Merge pull request #145 from griffithlab/v2-icons

attribute list-tables now up-to-date w/ client

Author: jmcmichael

README.md

@@ -11,7 +11,7 @@ We welcome contributions to the documentation. If you wish to contribute a clari
 After you've forked and cloned the repository, install [Sphinx](https://www.sphinx-doc.org/en/master/), a [reStructuredText](http://docutils.sourceforge.net/rst.html) documentation generator, and [sphinx-autobuild](https://pypi.org/project/sphinx-autobuild/), a utility that will host and update the documentation as you work:
 
 ```
-pip install sphinx sphinx-autobuild sphinx-fontawesome sphinxcontrib-images
+pip install sphinx sphinx-autobuild sphinx-fontawesome sphinxcontrib-images sphinx-rtd-theme
 ```
 
 These docs also depend on a custom fork of the `sphinxcontrib-programoutput` extension. It can be installed by running:
@@ -60,8 +60,8 @@ git push origin doc-update
 
 Then visit the [civic-docs pull requests page](https://github.com/griffithlab/civic-docs/pulls). Github should display a message asking you if you'd like to create a pull request from the new branch you just pushed. Create the pull request with a short description of your contribution. A CIViC maintainer will evaluate your contribution and will likely merge it with the master branch, which will then be published. Thanks for your contributions!
 
-
 ## Setting up Sphinx to work in Docker
+
 If you wind up in Python dependency hell getting Sphinx to work, you may want to try working in a Docker image by doing something like the following:
 
 ```
@@ -74,4 +74,3 @@ sphinx-autobuild --host 0.0.0.0 --port 8000 ./ ./_build/html
 ```
 
 To view the updated docs site in your web browser go to: http://0.0.0.0:8000/. Once you are satisfied, submit a pull request as described above.
-

docs/_static/css/civic.css

@@ -73,3 +73,36 @@ figcaption {
 .image-table td {
   vertical-align: top !important;
 }
+
+/* class applied to aliases defined in generated/civic.docs-aliases.rst */
+.cvc-icon {
+  display: inline-block;
+  width: 1em;
+  height: 1em;
+}
+
+/* custom styles for entity-icon-description tables */
+.cvc-icon-table tr td {
+  vertical-align: top !important;
+}
+
+/* display icons in a tag-like box */
+.cvc-icon-table tr td:nth-child(2) p {
+  background-color: #404040 !important;
+  display: block;
+  text-align: center;
+  padding: 1px 3px 3px 3px;
+  border-radius: 2px;
+}
+
+/* default icon color is a light grey, use css filter to brighten them */
+.cvc-icon-table tr td:nth-child(2) img.cvc-icon {
+  filter: brightness(5) !important;
+  vertical-align: middle !important;
+  margin-top: -2px !important;
+}
+
+/* align icon names to the right */
+.cvc-icon-table tr td:nth-child(1) p {
+  text-align: right !important;
+}

docs/_static/css/theme_overrides.css

@@ -1,12 +1,33 @@
 /* override table width restrictions */
 @media screen and (min-width: 767px) {
-    .wy-table-responsive table td {
-        /* !important prevents the common CSS stylesheets from overriding
+  .wy-table-responsive table td {
+    /* !important prevents the common CSS stylesheets from overriding
          this as on RTD they are loaded after this stylesheet */
-        white-space: normal !important;
-    }
+    white-space: normal !important;
+  }
 
-    .wy-table-responsive {
-        overflow: visible !important;
-    }
+  .wy-table-responsive {
+    overflow: visible !important;
+  }
+}
+
+/* improvements to theme's odd table defaults */
+table.docutils th {
+  padding: 6px 8px !important;
+  min-height: unset !important;
+}
+
+table.docutils th p {
+  line-height: 1.2em !important;
+  font-weight: normal !important;
+  font-size: 1em !important;
+  font-style: oblique;
+  margin: 0 !important;
+  color: #404040 !important;
+}
+table.docutils td {
+  padding: 6px 8px !important;
+}
+table.docutils td p {
+  line-height: 1.2em !important;
 }

docs/about/meetings.rst

@@ -13,6 +13,7 @@ Upcoming Meetings & Events
 :Sign Up: Via `CGC Registration page <https://www.cancergenomics.org/meetings/registration.php>`_
 :Topics: Propose topics on `GitHub <https://github.com/genome/civic-meeting/issues>`_
 :Agenda: `Hackathon Program (PDF) <https://www.cancergenomics.org/docs/cgc-hackathon-handout_2023.pdf>`_ 
+
 .. rubric:: Description
 
 The Jamboree/Hackathon will focus on promoting the standardization and dissemination of knowledge of the clinical significance of cancer variants. The hackathon and curation jamboree will be held as a pre-meeting of the 2023 Cancer Genomics Consortium (CGC) Annual Conference and co-hosted by the `Variant Interpretation for Cancer Consortium (VICC) <https://cancervariants.org/>`_, `CIViC <https://civicdb.org/>`_ and `ClinGen Somatic <https://www.clinicalgenome.org/working-groups/clinical-domain/somatic-cancer-cdwg/>`_.
@@ -102,6 +103,3 @@ The 2016 CIViC hackathon and jamboree took the form of an unconference with some
 
 :Hackathon: Software developers, engineers and computational biologists interested in learning and applying back-end and front-end web development skills. Prerequisites: Familiarity with either Ruby/Rails (back-end) or Javascript/Angular (front-end) would be beneficial.
 :Jamboree: Pathologists and oncologists (certified or in training), genome scientists, and other researchers interested in the problem of sequence variant interpretation for cancer precision medicine. Prerequisites: Basic understanding of the genetic basis of cancer.
-
-----
-

docs/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = u'CIViC'
-copyright = u'2022, The McDonnell Genome Institute at Washington University School of Medicine'
+copyright = u'2023, The McDonnell Genome Institute at Washington University School of Medicine'
 author = u'The McDonnell Genome Institute at Washington University School of Medicine'
 
 # The short X.Y version
@@ -63,7 +63,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -187,7 +187,6 @@
 # A list of files that should not be packed into the epub file.
 epub_exclude_files = ['search.html']
 
-
 def setup(app):
     app.add_css_file("css/civic.css")
     app.add_css_file("css/theme_overrides.css")