From 5a63d25e273f6f655f644cf1f5d240fa90aa0359 Mon Sep 17 00:00:00 2001 From: jen-reeve Date: Mon, 13 Jul 2026 15:15:03 +1200 Subject: [PATCH 1/4] update task to check all urls --- checks/run_a11y_check.sh | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/checks/run_a11y_check.sh b/checks/run_a11y_check.sh index 218b7025b..d7953f57a 100755 --- a/checks/run_a11y_check.sh +++ b/checks/run_a11y_check.sh @@ -4,7 +4,19 @@ set -euo pipefail CACHE_DIR="${HOME}/.cache/accesslint-audit" PORT="$(python3 -c 'import socket; s=socket.socket(); s.bind(("",0)); print(s.getsockname()[1]); s.close()')" -URLS="${1:-http://localhost:${PORT}/}" + +if [ ! -d "public" ]; then + echo "Error: 'public' directory does not exist. Run a build first!" >&2 + exit 1 +fi + +if [ -n "${1:-}" ]; then + URLS="$1" +else + # No URL given: audit every page from the built sitemap. + URLS="$(sed -n 's#.*\(.*\).*#\1#p' public/sitemap.xml \ + | sed "s#^https\?://[^/]*/#http://localhost:${PORT}/#")" +fi if [ ! -d "$CACHE_DIR" ]; then git clone --depth 1 --branch v0 https://github.com/AccessLint/audit.git "$CACHE_DIR" @@ -16,11 +28,6 @@ if [ ! -f "$READY_MARKER" ]; then touch "$READY_MARKER" fi -if [ ! -d "public" ]; then - echo "Error: 'public' directory does not exist. Run a build first!" >&2 - exit 1 -fi - python3 -m http.server "$PORT" --directory public & SERVER_PID=$! trap 'kill "$SERVER_PID" 2>/dev/null || true' EXIT From d4c186bb1871a936fb6d3d67ade734ffacb08c62 Mon Sep 17 00:00:00 2001 From: jen-reeve Date: Mon, 13 Jul 2026 16:18:40 +1200 Subject: [PATCH 2/4] updating task to allow for different scan scopes and violation levels --- .vscode/tasks.json | 16 +++++++++++++++- checks/run_a11y_check.sh | 9 ++++++--- 2 files changed, 21 insertions(+), 4 deletions(-) diff --git a/.vscode/tasks.json b/.vscode/tasks.json index 18414dca3..9e8c9ca28 100644 --- a/.vscode/tasks.json +++ b/.vscode/tasks.json @@ -178,7 +178,21 @@ "showReuseMessage": false }, "dependsOn": "test-build", - "command": "bash checks/run_a11y_check.sh" + "command": "bash checks/run_a11y_check.sh ${input:a11y_min_level} ${input:a11y_url}" }, + ], + "inputs": [ + { + "id": "a11y_min_level", + "description": "minimum violation level to report from run_a11y_check.sh", + "default": "minor", + "type": "promptString" + }, + { + "id": "a11y_url", + "description": "url to run a11y audit on", + "default": "", + "type": "promptString" + } ] } diff --git a/checks/run_a11y_check.sh b/checks/run_a11y_check.sh index d7953f57a..2057b6aa7 100755 --- a/checks/run_a11y_check.sh +++ b/checks/run_a11y_check.sh @@ -2,6 +2,8 @@ # Runs the same WCAG audit as the AccessLint/audit@v0 GitHub Action, locally. set -euo pipefail +MIN_IMPACT=$1 + CACHE_DIR="${HOME}/.cache/accesslint-audit" PORT="$(python3 -c 'import socket; s=socket.socket(); s.bind(("",0)); print(s.getsockname()[1]); s.close()')" @@ -10,8 +12,9 @@ if [ ! -d "public" ]; then exit 1 fi -if [ -n "${1:-}" ]; then - URLS="$1" +if [ -n "${2:-}" ]; then + PAGE=$2 + URLS="http://localhost:${PORT}/${PAGE}" else # No URL given: audit every page from the built sitemap. URLS="$(sed -n 's#.*\(.*\).*#\1#p' public/sitemap.xml \ @@ -47,5 +50,5 @@ env \ INPUT_URLS="$URLS" \ INPUT_WCAG-LEVEL="AA" \ INPUT_FAIL-ON="never" \ - INPUT_MIN-IMPACT="minor" \ + INPUT_MIN-IMPACT="$MIN_IMPACT" \ node "$CACHE_DIR/dist/index.js" From 65ab73cdabe9a26f2c12d943863edf34861ecabc Mon Sep 17 00:00:00 2001 From: jen-reeve Date: Mon, 13 Jul 2026 16:51:59 +1200 Subject: [PATCH 3/4] link fixes --- docs/CONTRIBUTING.md | 2 +- docs/Software/Available_Applications/AlphaFold.md | 10 +++++----- docs/Software/Available_Applications/Dorado.md | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index f3385c374..0daf50e6d 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -184,7 +184,7 @@ After a few minutes, a preview of the source branch will be deployed, a bot will Assign a reviewer if you wish. -Adding the tag will cause the request to be merged at midnight, if all checks passed. +Adding the tag will cause the request to be merged at midnight, if all checks passed. ### Reviewing A Merge Request diff --git a/docs/Software/Available_Applications/AlphaFold.md b/docs/Software/Available_Applications/AlphaFold.md index 9ded197e7..fca8fa8ba 100644 --- a/docs/Software/Available_Applications/AlphaFold.md +++ b/docs/Software/Available_Applications/AlphaFold.md @@ -99,7 +99,7 @@ complexes (with per-residue and per-pair confidence estimates). It does not compute binding affinities, docking scores or other measures of binding strength. -Home page is at . +Home page is at \ No newline at end of file +at: diff --git a/docs/Software/Available_Applications/Dorado.md b/docs/Software/Available_Applications/Dorado.md index 32c677c8b..0aa3e614f 100644 --- a/docs/Software/Available_Applications/Dorado.md +++ b/docs/Software/Available_Applications/Dorado.md @@ -21,7 +21,7 @@ zendesk_section_id: 360000040076 Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. -### [](https://github.com/nanoporetech/dorado#features)Features +### [Features](https://github.com/nanoporetech/dorado#features) - One executable with sensible defaults, automatic hardware detection and configuration. From 2b4baaf90011e09874e0122811c97a3a020dcb04 Mon Sep 17 00:00:00 2001 From: jen-reeve Date: Tue, 14 Jul 2026 09:11:44 +1200 Subject: [PATCH 4/4] code background color change for contrast --- docs/assets/stylesheets/theme.css | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/assets/stylesheets/theme.css b/docs/assets/stylesheets/theme.css index c79866038..c6b2dbfa7 100644 --- a/docs/assets/stylesheets/theme.css +++ b/docs/assets/stylesheets/theme.css @@ -19,7 +19,7 @@ --reannz-orange: rgb(241, 128, 0); --reannz-purple: rgb(132, 121, 183); -[data-md-color-scheme="default"] { +[data-md-color-scheme="default"] { /* original definitions of these colors here: https://github.com/squidfunk/mkdocs-material/blob/master/src/templates/assets/stylesheets/main/_colors.scss */ --md-primary-fg-color: var(--reannz-blue--dark); /* head bar background color */ --md-accent-fg-color: var(--reannz-blue); /* hover color for sidebar links */ /* --md-accent-bg-color: var(--reannz-orange); */ /* cannot figure what this one does */ @@ -28,8 +28,8 @@ /* --md-accent-fg-color--light: var(--reannz-orange); */ /* cannot figure what this one does */ /* --md-default-fg-color: var(--reannz-orange); */ /* main text color, sub H1 headers too */ /* --md-default-bg-color: var(--reannz-orange); */ /* main background color */ - /* --md-code-fg-color: var(--reannz-orange); */ /* main color for code text */ - /* --md-code-bg-color: var(--reannz-orange); */ /* main color for code background */ + /* --md-code-fg-color: rgb(53,69,77); */ /* main color for code text */ + --md-code-bg-color: var(--md-code-bg-color--light); /* main color for code background */ /* --md-typeset-color: var(--reannz-orange); */ /* main text color, sub H1 headers too */ }