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Merge branch 'galaxyproject:main' into main
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Swathi266 authored Oct 15, 2024
2 parents f720cbe + cfbc2ed commit 66252c1
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16 changes: 10 additions & 6 deletions .github/pull_request_template.md
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@@ -1,9 +1,13 @@
!!! DELETE THIS BEFORE SUBMITTING!!! It's just a checklist to help you :)
TODO: Describe your changes here..

1. Give your pull request a **good title**
- e.g. "Fix typo in ansible-galaxy tutorial" or "Add new transcriptomics tutorial covering a new sequencing technology"
2. Describe your changes in detail, list anything you still need some help with or things that are still TODO
3. Check that your images are allowed to be re-hosted by the GTN!
4. Not ready for review yet? Make it a **Draft** pull request
<!-- Contributor Checklist
1. Give your pull request a descriptive title
2. Describe your changes in detail at the top of this text box
3. List anything you still need some help with or things that are still TODO
4. Check that your images are allowed to be re-hosted by the GTN!
5. Not ready for review yet? Make it a **Draft** pull request
- Once you are done making changes, choose **Ready for Review**
- Then the automated tests will run and we will know to review and merge it
-->
6 changes: 3 additions & 3 deletions .github/workflows/ci-main.yml
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Expand Up @@ -17,7 +17,7 @@ on:
- 'news/**'
- 'events/**'
- CONTRIBUTORS.yaml
- FUNDERS.yaml
- GRANTS.yaml
- ORGANISATIONS.yaml


Expand Down Expand Up @@ -66,8 +66,8 @@ jobs:
- name: Check Tutorial Formatting
run: |
find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review
bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-on-error
find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review -fail-level=any
bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-level=any
env:
REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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6 changes: 3 additions & 3 deletions .github/workflows/deploy.yml
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Expand Up @@ -51,11 +51,12 @@ 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
sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config graphviz # for node
gem install bundler
bundle config path vendor/bundle
bundle install --jobs 4 --retry 3
npm install
rm -f package.json package-lock.json yarn.lock
npm install markdown-yaml-metadata-parser lunr
bundle pristine ffi
# END Dependencies

Expand All @@ -68,7 +69,6 @@ jobs:
make annotate ACTIVATE_ENV=pwd
curl -L https://docs.google.com/spreadsheets/d/1NfZhi5Jav7kl9zFCkeb7rIC2F8xW1isruv1TeO4WpNI/export\?format\=tsv | ruby bin/prepare_feedback.rb
curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
npm install
make rebuild-search-index ACTIVATE_ENV=pwd
cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
rdoc bin _plugins/ --output gtn_rdoc
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4 changes: 2 additions & 2 deletions .github/workflows/monthly-release-backfill.yml
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Expand Up @@ -47,7 +47,8 @@ jobs:
pip install pyyaml
bundle config path vendor/bundle
bundle install --jobs 4 --retry 3
npm install
rm -f package.json package-lock.json yarn.lock
npm install markdown-yaml-metadata-parser lunr
bundle pristine ffi
# END Dependencies

Expand All @@ -68,7 +69,6 @@ jobs:
sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml
sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml
curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
npm install
make rebuild-search-index ACTIVATE_ENV=pwd
cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material
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4 changes: 2 additions & 2 deletions .github/workflows/monthly-release.yml
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Expand Up @@ -54,7 +54,8 @@ jobs:
pip install pyyaml
bundle config path vendor/bundle
bundle install --jobs 4 --retry 3
npm install
rm -f package.json package-lock.json yarn.lock
npm install markdown-yaml-metadata-parser lunr
bundle pristine ffi
# END Dependencies

Expand All @@ -70,7 +71,6 @@ jobs:
sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml
sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml
curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
npm install
make rebuild-search-index ACTIVATE_ENV=pwd
cat metadata/swagger.yaml | ruby bin/yaml2json.rb > api/swagger.json
JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material
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75 changes: 75 additions & 0 deletions .github/workflows/social.yml
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@@ -0,0 +1,75 @@
name: "[Social] Autogenerate missing social media cards"

on:
schedule:
# * is a special character in YAML so you have to quote this string
# We'll run this weekly at noon.
- cron: '0 12 * * 0'
workflow_dispatch:
inputs:
all_old:
type: string
description: If you want to re-generate ALL images set to a non-empty value

jobs:
runner-job:
if: github.repository_owner == 'galaxyproject'
runs-on: ubuntu-latest
steps:
# Shallow should be fine for video
- uses: actions/checkout@v4
with:
fetch-depth: 500

# BEGIN Dependencies
- uses: actions/setup-python@v5
with:
python-version: '3.11'
architecture: 'x64'
- name: Install dependencies
run: |
sudo apt-get install -y imagemagick
pip install requests
mkdir -p ~/.fonts/
wget https://galaxy-training.s3.amazonaws.com/social/recursive.ttf -O ~/.fonts/recursive.ttf
fc-cache -rv
# END Dependencies


# We get the previous build ID to know how many videos were changed since
# then.
#
# We *could* fetch the diff in the past N days but if a build fails for
# any reason, we'd lose those changes permanently and things would never
# get built.
#
# So instead we just track the last successfully built timestamp
- name: Previous build ID
id: build_id
run: |
echo "timestamp=$(curl https://galaxy-training.s3.amazonaws.com/social/timestamp.txt -f 2>/dev/null || echo none)" >> $GITHUB_ENV
# Support regenerating all
if [[ "${{ github.event.inputs.selected_tag }}" != "" ]]; then
echo "timestamp=0" >> $GITHUB_ENV
fi
# The actual compilation process deposits everything in the ./social/ folder.
# And requires fetching metadata from the live website (api/social-meta.json)
- name: Build Social Media Cards
run: |
mkdir -p social/
python bin/social-cards.py $PREVIOUS_TIMESTAMP
env:
PREVIOUS_TIMESTAMP: ${{ env.timestamp }}

# Deploy step, scary.
- uses: jakejarvis/[email protected]
with:
args: --acl public-read --follow-symlinks
env:
AWS_S3_BUCKET: galaxy-training
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
SOURCE_DIR: './social/'
DEST_DIR: 'social/'
2 changes: 1 addition & 1 deletion .github/workflows/video.yml
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Expand Up @@ -10,7 +10,7 @@ on:
jobs:
runner-job:
if: github.repository_owner == 'galaxyproject'
runs-on: ubuntu-latest
runs-on: ubuntu-22.04
services:
# Label used to access the service container
mozillatts:
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