ensembl-py 2.0.1__tar.gz

ensembl_py-2.0.1/.github/actions/python_build/action.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: python-build
+description: "Common steps to build the Python environment"
+inputs:
+  python-version:
+    description: "Python version"
+    required: true
+    default: "3.10"
+  tags:
+    description: "Optional dependencies (via available tags) to install, e.g. [cicd]"
+    required: true
+    default: ""
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+        cache: 'pip'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .${{ inputs.tags }}
+      shell: bash

ensembl_py-2.0.1/.github/dependabot.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

ensembl_py-2.0.1/.github/workflows/ci.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: "CI"
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  license_check:
+    name: Check missing license headers
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Check license header
+        uses: apache/skywalking-eyes/header@v0.6.0
+        with:
+          config: .licenserc.yml
+
+  python_ci:
+    name: Python CI
+    uses: ./.github/workflows/python_ci.yml
+    with:
+      python-version: "3.10"

ensembl_py-2.0.1/.github/workflows/ci_dev.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: "CI (dev)"
+run-name: Run CI for Python ${{ inputs.python-version }} by @${{ github.actor }}
+
+on:
+  workflow_dispatch:
+    inputs:
+      python-version:
+        description: Python version
+        required: true
+        type: string
+
+jobs:
+  python_ci:
+    name: Python CI
+    uses: ./.github/workflows/python_ci.yml
+    with:
+      python-version: ${{ inputs.python-version }}

ensembl_py-2.0.1/.github/workflows/notice.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: "Update NOTICE copyright year at the start of every year"
+
+on:
+  schedule:
+    - cron:  '15 15 1 1 *'
+
+jobs:
+  notice_update:
+    name: Update NOTICE copyright year
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Update NOTICE file
+        run: |
+          sed -i "s/$(date +%Y --date='1 year ago')/$(date +%Y)/" NOTICE
+
+      - uses: EndBug/add-and-commit@v9
+        with:
+          add: 'NOTICE'
+          message: 'Update NOTICE copyright year'

ensembl_py-2.0.1/.github/workflows/publish.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: Upload Python package to PyPI when a release is created
+
+on:
+  release:
+    types: [created]
+
+defaults:
+  run:
+    working-directory: ./
+
+env:
+  PYTHON_VERSION: "3.10"
+
+jobs:
+  mkdocs:
+    name: Deploy documentation to GitHub Pages
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/python_build
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          tags: "[cicd,docs]"
+
+      - name: Generate coverage report
+        run: |
+          coverage run -m pytest
+          coverage html -d ./reports/htmlcov
+          coverage xml -o ./reports/coverage.xml
+          genbadge coverage -i ./reports/coverage.xml -o ./reports/htmlcov/coverage-badge.svg
+
+      - name: Run mkdocs
+        run: |
+          mkdocs gh-deploy --force
+
+  pypi-publish:
+    name: Publish release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ensembl-py
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/python_build
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          tags: "[build]"
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

ensembl_py-2.0.1/.github/workflows/python_ci.yml

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: "Python CI"
+
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: Python version to run the CI checks on
+        required: true
+        type: string
+
+defaults:
+  run:
+    working-directory: ./
+
+jobs:
+  pylint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/python_build
+        with:
+          python-version: ${{ inputs.python-version }}
+          tags: "[cicd]"
+
+      - name: Run pylint
+        run: |
+          pylint --rcfile pyproject.toml src/python/ensembl
+          pylint --rcfile pyproject.toml src/python/tests
+
+  mypy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/python_build
+        with:
+          python-version: ${{ inputs.python-version }}
+          tags: "[cicd]"
+
+      - name: Run mypy
+        run: |
+          mypy --config-file pyproject.toml src/python/ensembl
+          mypy --config-file pyproject.toml src/python/tests
+
+  black:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/python_build
+        with:
+          python-version: ${{ inputs.python-version }}
+          tags: "[cicd]"
+
+      - name: Run black
+        run: |
+          black --config pyproject.toml --check .
+
+  pytest:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      checks: write
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/python_build
+        with:
+          python-version: ${{ inputs.python-version }}
+          tags: "[cicd]"
+
+      - name: Run pytest with coverage
+        run: |
+          coverage run -m pytest --junitxml=./reports/test_results.xml
+          coverage xml -o ./reports/coverage.xml
+          coverage report -m
+
+      - name: Add coverage reports
+        if: ${{ github.event_name == 'pull_request' }}
+        continue-on-error: true
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-xml-coverage-path: ./reports/coverage.xml
+          junitxml-path: ./reports/test_results.xml

ensembl_py-2.0.1/.gitignore

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+# 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/
+pip-wheel-metadata/
+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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# ruff
+.ruff_cache/

ensembl_py-2.0.1/.licenserc.yml

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+header:
+  license:
+    content: |
+      See the NOTICE file distributed with this work for additional information
+      regarding copyright ownership.
+
+      Licensed under the Apache License, Version 2.0 (the "License");
+      you may not use this file except in compliance with the License.
+      You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+      Unless required by applicable law or agreed to in writing, software
+      distributed under the License is distributed on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+      See the License for the specific language governing permissions and
+      limitations under the License.
+
+  paths-ignore:
+    - '**/*.md'
+    - 'src/python/tests/**/test_*/**/*'
+    - '.gitignore'
+    - 'LICENSE'
+    - 'NOTICE'
+
+  comment: on-failure