Cleanup docs (#621)

Author: cthoyt

docs/cli_usage.rst

@@ -8,7 +8,7 @@ The main one is `convert`
 .. code-block:: bash
 
     sssom convert -i tests/data/basic.tsv -o basic.ttl
-    
+
 .. click:: sssom.cli:main
     :prog: sssom
     :nested: full

docs/developer_docs/api.rst

@@ -7,36 +7,33 @@ Datamodel
 Top-level Document object
 
 .. automodule:: sssom.sssom_document
-   :members:
-   :inherited-members:
-   :show-inheritance:
+    :members:
+    :inherited-members:
+    :show-inheritance:
 
 A Document holds a MappingSet which is a collection of mappings
 
 .. automodule:: sssom.sssom_datamodel
-   :members:
-   :inherited-members:
-   :show-inheritance:
-
+    :members:
+    :inherited-members:
+    :show-inheritance:
 
 I/O
 ---
 
 Conversion between TSV/pandas, internal datamodel and RDF
 
 .. automodule:: sssom.io
-   :members:
-   :inherited-members:
-   :show-inheritance:
-      
+    :members:
+    :inherited-members:
+    :show-inheritance:
 
 Utils
 -----
 
 Utils - currently boomer-specific
 
 .. automodule:: sssom.util
-   :members:
-   :inherited-members:
-   :show-inheritance:
-      
+    :members:
+    :inherited-members:
+    :show-inheritance:

docs/developer_docs/modules.rst

@@ -1,9 +1,9 @@
 Technical Documentation
-========
+=======================
 
 .. toctree::
-   :maxdepth: 4
+    :maxdepth: 4
 
-   api
-   sssom
-   sphinx
+    api
+    sssom
+    sphinx

docs/developer_docs/sphinx.rst

@@ -10,12 +10,12 @@ Using your terminal, ``cd`` to the 'docs' directory within the project.
 New page
 --------
 
-If you need to add a new page create a new file in this directory (docs/*filename*.rst). Update the content 
-within *filename*.rst to the documentation you wish to add using the guidance provided by the 
-`Sphinx <https://www.sphinx-doc.org/en/master/contents.html>`_ web page.
+If you need to add a new page create a new file in this directory (docs/*filename*.rst). Update the
+content within *filename*.rst to the documentation you wish to add using the guidance provided by
+the `Sphinx <https://www.sphinx-doc.org/en/master/contents.html>`_ web page.
 
 Update and page deployment
------------
+--------------------------
 
-This is done automatically by GitHub Actions through a workflow as soon as the 
-pull request is merged to the ``master`` branch.
+This is done automatically by GitHub Actions through a workflow as soon as the pull request is
+merged to the ``master`` branch.

docs/developer_docs/sssom.rst

@@ -5,92 +5,91 @@ sssom.cli module
 ----------------
 
 .. automodule:: sssom.cli
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 sssom.cliques module
 --------------------
 
 .. automodule:: sssom.cliques
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 sssom.context module
 --------------------
 
 .. automodule:: sssom.context
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 sssom.io module
 ---------------
 
 .. automodule:: sssom.io
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :noindex:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
 
 sssom.parsers module
 --------------------
 
 .. automodule:: sssom.parsers
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 sssom.sparql\_util module
 -------------------------
 
 .. automodule:: sssom.sparql_util
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :noindex:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
 
 sssom.sssom\_datamodel module
 -----------------------------
 
 .. automodule:: sssom.sssom_datamodel
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :noindex:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
 
 sssom.sssom\_document module
 ----------------------------
 
 .. automodule:: sssom.sssom_document
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :noindex:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
 
 sssom.util module
 -----------------
 
 .. automodule:: sssom.util
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :noindex:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
 
 sssom.writers module
 --------------------
 
 .. automodule:: sssom.writers
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 Module contents
 ---------------
 
 .. automodule:: sssom
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/examples.rst

@@ -2,18 +2,19 @@ Examples
 ========
 
 ``parse`` command
-------------------
+-----------------
 
-The ``parse`` command is a way to import a mapping file. In this example, the file `basic.tsv <https://github.com/mapping-commons/sssom-py/blob/master/tests/data/basic.tsv>`_
-will be parsed. The CLI command is as follows:
+The ``parse`` command is a way to import a mapping file. In this example, the file `basic.tsv
+<https://github.com/mapping-commons/sssom-py/blob/master/tests/data/basic.tsv>`_ will be parsed. The
+CLI command is as follows:
 
 .. code-block:: bash
 
     sssom parse basic.tsv
 
-This results in the contents of the file displayed on the terminal.
-If the result is needed to be exported into another tsv, an ``--output`` 
-parameter could be passed and the command will look like this:
+This results in the contents of the file displayed on the terminal. If the result is needed to be
+exported into another tsv, an ``--output`` parameter could be passed and the command will look like
+this:
 
 .. code-block:: bash
 
@@ -22,20 +23,18 @@ parameter could be passed and the command will look like this:
 ``convert`` command
 -------------------
 
-The ``convert`` command converts files from one format to another. In this example,
-we convert a tsv file into an owl format.
+The ``convert`` command converts files from one format to another. In this example, we convert a tsv
+file into an owl format.
 
 .. code-block:: bash
 
     sssom convert basic.tsv --output basic.owl --output-format owl
 
-
 ``diff`` command
--------------------
+----------------
 
 Mapping files can be compared and differences highlighted using the ``diff`` command.
 
 .. code-block:: bash
 
     sssom diff basic.tsv basic2.tsv -o diff_output.tsv
-

docs/index.rst

@@ -1,42 +1,40 @@
-.. sssom-py documentation master file, created by
-   sphinx-quickstart on Fri Aug 12 08:35:01 2022.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+..
+    sssom-py documentation master file, created by
+    sphinx-quickstart on Fri Aug 12 08:35:01 2022.
+    You can adapt this file completely to your liking, but it should at least
+    contain the root `toctree` directive.
 
 SSSOM Mapping Format Python Utilities
 =====================================
 
-SSSOM (Simple Standard for Sharing Ontology Mappings) is a TSV format
-for representing ontology mappings, or mappings between pairs of
-entities in general:
+SSSOM (Simple Standard for Sharing Ontology Mappings) is a TSV format for representing ontology
+mappings, or mappings between pairs of entities in general:
 
-GitHub: https://github.com/mapping-commons/sssom
-Documentation: https://mapping-commons.github.io/sssom/
-Publication: https://arxiv.org/abs/2112.07051
-Tutorials: https://mapping-commons.github.io/sssom/tutorial/
+- GitHub: https://github.com/mapping-commons/sssom
+- Documentation: https://mapping-commons.github.io/sssom/
+- Publication: https://arxiv.org/abs/2112.07051
+- Tutorials: https://mapping-commons.github.io/sssom/tutorial/
 
-sssom-py is a Python library and command line toolkit for working with
-SSSOM:
+sssom-py is a Python library and command line toolkit for working with SSSOM:
 
 GitHub: https://github.com/mapping-commons/sssom-py
 
-
 Contents
 --------
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+    :maxdepth: 2
+    :caption: Contents:
 
-   installation
-   cli_usage
-   examples
-   sphinx
-   developer_docs/modules
+    installation
+    cli_usage
+    examples
+    sphinx
+    developer_docs/modules
 
 Indices and tables
 ==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+- :ref:`genindex`
+- :ref:`modindex`
+- :ref:`search`