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docs folder for integration with sphinx (#10)
* docs folder for integration with sphinx
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‎docs/Makefile

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

‎docs/make.bat

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

‎docs/requirements.txt

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-r ../requirements.txt
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sphinx>=2.0.1
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myst-parser
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nbsphinx
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sphinx-autodoc-typehints
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sphinx-autodoc-annotation
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sphinx_rtd_theme
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sphinx_gallery

‎docs/source/_static/images/breast_stack_2d.png

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‎docs/source/_static/images/paste_overview.png

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‎docs/source/api.rst

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API
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===
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Import Paste as::
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from paste.visualization import plot_slice, stack_slices_pairwise, stack_slices_center
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from paste.PASTE import pairwise_align, center_align
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from paste.helper import filter_for_common_genes, match_spots_using_spatial_heuristic, match_spots_using_spatial_heuristic, apply_trsf
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.. automodule:: paste
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Alignment
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~~~~~~~~~
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.. autosummary::
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:toctree: api
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PASTE.pairwise_align
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PASTE.center_align
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Visualization
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~~~~~~~~~~~~~
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.. autosummary::
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:toctree: api
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visualization.stack_slices_pairwise
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visualization.stack_slices_center
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visualization.plot_slice
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Miscellaneous
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~~~~~~~~~~~~~
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.. autosummary::
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:toctree: api
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helper.filter_for_common_genes
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helper.match_spots_using_spatial_heuristic
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helper.apply_trsf
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‎docs/source/api/paste.PASTE.center_align.rst

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paste.PASTE.center\_align
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=========================
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.. currentmodule:: paste.PASTE
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.. autofunction:: center_align

‎docs/source/api/paste.PASTE.pairwise_align.rst

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paste.PASTE.pairwise\_align
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===========================
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.. currentmodule:: paste.PASTE
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.. autofunction:: pairwise_align

‎docs/source/api/paste.helper.apply_trsf.rst

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paste.helper.apply\_trsf
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========================
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.. currentmodule:: paste.helper
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.. autofunction:: apply_trsf

‎docs/source/api/paste.helper.filter_for_common_genes.rst

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paste.helper.filter\_for\_common\_genes
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=======================================
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.. currentmodule:: paste.helper
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.. autofunction:: filter_for_common_genes

‎docs/source/api/paste.helper.match_spots_using_spatial_heuristic.rst

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paste.helper.match\_spots\_using\_spatial\_heuristic
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====================================================
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.. currentmodule:: paste.helper
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.. autofunction:: match_spots_using_spatial_heuristic

‎docs/source/api/paste.visualization.plot_slice.rst

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paste.visualization.plot\_slice
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===============================
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.. currentmodule:: paste.visualization
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.. autofunction:: plot_slice

‎docs/source/api/paste.visualization.stack_slices_center.rst

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paste.visualization.stack\_slices\_center
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=========================================
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.. currentmodule:: paste.visualization
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.. autofunction:: stack_slices_center

‎docs/source/api/paste.visualization.stack_slices_pairwise.rst

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paste.visualization.stack\_slices\_pairwise
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===========================================
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.. currentmodule:: paste.visualization
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.. autofunction:: stack_slices_pairwise

‎docs/source/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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from pathlib import Path
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import sys
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HERE = Path(__file__).parent
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sys.path.insert(0, str(HERE.parent.parent) + '/src')
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# -- Project information -----------------------------------------------------
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project = 'paste3'
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copyright = '2022, Raphael Lab'
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author = 'Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J. Raphael'
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# The full version, including alpha/beta/rc tags
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release = '1.2.0'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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"myst_parser",
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'sphinx.ext.autosummary',
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"sphinx.ext.autodoc",
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'sphinx.ext.napoleon',
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"sphinx_autodoc_typehints",
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"nbsphinx",
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"sphinx_gallery.load_style",
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"sphinx.ext.viewcode"
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]
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# Moves Type hints from function header into description
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autodoc_typehints = "description"
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# If true, the current module name will be prepended to all description
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# unit titles (such as .. function::).
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add_module_names = False
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'sphinx_rtd_theme'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_show_sourcelink = False
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html_show_sphinx = False
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nbsphinx_thumbnails = {
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"notebooks/getting-started": "_static/images/breast_stack_2d.png",
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}

‎docs/source/index.rst

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|PyPI| |Downloads|
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PASTE: Probabilistic Alignment of Spatial Transcriptomics Experiments
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=====================================================================
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**PASTE** is a computational method that leverages both gene expression similarity and spatial distances between spots to align and integrate spatial transcriptomics data.
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In particular, PASTE provides two main functionalities:
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1. Pairwise Alignment: align spots across pairwise slices.
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2. Center Alignment: integrate multiple slices into one center slice.
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.. image:: _static/images/paste_overview.png
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:alt: PASTE Overview Figure
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:width: 800px
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:align: center
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|
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Manuscript
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----------
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You can view our `preprint <https://www.biorxiv.org/content/10.1101/2021.03.16.435604v1>`_ on **bioRxiv**.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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:hidden:
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installation
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api
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tutorial
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.. |PyPI| image:: https://img.shields.io/pypi/v/paste-bio.svg
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:target: https://pypi.org/project/paste-bio/
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:alt: PyPI
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.. |Downloads| image:: https://pepy.tech/badge/paste-bio
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:target: https://pepy.tech/project/paste-bio
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:alt: Downloads

‎docs/source/installation.md

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# Installation
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The easiest way is to install PASTE on pypi: https://pypi.org/project/paste-bio/.
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`pip install paste-bio`
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Or you can install PASTE on bioconda: https://anaconda.org/bioconda/paste-bio.
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`conda install -c bioconda paste-bio`
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Note: `pip` is our recommended choice of installation.

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