DVP image readers

.flake8

@@ -38,6 +38,8 @@ ignore =
     D400
     # First line should be in imperative mood; try rephrasing
     D401
+    # Abstract base class without abstractmethod.
+    B024
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
     tests/*: D

.github/release.yml

@@ -0,0 +1,22 @@
+changelog:
+    exclude:
+        labels:
+            - release-ignore
+        authors:
+            - pre-commit-ci
+    categories:
+        - title: Major
+          labels:
+              - "release-major"
+        - title: Minor
+          labels:
+              - "release-minor"
+        - title: Changed
+          labels:
+              - "release-changed"
+        - title: Fixed
+          labels:
+              - "release-fixed"
+        - title: Other Changes
+          labels:
+              - "*"

.github/workflows/prepare_test_data.yaml

@@ -18,15 +18,30 @@ jobs:
               run: |
                   mkdir -p ./data
                   cd ./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
+
+                  # Spatial Genomics seqFISH v2
+                  curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip
+
             - 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

.github/workflows/release.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/checkout@v3
+            - name: Set up Python 3.12
               uses: actions/setup-python@v4
               with:
-                  python-version: "3.10"
-
+                  python-version: "3.12"
+                  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/test.yaml

@@ -18,7 +18,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: ["3.9", "3.10"]
+                python: ["3.10", "3.12"]
                 os: [ubuntu-latest]
 
         env:
@@ -50,17 +50,19 @@ jobs:
             - name: Install dependencies
               run: |
                   pip install --pre -e ".[dev,test]"
+            - name: Install experimental dependencies
+              run: pip install --pre -e ".[dvp]"
 
             - name: Download artifact of test data
-              if: matrix.python == '3.10'
+              if: matrix.python == '3.12'
               uses: dawidd6/action-download-artifact@v2
               with:
                   workflow: prepare_test_data.yaml
                   name: data
                   path: ./data
 
             - name: List the data directory
-              if: matrix.python == '3.10'
+              if: matrix.python == '3.12'
               run: |
                   ls -l ./data
                   pwd

.mypy.ini

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

.pre-commit-config.yaml

@@ -2,28 +2,28 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.4.2
+      rev: 24.10.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
+      rev: 1.19.1
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
       rev: 5.13.2
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.11.0
+      rev: v1.14.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-PyYAML]
@@ -40,7 +40,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
+      rev: v5.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -59,7 +59,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 7.1.0
+      rev: 7.1.1
       hooks:
           - id: flake8
             additional_dependencies:
@@ -70,10 +70,10 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.17.0
+      rev: v3.19.1
       hooks:
           - id: pyupgrade
-            args: [--py3-plus, --py39-plus, --keep-runtime-typing]
+            args: [--py3-plus, --py310-plus, --keep-runtime-typing]
     - repo: local
       hooks:
           - id: forbid-to-commit
@@ -84,6 +84,6 @@ repos:
             language: fail
             files: '.*\.rej$'
     - repo: https://github.com/PyCQA/doc8
-      rev: v1.1.1
+      rev: v1.1.2
       hooks:
           - id: doc8

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
     os: ubuntu-20.04
     tools:
-        python: "3.9"
+        python: "3.10"
 sphinx:
     configuration: docs/conf.py
     fail_on_warning: true