Merge pull request #24 from dpeerlab/readthedocs

add modules

docs/docs_requirements.txt

@@ -1,2 +1,10 @@
-sphinx_rtd_theme >= 2.0.0
-myst_parser >= 3.0.0
+sphinxcontrib-autoprogram
+sphinxcontrib-napoleon
+sphinx-autodocgen
+sphinx-github-style
+sphinx-mdinclude
+m2r2
+nbsphinx
+furo
+typing-extensions
+IPython

docs/source/conf.py

@@ -6,33 +6,78 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-project = 'scenvi'
-copyright = '2024, DoronHav'
-author = 'DoronHav'
-release = '0.3.1'
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+# -- Path setup --------------------------------------------------------------
 
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+from pathlib import Path
+
+sys.path.insert(0, os.path.abspath("../../src"))
+
+this_directory = Path(__file__).parent
+
+
+
+
 
+# -- Project information -----------------------------------------------------
+
+project = "scenvi"
+copyright = "2024, " + 'Doron Haviv'
+author = 'Doron Haviv'
+
+# The full version, including alpha/beta/rc tags
+release = '3.0.2'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx_rtd_theme', 
-    'myst_parser']
+    "sphinx.ext.autodoc",
+    "nbsphinx",
+    "sphinx.ext.napoleon",
+    "sphinx_mdinclude",
+]
+if os.environ.get('READTHEDOCS') == 'True':
+    extensions.append("sphinx_github_style")
+
+source_suffix = [".rst", ".md"]
 
-templates_path = ['_templates']
-exclude_patterns = []
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
 
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
 
 # -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+pygments_style = "tango"
+
+highlight_language = "none"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = []
+
 
-autoclass_content = 'both'

docs/source/index.rst

@@ -3,58 +3,25 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to scenvi's documentation!
-==================================
-
-ENVI is a deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data.
-
-This implementation is written in Python3 and relies on jax, flax, sklearn, scipy and scanpy.  
-
-
-To install JAX, simply run the command:
-
-    pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
-
-And to install ENVI along with the rest of the requirements: 
-
-    pip install scenvi
-
-To run ENVI:
-
-    import scenvi 
-
-    envi_model = scenvi.ENVI(spatial_data = st_data, sc_data = sc_data)
-
-    envi_model.train()
-    envi_model.impute_genes()
-    envi_model.infer_niche_covet()
-    envi_model.infer_niche_celltype()
-
-    st_data.obsm['envi_latent'] = envi_model.spatial_data.obsm['envi_latent']
-    st_data.uns['COVET_genes'] =  envi_model.CovGenes
-    st_data.obsm['COVET'] = envi_model.spatial_data.obsm['COVET']
-    st_data.obsm['COVET_SQRT'] = envi_model.spatial_data.obsm['COVET_SQRT']
-    st_data.obsm['cell_type_niche'] = envi_model.spatial_data.obsm['cell_type_niche']
-    st_data.obsm['imputation'] = envi_model.spatial_data.obsm['imputation']
-
-
-    sc_data.obsm['envi_latent'] = envi_model.sc_data.obsm['envi_latent']
-    sc_data.uns['COVET_genes'] =  envi_model.CovGenes
-    sc_data.obsm['COVET'] = envi_model.sc_data.obsm['COVET']
-    sc_data.obsm['COVET_SQRT'] = envi_model.sc_data.obsm['COVET_SQRT']
-    sc_data.obsm['cell_type_niche'] = envi_model.sc_data.obsm['cell_type_niche']
-
-
-And to just compute COVET for spatial data:
-
-    st_data.obsm['COVET'], st_data.obsm['COVET_SQRT'], st_data.uns['CovGenes'] = scenvi.compute_covet(st_data)
-
 .. toctree::
    :hidden:
-   :maxdepth: 2
+   :maxdepth: 4
    :caption: Modules:
 
    modules <modules>
 
+.. toctree::
+   :hidden:
+   :caption: Tutorials:
+
+   MOp_MERFISH_tutorial.ipynb
+
+.. mdinclude:: ../../README.md
+
+Index
+=====
+
+* :ref:`genindex`
+