Merge branch 'develop' into dep-update-sphinx

Author: shaneahmed

.github/workflows/mypy-type-check.yml

@@ -35,8 +35,9 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-        pip install -r requirements/requirements_dev.txt
+        pip install uv
+        uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
+        uv pip install --system -r requirements/requirements_dev.txt
 
     - name: Debug typing environment
       run: |

.github/workflows/pip-install.yml

@@ -42,6 +42,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+            fetch-depth: 0
 
       - name: Install Miniconda
         uses: conda-incubator/setup-miniconda@v3
@@ -122,14 +124,16 @@ jobs:
         run: |
           source $CONDA/etc/profile.d/conda.sh
           conda activate test-env
-          pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+          pip install uv
+          uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
 
       - name: Install CPU-only PyTorch (Windows)
         if: runner.os == 'Windows'
         shell: pwsh
         run: |
           conda activate test-env
-          pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+          pip install uv
+          uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
 
       # -------------------------------
       # (Windows only) make console UTF-8 (extra safety)
@@ -151,14 +155,22 @@ jobs:
         run: |
           source $CONDA/etc/profile.d/conda.sh
           conda activate test-env
-          pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}
+          pip install uv
+          if [[ "${GITHUB_EVENT_NAME}" == "pull_request" ]]; then
+            REF="${{ github.event.pull_request.head.sha }}"
+          else
+            REF="${GITHUB_SHA}"
+          fi
+          echo "Installing tiatoolbox at ref: $REF"
+          uv pip install --system git+https://github.com/TissueImageAnalytics/tiatoolbox@$REF
 
       - name: Install tiatoolbox (Windows)
         if: runner.os == 'Windows'
         shell: pwsh
         run: |
           conda activate test-env
-          pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
+          pip install uv
+          uv pip install --system git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
 
       # -------------------------------
       # Test Imports

.github/workflows/python-package.yml

@@ -34,8 +34,9 @@ jobs:
         sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
         python -m pip install ruff==0.15.9 pytest pytest-cov pytest-runner
-        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-        pip install -r requirements/requirements.txt
+        pip install uv
+        uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
+        uv pip install --system -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v4
       with:
@@ -111,9 +112,10 @@ jobs:
       run: |
         sudo apt-get install -y libopenslide-dev libopenjp2-7
         python -m pip install --upgrade pip
-        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-        pip install -r requirements/requirements.txt
-        pip install build
+        pip install uv
+        uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
+        uv pip install --system -r requirements/requirements.txt
+        uv pip install --system build
     - name: Build package
       run: python -m build
 

docs/installation.rst

@@ -115,6 +115,16 @@ or
 
 An alternate way to install using conda on Windows could be to install it in `WSL2 with CUDA support <https://learn.microsoft.com/en-us/windows/ai/directml/gpu-cuda-in-wsl>`_. Depending on your hardware and workload, WSL2 may offer improved performance for some Python workflows, and therefore we **recommend** this option.
 
+Using uv
+--------
+
+To install using `uv <https://docs.astral.sh/uv/>`_, a fast Python package and project manager, written in Rust.
+
+.. code-block:: console
+
+    $ pip install uv
+    $ uv pip install tiatoolbox
+
 From Sources
 ------------
 

examples/01-wsi-reading.ipynb

@@ -74,7 +74,8 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install uv\n",
+    "uv pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },

examples/02-stain-normalization.ipynb

@@ -83,7 +83,8 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install uv\n",
+    "uv pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },

examples/03-tissue-masking.ipynb

@@ -73,7 +73,8 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install uv\n",
+    "uv pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },