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Deprecate Bio.Entrez.egquery #2371

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Deprecate Bio.Entrez.egquery

Deprecate Bio.Entrez.egquery #2371

Workflow file for this run

.github/workflows/ci.yml at d614a3c
name: CI
# Avoid running multiple jobs for the same branch
# in case of updates.
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
# Run on pull requests and push events to master only
on:
pull_request:
branches:
- master
push:
branches:
- master
permissions:
contents: read
jobs:
# Style Checking: Linux and Python version only.
style:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
# Check for changes only on files changed by the PR/push
- uses: tj-actions/changed-files@v44
id: changed-files
# Cache CI packages
- uses: actions/cache@v4
id: cache-precommit
with:
path: ~/.cache/pre-commit
key: ${{ runner.os }}-precommit-hooks-v2-${{ hashFiles('**/.pre-commit-config.yaml') }}
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: 3.9
- name: Installing pre-commit
run: |
python -m pip install pre-commit
- name: Installing pre-commit hooks (cached)
if: steps.cache-precommit.outputs.cache-hit != 'true'
run: |
pre-commit install --install-hooks
- name: Run style checking via pre-commit
run: |
pre-commit run --files ${{ steps.changed-files.outputs.all_changed_files }}
# Cache pip & python dependencies for Linux runner
# since it is used in most actions.
# Adapted from: https://medium.com/ai2-blog/python-caching-in-github-actions-e9452698e98d
linux_prep:
needs: [style]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.8", "3.10", "3.11"]
steps:
- uses: actions/checkout@v4
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- uses: actions/cache@v4
id: cache-pip
with:
path: ${{ env.pythonLocation }}
key: ${{runner.os}}-${{ env.pythonLocation }}-${{ matrix.python-version }}-v2-${{ hashFiles('setup.py') }}-${{ hashFiles('**/ci-dependencies.txt') }}
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Install Python dependencies
if: steps.cache-pip.outputs.cache-hit != 'true'
run: |
python -m pip install --upgrade --upgrade-strategy eager -r ci-dependencies.txt
# Try building package:
# - tarball on Linux
# - wheels on all supported OSes and Linux, MacOS, and Windows
build:
needs: [style]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.9
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Package tarball
run: |
python setup.py sdist --formats=gztar,zip
build_wheels:
needs: [style]
strategy:
matrix:
os: [ubuntu-latest, macos-latest, windows-2019]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Build wheel
run: |
python setup.py bdist_wheel
# - name: Archive wheels
# uses: actions/upload-artifact@v2
# with:
# name: biopython_wheels
# path: |
# dist/*whl
#
# - name: Fetch archived wheels from previous jobs
# uses: actions/download-artifact@v2
# with:
# name: biopython_wheels
# path: dist
# Run tests in parallel across Linux, MacOS, and Windows
# hosts (thus the three steps and not the single matrix entry).
#
# Linux tests install all the dev dependencies, while MacOS and Windows
# tests install only numpy (lightweight version).
# NOTE: PyPy only runs on Linux with minimal dependencies because it's running slowly.
#
# Tests trigger only of the style and build steps succeed.
#
# Linux is where the thorough tests run. Install all dependencies and run all (offline) tests.
test_linux:
timeout-minutes: 15
needs: [style, build, build_wheels, linux_prep]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.8", "3.10", "3.11"]
steps:
# Start MySQL server: required for some tests.
- run: |
sudo /etc/init.d/mysql start
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
# Retrieve cache to speed things up
- uses: actions/cache@v4
id: cache-pip
with:
path: ${{ env.pythonLocation }}
key: ${{runner.os}}-${{ env.pythonLocation }}-${{ matrix.python-version }}-v2-${{ hashFiles('setup.py') }}-${{ hashFiles('**/ci-dependencies.txt') }}
- name: Install dependencies
if: steps.cache-pip.outputs.cache-hit != 'true'
run: |
python -m pip install --upgrade --upgrade-strategy eager -r ci-dependencies.txt
- name: Debug Info
run: |
python -m pip list
- name: Install from source
run: |
python -m pip install .
- name: Run test suite and get coverage
run: |
cd Tests
rm -rf coverage.xml
coverage run run_tests.py --offline
coverage xml
shell: bash
test_macos:
timeout-minutes: 15
needs: [style, build, build_wheels]
runs-on: macos-latest
strategy:
matrix:
python-version: ["3.8", "3.12"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Install minimal Python dependencies
run: |
python -m pip install numpy
- name: Debug Info
run: |
python -m pip list
- name: Install from source
run: |
python -m pip install .
- name: Run test suite
run: |
cd Tests
python run_tests.py --offline
test_windows:
timeout-minutes: 15
needs: [style, build, build_wheels]
runs-on: windows-2019
strategy:
matrix:
# TODO - Try Python 3.11 again, was Python 3.11.0 was
# failing when trying to delete SQlite databases.
python-version: ["3.8", "3.10", "3.12"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Install minimal Python dependencies
run: |
python -m pip install numpy
- name: Debug Info
run: |
python -m pip list
- name: Install from source
run: |
python -m pip install .
- name: Run test suite
run: |
cd Tests
python run_tests.py --offline
test_pypy:
timeout-minutes: 20 # a little more time
needs: [style, build, build_wheels]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [pypy-3.9]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Install minimal Python dependencies
run: |
python -m pip install numpy
- name: Debug Info
run: |
python -m pip list
- name: Install from source
run: |
python -m pip install .
- name: Run test suite
run: |
cd Tests
python run_tests.py --offline
# Flag step
check_tests:
needs: [test_linux, test_macos, test_windows]
runs-on: ubuntu-latest
steps:
- run: echo All tests passed.
# Check and build (API) documentation if everything passes.
docs:
needs: [check_tests]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.9
- uses: actions/cache@v4
id: cache-pip
with:
path: ${{ env.pythonLocation }}
key: ${{runner.os}}-${{ env.pythonLocation }}-${{ matrix.python-version }}-v2-${{ hashFiles('setup.py') }}-${{ hashFiles('**/ci-dependencies.txt') }}
- name: Install Python packaging tools
run: |
python -m pip install --upgrade pip setuptools wheel
- name: Install dependencies
if: steps.cache-pip.outputs.cache-hit != 'true'
run: |
python -m pip install --upgrade --upgrade-strategy eager -r .circleci/requirements-sphinx.txt
- name: Debug Info
run: |
python -m pip list
- name: Install from source
run: |
python -m pip install .
- name: Make documentation
run: |
make -C Doc html
shell: bash
cleanup_wheels:
if: always()
needs: [build_wheels]
runs-on: ubuntu-latest
steps:
- uses: geekyeggo/delete-artifact@v5
with:
name: biopython_wheels