Add documentation structure

docs/Makefile

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+# 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) $(O)
+
+.PHONY: help Makefile
+
+deepclean:
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+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/source/_static/custom.css

@@ -0,0 +1,31 @@
+/*For type annotation in API documentation*/
+span.classifier {
+    margin-left: .5rem;
+}
+
+#left-sidebar a.expandable {
+    justify-content: start;
+}
+
+div.container.cell {
+    margin-top: 1rem;
+}
+
+#content h1 {
+    display: flex;
+    align-items: center;
+}
+
+span > svg {
+    margin-right: 2px !important;
+}
+
+nav[aria-label="breadcrumbs"] > span[aria-current="page"] {
+    display: flex;
+    align-items: center;
+}
+
+div.sd-card-title {
+    display: flex;
+    align-items: center;
+}

docs/source/api/.gitignore

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+_autogen/

docs/source/api/index.rst

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+:octicon:`file-directory;1em;mr-1` API Reference
+================================================
+
+WSI Object
+----------
+
+.. currentmodule:: lazyslide
+.. autosummary::
+    :toctree: _autogen
+
+    WSI
+
+pp
+--
+
+.. currentmodule:: lazyslide.pp
+.. autosummary::
+    :toctree: _autogen
+
+    find_tissue
+    tiles
+    tiles_qc
+
+
+tl
+--
+
+.. currentmodule:: lazyslide.tl
+.. autosummary::
+    :toctree: _autogen
+
+    tissue_props
+    feature_extraction
+    anatomical_domain
+    annotate
+
+
+pl
+--
+
+.. currentmodule:: lazyslide.pl
+.. autosummary::
+    :toctree: _autogen
+
+    tissue
+    tiles
+
+
+get
+---
+
+.. currentmodule:: lazyslide.get
+.. autosummary::
+    :toctree: _autogen
+
+
+    tissue_contours
+    tissue_images
+    tile_images
+    features_anndata
+    pyramids
+    n_tissue
+    n_tiles
+
+data
+----
+
+.. currentmodule:: lazyslide.data
+.. autosummary::
+    :toctree: _autogen
+
+    TileImagesDataset
+    DiskDatasetBuilder
+
+models
+------
+
+.. currentmodule:: lazyslide.models
+.. autosummary::
+    :toctree: _autogen
+
+    PLIP
+    PLIPVision
+    CONCH
+    CONCHVision
+
+

docs/source/cli.rst

@@ -0,0 +1,17 @@
+:octicon:`terminal;1em;mr-1` CLI Usage
+======================================
+
+tissue
+------
+
+.. code-block:: bash
+
+    $ lazyslide tissue --help
+
+.. option:: slide
+
+    The slide file to process
+
+.. option:: --output
+
+    By default will write to a zarr file with the same name as the slide file

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+from sphinxawesome_theme.postprocess import Icons
+
+project = "LazySlide"
+copyright = "2024, Yimin Zheng, Ernesto Abila, André F. Rendeiro"
+author = "LazySlide Contributors"
+release = "0.1.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "numpydoc",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autosectionlabel",
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "myst_nb",
+]
+autoclass_content = "class"
+autodoc_docstring_signature = True
+autodoc_default_options = {"members": None, "undoc-members": None}
+autodoc_typehints = "none"
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+html_theme = "sphinxawesome_theme"
+html_static_path = ["_static"]
+html_css_files = ["custom.css"]
+html_permalinks_icon = Icons.permalinks_icon
+html_theme_options = {
+    "main_nav_links": {
+        "Installation": "/installation",
+        "Tutorial": "/tutorial/index",
+        "API": "/api/index",
+    }
+}
+
+jupyter_execute_notebooks = "off"

docs/source/index.rst

@@ -0,0 +1,50 @@
+.. LazySlide documentation master file, created by
+   sphinx-quickstart on Sat Jun 15 08:19:55 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to LazySlide's documentation!
+=====================================
+
+
+LazySlide introduction here.
+
+
+
+.. toctree::
+    :maxdepth: 3
+    :hidden:
+
+    installation
+    tutorial/index
+    api/index
+    cli
+    nextflow
+
+
+.. grid :: 1 2 2 2
+   :gutter: 2
+
+   .. grid-item-card :: :octicon:`package;1em;mr-1` Installation
+      :link: installation
+      :link-type: doc
+
+      How to install LazySlide
+
+   .. grid-item-card :: :octicon:`telescope;1em;mr-1` Tutorial
+      :link: tutorial/index
+      :link-type: doc
+
+      A step-by-step guide to using LazySlide
+
+   .. grid-item-card :: :octicon:`file-directory;1em;mr-1` API
+      :link: api/index
+      :link-type: doc
+
+      LazySlide API documentation
+
+   .. grid-item-card :: :octicon:`terminal;1em;mr-1` CLI
+      :link: cli
+      :link-type: doc
+
+      LazySlide command line interface

docs/source/installation.rst

@@ -0,0 +1,48 @@
+:octicon:`package;1em;mr-1` Installation
+==========================================
+
+PIP
+---
+
+To install the released version, simply run:
+
+
+.. code-block:: bash
+
+    pip install lazyslide
+
+
+To install the latest development version, run:
+
+
+.. code-block:: bash
+
+    pip install git+https://github.com/rendeirolab/LazySlide.git
+
+
+Installation for openslide
+--------------------------
+
+By default, LazySlide will try to use :code:`openslide` when available to support wider range of image formats.
+
+It will also load :code:`tiffslide` when :code:`openslide` is not available. Especially on windows platform.
+
+For Linux and OSX users, it's suggested that you install :code:`openslide` with conda or mamba:
+
+.. code-block:: bash
+
+    conda install -c conda-forge openslide-python
+    # or
+    mamba install -c conda-forge openslide-python
+
+
+For Windows users, you need to download compiled :code:`openslide` from
+`GitHub Release <https://github.com/openslide/openslide-bin/releases>`_.
+
+Before import lazyslide in your code, you need to set the path to the :code:`openslide` library:
+
+.. code-block:: python
+
+    import os
+    with os.add_dll_directory("path/to/openslide/bin")):
+        import openslide

docs/source/nextflow.rst

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+Nextflow Usage
+==============
+
+How to run lazyslide in a nextflow pipeline.

docs/source/tutorial/.gitignore

@@ -0,0 +1 @@
+/tmp