Coerce SPE to SFE (#8)

- Supporting dolomite/alabaster workflows and refactoring image classes
- Coerce spatial experiment to spatial feature experiment
- Migrate to the newer github actions
- Update typehints, docs and tests

Author: jkanche

.github/workflows/publish-pypi.yml

@@ -24,6 +24,10 @@ jobs:
         with:
           python-version: 3.11
 
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install libxml2-dev libxslt-dev
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/run-tests.yml

@@ -1,33 +1,77 @@
-name: Run tests
+name: Test the library
 
 on:
   push:
-    branches: [master]
+    branches:
+      - master # for legacy repos
+      - main
   pull_request:
-    branches: [master]
+    branches:
+      - master # for legacy repos
+      - main
+  workflow_dispatch: # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: "0 0 1,16 * *"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  test:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-
-    name: Python ${{ matrix.python-version }}
+        python: ["3.9", "3.10", "3.11", "3.12"] # , "3.13"
+        platform:
+          - ubuntu-latest
+          # - macos-latest
+          # - windows-latest
+    runs-on: ${{ matrix.platform }}
+    name: Python ${{ matrix.python }}, ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
+        id: setup-python
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
+          python-version: ${{ matrix.python }}
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install libxml2-dev libxslt-dev
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tox
+          pip install tox coverage
 
-      - name: Test with tox
-        run: |
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
           tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
+
+      - name: Check for codecov token availability
+        id: codecov-check
+        shell: bash
+        run: |
+          if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
+            echo "codecov=true" >> $GITHUB_OUTPUT;
+          else
+            echo "codecov=false" >> $GITHUB_OUTPUT;
+          fi
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v5
+        if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          slug: ${{ github.repository }}
+          flags: ${{ matrix.platform }} - py${{ matrix.python }}

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## Version 0.0.3
+
+- Supporting dolomite/alabaster workflows and refactoring image classes
+- Coerce spatial experiment to spatial feature experiment
+- Migrate to the newer github actions
+
 ## Version 0.0.1 - 0.0.2
 
 - Migrating the class from the SpatialExperiment package

pyproject.toml

@@ -12,14 +12,14 @@ version_scheme = "no-guess-dev"
 line-length = 120
 src = ["src"]
 exclude = ["tests"]
-extend-ignore = ["F821"]
+lint.extend-ignore = ["F821"]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "google"
 
 [tool.ruff.format]
 docstring-code-format = true
 docstring-code-line-length = 20
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["E402", "F401"]

setup.cfg

@@ -57,6 +57,7 @@ install_requires =
     rasterio
     aicsimageio
     numcodecs<=0.15.1
+    libpysal
 
 [options.packages.find]
 where = src