Merge branch 'main' into kira/fix-deposition-links

chanzuckerberg · Oct 1, 2024 · 82334bc · 82334bc
2 parents 05f9a77 + ea1598d
commit 82334bc
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diff --git a/.github/workflows/client-python.yml b/.github/workflows/client-python.yml
@@ -6,13 +6,13 @@ on:
       - main
     paths:
       - 'client/python/**'
-      - '.github/workflows/**'
+      - '.github/workflows/client-python.yml'
   pull_request:
     branches:
       - '**'
     paths:
       - 'client/python/**'
-      - '.github/workflows/**'
+      - '.github/workflows/client-python.yml'
 
 jobs:
   test-client-python:

diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml
@@ -6,6 +6,7 @@ on:
       - 'client/**'
       - 'frontend/**'
       - 'backend/**'
+      - 'docs/_static/css/**'
       - '.github/workflows/**' # Re-run if a workflow is modified - useful to test workflow changes in PRs
   push:
     branches:

diff --git a/.github/workflows/frontend-e2e-tests.yml b/.github/workflows/frontend-e2e-tests.yml
@@ -155,13 +155,17 @@ jobs:
         working-directory: frontend/packages/data-portal
         env:
           API_URL: ${{ vars.API_URL }}
+          API_URL_V2: ${{ vars.API_URL_V2 }}
           ENV: ${{ inputs.environment }}
 
       - name: Run E2E tests
-        run: pnpm e2e --shard ${{ matrix.shardCurrent }}/${{ matrix.shardTotal }}
+        run: |
+          sleep 15
+          pnpm e2e --shard ${{ matrix.shardCurrent }}/${{ matrix.shardTotal }}
         working-directory: frontend/packages/data-portal
         env:
           API_URL: ${{ vars.API_URL }}
+          API_URL_V2: ${{ vars.API_URL_V2 }}
           E2E_BROWSER: ${{ matrix.browser }}
           E2E_CONFIG: ${{ secrets.E2E_CONFIG }}
           CI: true

diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -162,8 +162,8 @@ ul.md-nav__list > li.md-nav__item > a.md-nav__link > span.md-ellipsis {
 /* Footer */
 
 .md-footer {
-    background-color: #EFF2FC;
-    color: black;
+    background-color: #333333;
+    color: ffffff;
 }
 
 .md-footer-meta {
@@ -174,7 +174,7 @@ ul.md-nav__list > li.md-nav__item > a.md-nav__link > span.md-ellipsis {
 
 html .md-footer-meta.md-typeset a {
     color: var(--md-footer-fg-color--light);
-    text-decoration: underline;
+    text-decoration: none;
 }
 
 .md-footer-meta__inner {
@@ -189,6 +189,7 @@ html .md-footer-meta.md-typeset a {
   display: flex;
   flex-direction: row;
   justify-content: space-between;
+  padding-top: 0.4rem;
 }
 
 .czi-inner {
@@ -236,3 +237,91 @@ html .md-footer-meta.md-typeset a {
       align-items: baseline;
     }
 }
+
+/* Better display of attributes in class descriptions */
+dl.py.attribute.objdesc {
+  display: grid;
+  grid-template-columns: 1fr 2.5fr;
+}
+
+dl.py.attribute.objdesc > dt.sig.sig-object.highlight.py {
+  grid-column-start: 1;
+  background-color: var(--md-default-bg-color);
+  align-content: baseline;
+  font-size: 1em;
+}
+
+dl.py.attribute.objdesc > dd {
+  grid-column-start: 2;
+  margin-top: 0;
+  margin-bottom: 0;
+  align-content: baseline;
+}
+
+dl.py.attribute.objdesc > dd > p {
+  margin-top: 0;
+  margin-bottom: 0;
+}
+
+.md-typeset blockquote, .md-typeset dl, .md-typeset figure, .md-typeset ol, .md-typeset pre, .md-typeset ul {
+  margin-top: 0;
+  margin-bottom: 0;
+}
+
+dl.py.attribute.objdesc > dd > dl.field-list.simple {
+  display: grid;
+  line-height: 1;
+  margin-top: 0;
+  margin-bottom: 0;
+  grid-template: "a b" auto / 1fr 10fr;
+}
+
+dl.py.attribute.objdesc > dd > dl.field-list.simple > dd.field-odd > p {
+  margin-top: 10px;
+  margin-bottom: 10px;
+}
+
+dl.py.attribute.objdesc > dd > dl.field-list.simple > dt.field-odd {
+  margin-bottom: 10px;
+}
+
+
+dl.py.attribute.objdesc > dd > dl.field-list.simple >dt {
+  grid-column-start: 1;
+  grid-row-start: auto;
+  align-content: end;
+}
+
+dl.py.attribute.objdesc > dd > dl.field-list.simple >dd {
+  grid-column-start: 2;
+  grid-row-start: auto;
+  margin-top: 0;
+  margin-bottom: 0;
+  margin-left: 0;
+}
+
+dl.class > dd > dl:nth-child(27) {
+  margin-bottom: 20px;
+}
+
+/* FAQ Admonitions */
+.czi-faq.admonition {
+  border: none;
+  margin-top: 0;
+  margin-bottom: 0;
+}
+
+.czi-faq.admonition > summary.admonition-title {
+  background-color: var(--md-default-bg-color);
+  padding-left: 14px;
+}
+
+.czi-faq.admonition > summary.admonition-title::before {
+  content: none;
+}
+
+.md-typeset .admonition, .md-typeset details {
+  border-radius: 0;
+  box-shadow: none;
+  border-bottom: 0.01px solid var(--md-default-fg-color--lightest);
+}
diff --git a/docs/_static/js/faq.js b/docs/_static/js/faq.js
@@ -0,0 +1,18 @@
+// cryoet_data_portal_docsite_faq.html?target=data-schema&status=open
+document.addEventListener("DOMContentLoaded", function () {
+    const urlParams = new URLSearchParams(window.location.search);
+
+    // Get the value of the "open" or "closed" parameter
+    const status = urlParams.get("status");
+    const target = urlParams.get("target");
+
+    // Get the div element
+    const divElement = document.getElementById(target);
+
+    // Add the "open" attribute to the details class based
+    // on the value of the status parameter
+
+    if (status === "open") {
+        divElement.setAttribute('open', '');
+    }
+});
diff --git a/docs/_templates/partials/footer.html b/docs/_templates/partials/footer.html
@@ -88,13 +88,21 @@
   <div class="md-footer-meta md-typeset">
     <div class="md-footer-meta__inner md-grid">
       <div class="czi">
-        <div class="md-header__topic czi-footer">
-          <div class="md-ellipsis--cet">
-            CryoET Data Portal <img src="_static/img/beta.svg" alt="CryoET Data Portal">
+        <a
+          href="https://cryoetdataportal.czscience.com/"
+          title="CryoET Data Portal"
+          aria-label="CryoET Data Portal"
+          >
+          <div class="md-header__topic czi-footer">
+            <div class="md-ellipsis--cet">
+              CryoET Data Portal <img src="_static/img/beta.svg" alt="CryoET Data Portal">
+            </div>
+            <div class="hv"></div>
+            <div class="md-ellipsis--cet">
+              Documentation
+            </div>
           </div>
-          <div class="hv"></div>
-          <div class="md-ellipsis--cet">Documentation</div>
-        </div>
+        </a>
         <div class="czi-inner">
           <div class="czi-logo">
             <a href="https://chanzuckerberg.com/science/programs-resources/imaging/">

diff --git a/docs/_templates/partials/header.html b/docs/_templates/partials/header.html
@@ -53,9 +53,9 @@
     <div class="md-header__title">
       <div class="md-header__ellipsis">
         <a
-        href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}"
-        title="{{ config.site_name | e }}"
-        aria-label="{{ config.site_name }}"
+        href="https://cryoetdataportal.czscience.com/"
+        title="CryoET Data Portal"
+        aria-label="CryoET Data Portal"
         >
           <div class="md-header__topic">
             <div class="md-ellipsis--cet">

diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -15,5 +15,3 @@ subtrees:
     title: "FAQ"
   - file: cryoet_data_portal_docsite_aws.md
   - file: cryoet_data_portal_docsite_napari.md
-  - url: "https://cryoetdataportal.czscience.com/"
-    title: "CryoET Data Portal"
diff --git a/docs/conf.py b/docs/conf.py
@@ -58,6 +58,8 @@
 # Inject custom css files in `/_static/css/*`
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
+html_js_files = ["js/faq.js"]
+
 html_logo = ""
 html_title = "CryoET Data Portal Documentation"
 html_favicon = "_static/img/favicon-cryoet-data-portal.png"
@@ -117,13 +119,6 @@
     ("py:.*", dict(include_fields_in_toc=False)),
 ]
 
-# html_js_files = [
-#     (
-#         "https://plausible.io/js/script.js",
-#         {"data-domain": "chanzuckerberg.github.io/cryoet-data-portal", "defer": "defer"},
-#     ),
-# ]
-
 # -- Options for myst -------------------------------------------------
 myst_enable_extensions = ['colon_fence']
 myst_heading_anchors = 4