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Merge branch 'galaxyproject:main' into DASH-1256
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kkamieniecka authored Oct 16, 2023
2 parents 4612917 + 46b04fb commit 232a400
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5 changes: 4 additions & 1 deletion .github/labeler.yml
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Expand Up @@ -11,6 +11,8 @@ template-and-tools:
# topic labels
admin:
- topics/admin/**/*
ai4life:
- topics/ai4life/**/*
assembly:
- topics/assembly/**/*
climate:
Expand All @@ -29,6 +31,8 @@ epigenetics:
- topics/epigenetics/**/*
evolution:
- topics/evolution/**/*
fair:
- topics/fair/**/*
galaxy-interface:
- topics/galaxy-interface/**/*
genome-annotation:
Expand Down Expand Up @@ -61,4 +65,3 @@ variant-analysis:
- topics/variant-analysis/**/*
visualisation:
- topics/visualisation/**/*

2 changes: 2 additions & 0 deletions .github/workflows/ci-main.yml
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Expand Up @@ -12,6 +12,8 @@ on:
- '**/tutorial*.md'
- '**/slides.html'
- '**/slides/*.html'
- 'learning-pathways/*'
- 'faqs/**'

jobs:
lint:
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3 changes: 2 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -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: |
Expand All @@ -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
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3 changes: 2 additions & 1 deletion .github/workflows/deploy.yml
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Expand Up @@ -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: |
Expand All @@ -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
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3 changes: 2 additions & 1 deletion .github/workflows/monthly-release-backfill.yml
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Expand Up @@ -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: |
Expand All @@ -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
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3 changes: 2 additions & 1 deletion .github/workflows/monthly-release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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: |
Expand All @@ -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
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3 changes: 2 additions & 1 deletion .github/workflows/video-dry.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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: |
Expand All @@ -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
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3 changes: 2 additions & 1 deletion .github/workflows/video.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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: |
Expand All @@ -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
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20 changes: 18 additions & 2 deletions CONTRIBUTORS.yaml
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Expand Up @@ -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: [email protected]
linkedin: camila-goclowski

charitylaw:
name: Charity Law
joined: 2018-09
Expand Down Expand Up @@ -908,6 +914,11 @@ kxk302:
email: [email protected]
joined: 2021-02

kysrpex:
name: José Manuel Domínguez
joined: 2023-10
elixir_node: de

Lain-inrae:
name: Lain Pavot
email: [email protected]
Expand All @@ -920,6 +931,11 @@ lamouresparus:
twitter: lamouresparus
joined: 2021-10

Laura190:
name: Laura Cooper
email: [email protected]
joined: 2023-08

lecorguille:
name: Gildas Le Corguillé
joined: 2017-09
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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55 changes: 17 additions & 38 deletions Gemfile.lock
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@@ -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)
Expand All @@ -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
Expand All @@ -38,26 +28,22 @@ 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)
zeitwerk (~> 2.5)
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)
Expand Down Expand Up @@ -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
Expand All @@ -150,4 +129,4 @@ DEPENDENCIES
webrick

BUNDLED WITH
2.4.2
2.4.20
1 change: 1 addition & 0 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
63 changes: 49 additions & 14 deletions _includes/analytics.html
Original file line number Diff line number Diff line change
@@ -1,24 +1,59 @@
<!--
<script async defer data-domain="training.galaxyproject.org" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
-->
<!-- We let users opt-out, so if they've opted in, we need to append the plausible script to the body -->

<script>
var scriptElement = document.createElement("script");
scriptElement.async = true;
scriptElement.defer = true;
scriptElement.setAttribute("data-domain", "training.galaxyproject.org");
scriptElement.src = "https://plausible.galaxyproject.eu/js/plausible.js";

// Appending the script element to the body
if(localStorage.getItem('plausible-opt-out') !== 'opt-out' && navigator.doNotTrack !== "1") {
console.log("Plausible: opt-in");
// Wait for the document to be available
document.addEventListener("DOMContentLoaded", function(event) {
document.body.appendChild(scriptElement);
});
}
</script>

<!-- JavaScript Error Monitoring, and performance tracking. -->
<!--
<script
src="https://browser.sentry-cdn.com/7.52.1/bundle.tracing.min.js"
integrity="sha384-muuFXKS3752PNA4rPm9Uq6BLvOfV4CXyr9MHDBPvozOJJUWLKkogEFWOIRoVps43"
crossorigin="anonymous"
></script>
-->
<script type="text/javascript">
Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@{{ site.git_revision }}",
integrations: [new Sentry.BrowserTracing(), new Sentry.Replay()],
sampleRate: 0.1,
tracesSampleRate: 0.1,
// Capture Replay for no sessions by default
replaysSessionSampleRate: 0.01,
// plus for 1% of sessions with an error
replaysOnErrorSampleRate: 0.01,
// PII OFF
sendDefaultPii: false, // Off by default but just in case.
environment: "{{ jekyll.environment }}",
});
var scriptElement = document.createElement("script");
scriptElement.src = "https://browser.sentry-cdn.com/7.52.1/bundle.tracing.min.js";
scriptElement.integrity = "sha384-muuFXKS3752PNA4rPm9Uq6BLvOfV4CXyr9MHDBPvozOJJUWLKkogEFWOIRoVps43";
scriptElement.crossOrigin = "anonymous";

if(localStorage.getItem('sentry-opt-out') !== 'opt-out' && navigator.doNotTrack !== "1") {
console.log("Sentry: opt-in");
// Appending the script element to the body
document.addEventListener("DOMContentLoaded", function(event) {
document.body.appendChild(scriptElement);
});

Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@{{ site.git_revision }}",
integrations: [new Sentry.BrowserTracing(), new Sentry.Replay()],
sampleRate: 0.1,
tracesSampleRate: 0.1,
// Capture Replay for no sessions by default
replaysSessionSampleRate: 0.01,
// plus for 1% of sessions with an error
replaysOnErrorSampleRate: 0.01,
// PII OFF
sendDefaultPii: false, // Off by default but just in case.
environment: "{{ jekyll.environment }}",
});
}
</script>
2 changes: 1 addition & 1 deletion _includes/default-header.html
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<a class="navbar-brand" href="{{ site.baseurl }}/">
<img src="{{ site.baseurl }}/{{ site.small_logo }}" height="30" alt="Galaxy Training Network logo">
{% if topic.logo %}
<img src="{{ topic.logo }}" height="30" width="30" alt="{{ topic.logo_alt }}">
<img src="{{ topic.logo }}" height="30" alt="{{ topic.logo_alt }}">
{{ topic.logo_text }}
{% else %}
{{ site.title }}
Expand Down
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