IQSS · pdurbin · Oct 31, 2022 · Jul 29, 2022 · Jul 29, 2022 · Jul 29, 2022
diff --git a/doc/sphinx-guides/source/_static/docsdataverse_org.css b/doc/sphinx-guides/source/_static/docsdataverse_org.css
@@ -68,7 +68,7 @@ a.headerlink {
 #sidebar.bs-sidenav {
     background-color: #f8d5b8;
 }
-#sidebar.bs-sidenav .nav > li > a:hover, #sidebar.bs-sidenav .nav > li > a:focus {
+#sidebar.bs-sidenav .nav > li > a:hover, #sidebar.bs-sidenav .nav > li > a:focus, #sidebar.bs-sidenav .nav > li > a.current {
     background-color: #fbf4c5;
     border-right: 1px solid #dbd8e0;
     text-decoration: none;

diff --git a/doc/sphinx-guides/source/admin/integrations.rst b/doc/sphinx-guides/source/admin/integrations.rst
@@ -57,7 +57,7 @@ their research results and retain links to imported and exported data. Users
 can organize their data in "Datasets", which can be exported to a Dataverse installation via
 the command-line interface (CLI).
 
-Renku dataset documentation: https://renku-python.readthedocs.io/en/latest/reference/commands.html#module-renku.cli.dataset
+Renku documentation: https://renku-python.readthedocs.io
 
 Flagship deployment of the Renku platform: https://renkulab.io
 

diff --git a/doc/sphinx-guides/source/admin/metadatacustomization.rst b/doc/sphinx-guides/source/admin/metadatacustomization.rst
@@ -565,7 +565,7 @@ In general, the external vocabulary support mechanism may be a better choice for
 The specifics of the user interface for entering/selecting a vocabulary term and how that term is then displayed are managed by third-party Javascripts. The initial Javascripts that have been created provide auto-completion, displaying a list of choices that match what the user has typed so far, but other interfaces, such as displaying a tree of options for a hierarchical vocabulary, are possible. 
 Similarly, existing scripts do relatively simple things for displaying a term - showing the term's name in the appropriate language and providing a link to an external URL with more information, but more sophisticated displays are possible.
 
-Scripts supporting use of vocabularies from services supporting the SKOMOS protocol (see https://skosmos.org) and retrieving ORCIDs (from https:/orcid.org) are available https://github.com/gdcc/dataverse-external-vocab-support. (Custom scripts can also be used and community members are encouraged to share new scripts through the dataverse-external-vocab-support repository.)
+Scripts supporting use of vocabularies from services supporting the SKOMOS protocol (see https://skosmos.org) and retrieving ORCIDs (from https://orcid.org) are available https://github.com/gdcc/dataverse-external-vocab-support. (Custom scripts can also be used and community members are encouraged to share new scripts through the dataverse-external-vocab-support repository.)
 
 Configuration involves specifying which fields are to be mapped, whether free-text entries are allowed, which vocabulary(ies) should be used, what languages those vocabulary(ies) are available in, and several service protocol and service instance specific parameters.
 These are all defined in the :ref:`:CVocConf <:CVocConf>` setting as a JSON array. Details about the required elements as well as example JSON arrays are available at https://github.com/gdcc/dataverse-external-vocab-support, along with an example metadata block that can be used for testing.

diff --git a/doc/sphinx-guides/source/api/native-api.rst b/doc/sphinx-guides/source/api/native-api.rst
@@ -2614,7 +2614,7 @@ The fully expanded example above (without environment variables) looks like this
 
   curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X POST "https://demo.dataverse.org/api/files/:persistentId/prov-freeform?persistentId=doi:10.5072/FK2/AAA000" -H "Content-type:application/json" --upload-file provenance.json
 
-See a sample JSON file :download:`file-provenance.json <../_static/api/file-provenance.json>` from http://openprovenance.org (c.f. Huynh, Trung Dong and Moreau, Luc (2014) ProvStore: a public provenance repository. At 5th International Provenance and Annotation Workshop (IPAW'14), Cologne, Germany, 09-13 Jun 2014. pp. 275-277).
+See a sample JSON file :download:`file-provenance.json <../_static/api/file-provenance.json>` from https://openprovenance.org (c.f. Huynh, Trung Dong and Moreau, Luc (2014) ProvStore: a public provenance repository. At 5th International Provenance and Annotation Workshop (IPAW'14), Cologne, Germany, 09-13 Jun 2014. pp. 275-277).
 
 Delete Provenance JSON for an uploaded file
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst b/doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst
@@ -77,7 +77,7 @@ To delete metadata for a Dataset, send a json-ld representation of the fields to
 
     curl -X PUT -H X-Dataverse-key:$API_TOKEN -H 'Content-Type: application/ld+json' -d '{"https://dataverse.org/schema/core#restrictions":"No restrictions"}' "$SERVER_URL/api/datasets/:persistentId/metadata/delete?persistentId=$DATASET_PID"
 
-Note, this example uses the term URI directly rather than adding an '@context' element. You can use either form in any of these API calls. 
+Note, this example uses the term URI directly rather than adding an ``@context`` element. You can use either form in any of these API calls. 
 
 You should expect a 200 ("OK") response indicating whether a draft Dataset version was created or an existing draft was updated.
 

diff --git a/doc/sphinx-guides/source/index.rst b/doc/sphinx-guides/source/index.rst
@@ -73,6 +73,4 @@ If you have a **security issue** to report, please email `[email protected]
 Indices and Tables
 ------------------
 
-* :ref:`genindex`
-* :ref:`modindex`
 * :ref:`search`
diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
@@ -478,7 +478,7 @@ named config in the same folder")
 Console Commands to Set Up Access Configuration
 ###############################################
 
-Begin by installing the CLI tool `pip <https://pip.pypa.io//en/latest/>`_ to install the
+Begin by installing the CLI tool `pip (package installer for Python) <https://pip.pypa.io/en/latest/>`_ to install the
 `AWS command line interface <https://aws.amazon.com/cli/>`_ if you don't have it.
 
 First, we'll get our access keys set up. If you already have your access keys configured, skip this step.

diff --git a/doc/sphinx-guides/source/installation/prerequisites.rst b/doc/sphinx-guides/source/installation/prerequisites.rst
@@ -291,8 +291,8 @@ If the installed location of the convert executable is different from ``/usr/bin
 R
 -
 
-The Dataverse Software uses `R <https://https://cran.r-project.org/>`_ to handle
-tabular data files. The instructions below describe a **minimal** R
+The Dataverse Software uses `R <https://cran.r-project.org>`_ to handle
+tabular data files. The instructions below describe a **minimal** R Project
 installation. It will allow you to ingest R (.RData) files as tabular
 data and to export tabular data as .RData files.  R can be considered an optional component, meaning
 that if you don't have R installed, you will still be able to run and

diff --git a/doc/sphinx_bootstrap_theme/bootstrap/layout.html b/doc/sphinx_bootstrap_theme/bootstrap/layout.html
@@ -106,7 +106,7 @@
       {%- if hasdoc('copyright') %}
         {% trans path=pathto('copyright'), copyright=copyright|e %}<p><a href="{{ path }}">Copyright</a>  &#169; {{ copyright }}.</p>{% endtrans %}
       {%- else %}
-      {% trans copyright=copyright|e %}<p>Developed at the <a href="http://www.iq.harvard.edu/" title="Institute for Quantitative Social Science" target="_blank">Institute for Quantitative Social Science</a>  &nbsp;|&nbsp;  Code available at <a href="https://github.com/IQSS/dataverse" title="Dataverse on GitHub" target="_blank"><span class="socicon socicon-github"></span></a> &nbsp;|&nbsp; Created using <a href="http://sphinx.pocoo.org/" title="Sphinx" target="_blank">Sphinx</a> {{ sphinx_version }}<br/>Last updated on {{ last_updated }} &nbsp;|&nbsp; Dataverse v. {{ version }} &nbsp;|&nbsp; View the <a href="http://guides.dataverse.org/en/latest/" title="Dataverse Guides">latest version of Dataverse Guides</a></p>
+      {% trans copyright=copyright|e %}<p>Developed at the <a href="http://www.iq.harvard.edu/" title="Institute for Quantitative Social Science" target="_blank">Institute for Quantitative Social Science</a>  &nbsp;|&nbsp;  Code available at <a href="https://github.com/IQSS/dataverse" title="Dataverse on GitHub" target="_blank"><span class="socicon socicon-github"></span></a> &nbsp;|&nbsp; Created using <a href="https://www.sphinx-doc.org" title="Sphinx" target="_blank">Sphinx</a> {{ sphinx_version }}<br/>Last updated on {{ last_updated }} &nbsp;|&nbsp; Dataverse v. {{ version }} &nbsp;|&nbsp; View the <a href="http://guides.dataverse.org/en/latest/" title="Dataverse Guides">latest version of Dataverse Guides</a></p>
         <p>Copyright &#169; {{ copyright }}</p> {% endtrans %}
       {%- endif %}
     {%- endif %}