diff --git a/docs/source/api/data.rst b/docs/source/api/data.rst deleted file mode 100644 index 5cd3913..0000000 --- a/docs/source/api/data.rst +++ /dev/null @@ -1,25 +0,0 @@ -Data -==== - -networkcommons.data.omics.deseq2 --------------------------------- -.. automodule:: networkcommons._data._omics._deseq2 - :members: - :undoc-members: - :show-inheritance: - - -networkcommons.data.omics.decryptm ----------------------------------- -.. automodule:: networkcommons._data._omics._decryptm - :members: - :undoc-members: - :show-inheritance: - - -networkcommons.data.omics.panacea ---------------------------------- -.. automodule:: networkcommons._data._omics._panacea - :members: - :undoc-members: - :show-inheritance: \ No newline at end of file diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst deleted file mode 100644 index ea58777..0000000 --- a/docs/source/api/index.rst +++ /dev/null @@ -1,14 +0,0 @@ -API -=== -.. automodule:: networkcommons - - -networkcommons.data --------------------- - -.. toctree:: - :maxdepth: 4 - :hidden: - :caption: Main - - data \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py index ff42836..11e00c4 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -32,7 +32,7 @@ templates_path = ['_templates'] # -- Options for HTML output -master_doc = 'index' +master_doc = 'contents' html_theme = 'sphinx_rtd_theme' html_static_path = ["_static"] diff --git a/docs/source/contents.rst b/docs/source/contents.rst new file mode 100644 index 0000000..c25efb6 --- /dev/null +++ b/docs/source/contents.rst @@ -0,0 +1,15 @@ +.. toctree:: + :maxdepth: 2 + :caption: Main + + index + installation + data + + +.. toctree:: + :maxdepth: 2 + :caption: Vignettes + + vignettes/1_simple_example + vignettes/2_moon \ No newline at end of file diff --git a/docs/source/data.rst b/docs/source/data.rst new file mode 100644 index 0000000..8b2e032 --- /dev/null +++ b/docs/source/data.rst @@ -0,0 +1,55 @@ +### +API +### + +Omics data +========== + + +networkcommons.data.omics.deseq2 +-------------------------------- +.. automodule:: networkcommons._data._omics._deseq2 + :members: + :undoc-members: + :show-inheritance: + + +networkcommons.data.omics.decryptm +---------------------------------- +.. automodule:: networkcommons._data._omics._decryptm + :members: + :undoc-members: + :show-inheritance: + + +networkcommons.data.omics.panacea +--------------------------------- +.. automodule:: networkcommons._data._omics._panacea + :members: + :undoc-members: + :show-inheritance: + + +Prior knowledge resources +========================= + +networkcommons.data.network.omnipath +------------------------------------ +.. automodule:: networkcommons._data._network._omnipath + :members: + :undoc-members: + :show-inheritance: + +networkcommons.data.network.moon +------------------------------- +.. automodule:: networkcommons._data._network._moon + :members: + :undoc-members: + :show-inheritance: + +networkcommons.data.network.lianaplus +--------------------------------- +.. automodule:: networkcommons._data._network._lianaplus + :members: + :undoc-members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/index.rst b/docs/source/index.rst index 3244fb4..bcdb6ce 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,7 +1,8 @@ +############## NetworkCommons -============================================================== +############## -.. |MainBuild| |Codecov| +|MainBuild| |Codecov| |Docs| .. |MainBuild| image:: https://github.com/saezlab/networkcommons/actions/workflows/main.yml/badge.svg :target: https://github.com/saezlab/networkcommons/actions @@ -12,8 +13,8 @@ NetworkCommons .. .. |PyPIDownloads| image:: https://static.pepy.tech/badge/decoupler .. :target: https://pepy.tech/project/decoupler -.. .. |Docs| image:: https://readthedocs.org/projects/networkcommons/badge/?version=latest -.. :target: https://networkcommons.readthedocs.io/en/latest/?badge=latest +.. |Docs| image:: https://readthedocs.org/projects/networkcommons/badge/?version=latest + :target: https://networkcommons.readthedocs.io/en/22-add-documentation/?badge=22-add-documentation .. |Codecov| image:: https://codecov.io/github/saezlab/networkcommons/graph/badge.svg?token=RH438ALJC2 :target: https://codecov.io/gh/saezlab/networkcommons @@ -45,7 +46,7 @@ NetworkCommons .. For more information check the link. License -------- +======= The data redistributed by OmniPath does not have a license, each original resource carries their own. `Here `_ one can find the license information of all the resources in OmniPath. @@ -55,18 +56,3 @@ The data redistributed by OmniPath does not have a license, each original resour .. Ramirez Flores R.O. and Saez-Rodriguez J. 2022. decoupleR: ensemble of computational methods to infer biological activities .. from omics data. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbac016 -.. toctree:: - :maxdepth: 4 - :hidden: - :caption: Main - - installation - api/index - -.. toctree:: - :maxdepth: 1 - :hidden: - :caption: Vignettes - - vignettes/1_simple_example - vignettes/2_moon \ No newline at end of file diff --git a/docs/source/installation.rst b/docs/source/installation.rst index d55ce83..1a3d9a9 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -1,5 +1,6 @@ +############ Installation -============ +############ ``NetworkCommons`` requires Python version >= 3.10 to run.