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Merge pull request #68 from biocommons/andreasprlic-patch-1
Update python-package.yml
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‎.github/workflows/python-package.yml‎

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# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
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name: Python package
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on:
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push:
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tags:
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- '[0-9]+.[0-9]+.[0-9]+' # release
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- '[0-9]+.[0-9]+.[0-9]+a[0-9]+' # alpha
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- '[0-9]+.[0-9]+.[0-9]+b[0-9]+' # beta
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- '[0-9]+.[0-9]+.[0-9]+rc[0-9]+' # release candidate
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- '[0-9]+.[0-9]+.[0-9]+.dev[0-9]+' # dev (not semver compliant)
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- '[0-9]+.[0-9]+.[0-9]+.post[0-9]+' # post (not semver compliant)
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pull_request:
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jobs:
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cqa:
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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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- uses: actions/checkout@v4
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- uses: awalsh128/cache-apt-pkgs-action@latest
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with:
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packages: zsh
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version: 1.0
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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python-version: "3.12"
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cache: pip
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cache-dependency-path: '**/setup.cfg'
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cache-dependency-path: '**/pyproject.yaml'
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- name: Install test dependencies
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run: |
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python -m pip install --upgrade pip
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pip install --use-deprecated=legacy-resolver -e .[dev]
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pip install --use-deprecated=legacy-resolver -e .[dev,test]
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- name: Lint with flake8
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- name: Lint with Ruff
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Format check with isort
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run: |
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isort --check src
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ruff check .
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- name: Format check with Ruff
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run: |
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ruff format --check src
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# Disable bandit until issues are resolved
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# - name: Security check with bandit
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# run: |
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# bandit -ll -r src
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ruff format --check .
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test:
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runs-on: ubuntu-latest
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: awalsh128/cache-apt-pkgs-action@latest
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with:
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packages: zsh
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version: 1.0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: pip
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install --use-deprecated=legacy-resolver -e .[test]
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make develop
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- name: Test with pytest
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run: |
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make test
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deploy:
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- name: Upload coverage data to Codecov
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run: |
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# Verify integrity of codecov download
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curl https://uploader.codecov.io/verification.gpg | gpg --no-default-keyring --keyring trustedkeys.gpg --import
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curl -Os https://uploader.codecov.io/latest/linux/codecov
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curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
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curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
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gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
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shasum -a 256 -c codecov.SHA256SUM
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# Upload coverage report
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chmod +x codecov
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./codecov
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build:
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name: Build distribution
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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runs-on: ubuntu-latest
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needs:
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- cqa
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- test
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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cache: pip
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cache-dependency-path: '**/setup.cfg'
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- name: Install pypa/build
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run: >-
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python3 -m
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pip install
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build
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--user
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- name: Build a binary wheel and a source tarball
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run: python3 -m build
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- name: Store the distribution packages
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uses: actions/upload-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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publish-to-pypi:
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name: >-
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Publish Python distribution to PyPI
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/bioutils
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: hello world
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run: |
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echo "::group::Environment info"
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echo github.event_name = ${{ github.event_name }}
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echo refs = ${{ github.ref }}
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echo tags = ${{ startsWith(github.ref, 'refs/tags') }}
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echo "::endgroup::"
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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cache: pip
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cache-dependency-path: '**/setup.cfg'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build package
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run: python -m build --wheel
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- name: Publish package
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎Makefile‎

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SELF:=$(firstword $(MAKEFILE_LIST))
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PY_VERSION:=$(shell python3 --version | cut -d" " -f2 | cut -d. -f1-2)
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VE_DIR:=venv/${PY_VERSION}
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VE_DIR=venv
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$(info Using Python ${PY_VERSION})
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pip install --upgrade pip setuptools wheel
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#=> develop: install package in develop mode
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.PHONY: develop install
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#=> develop: install package in develop mode
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.PHONY: develop
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develop:
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@if [ -z "$${VIRTUAL_ENV}" ]; then echo "Not in a virtual environment; see README.md" 1>&2; exit 1; fi
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pip install -e .[dev,test]
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pip install -e ".[dev, test]"
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#=> install: install package
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install:

‎docs/source/conf.py‎

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# -- Project information -----------------------------------------------------
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project = 'bioutils'
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copyright = '2019, bioutils Contributors'
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author = 'bioutils Contributors'
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project = "bioutils"
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copyright = "2019, bioutils Contributors"
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author = "bioutils Contributors"
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
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'sphinx.ext.autosummary', 'sphinx.ext.viewcode', 'sphinx.ext.coverage',
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'sphinx.ext.doctest', 'sphinx.ext.ifconfig', 'sphinx.ext.mathjax',
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'sphinx.ext.napoleon']
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.intersphinx",
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"sphinx.ext.todo",
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"sphinx.ext.autosummary",
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"sphinx.ext.viewcode",
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"sphinx.ext.coverage",
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"sphinx.ext.doctest",
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"sphinx.ext.ifconfig",
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"sphinx.ext.mathjax",
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"sphinx.ext.napoleon",
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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templates_path = ["_templates"]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'alabaster'
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html_theme = "alabaster"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_static_path = ["_static"]

‎src/bioutils/normalize.py‎

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# -*- coding: utf-8 -*-
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"""Provides functionality for normalizing alleles, ensuring comparable representations."""
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import copy
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import enum
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import logging
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import math

‎tests/conftest.py‎

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import logging
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import os
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import pytest
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import vcr
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# set vcr logging level

‎tests/test_seqfetcher.py‎

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from bioutils.seqfetcher import (
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_add_eutils_api_key,
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_fetch_seq_ensembl,
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_fetch_seq_ncbi,
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fetch_seq,
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)

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