Deprecate ProteinAnalysis.get_amino_acids_percent() and create Protei… #64

Workflow file for this run

.github/workflows/ci.yml at 3d1980f

	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: ["3.9", "3.11", "3.12"]

	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: ["3.9", "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: ["3.9", "3.11", "3.12"]

	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
	run: \|
	cd Tests
	python run_tests.py --offline
	shell: bash

	test_macos:
	timeout-minutes: 15
	needs: [style, build, build_wheels]
	runs-on: macos-latest
	strategy:
	matrix:
	python-version: ["3.9", "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: ["3.9", "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

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Deprecate ProteinAnalysis.get_amino_acids_percent() and create Protei… #64

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Deprecate ProteinAnalysis.get_amino_acids_percent() and create Protei… #64

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Workflow file for this run