Docsite

.gitignore

@@ -120,6 +120,9 @@ venv.bak/
 # mkdocs documentation
 /site
 
+# sphinx documentation
+/doc/_build/
+
 # mypy
 .mypy_cache/
 .dmypy.json

api/python/cell_census/src/cell_census/_experiment.py

@@ -5,21 +5,21 @@
 
 def _get_experiment(census: soma.Collection, organism: str) -> soma.Experiment:
     """
-    Given a census soma.Collection, return the experiment for the named organism.
+    Given a census ``soma.Collection``, return the experiment for the named organism.
     Organism matching is somewhat flexible, attempting to map from human-friendly
-    names to the underlying collection element name.  Will raise a ValueError if
+    names to the underlying collection element name.  Will raise a ``ValueError`` if
     unable to find the specified organism [lifecycle: experimental].
 
     Parameters
     ----------
-    census - soma.Collection
+    census - ``soma.Collection``
         The census
-    organism - str
+    organism - ``str``
         The organism name, eg., ``Homo sapiens``
 
     Returns
     -------
-    soma.Experiment - the requested experiment.
+    ``soma.Experiment`` - the requested experiment.
 
     Examples
     --------

api/python/cell_census/src/cell_census/_get_anndata.py

@@ -24,37 +24,37 @@ def get_anndata(
     column_names: Optional[AxisColumnNames] = None,
 ) -> anndata.AnnData:
     """
-    Convience wrapper around soma.Experiment query, to build and execute a query,
-    and return it as an AnnData object [lifecycle: experimental].
+    Convience wrapper around ``soma.Experiment`` query, to build and execute a query,
+    and return it as an ``AnnData`` object [lifecycle: experimental].
 
     Parameters
     ----------
-    census : soma.Collection
+    census : ``soma.Collection``
         The census object, usually returned by `cell_census.open_soma()`
-    organism : str
+    organism : ``str``
         The organism to query, usually one of "Homo sapiens" or "Mus musculus"
-    measurement_name : str, default 'RNA'
+    measurement_name : ``str``, default ``"RNA"``
         The measurement object to query
-    X_name : str, default "raw"
-        The X layer to query
-    obs_value_filter: str, default None
+    X_name : str, default ``"raw"``
+        The ``X`` layer to query
+    obs_value_filter: ``str``, default ``None``
         Value filter for the ``obs`` metadata. Value is a filter query written in the
         SOMA ``value_filter`` syntax.
-    obs_coords: tuple[int, slice or NumPy ArrayLike of int], default None
+    obs_coords: ``tuple``[``int``, slice or NumPy ArrayLike of ``int``], default ``None``
         Coordinates for the ``obs`` axis, which is indexed by the ``soma_joinid`` value.
-        May be an int, a list of int, or a slice. The default, None, selects all.
-    var_value_filter: str, default None
+        May be an ``int``, a list of ``int``, or a slice. The default, ``None``, selects all.
+    var_value_filter: ``str``, default ``None``
         Value filter for the ``var`` metadata. Value is a filter query written in the
         SOMA ``value_filter`` syntax.
-    var_coords: tuple[int, slice or NumPy ArrayLike of int], default None
+    var_coords: ``tuple``[``int``, slice or NumPy ArrayLike of ``int``], default ``None``
         Coordinates for the ``var`` axis, which is indexed by the ``soma_joinid`` value.
-        May be an int, a list of int, or a slice. The default, None, selects all.
-    column_names: dict[Literal['obs', 'var'], List[str]]
-        Colums to fetch for obs and var dataframes.
+        May be an ``int``, a list of ``int``, or a slice. The default, ``None``, selects all.
+    column_names: ``dict[Literal['obs', 'var'], List[str]]``
+        Colums to fetch for ``obs`` and ``var`` dataframes.
 
     Returns
     -------
-    anndata.AnnData - containing the census slice
+    ``anndata.AnnData`` - containing the census slice
 
     Examples
     --------

api/python/cell_census/src/cell_census/_open.py

@@ -43,14 +43,14 @@ def open_soma(
     context: Optional[soma.options.SOMATileDBContext] = None,
 ) -> soma.Collection:
     """
-    Open the Cell Census by version or URI, returning a soma.Collection containing the
+    Open the Cell Census by version or URI, returning a ``soma.Collection`` containing the
     top-level census.  Raises error if ``census_version`` is specified and unknown, or
     if neither ``uri`` or ``census_version`` are specified, or if the ``uri`` can not
     be opened [lifecycle: experimental].
 
     Parameters
     ----------
-    census_version : Optional[str]
+    census_version : ``Optional[str]``
         The version of the Census, e.g., "latest"
     uri : Optional[str]
         The URI containing the Census SOMA objects. If specified, will take precedence
@@ -59,7 +59,7 @@ def open_soma(
 
     Returns
     -------
-    soma.Collection : returns a SOMA Collection object. Can be used as a context manager, which
+    ``soma.Collection`` : returns a SOMA Collection object. Can be used as a context manager, which
         will automatically close upon exit.
 
     Examples
@@ -71,19 +71,23 @@ def open_soma(
             ...
 
     Open and close:
+
     >>> census = cell_census.open_soma()
         ...
         census.close()
 
     Open a specific Cell Census by version:
+
     >>> with cell_census.open_soma("2022-12-31") as census:
             ...
 
     Open a Cell Census by S3 URI, rather than by version.
+
     >>> with cell_census.open_soma(uri="s3://bucket/path") as census:
             ...
 
     Open a Cell Census by path (file:// URI), rather than by version.
+
     >>> with cell_census.open_soma(uri="/tmp/census") as census:
             ...
     """
@@ -100,20 +104,20 @@ def open_soma(
 
 def get_source_h5ad_uri(dataset_id: str, *, census_version: str = "latest") -> CensusLocator:
     """
-    Open the named version of the census, and return the URI for the dataset_id. This
+    Open the named version of the census, and return the URI for the ``dataset_id``. This
     does not guarantee that the H5AD exists or is accessible to the user. Raises an
-    error if dataset_id or census_version are unknown [lifecycle: experimental].
+    error if ``dataset_id`` or ``census_version`` are unknown [lifecycle: experimental].
 
     Parameters
     ----------
-    dataset_id : str
-        The dataset_id of interest
-    census_version : Optional[str]
+    dataset_id : ``str``
+        The ``dataset_id`` of interest
+    census_version : ``Optional[str]``
         The census version
 
     Returns
     -------
-    CensusLocator : the URI and optional S3 region for the source H5AD
+    ``CensusLocator`` : the URI and optional S3 region for the source H5AD
 
     Examples
     --------
@@ -136,17 +140,17 @@ def get_source_h5ad_uri(dataset_id: str, *, census_version: str = "latest") -> C
 
 def download_source_h5ad(dataset_id: str, to_path: str, *, census_version: str = "latest") -> None:
     """
-    Download the source H5AD dataset, for the given dataset_id, to the user-specified
+    Download the source H5AD dataset, for the given ``dataset_id``, to the user-specified
     file name. Will raise an error if the path already exists (i.e., will not overwrite
     an existing file), or is not a file [lifecycle: experimental].
 
     Parameters
     ----------
-    dataset_id : str
-        Fetch the source (original) H5AD associated with this dataset_id.
-    to_path : str
+    dataset_id : ``str``
+        Fetch the source (original) H5AD associated with this ``dataset_id``.
+    to_path : ``str``
         The file name where the downloaded H5AD will be written.  Must not already exist.
-    census_version : str
+    census_version : ``str``
         The census version name. Defaults to ``latest``.
 
     Returns
@@ -155,7 +159,7 @@ def download_source_h5ad(dataset_id: str, to_path: str, *, census_version: str =
 
     See Also
     --------
-    get_source_h5ad_uri : Look up the location of the source H5AD.
+    ``get_source_h5ad_uri`` : Look up the location of the source H5AD.
 
     Examples
     --------

api/python/cell_census/src/cell_census/_presence_matrix.py

@@ -11,23 +11,23 @@ def get_presence_matrix(
 ) -> sparse.csr_matrix:
     """
     Read the gene presence matrix and return as a SciPy sparse CSR array
-    (scipy.sparse.csr_array). The returned sparse matrix is indexed on the
+    (``scipy.sparse.csr_array``). The returned sparse matrix is indexed on the
     first dimension by the dataset ``soma_joinid`` values, and on the
     second dimension by the ``var`` DataFrame ``soma_joinid`` values
     [lifecycle: experimental].
 
     Parameters
     ----------
-    census : soma.Collection
+    census : ``soma.Collection``
         The census from which to read the presence matrix.
-    organism : str
+    organism : ``str``
         The organism to query, usually one of "Homo sapiens" or "Mus musculus"
-    measurement_name : str, default 'RNA'
+    measurement_name : ``str``, default ``"RNA"``
         The measurement object to query
 
     Returns
     -------
-    scipy.sparse.csr_array - containing the presence matrix.
+    ``scipy.sparse.csr_array`` - containing the presence matrix.
 
     Examples
     --------

api/python/cell_census/src/cell_census/_release_directory.py

@@ -39,17 +39,17 @@ def get_census_version_description(census_version: str) -> CensusVersionDescript
 
     Parameters
     ----------
-    census_version : str
+    census_version : ``str``
         The census version name.
 
     Returns
     -------
-    CensusReleaseDescription
+    ``CensusVersionDescription``
         Dictionary containing a description of the release.
 
     See Also
     --------
-    get_census_version_directory : returns the entire directory as a dict.
+    ``get_census_version_directory`` : returns the entire directory as a dict.
 
     Examples
     --------
@@ -78,13 +78,13 @@ def get_census_version_directory() -> Dict[CensusVersionName, CensusVersionDescr
 
     Returns
     -------
-    Dict[CensusReleaseName, CensusReleaseDescription]
+    ``Dict[CensusVersionName, CensusVersionDescription]``
         Dictionary of release names and their corresponding
         release description.
 
     See Also
     --------
-    get_census_version_description : get description by census_version.
+    ``get_census_version_description`` : get description by census_version.
 
     Examples
     --------

doc/Makefile

@@ -0,0 +1,20 @@
+# 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)

doc/_static/custom.css

@@ -0,0 +1,39 @@
+.wy-side-nav-search {
+    background-color: #fafafa;
+    color: #404040;
+}
+
+.wy-side-nav-search > a {
+    color: #2980B9;
+}
+
+.wy-side-nav-search > div.version {
+    color: rgba(64, 64, 64, 0.3);
+}
+
+.red {
+    color: red;
+}
+
+.green {
+    color: green;
+}.wy-side-nav-search {
+    background-color: #fafafa;
+    color: #404040;
+}
+
+.wy-side-nav-search > a {
+    color: #2980B9;
+}
+
+.wy-side-nav-search > div.version {
+    color: rgba(64, 64, 64, 0.3);
+}
+
+.red {
+    color: red;
+}
+
+.green {
+    color: green;
+}

doc/conf.py

@@ -0,0 +1,37 @@
+# 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 = 'cell-census'
+copyright = '2022-2023 Chan Zuckerberg Initiative'
+author = 'Chan Zuckerberg Initiative'
+
+version = "0.5"
+release = "0.5.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# html_theme = 'alabaster'
+# html_static_path = ['_static']
+
+import sphinx_rtd_theme
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+def setup(app):
+    app.add_css_file("custom.css")

doc/index.rst

@@ -0,0 +1,28 @@
+.. cell-census documentation master file, created by
+   sphinx-quickstart on Thu Feb 16 11:22:43 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. meta::
+   :name=robots: noindex
+
+Welcome to cell-census documentation!
+=======================================
+
+Note: this site is currently under construction. The location will change in the future, so don't bookmark it.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 1
+
+   setup
+   python-api
+   schema