Initial sphinx docs

Author: Nathaniel-github

docs/api.rst

@@ -0,0 +1,28 @@
+API Reference
+=============
+
+.. automodule:: RISE
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: RISE.factorization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: RISE.imports
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: RISE.logisticReg
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: RISE.gating
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/conf.py

@@ -0,0 +1,73 @@
+"""Configuration file for the Sphinx documentation builder."""
+
+import sys
+from pathlib import Path
+
+# Add the parent directory to the path so we can import RISE
+# This allows Sphinx to find the RISE package
+project_root = Path(__file__).parent.parent.resolve()
+sys.path.insert(0, str(project_root))
+
+# Project information
+project = "RISE"
+copyright = "2024, Andrew Ramirez, Aaron Meyer"
+author = "Andrew Ramirez, Aaron Meyer"
+
+# General configuration
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# Napoleon settings for NumPy-style docstrings
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = True
+napoleon_use_admonition_for_notes = True
+napoleon_use_admonition_for_references = True
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_preprocess_types = False
+napoleon_attr_annotations = True
+
+# Autodoc configuration
+autodoc_default_options = {
+    "members": True,
+    "member-order": "bysource",
+    "undoc-members": True,
+    "show-inheritance": True,
+    "inherited-members": False,
+}
+
+# Intersphinx mapping for external documentation
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "tensorly": ("http://tensorly.org/stable/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+}
+
+# Options for HTML output
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+html_theme_options = {
+    "navigation_depth": 4,
+    "collapse_navigation": False,
+    "sticky_navigation": True,
+    "includehidden": True,
+    "titles_only": False,
+}
+

docs/index.rst

@@ -0,0 +1,18 @@
+.. RISE documentation master file
+
+Welcome to RISE's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   api
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

pyproject.toml

@@ -48,6 +48,8 @@ dev-dependencies = [
     "scanorama>=1.7.4",
     "harmonypy>=0.0.10",
     "scib>=1.1.5",
+    "sphinx>=7.0,<9.0",
+    "sphinx-rtd-theme>=3.0.0",
 ]
 
 

requirements-dev.lock

@@ -12,6 +12,8 @@
 -e file:.
 absl-py==2.1.0
     # via ortools
+alabaster==1.0.0
+    # via sphinx
 anndata==0.11.1
     # via doubletdetection
     # via parafac2
@@ -23,6 +25,8 @@ annoy==1.17.3
     # via scanorama
 array-api-compat==1.8
     # via anndata
+babel==2.17.0
+    # via sphinx
 certifi==2024.8.30
     # via requests
 charset-normalizer==3.3.2
@@ -51,6 +55,9 @@ datashader==0.16.3
     # via rise
 deprecated==1.2.14
     # via scib
+docutils==0.21.2
+    # via sphinx
+    # via sphinx-rtd-theme
 doubletdetection==4.3.0.post1
     # via rise
 fastrlock==0.8.2
@@ -79,12 +86,16 @@ idna==3.8
 igraph==0.11.6
     # via leidenalg
     # via scib
+imagesize==1.4.1
+    # via sphinx
 immutabledict==4.2.1
     # via ortools
 iniconfig==2.0.0
     # via pytest
 intervaltree==3.1.0
     # via scanorama
+jinja2==3.1.6
+    # via sphinx
 joblib==1.4.2
     # via pynndescent
     # via scanpy
@@ -102,6 +113,8 @@ llvmlite==0.44.0
     # via scib
 locket==1.0.0
     # via partd
+markupsafe==3.0.3
+    # via jinja2
 matplotlib==3.9.2
     # via doubletdetection
     # via gseapy
@@ -169,6 +182,7 @@ packaging==24.1
     # via matplotlib
     # via pytest
     # via scanpy
+    # via sphinx
     # via statsmodels
     # via xarray
 pacmap==0.7.3
@@ -215,6 +229,8 @@ pyct==0.5.0
     # via datashader
 pydot==3.0.1
     # via scib
+pygments==2.19.2
+    # via sphinx
 pynndescent==0.5.13
     # via scanpy
     # via umap-learn
@@ -235,7 +251,10 @@ pyyaml==6.0.2
 requests==2.32.3
     # via datashader
     # via gseapy
+    # via sphinx
     # via tlviz
+roman-numerals-py==3.1.0
+    # via sphinx
 scanorama==1.7.4
 scanpy==1.10.4
     # via doubletdetection
@@ -284,8 +303,28 @@ setuptools==74.1.2
 six==1.16.0
     # via patsy
     # via python-dateutil
+snowballstemmer==3.0.1
+    # via sphinx
 sortedcontainers==2.4.0
     # via intervaltree
+sphinx==8.2.3
+    # via sphinx-rtd-theme
+    # via sphinxcontrib-jquery
+sphinx-rtd-theme==3.0.2
+sphinxcontrib-applehelp==2.0.0
+    # via sphinx
+sphinxcontrib-devhelp==2.0.0
+    # via sphinx
+sphinxcontrib-htmlhelp==2.1.0
+    # via sphinx
+sphinxcontrib-jquery==4.1
+    # via sphinx-rtd-theme
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==2.0.0
+    # via sphinx
+sphinxcontrib-serializinghtml==2.0.0
+    # via sphinx
 statsmodels==0.14.2
     # via rise
     # via scanpy