diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 000000000..362ed038a --- /dev/null +++ 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 \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 2cf798b22..cbef75a56 100644 --- 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 index 81cb09e06..d6e27df45 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,4 +1,4 @@ -.. 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. @@ -6,10 +6,10 @@ .. 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 + R API schema examples diff --git a/docs/python-api.rst b/docs/python-api.rst index 57b279283..2891e6f78 100644 --- 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 \ No newline at end of file +.. autofunction:: cellxgene_census.get_census_version_description +.. autofunction:: cellxgene_census.get_census_version_directory \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 000000000..bfc3f807f --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +nbsphinx \ No newline at end of file diff --git a/docs/setup.rst b/docs/setup.rst index ebdf588a7..36faf995b 100644 --- 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/ \ No newline at end of file diff --git a/docs/soma.rst b/docs/soma.rst index 8c10e7d8b..f0610778f 100644 --- 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 `_). -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 `_. .. _SOMA API: https://github.com/single-cell-data/SOMA