linux tests and documentation build for 'kiara'

chore: first working version of sqlite data store #936

Workflow file for this run

.github/workflows/build-linux.yaml at c595892

	name: "linux tests and documentation build for 'kiara'"
	# This workflow is triggered on pushes to the repository.
	on: [push]

	jobs:

	commitlint:
	name: lint commit message
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- uses: wagoid/commitlint-github-action@v4

	test-linux:
	name: pytest on linux
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python_version: ["3.8", "3.9", "3.10", "3.11"]
	steps:
	- name: "Set up Python ${{ matrix.python_version }}"
	uses: actions/setup-python@v4
	with:
	python-version: "${{ matrix.python_version }}"
	- name: pip cache
	id: pip-cache
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('*/setup.') }}
	- uses: actions/checkout@v2
	- name: install core_types plugin
	run: pip install -U git+https://github.com/DHARPA-project/kiara_plugin.core_types@develop
	- name: install tabular types plugin
	run: pip install -U git+https://github.com/DHARPA-project/kiara_plugin.tabular@develop
	- name: install kiara
	run: pip install -U .[dev_testing]
	- name: display installed kiara and module package versions
	run: pip list \| grep kiara
	- name: test with pytest
	run: pytest --cov-report=xml --cov=kiara tests
	- name: Coveralls
	uses: coverallsapp/github-action@v2
	with:
	parallel: true
	flag-name: run ${{ join(matrix.*, ' - ') }}
	format: cobertura
	file: coverage.xml

	coverage:
	name: test coverage
	runs-on: ubuntu-latest
	needs:
	- test-linux
	steps:
	- name: Coveralls Finished
	uses: coverallsapp/github-action@v2
	with:
	parallel-finished: true
	# carryforward: "run-1,run-2"
	# - name: "Set up Python 3.10"
	# uses: actions/setup-python@v4
	# with:
	# python-version: "3.10"
	# - name: pip cache
	# id: pip-cache
	# uses: actions/cache@v3
	# with:
	# path: ~/.cache/pip
	# key: ${{ runner.os }}-pip-${{ hashFiles('*/setup.') }}
	# - uses: actions/checkout@v2
	# - name: install core_types plugin
	# run: pip install -U git+https://github.com/DHARPA-project/kiara_plugin.core_types@develop
	# - name: install tabular types plugin
	# run: pip install -U git+https://github.com/DHARPA-project/kiara_plugin.tabular@develop
	# - name: install kiara
	# run: pip install -U .[dev_testing]
	# - name: display installed kiara and module package versions
	# run: pip list \| grep kiara
	# - name: Run coverage
	# run: coverage run -m pytest tests
	# - name: coveralls
	# uses: coverallsapp/github-action@v2
	# with:
	# format: python
	# allow-empty: true
	# - name: Upload coverage data to coveralls.io
	# run: coveralls --service=github
	# env:
	# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	mypy-linux:
	name: mypy check on linux
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
	steps:
	- name: "Set up Python ${{ matrix.python_version }}"
	uses: actions/setup-python@v4
	with:
	python-version: "${{ matrix.python_version }}"
	- name: pip cache
	id: pip-cache
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('*/setup.') }}
	- uses: actions/checkout@v2
	- name: install kiara
	run: pip install -U .[dev_testing]
	- name: Test with mypy
	run: make mypy

	linting-linux:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Install Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.11"
	- name: pip cache
	id: pip-cache
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('*/setup.') }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install ruff==0.0.257
	# Include `--format=github` to enable automatic inline annotations.
	- name: Run Ruff
	run: ruff --format=github src/

	# build-docs:
	# name: build documentation
	# runs-on: ubuntu-latest
	# needs:
	# - test-linux
	# - mypy-linux
	# - linting-linux
	# steps:
	# - name: Set up Python 3.10
	# uses: actions/setup-python@v4
	# with:
	# python-version: "3.10"
	# - name: pip cache
	# id: pip-cache
	# uses: actions/cache@v3
	# with:
	# path: ~/.cache/pip
	# key: ${{ runner.os }}-pip-${{ hashFiles('*/setup.') }}
	# - uses: actions/checkout@v3
	# with:
	# fetch-depth: 0
	# - name: install kiara
	# run: pip install -U .[dev_documentation,doc]
	# - run: git config --global user.email "markus@frkl.io"
	# - run: git config --global user.name "Markus Binsteiner"
	# - name: create latest documentation
	# if: ${{ ( github.ref == 'refs/heads/develop') }}
	# run: FAIL_DOC_BUILD_ON_ERROR=true mike deploy --push latest && mike set-default --push latest
	# - name: extract tag name
	# run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
	# - name: create stable documentation
	# if: ${{ startsWith(github.ref, 'refs/tags/') }}
	# run: FAIL_DOC_BUILD_ON_ERROR=true mike deploy --push --update-alias --title "v ${RELEASE_VERSION}" "${RELEASE_VERSION}" stable

	build_python_package:
	name: build python package
	runs-on: ubuntu-latest
	needs:
	- test-linux
	- mypy-linux
	- linting-linux
	steps:
	- name: Set up Python 3.10
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0
	- name: install pip
	run: pip install -U pip setuptools setuptools_scm build wheel
	- name: create packages
	run: python -m build
	- name: upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: build-dists
	path: dist/

	publish_python_package:
	name: publish python package
	runs-on: ubuntu-latest
	needs:
	- build_python_package
	env:
	GEMFURY_PUSH_TOKEN: ${{ secrets.GEMFURY_PUSH_TOKEN }}
	permissions:
	id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
	steps:
	- name: Retrieve build distributions
	uses: actions/download-artifact@v3
	with:
	name: build-dists
	path: dist/
	- name: upload source package to gemfury
	if: ${{ ( github.ref == 'refs/heads/develop') \|\| startsWith(github.ref, 'refs/tags') }}
	run: curl -F package=@$(ls dist/kiara-*.tar.gz) https://${GEMFURY_PUSH_TOKEN}@dharpa.fury.land:443/pypi/
	- name: upload wheel to gemfury
	if: ${{ (github.ref == 'refs/heads/develop') \|\| startsWith(github.ref, 'refs/tags') }}
	run: curl -F package=@$(ls dist/kiara-*.whl) https://${GEMFURY_PUSH_TOKEN}@dharpa.fury.land:443/pypi/
	- name: Publish release distributions to PyPI
	if: startsWith(github.ref, 'refs/tags')
	uses: pypa/gh-action-pypi-publish@release/v1

	conda_package_build:
	name: conda package build (and upload if release)
	runs-on: ubuntu-latest
	needs:
	- test-linux
	- mypy-linux
	- linting-linux
	steps:
	- name: "Set up Python 3.10"
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"
	- name: pip cache
	id: pip-cache
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('*/setup.') }}
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0
	- name: install kiara
	run: pip install -U .
	- name: install required plugin packages
	run: pip install git+https://github.com/DHARPA-Project/kiara_plugin.develop.git@develop
	- name: build conda package
	if: ${{ ( github.ref == 'refs/heads/develop') }}
	run: kiara conda build-package --patch-data ci/conda/conda-pkg-patch.yaml .
	- name: extract tag name
	run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
	- name: build & publish conda package
	if: ${{ startsWith(github.ref, 'refs/tags/') }}
	run: kiara conda build-package --publish --user dharpa --token ${{ secrets.ANACONDA_PUSH_TOKEN }} --patch-data ci/conda/conda-pkg-patch.yaml .

	merge_tag_to_main:
	name: merge current tag to main branch
	runs-on: ubuntu-latest
	if: ${{ startsWith(github.ref, 'refs/tags') }}
	needs:
	- test-linux
	- mypy-linux
	- linting-linux
	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0
	- run: git config --global user.email "markus@frkl.io"
	- run: git config --global user.name "Markus Binsteiner"
	- name: extract tag name
	run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
	- name: checkout main branch
	run: git checkout main
	- name: merge tag
	run: git merge "${RELEASE_VERSION}"
	- name: push updated main branch
	run: git push https://${{ secrets.GITHUB_TOKEN }}@github.com/DHARPA-Project/kiara.git

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chore: first working version of sqlite data store #936

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chore: first working version of sqlite data store #936

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