version: python3 | ||
- repo: https://github.com/pycqa/pydocstyle | ||
rev: 6.3.0 | ||
hooks: | ||
- id: pydocstyle | ||
exclude: tests | ||
args: | ||
- --convention=google | ||
- --add-ignore=D100,D104,D212,D200,D415 | ||
- repo: https://github.com/pre-commit/mirrors-mypy | ||
rev: v1.3.0 | ||
hooks: | ||
- id: mypy | ||
exclude: tests | ||
args: ["--ignore-missing-imports", "--implicit-optional", "--follow-imports=skip"] | ||
- repo: https://github.com/pycqa/isort | ||
rev: 5.12.0 | ||
hooks: | ||
- id: isort | ||
args: ["--profile", "black"] | ||
- repo: https://github.com/rubik/xenon | ||
rev: v0.9.0 | ||
hooks: | ||
- id: xenon | ||
args: [ --max-absolute A, --max-modules A, --max-average A ] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,70 @@ | ||
# Code of Conduct - python-template | ||
|
||
## Our Pledge | ||
|
||
In the interest of fostering an open and welcoming environment, we as | ||
contributors and maintainers pledge to make participation in our project and | ||
our community a harassment-free experience for everyone, regardless of age, body | ||
size, disability, ethnicity, sex characteristics, gender identity and expression, | ||
level of experience, education, socio-economic status, nationality, personal | ||
appearance, race, religion, or sexual identity and orientation. | ||
|
||
## Our Standards | ||
|
||
Examples of behavior that contributes to a positive environment for our | ||
community include: | ||
|
||
* Demonstrating empathy and kindness toward other people | ||
* Being respectful of differing opinions, viewpoints, and experiences | ||
* Giving and gracefully accepting constructive feedback | ||
* Accepting responsibility and apologizing to those affected by our mistakes, | ||
and learning from the experience | ||
* Focusing on what is best not just for us as individuals, but for the | ||
overall community | ||
|
||
Examples of unacceptable behavior include: | ||
|
||
* The use of sexualized language or imagery, and sexual attention or | ||
advances | ||
* Trolling, insulting or derogatory comments, and personal or political attacks | ||
* Public or private harassment | ||
* Publishing others' private information, such as a physical or email | ||
address, without their explicit permission | ||
* Other conduct which could reasonably be considered inappropriate in a | ||
professional setting | ||
|
||
## Our Responsibilities | ||
|
||
Project maintainers are responsible for clarifying and enforcing our standards of | ||
acceptable behavior and will take appropriate and fair corrective action in | ||
response to any instances of unacceptable behavior. | ||
|
||
Project maintainers have the right and responsibility to remove, edit, or reject | ||
comments, commits, code, wiki edits, issues, and other contributions that are | ||
not aligned to this Code of Conduct, or to ban | ||
temporarily or permanently any contributor for other behaviors that they deem | ||
inappropriate, threatening, offensive, or harmful. | ||
|
||
## Scope | ||
|
||
This Code of Conduct applies within all community spaces, and also applies when | ||
an individual is officially representing the community in public spaces. | ||
Examples of representing our community include using an official e-mail address, | ||
posting via an official social media account, or acting as an appointed | ||
representative at an online or offline event. | ||
|
||
## Enforcement | ||
|
||
Instances of abusive, harassing, or otherwise unacceptable behavior may be | ||
reported to the community leaders responsible for enforcement. | ||
All complaints will be reviewed and investigated promptly and fairly. | ||
|
||
All community leaders are obligated to respect the privacy and security of the | ||
reporter of any incident. | ||
|
||
## Attribution | ||
|
||
This Code of Conduct is adapted from the [Contributor Covenant](https://contributor-covenant.org/), version | ||
[1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct/code_of_conduct.md) and | ||
[2.0](https://www.contributor-covenant.org/version/2/0/code_of_conduct/code_of_conduct.md), | ||
and was generated by [contributing-gen](https://github.com/bttger/contributing-gen). |
Oops, something went wrong.