Change to image handling for consistency (#51)

- Add an affine function that computes a `rasterio.Affine` object given a `scale_factor`. This assumes a simple scaling where the origin is (0,0) in the spatial coordinate system corresponding to the top-left pixel (0,0). More complex alignments would require explicit affine transforms.
- Ensure `img_raster()` consistently returns a PIL.Image.Image.
- Add `to_numpy()` method.
- Changes to how caching works in remote images.

Author: jkanche

.github/workflows/run-tests.yml

@@ -1,33 +1,73 @@
-name: Run tests
+name: Test the library
 
 on:
   push:
-    branches: [main]
+    branches:
+      - master # for legacy repos
+      - main
   pull_request:
-    branches: [main]
+    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", "3.13"]
-
-    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 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 +1,13 @@
 # Changelog
 
+## Version 0.0.10
+
+- Add an affine function that computes a `rasterio.Affine` object given a `scale_factor`. This assumes a simple scaling where the origin is (0,0) in the spatial coordinate system corresponding to the top-left pixel (0,0). More complex alignments would require explicit affine transforms.
+- Ensure img_raster() consistently returns a PIL.Image.Image.
+- Add to_numpy() method.
+- Changes to how caching works in remote images.
+
+
 ## Version 0.0.9
 - Added `to_anndata()` in main `SpatialExperiment` class (PR #50)
 

setup.cfg

@@ -51,11 +51,11 @@ install_requires =
     importlib-metadata; python_version<"3.8"
     biocframe>=0.6.3
     biocutils>=0.2
-    summarizedexperiment>=0.5
     singlecellexperiment>=0.5.7
     pillow>=11.0
     requests
     scipy~=1.13
+    rasterio
 
 
 [options.packages.find]