Update from upstream again

.github/workflows/demo_deploy.yml

@@ -0,0 +1,78 @@
+name: Deploy PR branches
+on: 
+  pull_request:
+  workflow_dispatch:
+env:
+  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  TARGET_REPO: "mkdocs-demo-deploy"
+  TARGET_OWNER: "CallumWalley"
+  WORKFLOW_ID: "deploy.yml"
+  DEPLOY_URL: "https://callumwalley.github.io/mkdocs-demo-deploy"
+  HEAD: ${{ github.event.pull_request.head.ref }}
+permissions: write-all
+jobs:
+  demo-deploy:
+    continue-on-error: true
+    name: Trigger test deployments
+    runs-on: ubuntu-latest
+    steps:
+      - name: Trigger Workflow in Another Repository
+        run: |
+          set -x
+          set -o xtrace 
+          curl -L \
+            -X POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer ${{ secrets.PAT }}" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            https://api.github.com/repos/${TARGET_OWNER}/${TARGET_REPO}/dispatches \
+            -d "{\"event_type\":\"deploy\",\"client_payload\":{\"targets\":\"${GITHUB_REPOSITORY}:${HEAD}\", \"use-cache\":\"true\"}}"
+            
+      # This would be better if it worked
+      # - name: Run 'deploy.yml' Workflow
+      #   uses: convictional/trigger-workflow-and-wait@v1.6.1
+      #   with:
+      #     owner: ${TARGET_OWNER}
+      #     repo: ${TARGET_REPO}
+      #     github_token: ${{ secrets.PAT }}
+      #     workflow_file_name: deploy.yml
+      #     client_payload: '{"targets":"${GITHUB_REPOSITORY}:${HEAD}", "use-cache":"true"}'
+      - name: Wait for Workflow Action
+        run: |
+          curl -L \
+              -X POST \
+              -H "Accept: application/vnd.github+json" \
+              -H "Authorization: Bearer ${{ secrets.PAT }}" \
+              -H "X-GitHub-Api-Version: 2022-11-28" \
+              https://api.github.com/repos/${TARGET_OWNER}/${TARGET_REPO}/actions/runs/deploy.yml
+      - name: Wait for Workflow Action
+        run: |
+          # Just give a minute or so to deploy
+            sleep 60
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Post messages open requests
+        run: |
+            msg="Test deployment available at <a href=\"${DEPLOY_URL}/${GITHUB_REPOSITORY}/${HEAD}\">${DEPLOY_URL}/${GITHUB_REPOSITORY}/${HEAD}</a>"
+            changed_pages="$(git diff --name-only origin/main -- '*.md')"
+            # Logic for truncating out long sections commented out.
+            # maxlines=-5
+            if [ -n "${changed_pages}" ]; then
+                msg="${msg}<br><br>Seems the following pages differ;<br><ul>"
+                for f in ${changed_pages};do
+                    # maxlines=((maxlines+1))
+                    #if [ ${maxlines} -lt 1 ]; then
+                    g=${f#*/}; h=${g%.*}
+                    msg="${msg}<li><a href=\"${DEPLOY_URL}/${GITHUB_REPOSITORY}/${HEAD}/${h}\" target=_blank>${h##*/}</a></li>"
+                    #fi
+                done
+                # if [ ${maxlines} -gt 0 ];then
+                #     msg="${msg}<li>   ... and ${maxlines} more.</li>"
+                # fi
+                msg="${msg}</ul>"
+            fi
+            msg="${msg}<br><br><em><a href="${DEPLOY_URL}">See all deployed demo sites</a></em>"
+            (gh pr comment ${HEAD} --edit-last --body "${msg}") || (gh pr comment ${HEAD} --body "${msg}")
+            echo "::info title=Deploy successful::${DEPLOY_URL}/${GITHUB_REPOSITORY}/${HEAD}" 

.vscode/tasks.json

@@ -48,6 +48,7 @@
                     "column": 4,
                     "endLine": 5,
                     "message": 7,
+                    "loop": true
                 },
                 "owner": "proselint",
                 "fileLocation": "autoDetect",
@@ -94,7 +95,7 @@
                     "column": 4,
                     "endColumn": 5,
                     "line": 6,
-                    "message": 7
+                    "message": 7,
                 },
                 "owner": "test-build",
                 "fileLocation": [

checks/README.md

@@ -16,6 +16,12 @@ Spellcheck pipeline settings can be modified in [.spellcheck.yml](../.spellcheck
 List of custom words can be found in [dictionary.txt](../docs/assets/glossary/dictionary.txt),
 however you **should not edit this manually**, see [adding-words-to-dictionary](../docs/CONTRIBUTING.md#adding-words-to-dictionary).
 
+This list is automatically updated daily in the case of docs.nesi, but not the other sites.
+You should occasionally run 
+`wget -O docs/assets/glossary/dictionary.txt https://raw.githubusercontent.com/nesi/nesi-wordlist/main/outputs/dictionary.txt`
+to keep it up to date.
+
+
 ### Limitations
 
 Spellchecker does not provide output lineumber / column.

checks/run_meta_check.py

@@ -100,6 +100,8 @@ def _run_check(f):
     for r in f():
         print(f"::{r.get('level', 'warning')} file={input_path},title={f.__name__},col={r.get('col', 0)},endColumn={r.get('endColumn', 99)},line={r.get('line', 1)}::{r.get('message', 'something wrong')}")
         sys.stdout.flush()
+        time.sleep(0.01)
+
 
 
 def _title_from_filename():
@@ -136,26 +138,29 @@ def _unpack(toc, a):
             return toc[a[0]]
         return _unpack(toc[a[0]]["children"], a[1:])
 
-    if in_code_block:
-        return
+    try:
+        if in_code_block:
+            return
 
-    header_match = re.match(r"^(#+)\s*(.*)$", line)
+        header_match = re.match(r"^(#+)\s*(.*)$", line)
 
-    if not header_match:
-        return
-
-    header_level = len(header_match.group(1))
-    header_name = header_match.group(2)
+        if not header_match:
+            return
+        
+        header_level = len(header_match.group(1))
+        header_name = header_match.group(2)
 
-    if header_level == 1:
-        toc = {header_name: {"lineno": lineno, "children": {}}}
-        toc_parents = [header_name]
+        if header_level == 1:
+            toc = {header_name: {"lineno": lineno, "children": {}}}
+            toc_parents = [header_name]
 
-    while header_level < len(toc_parents)+1:
-        toc_parents.pop(-1)
+        while header_level < len(toc_parents)+1:
+            toc_parents.pop(-1)
 
-    _unpack(toc, toc_parents)["children"][header_name] = {"level": header_level, "lineno": lineno, "children": {}}
-    toc_parents += [header_name]
+        _unpack(toc, toc_parents)["children"][header_name] = {"level": header_level, "lineno": lineno, "children": {}}
+        toc_parents += [header_name]
+    except Exception:
+        print(f"::error file={input_path},title=misc-nav,col=0,endColumn=0,line=1 ::Failed to parse Nav tree. Something is wrong.")
 
 
 def _nav_check():
@@ -268,4 +273,3 @@ def _count_children(d):
 
     # FIXME terrible hack to make VSCode in codespace capture the error messages
     # see https://github.com/microsoft/vscode/issues/92868 as a tentative explanation
-    time.sleep(5)

checks/run_proselint.py

@@ -6,6 +6,7 @@
 
 import sys
 from pathlib import Path
+import time
 
 import proselint
 from proselint import config, tools
@@ -22,10 +23,11 @@
     for file in files:
         print(f"Running proselint on {file}")
         content = Path(file).read_text(encoding="utf8")
+        fails = proselint.tools.lint(content, config=config_custom)
         for notice in proselint.tools.lint(content, config=config_custom):
             print(
                 f"::{notice[7]} file={file},line={notice[2]+1},"
                 f"col={notice[3]+2},endColumn={notice[2]+notice[6]+1},"
                 f"title={notice[0]}::'{notice[1]}'",
-                flush=True,
             )
+            time.sleep(0.01)

checks/run_test_build.py

@@ -6,11 +6,14 @@
 import logging
 import sys
 import re
+import time
+
 
 """ 
-This doesnt work and I have no idea why.
+This works but is a bit messy
 """
 
+
 def parse_macro(record):
 
     # These are not useful messages
@@ -29,6 +32,13 @@ def parse_macro(record):
         record.name = g["title"]
         record.filename = g["file"]
         record.msg = g["message"]
+
+    # Does not give correct path to file in question in 'title'.
+    # Infer from message.
+    m = re.search(r"'(.*?\.md)'",  record.msg)
+    if m:
+        record.filename = m.group(1)
+
     return True
 
 
@@ -42,3 +52,4 @@ def parse_macro(record):
     log.addHandler(sh)
     config = load_config(config_file_path="./mkdocs.yml")
     build.build(config)
+    time.sleep(5)

docs/assets/glossary/dictionary.txt

@@ -1750,6 +1750,7 @@ json-c's
 json-c
 jvarkit's
 jvarkit
+kaitiaki
 kaitiakitanga
 kalign2's
 kalign2
@@ -2168,6 +2169,7 @@ tabix's
 tabix
 tabixpp's
 tabixpp
+taonga
 tbb's
 tbb
 tbl2asn's

docs/assets/glossary/update_dictionary.sh

@@ -1,5 +1,3 @@
 #!/bin/bash
 
-# Updates dictionary for spellcheck
-
-wget -O docs/assets/glossary/dictionary.txt https://raw.githubusercontent.com/nesi/nesi-wordlist/main/outputs/dictionary.txt
+( cd "${PWD/\/docs\/*/}" && wget -O docs/assets/glossary/dictionary.txt https://raw.githubusercontent.com/nesi/nesi-wordlist/main/outputs/dictionary.txt )

docs/assets/stylesheets/theme.css

@@ -14,21 +14,62 @@
     --md-accent-bg-color:                rgb(210,227,235);
     --md-accent-bg-color--light:         rgb(210,227,235,0.5);
   }
+/* :root{
+  --nesi-grey : #414f5c;
+  --nesi-grey--light: #94a5ad;
+  --nesi-yellow :#fcce06;
+  --nesi-purple: rgb(202, 159, 213);
+  --nesi-orange : rgb(244, 121, 37);
+  --nesi-blue : #4fbaed;
+  --nesi-red:#ef315e;
+  --nesi-green: #cce310;
+
+  [data-md-color-scheme="default"]{
+    --md-primary-fg-color:               var(--nesi-red);
+    
+    --md-accent-fg-color:                var(--nesi-orange);;
+    --md-accent-fg-color--transparent:   rgb(244, 121, 37, 0.25);
+  }
+
+   --md-accent-bg-color:                rgb(210,227,235); 
+  [data-md-color-scheme="slate"] {
+    --md-primary-fg-color:               var(--nesi-red);
+    --md-accent-fg-color:                var(--nesi-orange);;
+    --md-accent-fg-color--transparent:   rgb(244, 121, 37, 0.25);
+
+    .nt-card-image>img {
+      filter: brightness(0) invert(1);
+    }
+  }
+} 
+// Logo biggification
+/* .md-header__button.md-logo img, .md-header__button.md-logo svg {
+  height: 4rem;
+  margin: -2rem;
+} */
+
+/* Version table stuff */
 .md-tag.md-tag-ver{
   color: var(--md-code-fg-color);
 }
 .md-tag.md-tag-ver-shown {
     outline: var(--md-primary-fg-color) 2px solid;
 }
+
+.md-tag-ver-warn {
+  text-decoration: line-through;
+}
 .md-typeset__table {
   width: 100%;
 }
 .md-typeset__table table:not([class]) {
   display: table
 }
+/* convenience class. Not sure if it is used */
 .hidden{
     display: none;
 }
+/* Get support button */
 .md-button-support{
   position: absolute;
   margin: -2rem 0 0 1rem;

overrides/README.md

@@ -20,6 +20,7 @@ This is for customising the [material theme](https://squidfunk.github.io/mkdocs-
 
 When possible, it is best to _extend_ a template (using 'super') rather than straight replacing.
 
+
 Overriding files must mirror the original file structure if you are replacing an existing file.
 However, you can put your own custom stuff in here.
 Here is a list of the original available files, before override: