ADD: sphinx docs (#53)

* make patchlib private: _patchlib

* update code to use private patchlib

* add sphinx docs + dependencies

* move Weights validation to separate validate staticmethod

* use map_location="cpu" when loading state dict from URL

* fix pip install + add model inference example

* add requirements.txt file for docs

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,39 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "wsinfer"
+copyright = "2022, Jakub Kaczmarzyk"
+author = "Jakub Kaczmarzyk"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "autoapi.extension",
+]
+
+autoapi_type = "python"
+autoapi_dirs = ["../wsinfer"]
+autoapi_options = [
+    "members",
+    "undoc-members",
+    # "private-members",
+    "show-inheritance",
+    "show-module-summary",
+    "special-members",
+    "imported-members",
+]
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]

docs/index.rst

@@ -0,0 +1,22 @@
+Welcome to WSInfer!
+===================
+
+**WSInfer** is a program to run patch-based classification inference on whole
+slide images.
+
+Check out the :doc:`user_guide` for further information, including how to install the
+project.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   user_guide
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,2 @@
+pydata-sphinx-theme
+sphinx-autoapi

docs/user_guide.rst

@@ -0,0 +1,41 @@
+User Guide
+==========
+
+.. _installation:
+
+Installation
+------------
+
+To use WSInfer, first install it using pip:
+
+.. code-block:: console
+
+   pip install wsinfer --find-links https://girder.github.io/large_image_wheels
+
+Examples
+-------
+
+List available models
+^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: console
+
+   wsinfer list
+
+Run model inference
+^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: console
+
+   mkdir -p example-wsi-inference/sample-images
+   cd example-wsi-inference/sample-images
+   # Download a sample slide.
+   wget -nc https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs
+   cd ..
+   # Run inference on the slide.
+   CUDA_VISIBLE_DEVICES=0 wsinfer run \
+      --wsi-dir sample-images/ \
+      --results-dir results/ \
+      --model resnet34 \
+      --weights TCGA-BRCA-v1 \
+      --num-workers 8

setup.cfg

@@ -56,6 +56,10 @@ dev =
     types-Pillow
     types-PyYAML
     types-tqdm
+docs =
+    pydata-sphinx-theme
+    sphinx
+    sphinx-autoapi
 
 [options.entry_points]
 console_scripts =

wsinfer/cli/infer.py

@@ -13,8 +13,8 @@
 
 from ..modellib.run_inference import run_inference
 from ..modellib import models
-from ..patchlib.create_dense_patch_grid import create_grid_and_save_multi_slides
-from ..patchlib.create_patches_fp import create_patches
+from .._patchlib.create_dense_patch_grid import create_grid_and_save_multi_slides
+from .._patchlib.create_patches_fp import create_patches
 
 PathType = typing.Union[str, Path]
 

wsinfer/cli/patch.py

@@ -2,7 +2,7 @@
 
 import click
 
-from ..patchlib.create_patches_fp import create_patches as _create_patches
+from .._patchlib.create_patches_fp import create_patches as _create_patches
 
 
 @click.command()

wsinfer/modellib/models.py

@@ -79,13 +79,12 @@ def __post_init__(self):
         if len(self.class_names) != self.num_classes:
             raise ValueError("length of class_names must be equal to num_classes")
 
-    @classmethod
-    def from_yaml(cls, path):
-        with open(path) as f:
-            d = yaml.safe_load(f)
+    @staticmethod
+    def _validate_input(d) -> None:
+        """Raise error if invalid input."""
 
         if not isinstance(d, dict):
-            raise ValueError("expected YAML config to be a dictionary")
+            raise ValueError("expected config to be a dictionary")
 
         # Validate contents.
         # Validate keys.
@@ -171,6 +170,14 @@ def from_yaml(cls, path):
             if not file.exists():
                 raise FileNotFoundError(f"'file' not found: {file}")
 
+    @classmethod
+    def from_yaml(cls, path):
+        """Create a new instance of Weights from a YAML file."""
+
+        with open(path) as f:
+            d = yaml.safe_load(f)
+        cls._validate_input(d)
+
         transform = PatchClassification(
             resize_size=d["transform"]["resize_size"],
             mean=d["transform"]["mean"],
@@ -189,13 +196,17 @@ def from_yaml(cls, path):
             class_names=d["class_names"],
         )
 
-    def load_model(self):
+    def load_model(self) -> torch.nn.Module:
+        """Return the pytorch implementation of the architecture with weights loaded."""
         model = _create_model(name=self.architecture, num_classes=self.num_classes)
 
         # Load state dict.
         if self.url and self.url_file_name:
             state_dict = load_state_dict_from_url(
-                url=self.url, check_hash=True, file_name=self.url_file_name
+                url=self.url,
+                map_location="cpu",
+                check_hash=True,
+                file_name=self.url_file_name,
             )
         elif self.file:
             state_dict = torch.load(self.file, map_location="cpu")
@@ -209,6 +220,7 @@ def load_model(self):
         return model
 
     def get_sha256_of_weights(self) -> str:
+        """Return the sha256 of the weights file."""
         if self.url and self.url_file_name:
             p = Path(torch.hub.get_dir()) / "checkpoints" / self.url_file_name
         elif self.file: