Fix test of CLI tool across OSes and Python versions (#1)

* add runs-on

* make ~/wsi directory

* add "from __future__ import annotations"

* quiet wget + test only on ubuntu temporarily

* set cache key + test wsinfer-mil twice

* install jsonschema in main deps

* run ruff once per pr

* mk ~/wsi only if it does not exist

* run only on ubuntu

* rename to Linux

* add tests on windows and macos

* add mypy workflow

* [skip ci] rename job

* use invoke webrequest for windows

* use dir other than /tmp

* set default num_workers=-1

.github/workflows/cli-test.yml → .github/workflows/cli-test-linux.yml

@@ -1,20 +1,21 @@
-name: Test CLI
+name: Linux
 on:
   push:
     branches: [ main ]
   pull_request:
     branches: [ main ]
 jobs:
   Test-CLI:
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Cache sample WSI
         uses: actions/cache@v3
         with:
           path: ~/wsi/
+          key: sample-wsi
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -24,14 +25,17 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu
-          python -m pip install .[dev]
+          python -m pip install .
       - name: Download sample WSI
         run: |
+          mkdir -p ~/wsi
           cd ~/wsi
-          wget -nc https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs
+          wget -nc -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs
           cd -
       - name: Run tests
         # Go to a different directory to test that WSInfer-MIL still finds everything it needs.
+        # Test it twice so the second time we get cache hits.
         run: |
           cd /tmp
           wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs
+          wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs

.github/workflows/cli-test-macos.yml

@@ -0,0 +1,41 @@
+name: macOS
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+jobs:
+  Test-CLI:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+      - name: Cache sample WSI
+        uses: actions/cache@v3
+        with:
+          path: ~/wsi/
+          key: sample-wsi
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install WSInfer-CLI
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+          python -m pip install .
+      - name: Download sample WSI
+        run: |
+          mkdir -p ~/wsi
+          cd ~/wsi
+          wget -nc -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs
+          cd -
+      - name: Run tests
+        # Go to a different directory to test that WSInfer-MIL still finds everything it needs.
+        # Test it twice so the second time we get cache hits.
+        run: |
+          cd /tmp
+          wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs
+          wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs

.github/workflows/cli-test-windows.yml

@@ -0,0 +1,44 @@
+name: Windows
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+jobs:
+  Test-CLI:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+      - name: Cache sample WSI
+        id: cache-wsi
+        uses: actions/cache@v3
+        with:
+          path: ~/wsi/
+          key: sample-wsi
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install WSInfer-CLI
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+          python -m pip install .
+      - name: Download sample WSI
+        if: steps.cache-wsi.outputs.cache-hit != 'true'
+        run: |
+          mkdir -p ~/wsi
+          cd ~/wsi
+          Invoke-WebRequest -URI https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs -OutFile CMU-1.svs
+          cd -
+      - name: Run tests
+        # Go to a different directory to test that WSInfer-MIL still finds everything it needs.
+        # Test it twice so the second time we get cache hits.
+        run: |
+          mkdir -p ~/foobar
+          cd ~/foobar
+          wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs
+          wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs

.github/workflows/mypy.yml

@@ -0,0 +1,25 @@
+name: Static Analysis
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+jobs:
+  MyPy:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install WSInfer-CLI
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+          python -m pip install .[dev] mypy
+      - name: Run mypy
+        run: python -m mypy --install-types --non-interactive wsinfer_mil

.github/workflows/ruff.yml

@@ -1,5 +1,9 @@
 name: Ruff
-on: [push, pull_request]
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
 jobs:
   ruff:
     runs-on: ubuntu-latest

pyproject.toml

@@ -37,6 +37,7 @@ dependencies = [
     "click>=8.0,<9,!=8.1.4,!=8.1.5",
     "h5py",
     "huggingface_hub",
+    "jsonschema",
     # This is when numpy.typing.NDArray was introduced.
     "numpy>=1.21.0",
     "opencv-python-headless>=4.0.0",
@@ -64,7 +65,6 @@ dynamic = ["version"]
 [project.optional-dependencies]
 dev = [
     "geojson",
-    "jsonschema",
     "mypy",
     "pre-commit",
     "pytest",

wsinfer_mil/__main__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from wsinfer_mil.cli import cli
 
 if __name__ == "__main__":

wsinfer_mil/cli.py

@@ -1,5 +1,7 @@
 """Command line interface for WSInfer MIL."""
 
+from __future__ import annotations
+
 import logging
 import os
 from pathlib import Path
@@ -80,9 +82,10 @@ def cli() -> None:
 @click.option(
     "-j",
     "--num-workers",
-    help="Number of workers to use during patch feature extraction",
-    type=click.IntRange(min=0, max=os.cpu_count()),
-    default=4,
+    help="Number of workers to use during patch feature extraction. -1 (default) uses"
+    " all cores.",
+    type=click.IntRange(min=-1, max=os.cpu_count()),
+    default=-1,
     show_default=True,
 )
 @click.option(
@@ -104,6 +107,8 @@ def run(
     json: bool,
 ) -> None:
     model = load_torchscript_model_from_hf(hf_repo_id, hf_repo_revision)
+    if num_workers == -1:
+        num_workers = os.cpu_count() or 0
     _run_impl(
         wsi_path=wsi_path,
         model=model,

wsinfer_mil/client/__init__.py

@@ -0,0 +1 @@
+from __future__ import annotations

wsinfer_mil/defaults.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 
 from platformdirs import user_cache_dir

wsinfer_mil/errors.py

@@ -1,5 +1,7 @@
 """Errors for WSInfer MIL."""
 
+from __future__ import annotations
+
 
 class WSInferMILException(Exception):
     """Base exception for WSInfer MIL."""

wsinfer_mil/wsi_utils.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import tiffslide
 from tiffslide.tiffslide import PROPERTY_NAME_MPP_X
 from tiffslide.tiffslide import PROPERTY_NAME_MPP_Y