add docs

.readthedocs.yaml

@@ -0,0 +1,14 @@
+# .readthedocs.yaml
+version: 2
+sphinx:
+  configuration: docs/source/conf.py
+build:
+  os: ubuntu-22.04
+  apt_packages:
+    - openslide-tools
+  tools:
+    python: "3.10"
+python:
+  install:
+    - method: pip
+      path: .[doc]

README.md

@@ -1,5 +1,9 @@
 WSI
 ====
+
+[![Documentation Status](https://readthedocs.org/projects/wsi/badge/?version=stable&style=flat-square)](https://wsi.readthedocs.io/en/stable)
+
+
 This is a fork of the repository from [Mahmood lab's CLAM repository](https://github.com/mahmoodlab/CLAM).
 It is made available under the GPLv3 License and is available for non-commercial academic purposes.
 

docs/Makefile

@@ -0,0 +1,24 @@
+# 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     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+clean:
+	rm -rf "$(BUILDDIR)"
+	rm -rf $(SOURCEDIR)/api/_autogen/*
+
+# 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/source/api.rst

@@ -0,0 +1,35 @@
+API reference
+---------------
+
+.. currentmodule:: wsi
+
+.. autoclass:: WholeSlideImage
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~WholeSlideImage.__init__
+      ~WholeSlideImage.get_thumbnail
+      ~WholeSlideImage.segment
+      ~WholeSlideImage.plot_segmentation
+      ~WholeSlideImage.save_segmentation
+      ~WholeSlideImage.load_segmentation
+      ~WholeSlideImage.tile
+      ~WholeSlideImage.plot_tile_graph
+      ~WholeSlideImage.save_tile_images
+      ~WholeSlideImage.has_tile_coords
+      ~WholeSlideImage.has_tile_images
+      ~WholeSlideImage.has_tissue_contours
+      ~WholeSlideImage.get_tile_coordinate_level_size
+      ~WholeSlideImage.get_tile_coordinates
+      ~WholeSlideImage.get_tile_graph
+      ~WholeSlideImage.get_tile_images
+      ~WholeSlideImage.get_tile_polygons
+      ~WholeSlideImage.get_tile_tissue_piece
+      ~WholeSlideImage.inference
+      ~WholeSlideImage.as_tile_bag
+      ~WholeSlideImage.as_data_loader
+      ~WholeSlideImage.as_torch_geometric_data

docs/source/conf.py

@@ -0,0 +1,45 @@
+from datetime import datetime
+
+import wsi
+
+project = "wsi"
+copyright = f"{datetime.now().year}, Rendeiro Lab"
+author = "wsi contributors"
+release = wsi.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "numpydoc",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+]
+autoclass_content = "class"
+autodoc_docstring_signature = True
+autodoc_default_options = {"members": None, "undoc-members": None}
+autodoc_typehints = "none"
+# setting autosummary
+autosummary_generate = True
+numpydoc_show_class_members = False
+add_module_names = False
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+html_theme = "pydata_sphinx_theme"
+html_sidebars = {"installation": [], "api": []}
+copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5," r"8}: "
+copybutton_prompt_is_regexp = True
+
+# Plot directive
+plot_include_source = True
+plot_html_show_source_link = False
+plot_html_show_formats = False
+plot_formats = [("png", 200)]
+
+intersphinx_mapping = {
+    "torch": ("https://pytorch.org/docs/stable/", None),
+    "torch_geometric": ("https://pytorch-geometric.readthedocs.io/en/stable/", None),
+}

docs/source/index.rst

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+wsi
+===
+
+**wsi** is a Python library for processing whole slide images (WSI).
+
+It is a simple library with an object-oriented interface where all operations are performed with a WholeSlideImage object.
+
+It has the goal of doing basic processing of WSIs with reasonable defaults, but high customizability.
+
+For example, to go from a slide remotely hosted to a torch geometric graph with ResNet50 features, the following lines suffice:
+
+.. code-block:: python
+
+   from wsi import WholeSlideImage
+   slide = WholeSlideImage("https://brd.nci.nih.gov/brd/imagedownload/GTEX-O5YU-1426")
+   slide.segment()
+   slide.tile()
+   data = slide.as_torch_geometric_data(model_name='resnet50')
+
+Head over to the `Installation <install.html>`_ and `API reference <api.html>`_ pages to learn more.
+
+
+.. toctree::
+    :maxdepth: 1
+    :hidden:
+
+    install
+    api
+
+
+.. grid:: 1 2 2 2
+   :gutter: 2
+
+   .. grid-item-card:: Installation
+      :link: install
+      :link-type: doc
+
+      Instructions for installation
+
+   .. grid-item-card:: API
+      :link: api
+      :link-type: doc
+
+      API documentation

docs/source/install.rst

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+Installation
+============
+
+To install the package from the GitHub repository, follow the steps below.
+
+1. Ensure you have Python 3.10 or higher installed.
+2. Install the package using `pip` by running the following command:
+
+.. code-block:: bash
+
+   pip install git+https://github.com/rendeirolab/wsi.git
+
+3. Verify that the package is correctly installed by importing it in Python:
+
+.. code-block:: python
+
+   import wsi
+
+If the installation was successful, you should not encounter any errors.
+
+For further details, please visit our `GitHub repository <https://github.com/rendeirolab/wsi>`_.

pyproject.toml

@@ -54,7 +54,9 @@ doc = [
     "Sphinx",
     "sphinx-issues",
     "sphinx-rtd-theme",
-    "sphinx-autodoc-typehints"
+    "sphinx-autodoc-typehints",
+    "pydata-sphinx-theme",
+    "numpydoc",
 ]
 
 [project.urls]