Creat sphinx documentation architechture

.gitignore

@@ -1,4 +1,5 @@
 pyNote.py
+test.h5ad
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt

README.md

@@ -1,6 +1,6 @@
-<img src="docs/logo.png" align="right" width="120" />
+<img src="docs/images/logo.png" align="right" width="120" />
 
-# CytoSimplex 
+# CytoSimplex
 [![Python3_10_test](https://github.com/mvfki/pyCytoSimplex/actions/workflows/python-package.yml/badge.svg)](https://github.com/mvfki/pyCytoSimplex/actions/workflows/python-package.yml)[![codecov](https://codecov.io/gh/mvfki/pyCytoSimplex/branch/main/graph/badge.svg?token=L839lYPVon)](https://codecov.io/gh/mvfki/pyCytoSimplex)[![AnnData-0.9.1](https://img.shields.io/badge/AnnData-0.9.1-blue)](https://pypi.org/project/anndata/)
 
 "CytoSimplex" is a Python module that creates simplex plot showing similarity between single-cells and terminals represented by clusters of cells.

cleanup

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+rm -rf build
+rm -rf dist
+rm -rf htmlcov
+rm -rf src/CytoSimplex.egg-info
+rm -rf src/CytoSimplex/__pycache__
+rm -rf src/CytoSimplex/tests/__pycache__
+rm src/CytoSimplex/tests/.coverage
+rm -rf .pytest_cache
+
+cd docs
+make clean
+cd ..
+

docs/.gitignore

@@ -0,0 +1,2 @@
+test.h5ad
+

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     = .
+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

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+from sphinx.application import Sphinx
+
+
+# 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 = 'CytoSimplex'
+copyright = '2023, Yichen Wang, Jialin Liu, Joshua D. Welch'
+author = 'Yichen Wang, Jialin Liu, Joshua D. Welch'
+release = '0.1.0'
+repository_url = "https://github.com/mvfki/pyCytoSimplex"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
+nitpick_ignore = [('py:class', 'type')]
+needs_sphinx = '4.0'  # Nicer param docs
+
+
+def setup(app: Sphinx):
+    """App setup hook."""
+    app.add_config_value(
+        "recommonmark_config",
+        {
+            "auto_toc_tree_section": "Contents",
+            "enable_auto_toc_tree": True,
+            "enable_math": True,
+            "enable_inline_math": False,
+            "enable_eval_rst": True,
+        },
+        True,
+    )
+
+
+extensions = [
+    'myst_nb',
+    'sphinx_copybutton',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.extlinks',
+    'matplotlib.sphinxext.plot_directive',
+    'sphinx_autodoc_typehints',  # needs to be after napoleon
+    # 'git_ref',  # needs to be before scanpydoc.rtd_github_links
+    'sphinx_design',
+    'sphinxext.opengraph',
+    'sphinx.ext.viewcode',
+    'nbsphinx'
+]
+napoleon_attr_annotations = True
+# Generate the API documentation when building
+autosummary_generate = True
+autodoc_member_order = 'bysource'
+# autodoc_default_flags = ['members']
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_use_rtype = True  # having a separate entry generally helps readability
+napoleon_use_param = True
+napoleon_custom_sections = [('Params', 'Parameters')]
+todo_include_todos = False
+# api_dir = HERE / 'api'  # function_images
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "html_admonition",
+]
+myst_url_schemes = ("http", "https", "mailto")
+nb_output_stderr = "remove"
+nb_execution_mode = "off"
+nb_merge_streams = True
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+plot_include_source = True
+plot_formats = [("png", 90)]
+plot_html_show_formats = False
+plot_html_show_source_link = False
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_book_theme'
+html_theme_options = {
+    "repository_url": repository_url,
+    "use_repository_button": True,
+}
+# html_css_files = ["css/override.css"]
+html_show_sphinx = False
+# html_logo = 'images/logo_bright.svg'
+html_theme_options = {
+   "logo": {
+      "image_light": "images/logo_bright.png",
+      "image_dark": "images/logo_dark.png",
+   }
+}
+html_title = "CytoSimplex"
+html_static_path = ['_static']
+html_css_files = ["css/override.css"]
+master_doc = 'source/index'
+
+intersphinx_mapping = dict(
+    anndata=('https://anndata.readthedocs.io/en/stable/', None),
+    matplotlib=('https://matplotlib.org/stable/', None),
+    numpy=('https://numpy.org/doc/stable/', None),
+    pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
+    pytest=('https://docs.pytest.org/en/latest/', None),
+    python=('https://docs.python.org/3', None),
+    scipy=('https://docs.scipy.org/doc/scipy/', None),
+    sklearn=('https://scikit-learn.org/stable/', None),
+)

docs/make.bat

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+@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/source/api/index.rst

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+========================================================================
+API
+========================================================================
+
+To use CytoSimplex functions, import the package in Python script:
+
+.. code-block:: python
+
+    import CytoSimplex as csx
+
+
+.. toctree::
+   :maxdepth: 2
+
+   preprocessing
+   visualization

docs/source/api/preprocessing.rst

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+
+Preprocessing
+^^^^^^^^^^^^^
+
+.. currentmodule:: CytoSimplex
+.. autosummary::
+   :toctree: ../generated/
+
+   row_normalize
+   select_top_features

docs/source/api/visualization.rst

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+
+Visualization
+^^^^^^^^^^^^^
+
+.. currentmodule:: CytoSimplex
+.. autosummary::
+   :toctree: ../generated/
+
+   plot_binary
+   plot_ternary
+   plot_quaternary

docs/source/example/index.rst

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+=======
+Example
+=======
+
+This package use simplex barycentric coordinate approach to assist exploration in the similarity between single cells
+between selected cell clusters. We denote a number (2-4) of selected clusters, or groups of clusters, as vertices.
+We calculate the similarity between each single cell and the average point of each vertex. By normalizing the similarity
+between each single cell and all specified vertices to a unit sum, we can derive the barycentric coordinates for each single cell.
+Visualization method for binary (ended line), ternary (equilateral triangle) and quaternary (tetrahedron) simplex are developed.
+The main plotting functions are :func:`~CytoSimplex.plot_binary`, :func:`~CytoSimplex.plot_ternary` and :func:`~CytoSimplex.plot_quaternary`, respectively.
+
+Test Dataset
+^^^^^^^^^^^^
+
+The dataset used in all example can be found on `figshare <https://figshare.com/ndownloader/files/41034857>`_.
+This is a small subset of publicly available single cell RNA-seq data from the human bone marrow mononuclear cells (BMMC)
+generated in our previous study [1]_. The data is stored in a ``.h5ad`` file format, which can be read by the
+`AnnData <https://anndata.readthedocs.io/en/stable/index.html>`_ package. Users can load the dataset following the code below.
+
+.. code-block:: python
+
+    import CytoSimplex as csx
+    import anndata
+    adata = anndata.read(filename='test.h5ad',
+                         backup_url="https://figshare.com/ndownloader/files/41034857")
+
+The contents included in the ``adata`` object include:
+
+- ``adata.X``: A CSR sparse matrix of 250 rows (cells) by 20,243 columns (genes) containing the raw gene count matrix.
+- ``adata.obs["cluster"]``: A categorical annotation of cell clusters. There are totally 12 clusters which can be viewed via ``adata.obs["cluster"].cat.categories``.
+  Namingly, 'Chondrocyte_1', 'Chondrocyte_2', 'Chondrocyte_3', 'OCT_Stem', 'ORT_1', 'ORT_2', 'ORT_3', 'Osteoblast_1', 'Osteoblast_2', 'Osteoblast_3', 'Reticular_1' and 'Reticular_2'.
+- ``adata.uns["velo"]``: A 250 by 250 CSR sparse matrix of velocity neighbor graph. This is derived with `veloVAE <https://github.com/welch-lab/VeloVAE>`_ [2]_.
+  We will have more introduction to this in detailed examples.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   select_top_features
+   ternary
+   binary
+   quaternary
+
+.. [1] Matsushita, Y., Liu, J., Chu, A.K.Y. et al. Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis. Nat Commun 14, 2383 (2023). https://doi.org/10.1038/s41467-023-38034-2
+.. [2] Gu, Y., Blaauw, D., Welch, J. D.. Bayesian Inference of RNA Velocity from Multi-Lineage Single-Cell Data. bioRxiv (2022). https://doi.org/10.1101/2022.07.08.499381