diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index b370982..24b3f6e 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -27,136 +27,113 @@ jobs: fetch-depth: 0 ref: ${{ github.event.pull_request.head.sha }} - - name: Setup python - uses: actions/setup-python@v4 + - name: Setup Python + uses: actions/setup-python@v6 with: - python-version: 3.9 - cache: "pip" - cache-dependency-path: requirements.txt + python-version-file: ".python-version" - - name: Install Dependencies - run: | - pip install --upgrade pip - pip install -r requirements.txt - - - name: Run black - shell: bash - run: pre-commit run black --all-files + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true - - name: Run flake8 - shell: bash - run: pre-commit run flake8 --all-files + - name: Install Dependencies + run: uv sync --locked --all-extras --dev - - name: Run docformatter + - name: Run ruff linter shell: bash - run: pre-commit run docformatter --all-files + run: uv run pre-commit run ruff-check --all-files - - name: Run pydocstyle + - name: Run ruff formatter shell: bash - run: pre-commit run pydocstyle --all-files + run: uv run pre-commit run ruff-format --all-files - name: Run mypy shell: bash - run: pre-commit run mypy --all-files - + run: uv run pre-commit run mypy --all-files + - name: Run pytest with code coverage run: | - pytest --junitxml pytest.xml --cov=. --cov-report=term-missing --cov-report=xml:coverage.xml --cov-branch | tee pytest-coverage.txt - - - name: Upload Coverage Results - uses: actions/upload-artifact@v3 - with: - name: coverage-results - path: coverage.xml - if: ${{ always() }} + uv run pytest --junitxml pytest.xml --cov=. --cov-report=term-missing --cov-report=xml:coverage.xml --cov-branch | tee pytest-coverage.txt - name: Upload Unit Test Results if: always() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: - name: unit-test-py39 - path: pytest.xml + name: unit-test-py312 + path: | + pytest.xml + coverage.xml + pytest-coverage.txt - - name: Upload Unit Test Results - if: always() - uses: actions/upload-artifact@v3 - with: - name: unit-test-py39 - path: pytest-coverage.txt - publish-test-results: - name: "Publish Unit Tests Results" - needs: pre-commit-and-test - runs-on: ubuntu-latest - if: always() - timeout-minutes: 20 - - steps: - - name: Download Artifacts - uses: actions/download-artifact@v3 - with: - name: unit-test-py39 - path: unit-test-py39 - - - name: Download coverage report - uses: actions/download-artifact@v3 - with: - name: coverage-results - - - name: Pytest coverage comment in pull-request - uses: MishaKav/pytest-coverage-comment@main - with: - default-branch: main - pytest-coverage-path: unit-test-py39/pytest-coverage.txt - junitxml-path: unit-test-py39/pytest.xml - hide-badge: true - hide-report: false - create-new-comment: false - hide-comment: false - report-only-changed-files: true - - - name: Get the Coverage - shell: bash - run: | - regex='' - line=$(grep -oP $regex coverage.xml) - [[ $line =~ $regex ]] - coverage=$( bc <<< ${BASH_REMATCH[1]}*100 ) - if (( $(echo "$coverage > 90" |bc -l) )); then - COLOR=green - else - COLOR=red - fi - echo "COVERAGE=${coverage%.*}%" >> $GITHUB_ENV - echo "COLOR=$COLOR" >> $GITHUB_ENV - - - name: Create Coverage Badge - uses: schneegans/dynamic-badges-action@v1.7.0 - with: - auth: ${{ secrets.GIST_SECRET }} - gistID: ${{ secrets.GIST_ID }} - filename: coverage.${{ env.REPO_NAME }}.${{ github.event.number }}.json - label: coverage - message: ${{ env.COVERAGE }} - color: ${{ env.COLOR }} - - - name: Find Comment - uses: peter-evans/find-comment@v2 - id: fc - with: - issue-number: ${{ github.event.pull_request.number }} - comment-author: "github-actions[bot]" - body-includes: Current Branch | Main Branch - - - name: Create coverage comment - uses: peter-evans/create-or-update-comment@v2 - with: - comment-id: ${{ steps.fc.outputs.comment-id }} - issue-number: ${{ github.event.pull_request.number }} - reactions: eyes - body: | - Current Branch | Main Branch | - | ------ | ------ | - ![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/${{ env.GIST_OWNER }}/${{ secrets.GIST_ID }}/raw/coverage.${{ env.REPO_NAME }}.${{ github.event.number }}.json) | ![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/${{ github.repository_owner }}/${{ secrets.GIST_ID }}/raw/coverage.${{ env.REPO_NAME }}.main.json) | - edit-mode: replace + name: Publish Unit Tests Results + needs: pre-commit-and-test + runs-on: ubuntu-latest + if: always() + timeout-minutes: 20 + + steps: + - name: Download Artifacts + uses: actions/download-artifact@v4 + with: + name: unit-test-py312 + path: unit-test-py312 + + - name: Pytest coverage comment in pull-request + uses: MishaKav/pytest-coverage-comment@main + with: + default-branch: main + pytest-coverage-path: unit-test-py312/pytest-coverage.txt + pytest-xml-coverage-path: unit-test-py312/coverage.xml + junitxml-path: unit-test-py312/pytest.xml + hide-badge: true + hide-report: false + create-new-comment: false + hide-comment: false + report-only-changed-files: true + + - name: Get the Coverage + shell: bash + run: | + regex='' + line=$(grep -oP $regex unit-test-py312/coverage.xml) + [[ $line =~ $regex ]] + coverage=$( bc <<< ${BASH_REMATCH[1]}*100 ) + if (( $(echo "$coverage > 90" |bc -l) )); then + COLOR=green + else + COLOR=red + fi + echo "COVERAGE=${coverage%.*}%" >> $GITHUB_ENV + echo "COLOR=$COLOR" >> $GITHUB_ENV + + - name: Create Coverage Badge + uses: schneegans/dynamic-badges-action@v1.7.0 + with: + auth: ${{ secrets.GIST_SECRET }} + gistID: ${{ secrets.GIST_ID }} + filename: coverage.${{ env.REPO_NAME }}.${{ github.event.number }}.json + label: coverage + message: ${{ env.COVERAGE }} + color: ${{ env.COLOR }} + + - name: Find Comment + uses: peter-evans/find-comment@v2 + id: fc + with: + issue-number: ${{ github.event.pull_request.number }} + comment-author: "github-actions[bot]" + body-includes: Current Branch | Main Branch + - name: Create coverage comment + uses: peter-evans/create-or-update-comment@v2 + with: + comment-id: ${{ steps.fc.outputs.comment-id }} + issue-number: ${{ github.event.pull_request.number }} + reactions: eyes + body: | + Current Branch | Main Branch | + | ------ | ------ | + ![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/${{ env.GIST_OWNER }}/${{ secrets.GIST_ID }}/raw/coverage.${{ env.REPO_NAME }}.${{ github.event.number }}.json) | ![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/${{ github.repository_owner }}/${{ secrets.GIST_ID }}/raw/coverage.${{ env.REPO_NAME }}.main.json) | + edit-mode: replace diff --git a/.github/workflows/merge.yaml b/.github/workflows/merge.yaml index 0b2a488..6f4675b 100644 --- a/.github/workflows/merge.yaml +++ b/.github/workflows/merge.yaml @@ -6,32 +6,36 @@ on: jobs: pre-commit-and-test: - name: "Pre-commit and Test Python 3.9" + name: Pre-commit and Test Python 3.12 runs-on: ubuntu-latest if: always() timeout-minutes: 20 steps: - - uses: actions/checkout@v3 - - name: Setup python - uses: actions/setup-python@v4 + - uses: actions/checkout@v5 + + - name: Setup Python + uses: actions/setup-python@v6 + with: + python-version-file: ".python-version" + + - name: Install uv + uses: astral-sh/setup-uv@v6 with: - python-version: "3.9" - cache: "pip" + enable-cache: true - name: Install Dependencies run: | - pip install --upgrade pip - pip install -r requirements.txt - pip install pytest-github-actions-annotate-failures - + uv sync --locked --all-extras --dev + uv pip install pytest-github-actions-annotate-failures + - name: Install Graphviz uses: tlylt/install-graphviz@v1 - name: PyTest with code coverage continue-on-error: true run: | - pytest --cov=. --cov-report=term-missing --cov-report=xml --cov-branch + uv run pytest --junitxml pytest.xml --cov=. --cov-report=term-missing --cov-report=xml:coverage.xml --cov-branch | tee pytest-coverage.txt - name: Get the Coverage shell: bash @@ -47,7 +51,7 @@ jobs: fi echo "COVERAGE=${coverage%.*}%" >> $GITHUB_ENV echo "COLOR=$COLOR" >> $GITHUB_ENV - + - name: Create Coverage Badge uses: schneegans/dynamic-badges-action@v1.7.0 with: diff --git a/.github/workflows/python-package-conda.yaml b/.github/workflows/python-package-conda.yaml index cb4e550..8e635ac 100644 --- a/.github/workflows/python-package-conda.yaml +++ b/.github/workflows/python-package-conda.yaml @@ -21,38 +21,32 @@ jobs: ref: ${{ github.event.pull_request.head.sha }} - name: Setup python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: architecture: x64 - python-version: 3.9 - cache: "pip" - cache-dependency-path: requirements.txt + python-version-file: ".python-version" + + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true - name: Install Dependencies run: | - pip install --upgrade pip - pip install -r requirements.txt - - - name: Run black - shell: bash - run: pre-commit run black --all-files + uv sync --locked --all-extras --dev - - name: Run flake8 + - name: Run ruff linter shell: bash - run: pre-commit run flake8 --all-files + run: uv run pre-commit run ruff-check --all-files - - name: Run docformatter + - name: Run ruff formatter shell: bash - run: pre-commit run docformatter --all-files - - - name: Run pydocstyle - shell: bash - run: pre-commit run pydocstyle --all-files + run: uv run pre-commit run ruff-format --all-files - name: Run mypy shell: bash - run: pre-commit run mypy --all-files - + run: uv run pre-commit run mypy --all-files + - name: Run pytest with code coverage run: | - pytest --junitxml pytest.xml --cov=. --cov-report=term-missing --cov-report=xml:coverage.xml --cov-branch | tee pytest-coverage.txt \ No newline at end of file + uv run pytest --junitxml pytest.xml --cov=. --cov-report=term-missing --cov-report=xml:coverage.xml --cov-branch | tee pytest-coverage.txt diff --git a/.gitignore b/.gitignore index b6e4761..e53afe4 100644 --- a/.gitignore +++ b/.gitignore @@ -81,9 +81,6 @@ target/ profile_default/ ipython_config.py -# pyenv -.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 @@ -127,3 +124,6 @@ dmypy.json # Pyre type checker .pyre/ + +# Ruff +.ruff_cache/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 897a5d1..34741f9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,55 +1,29 @@ fail_fast: true repos: - - repo: https://github.com/ambv/black - rev: 22.6.0 + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.12.12 hooks: - - id: black - language_version: python3.9 + - id: ruff-check + args: [--fix] + stages: [pre-commit] + - id: ruff-format + stages: [pre-commit] - - repo: https://github.com/pycqa/flake8 - rev: 5.0.4 - hooks: - - id: flake8 - - - repo: https://github.com/PyCQA/docformatter - rev: v1.7.5 - hooks: - - id: docformatter - name: docformatter - language: python - types: [python] - description: "Formats docstrings to follow PEP 257." - entry: docformatter - args: - - --in-place - - --wrap-summaries=80 - - --wrap-descriptions=80 - - - repo: https://github.com/pycqa/pydocstyle - rev: 6.1.1 - hooks: - - id: pydocstyle - args: - - --ignore=D101,D104,D105,D203,D213,D401,D406,D407,D413 - - --ignore-decorators - - - repo: local + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.17.1 hooks: - id: mypy - name: mypy - entry: mypy - language: python - types: [python] - exclude: ^(tests|data|docs)/ args: - --no-strict-optional - --ignore-missing-imports - --no-incremental - --disable-error-code=override + - repo: local + hooks: - id: pytest name: run tests entry: pytest tests -vv language: system always_run: true - pass_filenames: false \ No newline at end of file + pass_filenames: false diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..56bb660 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12.7 diff --git a/README.md b/README.md index 4f1b7cd..4e6454c 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,16 @@ # IAI Project Template -[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) +[![mypy](https://img.shields.io/badge/type--checked-mypy-blue?style=flat-square&logo=python)](https://github.com/python/mypy) ![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/vinaysetty/1cc32e6b43d911995bf07adb1cce4e89/raw/coverage.template-project.main.json) This repository serves as a template for software projects. -# Testing and GitHub actions +## Testing and GitHub actions Using `pre-commit` hooks, `flake8`, `black`, `mypy`, `docformatter`, `pydocstyle` and `pytest` are locally run on every commit. For more details on how to use `pre-commit` hooks see [here](https://github.com/iai-group/guidelines/tree/main/python#install-pre-commit-hooks). Similarly, Github actions are used to run `flake8`, `black`, `mypy`, `docformatter`, `pydocstyle` and `pytest` on every push and pull request and merge to main. The `pytest` also runs coverage. GitHub actions are explained in detail [here](https://github.com/iai-group/guidelines/blob/main/github/Actions.md). -For GitHub actions/CI Setup see [here](docs/CI_setup.md) \ No newline at end of file +For GitHub actions/CI Setup see [here](docs/CI_setup.md) diff --git a/pyproject.toml b/pyproject.toml index 1dc6036..29f2353 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,59 @@ -[tool.black] +[project] +name = "iai-template" +version = "0.1.0" +description = "Add your description here" +readme = "README.md" +requires-python = ">=3.12" +dependencies = [] + +[dependency-groups] +dev = [ + "ipykernel>=6.30.1", + "mypy>=1.17.1", + "pre-commit>=4.3.0", + "pytest>=8.4.2", + "pytest-cov>=7.0.0", + "ruff>=0.12.12", +] + + +[tool.uv] +package = false +required-version = "~= 0.8" +# https://docs.astral.sh/uv/reference/settings/#python-preference +python-preference = "system" + + +[tool.ruff] +# https://docs.astral.sh/ruff/configuration/ +preview = false line-length = 80 -target-version = ['py39'] +target-version = "py312" + + +[tool.ruff.lint] +select = [ + "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + "D", # https://docs.astral.sh/ruff/rules/#pydocstyle-d + "E", # https://docs.astral.sh/ruff/rules/#error-e + "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f + "I", # https://docs.astral.sh/ruff/rules/#isort-i + "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl + "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up + "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n + "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf +] +ignore = [ + "D101", # https://docs.astral.sh/ruff/rules/undocumented-public-class/ + "D104", # https://docs.astral.sh/ruff/rules/undocumented-public-package/ + "D105", # https://docs.astral.sh/ruff/rules/undocumented-magic-method/ + "N818", # https://github.com/astral-sh/ruff/issues/5367 +] + + +[tool.ruff.lint.pydocstyle] +convention = "google" + + +[tool.ruff.format] 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