Merge branch 'develop' into fix-dicom-reader

Author: measty

.github/workflows/pip-install.yml

@@ -5,6 +5,8 @@ name: pip Install
 on:
     push:
         paths: [ "requirements*.yml", "conda-env-create.yml", "requirements/requirement*.txt", "setup*py", "setup*cfg", "pytproject*toml", "MANIFEST*in"]
+    pull_request:
+        paths: [ "requirements*.yml", "conda-env-create.yml", "requirements/requirement*.txt", "setup*py", "setup*cfg", "pytproject*toml", "MANIFEST*in"]
 
 jobs:
   build:
@@ -19,16 +21,16 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - name: 🐧 Install OpenSlide & OpenJPEG
+    - name: 🐧 Install OpenJPEG
       if: runner.os == 'Linux'
       run: |
         sudo apt update
-        sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
+        sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-    - name: 🍎 Install OpenSlide & OpenJPEG
+    - name: 🍎 Install OpenJPEG
       if: runner.os == 'macOS'
       run: |
-        brew install openslide openjpeg
+        brew install openjpeg
         python -m pip install --upgrade pip
     - name: 🪟 Install OpenJPEG
       if: runner.os == 'Windows'
@@ -43,47 +45,28 @@ jobs:
         make -j4
         make install
         make clean
-    - name: 🪟 Install OpenSlide
-      if: runner.os == 'Windows'
-      run: |
-        choco install wget --no-progress
-        wget https://github.com/openslide/openslide-winbuild/releases/download/v20220811/openslide-win64-20220811.zip
-        7z x openslide-win64-20220811.zip
-        ls openslide-win64-20220811
-        # Add to PATH
-        echo "$(realpath ./openslide-win64-20220811/bin)" >> $GITHUB_PATH
-        echo "$(realpath ./openslide-win64-20220811/lib)" >> $GITHUB_PATH
-        # Install
-        mkdir "C:\Program Files\openslide"
-        Copy-Item -Path ".\openslide-win64-20220811\*" -Destination "C:\Program Files\openslide" -Recurse
-        ls "C:/Program Files/openslide"
     - name: 🪟 Install SQLite Shell
       if: runner.os == 'Windows'
       run: choco install sqlite.shell --no-progress
     - name: SQLite Version Information
       run: |
         sqlite3 --version
         sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
-    - name: OpenSlide Version Information
-      if: runner.os == 'Linux'
-      run: openslide-quickhash1sum --version
     - name: OpenJPEG Version Information
       continue-on-error: true  # This -h option has exit code 1 for some reason
       run: opj_dump -h
     - name: pip Install From GitHub Repo on Linux and macOS
       if: runner.os != 'Windows'
-      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_REF_NAME}
+      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}
     - name: pip Install From GitHub on Windows
       if: runner.os == 'Windows'
-      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_REF_NAME
-    - name: Test TIAToolbox Import
+      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
+    - name: Test Imports
       shell: python
       run: |
-        import os
-        if hasattr(os, "add_dll_directory"):
-          # Required for Python>=3.8 on Windows
-          with os.add_dll_directory(r"D:\a\tiatoolbox\tiatoolbox\openslide-win64-20220811\bin"):
-            import tiatoolbox
-        else:
-          os.environ["PATH"] = r"D:\a\tiatoolbox\tiatoolbox\openslide-win64-20220811\bin;"
-          import tiatoolbox
+        import tiatoolbox
+        print(tiatoolbox.__version__)
+        import openslide
+        print(openslide.__version__)
+        import torch
+        print(torch.__version__)

.github/workflows/python-package.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt update
-        sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
+        sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
         python -m pip install ruff==0.11.8 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
@@ -42,8 +42,6 @@ jobs:
         echo "---SQlite---"
         sqlite3 --version
         sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
-        echo "---Openslide---"
-        openslide-quickhash1sum --version
         echo "---OpenJPEG---"
         opj_dump -h | head -n 5
         echo "---Python---"

docs/installation.rst

@@ -17,16 +17,14 @@ On Linux, the prerequisite software can be installed using the following command
 
 .. code-block:: console
 
-    $ apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools
+    $ apt-get -y install libopenjp2-7-dev libopenjp2-tools
 
 The same command is used when working on the Colab or Kaggle platforms. When working on Google Colab, we remove the packages ``datascience`` and ``albumentations`` because they conflict and produce an error message.
 
 Windows (10+)
 -------------
 
-1. Download OpenSlide binaries from `this page <https://openslide.org/download/>`_. Extract the folder and add the ``bin`` and ``lib`` subdirectories to the Windows `system path <https://docs.microsoft.com/en-us/previous-versions/office/developer/sharepoint-2010/ee537574(v=office.14)>`_. If you are using a conda environment, you can also copy the ``bin`` and ``lib`` subdirectories to ``[Anaconda Installation Path]/envs/[tiatoolbox-environment]/Library/``.
-
-2. Install OpenJPEG. The easiest way to install OpenJPEG is through conda:
+On Windows, ``OpenJPEG`` can be installed using the following ``conda`` command:
 
 .. code-block:: console
 
@@ -45,14 +43,14 @@ Homebrew
 
 .. code-block:: console
 
-    $ brew install openjpeg openslide
+    $ brew install openjpeg
 
 MacPorts
 ^^^^^^^^
 
 .. code-block:: console
 
-    $ port install openjpeg openslide
+    $ port install openjpeg
 
 Installing Stable Release
 =========================

requirements/requirements.txt

@@ -3,7 +3,7 @@
 aiohttp>=3.8.1
 albumentations>=1.3.0
 bokeh>=3.1.1, <3.6.0
-Click>=8.1.3
+Click>=8.1.3, <8.2.0
 defusedxml>=0.7.1
 filelock>=3.9.0
 flask>=2.2.2
@@ -16,7 +16,8 @@ matplotlib>=3.6.2
 numba>=0.57.0
 numpy>=1.23.5, <2.0.0
 opencv-python>=4.6.0
-openslide-python>=1.2.0
+openslide-bin>=4.0.0.2
+openslide-python>=1.4.0
 pandas>=2.0.0
 pillow>=9.3.0
 pydicom>=2.3.1 # Used by wsidicom
@@ -28,7 +29,7 @@ scipy>=1.8
 shapely>=2.0.0
 SimpleITK>=2.2.1
 sphinx>=5.3.0
-tifffile>=2022.10.10
+tifffile>=2022.10.10, <=2025.5.10
 timm>=1.0.3
 torch>=2.1.0
 torchvision>=0.15.0

tests/test_tileserver.py

@@ -734,3 +734,44 @@ def test_prop_range(app: TileServer) -> None:
         assert response.status_code == 200
         # should be back to no scaling
         assert layer.renderer.score_fn(0.5) == 0.5
+
+
+def test_healthcheck(empty_app: TileServer) -> None:
+    """Test the /tileserver/healthcheck endpoint."""
+    with empty_app.test_client() as client:
+        response = client.get("/tileserver/healthcheck")
+        assert response.status_code == 200
+        assert response.content_type == "application/json"
+        assert response.get_json() == {"status": "OK"}
+
+
+def test_sessions_no_slide_loaded(empty_app: TileServer) -> None:
+    """Test /tileserver/sessions when no slides are loaded."""
+    with empty_app.test_client() as client:
+        setup_app(client)
+        response = client.get("/tileserver/sessions")
+        assert response.status_code == 200
+        assert response.is_json
+        assert response.get_json() == {}
+
+
+def test_sessions_one_slide_loaded(
+    empty_app: TileServer, remote_sample: Callable
+) -> None:
+    """Test /tileserver/sessions after loading one slide."""
+    with empty_app.test_client() as client:
+        setup_app(client)
+        slide_path = safe_str(remote_sample("svs-1-small"))
+
+        response = client.put(
+            "/tileserver/slide",
+            data={"slide_path": slide_path},
+        )
+        assert response.status_code == 200
+
+        response = client.get("/tileserver/sessions")
+        assert response.status_code == 200
+        sessions = response.get_json()
+
+        assert isinstance(sessions, dict)
+        assert len(sessions) == 1