Update dependencies and actions (#81)

.github/workflows/run_pytests.yaml

@@ -12,18 +12,16 @@ jobs:
           git config --global core.autocrlf false
           git config --global core.eol lf
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Load test images from cache
         id: cache-test-images
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: test-images-cache-${{ hashFiles('tests/download_test_images.py') }}
-          path: OPENTILE_TESTDATA
+          path: tests/testdata/slides
           enableCrossOsArchive: true
-      - name: Load test images
-        if: steps.cache-test-images.outputs.cache-hit != 'true'
-        env:
-          OPENTILE_TESTDIR: OPENTILE_TESTDATA
+      - name: Download test images
+        if: ${{ steps.cache-test-images.outputs.cache-hit != 'true' }}
         run: |
           python -m pip install -U pip
           python -m pip install requests
@@ -38,36 +36,27 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Prevent cache-miss on windows
         run: |
           git config --global core.autocrlf false
           git config --global core.eol lf
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Use GNU tar instead BSD tar
-        if: matrix.os == 'windows-latest'
-        shell: cmd
-        run: echo C:\Program Files\Git\usr\bin>>"%GITHUB_PATH%"
       - name: Load test images from cache
         id: cache-test-images
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: test-images-cache-${{ hashFiles('tests/download_test_images.py') }}
-          path: OPENTILE_TESTDATA
+          path: tests/testdata/slides
           enableCrossOsArchive: true
-      - name: Check test images are loaded
-        if: steps.cache-test-images.outputs.cache-hit != 'true'
-        uses: actions/github-script@v6
-        with:
-          script: |
-            core.setFailed('test images were not cached')
+          fail-on-cache-miss: true
       - name: Set up Ubuntu
         if: matrix.os == 'ubuntu-latest'
         run: sudo apt-get install -y libturbojpeg
@@ -82,7 +71,7 @@ jobs:
           7z e libjpeg-turbo-2.1.4-vc64.exe -oC:\turbojpeg bin/turbojpeg.dll
       - name: Set up paths in windows
         if: matrix.os == 'windows-latest'
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             core.addPath('C:\\turbojpeg')
@@ -102,6 +91,4 @@ jobs:
           python -m poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
 
       - name: Test with pytest.
-        env:
-          OPENTILE_TESTDIR: OPENTILE_TESTDATA
         run: python -m poetry run pytest

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] -
 
+## [0.11.2] - 2024-02-20
+
+### Fixed
+
+- Updated `ome-types` to 0.5.0.
+
 ## [0.11.1] - 2023-12-06
 
 ### Fixed
@@ -181,7 +187,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Initial release of opentile.
 
-[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.11.1..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.11.2..HEAD
+[0.11.2]: https://github.com/imi-bigpicture/opentile/compare/v0.11.1..v0.11.2
 [0.11.1]: https://github.com/imi-bigpicture/opentile/compare/v0.11.0..v0.11.1
 [0.11.0]: https://github.com/imi-bigpicture/opentile/compare/v0.10.4..v0.11.0
 [0.10.4]: https://github.com/imi-bigpicture/opentile/compare/v0.10.3..v0.10.4

opentile/__init__.py

@@ -17,4 +17,4 @@
 from opentile.opentile import OpenTile
 from opentile.metadata import Metadata
 
-__version__ = "0.11.1"
+__version__ = "0.11.2"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "opentile"
-version = "0.11.1"
+version = "0.11.2"
 description = "Read tiles from wsi-TIFF files"
 authors = ["Erik O Gabrielsson <erik.o.gabrielsson@sectra.com>"]
 license = "Apache-2.0"
@@ -22,15 +22,14 @@ PyTurboJPEG = "^1.7.3"
 Pillow = "^10.1.0"
 imagecodecs = ">=2022.12.24"
 defusedxml = "^0.7.1"
-ome-types = "^0.4.0"
+ome-types = "^0.5.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.0"
 pytest-watch = "^4.2.0"
-pycodestyle = "^2.8.0"
 requests = "^2.28.1"
-flake8 = "^4.0.1"
-black = "^22.12.0"
+black = "^24.2.0"
+flake8 = "^7.0.0"
 codespell = "^2.2.5"
 
 [build-system]

tests/download_test_images.py

@@ -19,17 +19,17 @@
 from hashlib import md5
 
 FILES: Dict[str, Dict[str, Any]] = {
-    "slides/svs/CMU-1/CMU-1.svs": {
+    "svs/CMU-1/CMU-1.svs": {
         "url": "https://data.cytomine.coop/open/openslide/aperio-svs/CMU-1.svs",  # NOQA
         "md5": {"CMU-1.svs": "751b0b86a3c5ff4dfc8567cf24daaa85"},
     },
-    "slides/ndpi/CMU-1/CMU-1.ndpi": {
+    "ndpi/CMU-1/CMU-1.ndpi": {
         "url": "https://data.cytomine.coop/open/openslide/hamamatsu-ndpi/CMU-1.ndpi",  # NOQA
         "md5": {"CMU-1.ndpi": "fb89dea54f85fb112e418a3cf4c7888a"},
     },
 }
 
-DEFAULT_DIR = "testdata"
+DEFAULT_SLIDE_FOLDER = "tests/testdata/slides"
 DOWNLOAD_CHUNK_SIZE = 8192
 
 
@@ -43,19 +43,20 @@ def download_file(url: str, filename: Path):
 
 def main():
     print("Downloading and/or checking testdata from cytomine.")
-    test_data_path = os.environ.get("OPENTILE_TESTDIR")
-    if test_data_path is None:
-        test_data_dir = Path(DEFAULT_DIR)
+
+    test_data_folder = os.environ.get("OPENTILE_TESTDIR")
+    if test_data_folder is None:
+        slide_folder = Path(DEFAULT_SLIDE_FOLDER)
         print(
             'Env "OPENTILE_TESTDIR"" not set, downloading to default folder '
-            f"{test_data_dir}."
+            f"{slide_folder}."
         )
     else:
-        test_data_dir = Path(test_data_path)
-        print(f"Downloading to {test_data_dir}")
-    os.makedirs(test_data_dir, exist_ok=True)
+        slide_folder = Path(test_data_folder).joinpath("slides")
+        print(f"Downloading to {slide_folder}")
+    os.makedirs(slide_folder, exist_ok=True)
     for file, file_settings in FILES.items():
-        file_path = test_data_dir.joinpath(file)
+        file_path = slide_folder.joinpath(file)
         if file_path.exists():
             print(f"{file} found, skipping download")
         else:

tests/filepaths.py

@@ -16,14 +16,11 @@
 from pathlib import Path
 
 test_data_dir = os.environ.get("OPENTILE_TESTDIR", "tests/testdata")
-svs_file_path = Path(test_data_dir).joinpath("slides/svs/CMU-1/CMU-1.svs")
-philips_file_path = Path(test_data_dir).joinpath(
-    "slides/philips_tiff/philips1/input.tif"
-)
-ndpi_file_path = Path(test_data_dir).joinpath("slides/ndpi/CMU-1/CMU-1.ndpi")
-histech_file_path = Path(test_data_dir).joinpath(
-    "slides/3dhistech_tiff/CMU-1/CMU-1_Default_Extended.tif"
-)
-ome_tiff_file_path = Path(test_data_dir).joinpath(
-    "slides/ome_tiff/CMU-1/CMU-1.ome.tiff"
+slide_folder = Path(test_data_dir).joinpath("slides")
+svs_file_path = slide_folder.joinpath("svs/CMU-1/CMU-1.svs")
+philips_file_path = slide_folder.joinpath("philips_tiff/philips1/input.tif")
+ndpi_file_path = slide_folder.joinpath("ndpi/CMU-1/CMU-1.ndpi")
+histech_file_path = slide_folder.joinpath(
+    "3dhistech_tiff/CMU-1/CMU-1_Default_Extended.tif"
 )
+ome_tiff_file_path = slide_folder.joinpath("ome_tiff/CMU-1/CMU-1.ome.tiff")

tests/test_jpeg.py

@@ -22,8 +22,9 @@
 from tifffile import TiffFile, TiffPage
 
 test_data_dir = os.environ.get("OPENTILE_TESTDIR", "tests/testdata")
-ndpi_file_path = Path(test_data_dir).joinpath("slides/ndpi/CMU-1/CMU-1.ndpi")
-svs_file_path = Path(test_data_dir).joinpath("slides/svs/CMU-1/CMU-1.svs")
+slide_folder = Path(test_data_dir).joinpath("slides")
+ndpi_file_path = slide_folder.joinpath("ndpi/CMU-1/CMU-1.ndpi")
+svs_file_path = slide_folder.joinpath("svs/CMU-1/CMU-1.svs")
 
 
 @pytest.fixture()