readthedocs setup (#335)

chanzuckerberg · Apr 7, 2023 · 4ff2e31 · 4ff2e31
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,19 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+sphinx:
+   configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: api/python/cellxgene_census
+    - requirements: docs/requirements.txt
diff --git a/docs/conf.py b/docs/conf.py
@@ -6,7 +6,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'cell-census'
+project = 'cellxgene-census'
 copyright = '2022-2023 Chan Zuckerberg Initiative'
 author = 'Chan Zuckerberg Initiative'
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,15 +1,15 @@
-.. cell-census documentation master file, created by
+.. cellxgene-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!
+Welcome to cellxgene-census documentation!
 =======================================
 
-Note: this site is currently under construction. The location will change in the future, so don't bookmark it.
+Note: this site is currently under construction.
 
 .. toctree::
    :maxdepth: 2
@@ -26,6 +26,6 @@ Contents
    setup
    soma
    python-api
-   R API <https://chanzuckerberg.github.io/cell-census/r/index.html>
+   R API <https://chanzuckerberg.github.io/cellxgene-census/r/index.html>
    schema
    examples
diff --git a/docs/python-api.rst b/docs/python-api.rst
@@ -6,19 +6,19 @@ Python API
 
 Open/retrieve Cell Census data
 ----
-.. autofunction:: cell_census.open_soma
-.. autofunction:: cell_census.get_source_h5ad_uri
-.. autofunction:: cell_census.download_source_h5ad
+.. autofunction:: cellxgene_census.open_soma
+.. autofunction:: cellxgene_census.get_source_h5ad_uri
+.. autofunction:: cellxgene_census.download_source_h5ad
 
 Get slice as AnnData
 ----
-.. autofunction:: cell_census.get_anndata
+.. autofunction:: cellxgene_census.get_anndata
 
 Feature presence matrix
 ----
-.. autofunction:: cell_census.get_presence_matrix
+.. autofunction:: cellxgene_census.get_presence_matrix
 
 Versioning of Cell Census builds
 ----
-.. autofunction:: cell_census.get_census_version_description
-.. autofunction:: cell_census.get_census_version_directory
+.. autofunction:: cellxgene_census.get_census_version_description
+.. autofunction:: cellxgene_census.get_census_version_directory
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1 @@
+nbsphinx
diff --git a/docs/setup.rst b/docs/setup.rst
@@ -57,6 +57,6 @@ If you want to work with the latest development version of cell-census, you can
 and, from the root directory, install locally via pip:
 ::
 
-  $ git clone https://github.com/chanzuckerberg/cell-census.git
-  $ cd cell-census
+  $ git clone https://github.com/chanzuckerberg/cellxgene-census.git
+  $ cd cellxgene-census
   $ pip install -e api/python/cell_census/
diff --git a/docs/soma.rst b/docs/soma.rst
@@ -1,10 +1,10 @@
 What is SOMA
 =====
 
-The Cell Census is a data object publicly hosted online and a convenience API to open it. 
+The CELLxGENE Census is a data object publicly hosted online and a convenience API to open it. 
 The object is built using the `SOMA API`_ and data model via its implementation `TileDB-SOMA`_ (`documentation <https://tiledb-inc-tiledb-soma.readthedocs-hosted.com/en/latest/index.html>`_). 
 
-As such, the Cell Census has all the data capabilities offered by TileDB-SOMA and currently absent in the single-cell field, 
+As such, the CELLxGENE Census has all the data capabilities offered by TileDB-SOMA and currently absent in the single-cell field, 
 including:
 
 - Cloud-based data storage and access.
@@ -13,7 +13,7 @@ including:
 - R and Python support.
 - Export to AnnData and Seurat.
 
-To get the most value out of the Cell Census it is highly recommended to be familiar with TileDB-SOMA capabilities. 
+To get the most value out of the CELLxGENE Census it is highly recommended to be familiar with TileDB-SOMA capabilities. 
 Please take a look at their `documentation page <https://tiledb-inc-tiledb-soma.readthedocs-hosted.com/en/latest/index.html>`_.
 
 .. _SOMA API: https://github.com/single-cell-data/SOMA