Merge branch 'main' into steinbock_reader

Author: LucaMarconato

.flake8

@@ -0,0 +1,29 @@
+changelog:
+    exclude:
+        labels:
+            - release-ignore
+        authors:
+            - pre-commit-ci
+            - pre-commit-ci[bot]
+    categories:
+        - title: Added
+          labels:
+              - "release-added"
+        - title: Changed
+          labels:
+              - "release-changed"
+        - title: Deprecated
+          labels:
+              - "release-deprecated"
+        - title: Removed
+          labels:
+              - "release-removed"
+        - title: Fixed
+          labels:
+              - "release-fixed"
+        - title: Security
+          labels:
+              - "release-security"
+        - title: Other Changes
+          labels:
+              - "*"

.github/release.yml

@@ -1,8 +1,11 @@
 name: Prepare test data
 
 on:
+    schedule:
+        - cron: "0 0 1 * *" # run once a month to prevent artifact expiration
     workflow_dispatch:
-# uncomment and adjust the branch name if you need to add new datasets to the artifact
+    # Uncomment and adjust the branch name if you need to add new datasets to the artifact.
+    # It needs to be a branch in the spatialdata-io origin repository, not from a fork.
 #    push:
 #        branches:
 #            - main
@@ -12,24 +15,69 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
 
             - name: Download test datasets
               run: |
                   mkdir -p ./data
                   cd ./data
+
+                  # -------
+                  # the Xenium datasets are licensed as CC BY 4.0, as shown here
+                  # https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/resources/xenium-example-data
+
+                  # 10x Genomics Xenium 2.0.0
                   curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip
                   curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip
 
+                  # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, multimodal cell segmentation
+                  # this file seems to be corrupted; skipping it for now
+                  # curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip
+
+                  # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, nuclear expansion
+                  curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip
+
+                  # 10x Genomics Xenium 4.0.0 (v1) Human ovary, nuclear expansion
+                  curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Ovary_tiny/Xenium_V1_Human_Ovary_tiny_outs.zip
+
+                  # 10x Genomics Xenium 4.0.0 (v1) Human ovary, multimodal cell segmentation
+                  curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_MultiCellSeg_Human_Ovary_tiny/Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip
+
+                  # 10x Genomics Xenium 4.0.0 (v1+Protein) Human kidney, multimodal cell segmentation
+                  curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Protein_Human_Kidney_tiny/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip
+
+                  # -------
+                  # the Visium HD dataset is licensed as CC BY 4.0, as shown here
+                  # https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data
+
+                  # 10x Genomics Visium HD 4.0.1 3' Mouse Brain Chunk
+                  curl -O https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip
+
+                  # -------
+                  # we received written permission to make the following dataset public and integrate it in the CI system of spatialdata-io
+                  # Spatial Genomics seqFISH v2
+                  curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip
+
+                  # -------
+                  # MACSima OMAP datasets are licensed as CC BY 4.0
+                  # OMAP23 for format v1.x.x
+                  curl -o OMAP23_small.zip "https://zenodo.org/api/records/18196452/files-archive"
+
+                  # OMAP10 for format v0.x.x
+                  curl -o OMAP10_small.zip "https://zenodo.org/api/records/18196366/files-archive"
+
             - name: Unzip files
               run: |
-                  unzip ./data/Xenium_V1_human_Breast_2fov_outs.zip -d ./data/Xenium_V1_human_Breast_2fov_outs
-                  unzip ./data/Xenium_V1_human_Lung_2fov_outs.zip -d ./data/Xenium_V1_human_Lung_2fov_outs
-                  rm ./data/Xenium_V1_human_Breast_2fov_outs.zip
-                  rm ./data/Xenium_V1_human_Lung_2fov_outs.zip
+                  cd ./data
+                  for file in *.zip; do
+                      dir="${file%.zip}"
+                      mkdir -p "$dir"
+                      unzip "$file" -d "$dir"
+                      rm "$file"
+                  done
 
             - name: Upload artifacts
-              uses: actions/upload-artifact@v3
+              uses: actions/upload-artifact@v4
               with:
                   name: data
                   path: ./data

.github/workflows/build.yaml

@@ -5,26 +5,26 @@ on:
         types: [published]
 
 jobs:
-    release:
-        # requires that you have put your twine API key in your
-        # github secrets (see readme for details)
+    package_and_release:
         runs-on: ubuntu-latest
-        if: contains(github.ref, 'tags')
+        if: startsWith(github.ref, 'refs/tags/v')
         steps:
-            - name: Checkout code
-              uses: actions/checkout@v3
-
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
+            - uses: actions/checkout@v4
+            - name: Set up Python 3.12
+              uses: actions/setup-python@v5
               with:
-                  python-version: "3.10"
-
+                  python-version: "3.13"
+                  cache: pip
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+            - name: Build package
+              run: python -m build
+            - name: Check package
+              run: twine check --strict dist/*.whl
             - name: Install hatch
               run: pip install hatch
-
             - name: Build project for distribution
               run: hatch build
-
             - name: Publish a Python distribution to PyPI
               uses: pypa/gh-action-pypi-publish@release/v1
               with:

.github/workflows/prepare_test_data.yaml

@@ -18,17 +18,17 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: ["3.9", "3.10"]
+                python: ["3.11", "3.12", "3.13"]
                 os: [ubuntu-latest]
 
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
 
@@ -37,7 +37,7 @@ jobs:
               run: |
                   echo "::set-output name=dir::$(pip cache dir)"
             - name: Restore pip cache
-              uses: actions/cache@v2
+              uses: actions/cache@v4
               with:
                   path: ${{ steps.pip-cache-dir.outputs.dir }}
                   key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
@@ -52,19 +52,13 @@ jobs:
                   pip install --pre -e ".[dev,test]"
 
             - name: Download artifact of test data
-              if: matrix.python == '3.10'
-              uses: dawidd6/action-download-artifact@v2
+              if: matrix.python == '3.13'
+              uses: dawidd6/action-download-artifact@v9
               with:
                   workflow: prepare_test_data.yaml
                   name: data
                   path: ./data
 
-            - name: List the data directory
-              if: matrix.python == '3.10'
-              run: |
-                  ls -l ./data
-                  pwd
-
             - name: Test
               env:
                   MPLBACKEND: agg

.github/workflows/release.yaml

@@ -6,6 +6,7 @@ temp/
 
 # Compiled files
 __pycache__/
+.ipynb_checkpoints/
 
 # Distribution / packaging
 /build/
@@ -37,6 +38,17 @@ node_modules/
 .asv/
 uv.lock
 
+# memray report
+*.bin
+
+# speedscope report
+profile.speedscope.json
+
 # test datasets (e.g. Xenium ones)
+# symlinks
+data
+# data folder
 data/
 tests/data
+uv.lock
+.asv/

.github/workflows/test.yaml

@@ -1,6 +1,5 @@
 [mypy]
-python_version = 3.9
-plugins = numpy.typing.mypy_plugin
+python_version = 3.10
 
 ignore_errors = False
 warn_redundant_casts = True