test that openslide.OpenSlide is available (#199)

* test that openslide.OpenSlide is available

* do not bound sphinx version

* use PYTORCH_MPS_HIGH_WATERMARK_RATIO=0.0 for macos test

* add WSINFER_FORCE_CPU env var

This forces CPU device, even if CUDA or MPS are available. The main use
case is for testing on github actions, where I faced failures with MPS.

.github/workflows/ci.yml

@@ -101,7 +101,7 @@ jobs:
           mkdir slides && cd slides
           wget -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs
           cd ..
-          wsinfer run --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca
+          WSINFER_FORCE_CPU=1 wsinfer run --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca
           test -f results/run_metadata_*.json
           test -f results/patches/JP2K-33003-1.h5
           test -f results/model-outputs-csv/JP2K-33003-1.csv

pyproject.toml

@@ -74,7 +74,7 @@ dev = [
 ]
 docs = [
     "pydata-sphinx-theme",
-    "sphinx<6.0.0",
+    "sphinx",
     "sphinx-autoapi",
     "sphinx-click",
     "sphinx-copybutton",

wsinfer/modellib/run_inference.py

@@ -6,6 +6,7 @@
 """
 from __future__ import annotations
 
+import os
 from pathlib import Path
 from typing import TYPE_CHECKING
 from typing import cast as type_cast
@@ -93,7 +94,14 @@ def run_inference(
     model.eval()
 
     # Set the device.
-    if torch.cuda.is_available():
+    # Use CPU if env var specifies. Prefer checking if this is false, because
+    # if the var is set to almost anything (other than 0, False, f), then it
+    # should be true.
+    # This env var was introduced mainly for continuous integration tests that
+    # failed on apple silicon in github actions. Forcing to cpu avoids failures.
+    if os.getenv("WSINFER_FORCE_CPU", "0").lower() not in {"0", "f", "false"}:
+        device = torch.device("cpu")
+    elif torch.cuda.is_available():
         device = torch.device("cuda")
         if torch.cuda.device_count() > 1:
             model = torch.nn.DataParallel(model)

wsinfer/wsi.py

@@ -21,6 +21,10 @@
 try:
     import openslide
 
+    # Test that OpenSlide object exists. If it doesn't, an error will be thrown and
+    # caught. For some reason, it is possible that openslide-python can be installed
+    # but the OpenSlide object (and other openslide things) are not available.
+    openslide.OpenSlide
     HAS_OPENSLIDE = True
     logger.debug("Imported openslide")
 except Exception as err: