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‎.github/CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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[email protected] (Christopher J Mungall).
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
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For answers to common questions about this code of conduct, see the FAQ at
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[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
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[https://www.contributor-covenant.org/translations][translations].
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[homepage]: https://www.contributor-covenant.org
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[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
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[Mozilla CoC]: https://github.com/mozilla/diversity
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[FAQ]: https://www.contributor-covenant.org/faq
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[translations]: https://www.contributor-covenant.org/translations

‎.github/CONTRIBUTING.md‎

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# Contributing
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### Code Style
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This project uses [`black`](https://github.com/psf/black) to automatically
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enforce a consistent code style. You can apply `black` and other pre-configured
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linters with `tox -e lint`.
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This project uses [`flake8`](https://flake8.pycqa.org) and several plugins for
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additional checks of documentation style, security issues, good variable
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nomenclature, and more (
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see [`tox.ini`](tox.ini) for a list of flake8 plugins). You can check if your
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code passes `flake8` with `tox -e flake8`.
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Each of these checks are run on each commit using GitHub Actions as a continuous
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integration service. Passing all of them is required for accepting a
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contribution. If you're unsure how to address the feedback from one of these
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tools, please say so either in the description of your pull request or in a
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comment, and we will help you.
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These code style contribution guidelines have been adapted from the
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[cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack/blob/main/%7B%7Bcookiecutter.package_name%7D%7D/.github/CODE_OF_CONDUCT.md)
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Python package template.

‎.github/workflows/deploy_documentation.yml‎

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name: Deploy Documentation
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# Controls when the action will run. Triggers the workflow on push
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on:
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workflow_dispatch:
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push:
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branches: [ main ]
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paths:
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- 'src/docs/*'
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- 'src/schema/*.yaml'
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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build-docs:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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#----------------------------------------------
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v3
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with:
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# persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
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fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
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- name: Set up Python3
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uses: actions/setup-python@v3
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with:
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python-version: 3.9
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#----------------------------------------------
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# install & configure poetry
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#----------------------------------------------
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- name: Install Poetry
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uses: snok/[email protected]
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#----------------------------------------------
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# install dependencies if cache does not exist
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#----------------------------------------------
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- name: Install dependencies
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# if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install --no-interaction
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#----------------------------------------------
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# Create documentation and deploy.
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#----------------------------------------------
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- name: Create local docs
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run: |
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mkdir docs
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touch docs/.nojekyll
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cp -r src/docs/* docs/
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make deploy-gh-doc

‎.github/workflows/main.yaml‎

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# Built from:
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# https://docs.github.com/en/actions/guides/building-and-testing-python
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# https://github.com/snok/install-poetry#workflows-and-tips
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name: Build and test
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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lint:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.9' ]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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pip install tox
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- name: Check code quality with flake8
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run: tox -e flake8
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.9' ]
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steps:
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#----------------------------------------------
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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#----------------------------------------------
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# install & configure poetry
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#----------------------------------------------
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- name: Install Poetry
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uses: snok/[email protected]
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with:
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virtualenvs-create: true
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virtualenvs-in-project: true
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#----------------------------------------------
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# load cached venv if cache exists
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#----------------------------------------------
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- name: Load cached venv
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id: cached-poetry-dependencies
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uses: actions/cache@v3
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with:
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path: .venv
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key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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#----------------------------------------------
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# install dependencies if cache does not exist
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#----------------------------------------------
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- name: Install dependencies
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if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install --no-interaction --no-root
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#----------------------------------------------
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# install your root project, if required
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#----------------------------------------------
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- name: Install library
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run: poetry install --no-interaction --extras gilda
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#----------------------------------------------
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# run test suite
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#----------------------------------------------
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- name: Run tests
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run: poetry run python -m unittest discover
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#----------------------------------------------
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# coverage report
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#----------------------------------------------
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- name: Generate coverage results
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run: |
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poetry run coverage run -m unittest discover
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poetry run coverage xml
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poetry run coverage report -m
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#----------------------------------------------
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# upload coverage results
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#----------------------------------------------
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- name: Upload coverage report
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uses: codecov/[email protected]
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with:
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name: codecov-results-${{ matrix.python-version }}
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml
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fail_ci_if_error: true

‎.github/workflows/pypi-publish.yaml‎

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name: Publish Python Package
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on:
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release:
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types: [created]
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jobs:
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build-n-publish:
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name: Build and publish Python 🐍 distributions 📦 to PyPI
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: 3.9
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- name: Install Poetry
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uses: snok/[email protected]
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with:
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virtualenvs-create: true
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virtualenvs-in-project: true
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- name: Install dependencies
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run: poetry install --no-interaction
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- name: Build source and wheel archives
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run: |
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poetry version $(git describe --tags --abbrev=0)
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poetry build
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- name: Publish distribution 📦 to PyPI
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uses: pypa/[email protected]
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with:
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user: __token__
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password: ${{ secrets.pypi_password }}

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