ENH: update app dockerfiles + add mypy/flake8 to github ci + support weights from timm

.github/workflows/ci.yml

@@ -23,6 +23,9 @@ jobs:
           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 --editable .[dev] --find-links https://girder.github.io/large_image_wheels
+      - name: Check style
+        run: python -m flake8 wsinfer/
+      - name: Check types
+        run: python -m mypy wsinfer/
       - name: Run tests
-        run: |
-          python -m pytest --verbose tests/
+        run: python -m pytest --verbose tests/

Dockerfile

@@ -1,5 +1,5 @@
 FROM pytorch/pytorch:1.12.1-cuda11.3-cudnn8-runtime
-WORKDIR /opt/wsi-classification
+WORKDIR /opt/wsinfer
 COPY . .
 RUN apt-get update \
     && apt-get install -y --no-install-recommends gcc git libopenslide0 \
@@ -15,4 +15,5 @@ RUN mkdir -p "$TORCH_HOME" \
     && chmod a+s "$TORCH_HOME"
 WORKDIR /work
 ENTRYPOINT ["wsinfer"]
+CMD ["--help"]
 LABEL maintainer="Jakub Kaczmarzyk <[email protected]>"

README.md

@@ -7,6 +7,8 @@ Original H&E                        |  Heatmap of Tumor Probability
 🔥 🚀 Blazingly fast pipeline to run patch-based classification models on whole slide images.
 
 ![Continuous Integration](https://github.com/kaczmarj/patch-classification-pipeline/actions/workflows/ci.yml/badge.svg)
+![Supported Python versions](https://img.shields.io/pypi/pyversions/wsinfer)
+![Version on PyPI](https://img.shields.io/pypi/v/wsinfer.svg)
 
 # Table of contents
 
@@ -268,6 +270,8 @@ Define a new model with a YAML configuration file. Please see the example below
 an overview of the specification.
 
 ```yaml
+# The version of the spec. At this time, only "1.0" is valid. (str)
+version: "1.0"
 # Models are referenced by the pair of (architecture, weights), so this pair must be unique.
 # The name of the architecture. We use timm to supply hundreds or network architectures,
 # so the name can be one of those models. If the architecture is not provided in timm,

dockerfiles/tils.dockerfile

@@ -2,13 +2,13 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
-ENV WSINFER_MODEL="inceptionv4"
+ENV WSINFER_MODEL="inceptionv4nobn"
 ENV WSINFER_WEIGHTS="TCGA-TILs-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib import models; models.$WSINFER_MODEL(\"$WSINFER_WEIGHTS\")" \
+RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/

dockerfiles/tumor-brca.dockerfile

@@ -2,13 +2,13 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"
 ENV WSINFER_WEIGHTS="TCGA-BRCA-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib import models; models.$WSINFER_MODEL(\"$WSINFER_WEIGHTS\")" \
+RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/

dockerfiles/tumor-luad.dockerfile

@@ -2,13 +2,13 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"
 ENV WSINFER_WEIGHTS="TCGA-LUAD-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib import models; models.$WSINFER_MODEL(\"$WSINFER_WEIGHTS\")" \
+RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/

dockerfiles/tumor-paad.dockerfile

@@ -2,13 +2,13 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
-ENV WSINFER_MODEL="resnet34_preact"
+ENV WSINFER_MODEL="preactresnet34"
 ENV WSINFER_WEIGHTS="TCGA-PAAD-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib import models; models.$WSINFER_MODEL(\"$WSINFER_WEIGHTS\")" \
+RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/

dockerfiles/tumor-prad.dockerfile

@@ -2,13 +2,13 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"
 ENV WSINFER_WEIGHTS="TCGA-PRAD-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib import models; models.$WSINFER_MODEL(\"$WSINFER_WEIGHTS\")" \
+RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/

scripts/build_docker_images.sh

@@ -24,33 +24,33 @@ fi
 version=$1
 
 # Main image.
-docker build -t kaczmarj/patch-classification-pipeline:$version .
+docker build -t kaczmarj/wsinfer:$version .
 
 # TILs
-docker build -t kaczmarj/patch-classification-pipeline:$version-tils - < dockerfiles/tils.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tils - < dockerfiles/tils.dockerfile
 
 # Tumor BRCA
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-brca - < dockerfiles/tumor-brca.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-brca - < dockerfiles/tumor-brca.dockerfile
 
 # Tumor LUAD
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-luad - < dockerfiles/tumor-luad.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-luad - < dockerfiles/tumor-luad.dockerfile
 
 # Tumor PAAD
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-paad - < dockerfiles/tumor-paad.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-paad - < dockerfiles/tumor-paad.dockerfile
 
 # Tumor PRAD
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-prad - < dockerfiles/tumor-prad.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-prad - < dockerfiles/tumor-prad.dockerfile
 
 # Push images.
 push_images="${2:-0}"
 if [ $push_images -eq 0 ]; then
     echo "Not pushing images. Pass a 1 to the script to push images."
 else
     echo "Pushing images."
-    docker push kaczmarj/patch-classification-pipeline:$version
-    docker push kaczmarj/patch-classification-pipeline:$version-tils
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-brca
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-luad
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-paad
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-prad
+    docker push kaczmarj/wsinfer:$version
+    docker push kaczmarj/wsinfer:$version-tils
+    docker push kaczmarj/wsinfer:$version-tumor-brca
+    docker push kaczmarj/wsinfer:$version-tumor-luad
+    docker push kaczmarj/wsinfer:$version-tumor-paad
+    docker push kaczmarj/wsinfer:$version-tumor-prad
 fi

setup.cfg

@@ -53,6 +53,9 @@ dev =
     mypy
     pytest
     tifffile
+    types-Pillow
+    types-PyYAML
+    types-tqdm
 
 [options.entry_points]
 console_scripts =
@@ -68,6 +71,24 @@ max-line-length = 88
 extend-ignore = E203
 exclude = wsinfer/_version.py
 
+[mypy]
+[mypy-h5py]
+ignore_missing_imports = True
+[mypy-large_image]
+ignore_missing_imports = True
+[mypy-cv2]
+ignore_missing_imports = True
+[mypy-torchvision.*]
+ignore_missing_imports = True
+[mypy-openslide]
+ignore_missing_imports = True
+[mypy-pandas]
+ignore_missing_imports = True
+[mypy-timm]
+ignore_missing_imports = True
+[mypy-scipy.stats]
+ignore_missing_imports = True
+
 [versioneer]
 VCS = git
 style = pep440