diff --git a/.github/labeler.yml b/.github/labeler.yml index 61650f564ce6d7..a55f6eddc52371 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -11,6 +11,8 @@ template-and-tools: # topic labels admin: - topics/admin/**/* +ai4life: + - topics/ai4life/**/* assembly: - topics/assembly/**/* climate: @@ -29,6 +31,8 @@ epigenetics: - topics/epigenetics/**/* evolution: - topics/evolution/**/* +fair: + - topics/fair/**/* galaxy-interface: - topics/galaxy-interface/**/* genome-annotation: @@ -61,4 +65,3 @@ variant-analysis: - topics/variant-analysis/**/* visualisation: - topics/visualisation/**/* - diff --git a/.github/workflows/ci-main.yml b/.github/workflows/ci-main.yml index 3f5de067fa2551..f25406506b5797 100644 --- a/.github/workflows/ci-main.yml +++ b/.github/workflows/ci-main.yml @@ -12,6 +12,8 @@ on: - '**/tutorial*.md' - '**/slides.html' - '**/slides/*.html' + - 'learning-pathways/*' + - 'faqs/**' jobs: lint: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7ea5b8e005c73d..79d627839052a3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -39,7 +39,7 @@ jobs: ruby-version: "3.0" - uses: actions/setup-node@v2 with: - node-version: '14' + node-version: '19' - uses: actions/cache@v2 with: path: | @@ -51,6 +51,7 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node gem install bundler bundle config path vendor/bundle bundle install --jobs 4 --retry 3 diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 96c9d69ba978a7..b1c8356972f371 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -27,7 +27,7 @@ jobs: ruby-version: "3.0" - uses: actions/setup-node@v2 with: - node-version: '14' + node-version: '19' - uses: actions/cache@v2 with: path: | @@ -39,6 +39,7 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node gem install bundler bundle config path vendor/bundle bundle install --jobs 4 --retry 3 diff --git a/.github/workflows/monthly-release-backfill.yml b/.github/workflows/monthly-release-backfill.yml index 655c050de1bf73..2205678029587f 100644 --- a/.github/workflows/monthly-release-backfill.yml +++ b/.github/workflows/monthly-release-backfill.yml @@ -28,7 +28,7 @@ jobs: ruby-version: "3.0" - uses: actions/setup-node@v2 with: - node-version: '14' + node-version: '19' - uses: actions/cache@v2 with: path: | @@ -41,6 +41,7 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node gem install bundler pip install pyyaml bundle config path vendor/bundle diff --git a/.github/workflows/monthly-release.yml b/.github/workflows/monthly-release.yml index 1f9d23b90fc4c9..ff658011cce2dd 100644 --- a/.github/workflows/monthly-release.yml +++ b/.github/workflows/monthly-release.yml @@ -44,7 +44,7 @@ jobs: ruby-version: "3.0" - uses: actions/setup-node@v2 with: - node-version: '14' + node-version: '19' - uses: actions/cache@v2 with: path: | @@ -57,6 +57,7 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node gem install bundler pip install pyyaml bundle config path vendor/bundle diff --git a/.github/workflows/video-dry.yml b/.github/workflows/video-dry.yml index 6e3d773b92697f..43ae802d384213 100644 --- a/.github/workflows/video-dry.yml +++ b/.github/workflows/video-dry.yml @@ -32,7 +32,7 @@ jobs: ruby-version: "3.0" - uses: actions/setup-node@v2 with: - node-version: '14' + node-version: '19' - uses: actions/cache@v2 with: path: | @@ -44,6 +44,7 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node gem install bundler bundle config path vendor/bundle bundle install --jobs 4 --retry 3 diff --git a/.github/workflows/video.yml b/.github/workflows/video.yml index 517de43682993f..e1b88f43ee43d6 100644 --- a/.github/workflows/video.yml +++ b/.github/workflows/video.yml @@ -33,7 +33,7 @@ jobs: ruby-version: "3.0" - uses: actions/setup-node@v2 with: - node-version: '14' + node-version: '19' - uses: actions/cache@v2 with: path: | @@ -45,6 +45,7 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node gem install bundler bundle config path vendor/bundle bundle install --jobs 4 --retry 3 diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 868ae0592d025f..f0b58b34e335a8 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -319,6 +319,12 @@ cfusterbarcelo: orcid: 0000-0002-4784-6957 bio: Post-doctoral researcher at UC3M +Camila-goclowski: + name: Camila Goclowski + joined: 2023-01 + email: camila.goclowski@gmail.com + linkedin: camila-goclowski + charitylaw: name: Charity Law joined: 2018-09 @@ -908,6 +914,11 @@ kxk302: email: kxk302@gmail.com joined: 2021-02 +kysrpex: + name: José Manuel Domínguez + joined: 2023-10 + elixir_node: de + Lain-inrae: name: Lain Pavot email: lain.pavot@inrae.fr @@ -920,6 +931,11 @@ lamouresparus: twitter: lamouresparus joined: 2021-10 +Laura190: + name: Laura Cooper + email: L.Cooper.5@warwick.ac.uk + joined: 2023-08 + lecorguille: name: Gildas Le Corguillé joined: 2017-09 @@ -1510,7 +1526,7 @@ stain: elixir_node: uk location: country: UK - lat: 53.46724379071192 + lat: 53.46724379071192 lon: -2.233631283105614 fediverse: https://scholar.social/@soilandreyes fediverse_flavor: mastodon @@ -1854,7 +1870,7 @@ nhgri-anvil: url: https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL funder: true funding_id: U24HG010263 - + ai4life: name: AI4Life github: false diff --git a/Gemfile.lock b/Gemfile.lock index 6ff976f294df95..c7d6bf24498f29 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,15 +1,8 @@ GEM remote: https://rubygems.org/ specs: - Ascii85 (1.1.0) - addressable (2.8.4) + addressable (2.8.5) public_suffix (>= 2.0.2, < 6.0) - afm (0.2.2) - async (2.6.2) - console (~> 1.10) - fiber-annotation - io-event (~> 1.1) - timers (~> 4.1) awesome_bot (1.20.0) parallel (= 1.20.1) bibtex-ruby (6.0.0) @@ -23,9 +16,6 @@ GEM commander (4.6.0) highline (~> 2.0.0) concurrent-ruby (1.2.2) - console (1.17.2) - fiber-annotation - fiber-local csl (2.0.0) namae (~> 1.0) rexml @@ -38,18 +28,15 @@ GEM ffi (>= 1.15.0) eventmachine (1.2.7) fastimage (2.2.7) - ffi (1.15.5) - fiber-annotation (0.2.0) - fiber-local (1.0.0) + ffi (1.16.2) forwardable-extended (2.6.0) - google-protobuf (3.23.3-x86_64-linux) - hashery (2.1.2) + google-protobuf (3.24.3-x86_64-linux) highline (2.0.3) - html-proofer (5.0.7) + html-proofer (4.4.3) addressable (~> 2.3) - async (~> 2.1) + mercenary (~> 0.3) nokogiri (~> 1.13) - pdf-reader (~> 2.11) + parallel (~> 1.10) rainbow (~> 3.0) typhoeus (~> 1.3) yell (~> 2.0) @@ -57,7 +44,6 @@ GEM http_parser.rb (0.8.0) i18n (1.14.1) concurrent-ruby (~> 1.0) - io-event (1.2.2) jekyll (4.3.2) addressable (~> 2.4) colorator (~> 1.0) @@ -94,40 +80,33 @@ GEM rb-inotify (~> 0.9, >= 0.9.10) mercenary (0.4.0) namae (1.1.1) - nokogiri (1.15.2-x86_64-linux) + nokogiri (1.15.4-x86_64-linux) racc (~> 1.4) parallel (1.20.1) pathutil (0.16.2) forwardable-extended (~> 2.6) - pdf-reader (2.11.0) - Ascii85 (~> 1.0) - afm (~> 0.2.1) - hashery (~> 2.0) - ruby-rc4 - ttfunk - pkg-config (1.5.2) - public_suffix (5.0.1) + pkg-config (1.5.5) + public_suffix (5.0.3) racc (1.7.1) rainbow (3.1.1) + rake (13.0.6) rb-fsevent (0.11.2) rb-inotify (0.10.1) ffi (~> 1.0) - rexml (3.2.5) - rouge (4.1.2) - ruby-rc4 (0.1.5) + rexml (3.2.6) + rouge (4.1.3) safe_yaml (1.0.5) - sass-embedded (1.63.5-x86_64-linux-gnu) + sass-embedded (1.68.0) google-protobuf (~> 3.23) + rake (>= 13.0.0) terminal-table (3.0.2) unicode-display_width (>= 1.1.1, < 3) - timers (4.3.5) - ttfunk (1.7.0) typhoeus (1.4.0) ethon (>= 0.9.0) - unicode-display_width (2.4.2) + unicode-display_width (2.5.0) webrick (1.8.1) yell (2.2.2) - zeitwerk (2.6.8) + zeitwerk (2.6.12) PLATFORMS x86_64-linux @@ -150,4 +129,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.4.2 + 2.4.20 diff --git a/Makefile b/Makefile index 316d9bfae1bc1a..2430c43e38c304 100644 --- a/Makefile +++ b/Makefile @@ -234,6 +234,7 @@ annotate: ## annotate the tutorials with usable Galaxy instances ${ACTIVATE_ENV} && \ wget https://github.com/hexylena/toolshed-version-database/raw/main/guid-rev.json -O metadata/toolshed-revisions.json && \ python bin/supported-fetch.py + bin/workflows-fetch.rb .PHONY: annotate rebuild-search-index: ## Rebuild search index diff --git a/_includes/analytics.html b/_includes/analytics.html index 7be1cc37033cc3..d2e0fa529447fe 100644 --- a/_includes/analytics.html +++ b/_includes/analytics.html @@ -1,24 +1,59 @@ + + + + + diff --git a/_includes/default-header.html b/_includes/default-header.html index 930e89b1a489e0..6301b29168cad7 100644 --- a/_includes/default-header.html +++ b/_includes/default-header.html @@ -4,7 +4,7 @@ Galaxy Training Network logo {% if topic.logo %} - {{ topic.logo_alt }} + {{ topic.logo_alt }} {{ topic.logo_text }} {% else %} {{ site.title }} diff --git a/_includes/extras.html b/_includes/extras.html index fc4de6db2f0ae1..521f174b026dc6 100644 --- a/_includes/extras.html +++ b/_includes/extras.html @@ -45,23 +45,9 @@ {% endif %} -
-
- {% icon gtn-theme %} Theme -
- -
- - - - - - - - -
- -
+ + {% icon gtn-theme %} Themes have moved New +
diff --git a/_includes/help.html b/_includes/help.html index 924f61fa768e82..6825e208690393 100644 --- a/_includes/help.html +++ b/_includes/help.html @@ -11,7 +11,7 @@ --> - + {% icon question %} FAQs {% if topic %} diff --git a/_includes/instance-dropdown.html b/_includes/instance-dropdown.html index 4ea810c557d5b0..834f6c1bf2ae82 100644 --- a/_includes/instance-dropdown.html +++ b/_includes/instance-dropdown.html @@ -1,13 +1,15 @@ {% assign locale = site.data.lang[page.lang] %} -{% assign supported_exactly = own_material.supported_servers.exact | length %} -{% assign supported_inexactly = own_material.supported_servers.inexact | length %} +{% assign supported_exactly = own_material.supported_servers.exact | size %} +{% assign supported_inexactly = own_material.supported_servers.inexact | size %} {% assign supported = supported_exactly | plus: supported_inexactly %} + {% if supported > 0 or include.docker %}