Ci and pixi

.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 }}

.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

.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

.github/workflows/python-ci.yml

@@ -10,78 +10,86 @@
 #
 # 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]
 
 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:
 
     runs-on: ubuntu-latest
     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 ../
+    - name: Run tox tests
+      run: pixi run tox

.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

.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 }}
+        password: ${{ secrets.PYPI_TOKEN_ES }}

.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"
+

.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

.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
 ..*