Support readers for newer image formats (#2)

- Support other image formats, e.g. coming from the SFE package
- Realize spatial coordinates as either numpy or sparse arrays
- Migrate Github actions to the new versions in biocsetup

Author: jkanche

.github/workflows/run-tests.yml

@@ -1,33 +1,73 @@
-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", "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 +1,7 @@
 # Changelog
 
-## Version 0.1
+## Version 0.1.0 - 0.1.1
 
 - Initial version of the readers and writers for `SpatialExperiment`.
+- Support other image formats, e.g. coming from the SFE package
+- Migrate Github actions to the new versions in biocsetup

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"]

src/dolomite_spatial/read_spatial_experiment.py

@@ -1,16 +1,38 @@
-import json
 import os
 
 import dolomite_base as dl
 import dolomite_sce as dlsce
 import h5py
 from biocframe import BiocFrame
+from delayedarray import is_sparse, to_dense_array, to_scipy_sparse_matrix
 from dolomite_base.read_object import read_object_registry
 from spatialexperiment import SpatialExperiment, construct_spatial_image_class
 
 read_object_registry["spatial_experiment"] = "dolomite_spatial.read_spatial_experiment"
 
 
+def realize_array(x):
+    """Realize a `ReloadedArray` into a dense array or sparse matrix.
+
+    Args:
+        x:
+            `ReloadedArray` object.
+
+    Returns:
+
+        Realized array or matrix.
+    """
+    from dolomite_matrix import ReloadedArray
+
+    if isinstance(x, ReloadedArray):
+        if is_sparse(x):
+            x = to_scipy_sparse_matrix(x, "csc")
+        else:
+            x = to_dense_array(x)
+
+    return x
+
+
 def read_spatial_experiment(path: str, metadata: dict, **kwargs) -> SpatialExperiment:
     """Load a
     :py:class:`~spatialexperiment.SpatialExperiment.SpatialExperiment`
@@ -50,7 +72,7 @@ def read_spatial_experiment(path: str, metadata: dict, **kwargs) -> SpatialExper
     _sp_coords_path = os.path.join(path, "coordinates")
     if os.path.exists(_sp_coords_path):
         _coords = dl.alt_read_object(_sp_coords_path, **kwargs)
-        spe = spe.set_spatial_coordinates(_coords)
+        spe = spe.set_spatial_coordinates(realize_array(_coords))
     else:
         raise FileNotFoundError(f"cannot find spatial coordinates at {path}.")
 
@@ -77,8 +99,14 @@ def read_spatial_experiment(path: str, metadata: dict, **kwargs) -> SpatialExper
         image_data = []
         if len(image_samples) > 0:
             for i, _ in enumerate(image_samples):
-                # TODO: write reader for SpatialImage class
-                image_data.append(construct_spatial_image_class(os.path.join(_img_path, f"{i}.{str(image_formats[i]).lower()}")))
+                if str(image_formats[i]).lower() == "other":
+                    image_data.append(dl.alt_read_object(os.path.join(_img_path, str(i)), **kwargs))
+                else:
+                    image_data.append(
+                        construct_spatial_image_class(
+                            os.path.join(_img_path, f"{i}.{str(image_formats[i]).lower()}"), is_url=False
+                        )
+                    )
 
         _image_frame = BiocFrame(
             {