diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml new file mode 100644 index 0000000..8c68f51 --- /dev/null +++ b/.github/actions/setup-pixi/action.yml @@ -0,0 +1,34 @@ +name: 'Setup Pixi Environment' +description: 'Sets up pixi with common configuration' +inputs: + environments: + description: 'Pixi environments to setup' + required: false + default: 'dev' + activate-environment: + description: 'Environment to activate' + required: false + default: 'dev' + run-install: + description: 'Whether to run install' + required: false + default: 'true' + cache: + description: 'Whether to use cache' + required: false + default: 'false' + post-cleanup: + description: 'Whether to run post cleanup' + required: false + default: 'false' + +runs: + using: 'composite' + steps: + - uses: prefix-dev/setup-pixi@v0.9.0 + with: + environments: ${{ inputs.environments }} + activate-environment: ${{ inputs.activate-environment }} + run-install: ${{ inputs.run-install }} + cache: ${{ inputs.cache }} + post-cleanup: ${{ inputs.post-cleanup }} \ No newline at end of file diff --git a/.github/workflows/documentation-build.yml b/.github/workflows/documentation-build.yml index 30f4942..b238f74 100644 --- a/.github/workflows/documentation-build.yml +++ b/.github/workflows/documentation-build.yml @@ -25,25 +25,22 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@master + uses: actions/checkout@v5 with: fetch-depth: 0 # otherwise, you will failed to push refs to dest repo - - name: Upgrade pip - run: | - python -m pip install --upgrade pip - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - - name: Install Pandoc, repo and dependencies - run: | - sudo apt install pandoc - pip install . '.[dev,docs]' + + - name: Setup Pixi + uses: ./.github/actions/setup-pixi + + - name: Build documentation + run: pixi run docs-build + - name: Build and Commit uses: sphinx-notes/pages@master with: install_requirements: true documentation_path: docs/src + - name: Push changes uses: ad-m/github-push-action@master continue-on-error: true diff --git a/.github/workflows/nightly-check.yml b/.github/workflows/nightly-check.yml new file mode 100644 index 0000000..133ba4d --- /dev/null +++ b/.github/workflows/nightly-check.yml @@ -0,0 +1,24 @@ +# Nightly Check - install dependencies and run tests after pixi update-lock +name: Nightly Check +on: + schedule: + - cron: '0 0 * * *' # Runs every day at midnight UTC + workflow_dispatch: + +jobs: + nightly-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v5 + + - name: Setup Pixi + uses: ./.github/actions/setup-pixi + + - name: Update lock file + run: pixi run update-lock + + - name: Build package + run: pixi run build + + - name: Run tox tests + run: pixi run tox diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 4c8efaf..3fc3cfb 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -10,7 +10,7 @@ # # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries -name: CI using pip +name: CI using Pixi on: [push, pull_request] @@ -18,51 +18,64 @@ jobs: Code_Consistency: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: chartboost/ruff-action@v1 - - name: Suggestion to fix issues + - uses: actions/checkout@v5 + - name: Setup Pixi + uses: ./.github/actions/setup-pixi + - name: Run linting + run: pixi run lint + + - name: Suggestion to fix lint issues if: ${{ failure() }} run: | - echo "::notice::In project root run 'python.exe -m ruff . --fix' and commit changes to fix issues." + echo "::notice::In project root run 'pixi run lint-fix' and commit changes to fix issues." + exit 1 + + - name: Run formatting + run: pixi run format-check + + - name: Suggestion to fix format issues + if: ${{ failure() }} + run: | + echo "::notice::In project root run 'pixi run format' and commit changes to fix issues." exit 1 Code_Testing: strategy: max-parallel: 4 matrix: - python-version: ['3.9', '3.10', '3.11'] - os: [ubuntu-latest, macos-latest, windows-latest] + python-version: ['3.11', '3.12', '3.13'] + os: [ubuntu-latest, macos-latest, macos-15-intel, windows-latest] runs-on: ${{ matrix.os }} if: "!contains(github.event.head_commit.message, '[ci skip]')" steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - - uses: actions/setup-python@v5 + - name: Setup Pixi + uses: prefix-dev/setup-pixi@v0.9.0 with: - python-version: ${{ matrix.python-version }} + run-install: false + cache: false + post-cleanup: false - - name: Upgrade pip - run: | - python -m pip install --upgrade pip + - name: Set Python version + run: pixi add python=${{ matrix.python-version }} - - name: Install dependencies - run: pip install -e '.[dev]' - - name: Test with tox - run: | - pip install tox tox-gh-actions coverage - tox + - name: Install dependencies and run tests + run: pixi run -e dev test - - name: Upload coverage - uses: codecov/codecov-action@v4 + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v5 with: - name: Pytest coverage - env_vars: OS,PYTHON,GITHUB_ACTIONS,GITHUB_ACTION,GITHUB_REF,GITHUB_REPOSITORY,GITHUB_HEAD_REF,GITHUB_RUN_ID,GITHUB_SHA,COVERAGE_FILE - env: - OS: ${{ matrix.os }} - PYTHON: ${{ matrix.python-version }} + name: unit-tests-job + flags: unittests + files: ./coverage-unit.xml + fail_ci_if_error: true + verbose: true + token: ${{ secrets.CODECOV_TOKEN }} + slug: EasyScience/imaging-lib Package_Testing: @@ -70,18 +83,13 @@ jobs: if: "!contains(github.event.head_commit.message, '[ci skip]')" steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - - uses: actions/setup-python@v5 - with: - python-version: 3.9 + - name: Setup Pixi + uses: ./.github/actions/setup-pixi - - name: Install dependencies and build - run: | - pip install -e '.[dev]' - python -m build + - name: Build package + run: pixi run build - - name: Check Build - run: | - cd ./dist - pytest ../ \ No newline at end of file + - name: Run tox tests + run: pixi run tox \ No newline at end of file diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index e069cfa..1b4b1b8 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -18,25 +18,26 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9', '3.10', '3.11'] + python-version: ['3.11', '3.12', '3.13'] if: "!contains(github.event.head_commit.message, '[ci skip]')" steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies and build - run: | - pip install -e '.[dev]' - python -m build - - name: Test with pytest - run: | - cd ./dist - pytest ../ + - uses: actions/checkout@v5 + + - name: Setup Pixi + uses: ./.github/actions/setup-pixi + + - name: Set Python version + run: pixi add python=${{ matrix.python-version }} + + - name: Build package + run: pixi run build + + - name: Run tests with tox + run: pixi run tox + - uses: actions/upload-artifact@v4 with: - name: Upload - Python ${{ matrix.python-version }} + name: EasyImaging - Python ${{ matrix.python-version }} path: ${{ github.workspace }}/dist/* overwrite: true \ No newline at end of file diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 4ff0448..d3775cb 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -21,20 +21,20 @@ jobs: deploy: runs-on: ubuntu-latest + permissions: + id-token: write + contents: read steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - - uses: actions/setup-python@v5 - with: - python-version: 3.9 + - name: Setup Pixi + uses: ./.github/actions/setup-pixi - - name: Install dependencies and build - run: | - pip install -e '.[dev]' - python -m build + - name: Build package + run: pixi run build - name: Publish distribution 📦 to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - password: ${{ secrets.PYPI_PASSWORD }} \ No newline at end of file + password: ${{ secrets.PYPI_TOKEN_ES }} \ No newline at end of file diff --git a/.github/workflows/verify_issue_labels.yml b/.github/workflows/verify_issue_labels.yml new file mode 100644 index 0000000..69ec3a1 --- /dev/null +++ b/.github/workflows/verify_issue_labels.yml @@ -0,0 +1,31 @@ +# This workflow will verify that all issues have at +# least one of the [scope] labels and one of the [priority] labels + +name: Verify issue labels +on: + issues: + types: [opened, labeled, unlabeled] + +jobs: + check_issue_labels: + runs-on: ubuntu-latest + permissions: + issues: write + steps: + - name: Require [scope] label + uses: trstringer/require-label-prefix@v1 + with: + secret: ${{ github.TOKEN }} + prefix: "[scope]" + addLabel: true + defaultLabel: "[scope] ⚠️ label needed" + + - name: Require [priority] label + if: always() + uses: trstringer/require-label-prefix@v1 + with: + secret: ${{ github.TOKEN }} + prefix: "[priority]" + addLabel: true + defaultLabel: "[priority] ⚠️ label needed" + diff --git a/.github/workflows/verify_pr_labels.yml b/.github/workflows/verify_pr_labels.yml new file mode 100644 index 0000000..e7eb0f5 --- /dev/null +++ b/.github/workflows/verify_pr_labels.yml @@ -0,0 +1,23 @@ +# This workflow will verify that all PRs have at +# least one of the [scope] labels before they can be merged. + +name: Verify PR labels +on: + pull_request_target: + types: [opened, labeled, unlabeled, synchronize] + +jobs: + check_pr_label: + runs-on: ubuntu-latest + permissions: + pull-requests: write + name: Verify that the PR has a valid label + steps: + - name: Verify PR label action + uses: jesusvasquez333/verify-pr-label-action@v1.4.0 + id: verify-pr-label + with: + github-token: ${{ github.TOKEN }} + valid-labels: '[scope] bug, [scope] enhancement, [scope] documentation, [scope] significant, [scope] maintenance' + pull-request-number: ${{ github.event.pull_request.number }} + disable-reviews: false diff --git a/.gitignore b/.gitignore index c756032..772dbfe 100644 --- a/.gitignore +++ b/.gitignore @@ -41,12 +41,16 @@ docs/_build # VSCode .vscode +# Pixi +.pixi/ + # Large files *.hdf *normalized.tiff *sample.tiff *open_beam.tiff ProofOfConcept/sample_data/*.tiff +ProofOfConcept/sample_data/* # Misc ..* diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..1e49ef9 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,6257 @@ +version: 6 +environments: + default: + channels: + - 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"Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Development Status :: 3 - Alpha" ] -requires-python = ">=3.9,<3.12" +requires-python = ">=3.10,<3.13" dependencies = [ - "easyscience>=0.6.0", - "scipp>=23.12.0", + "easyscience>=2.0.0", + "scitiff", + "plopp", + "ncrystal[composer]" ] [project.optional-dependencies] +build = [ + "hatchling <= 1.21.0", + "setuptools-git-versioning", + "build" +] dev = [ "build", "codecov>=2.1.11", - "coverage", - "coveralls", "flake8>=6.0.0", "ipykernel", "jupyter>=1.0.0", @@ -47,15 +51,14 @@ dev = [ "pytest>=5.2", "pytest-cov>=3.0.0", "ruff", - "toml>=0.10", - "yapf>=0.31.0", + "tox-gh-actions" ] docs = [ - "myst_parser", - "nbsphinx", - "sphinx_autodoc_typehints", + "doc8", + "readme-renderer", + "sphinx_autodoc_typehints", "sphinx_book_theme", - "sphinx-copybutton", + "sphinx_gallery", "toml" ] @@ -126,17 +129,17 @@ force-single-line = true legacy_tox_ini = """ [tox] isolated_build = True -envlist = py{3.9,3.10,3.11,3.12} +envlist = py{3.11,3.12,3.13} [gh-actions] python = - 3.9: py39 - 3.10: py310 3.11: py311 3.12: py312 + 3.13: py313 [gh-actions:env] PLATFORM = ubuntu-latest: linux macos-latest: macos + macos-15-intel: macos-intel windows-latest: windows [testenv] passenv = diff --git a/src/easyimaging/__init__.py b/src/easyimaging/__init__.py index 1b39cf9..31d73b7 100644 --- a/src/easyimaging/__init__.py +++ b/src/easyimaging/__init__.py @@ -7,6 +7,6 @@ try: __version__ = importlib.metadata.version(__package__ or __name__) except importlib.metadata.PackageNotFoundError: - __version__ = "0.0.0" + __version__ = '0.0.0' del importlib diff --git a/src/easyimaging/__version__.py b/src/easyimaging/__version__.py index 6c8e6b9..c57bfd5 100644 --- a/src/easyimaging/__version__.py +++ b/src/easyimaging/__version__.py @@ -1 +1 @@ -__version__ = "0.0.0" +__version__ = '0.0.0' diff --git a/tests/package_test.py b/tests/package_test.py index 0ee0f3e..4197cf3 100644 --- a/tests/package_test.py +++ b/tests/package_test.py @@ -4,4 +4,4 @@ def test_has_version(): - assert hasattr(pkg, '__version__') # noqa S101 + assert hasattr(pkg, '__version__') # noqa S101