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V1.2.0 #244

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merged 48 commits into from
Mar 8, 2024
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e4d721c
tweak dark mode for easier default
vincerubinetti Oct 27, 2023
900bbc7
tweak dark mode for easier default
vincerubinetti Oct 27, 2023
e9ce141
fix object_items bug
vincerubinetti Feb 21, 2024
78d9474
update all gh-actions versions
vincerubinetti Feb 21, 2024
2a14d23
add tmate for debugging
vincerubinetti Feb 21, 2024
88b4dab
remove table wrapper
vincerubinetti Feb 22, 2024
a923a28
add option to explicitly flag source for removal from citations
vincerubinetti Feb 22, 2024
e4195fe
fix site.location
vincerubinetti Feb 22, 2024
4d3748b
update font awesome and improve async load technique
vincerubinetti Feb 22, 2024
3a115b6
add discussion templates
vincerubinetti Feb 22, 2024
e2d22ac
fix font awesome load
vincerubinetti Feb 22, 2024
59d16cf
add table wrap js plugin
vincerubinetti Feb 22, 2024
d97cfa1
add html proofer, update bundler version
vincerubinetti Feb 22, 2024
09780ca
ignore localhost for html-proofer
vincerubinetti Feb 22, 2024
321f2e9
update citations
vincerubinetti Feb 22, 2024
41262d5
add commented out html-proofer critical error
vincerubinetti Feb 22, 2024
f9a9d7b
fix lookup citation bug
vincerubinetti Feb 27, 2024
09082f1
add config option to turn proofer off
vincerubinetti Feb 27, 2024
b45fb6b
fix header css, thanks to @Maruuka (Inna Goncearenco)
vincerubinetti Mar 4, 2024
8b1d913
tweak citation styles
vincerubinetti Mar 4, 2024
2e99677
remove unnecessary * selectors
vincerubinetti Mar 4, 2024
aab9795
add markdownify tweaks to some components
vincerubinetti Mar 4, 2024
eee5d27
make citation detail class names more specific
vincerubinetti Mar 4, 2024
0c80bb2
add h5/6 styles, fix nested list styles
vincerubinetti Mar 4, 2024
0e95529
tweak heading styles more
vincerubinetti Mar 4, 2024
a723604
darken default theme color
vincerubinetti Mar 4, 2024
ef59b16
css tweaks
vincerubinetti Mar 4, 2024
fb4f1b1
move debug workflow steps
vincerubinetti Mar 5, 2024
abc9e6d
update cache
vincerubinetti Mar 5, 2024
96997fb
fix header subtitle css for real
vincerubinetti Mar 5, 2024
e20125c
change cite process to ignore uncitable metasources by default
vincerubinetti Mar 5, 2024
4d5b898
add blog post image thumbnail support
vincerubinetti Mar 5, 2024
7a9eb4c
incorporate now widely supported container queries
vincerubinetti Mar 5, 2024
1b13a50
update version
vincerubinetti Mar 5, 2024
250c1b2
update ruby version in workflows
vincerubinetti Mar 5, 2024
b5cacf2
temporarily add pull_request target
vincerubinetti Mar 5, 2024
0e09590
revert previous commit
vincerubinetti Mar 5, 2024
db60199
uncomment "remove" cite process option
vincerubinetti Mar 5, 2024
1943386
update changelog
vincerubinetti Mar 5, 2024
c955b19
update changelog
vincerubinetti Mar 5, 2024
09787a4
change blog photo
vincerubinetti Mar 5, 2024
3bc4c35
revert action-create-branch
vincerubinetti Mar 5, 2024
f11d7f7
add version to html-proofer
vincerubinetti Mar 6, 2024
ac6463b
move remove keyword to top of loop
vincerubinetti Mar 6, 2024
172f7ae
update nested list testbed, update gem lockfile
vincerubinetti Mar 6, 2024
bad10ea
update testbed list
vincerubinetti Mar 6, 2024
231ba55
update date
vincerubinetti Mar 8, 2024
3c685c2
trim url whitespace
vincerubinetti Mar 8, 2024
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35 changes: 35 additions & 0 deletions .github/DISCUSSION_TEMPLATE/general.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
body:
- type: checkboxes
attributes:
label: Checks
options:
- label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first.
required: true

- type: input
id: repo
attributes:
label: Link to your website repo
description: "In almost all cases, **we cannot help you if you don't provide this**."
placeholder: ex. https://github.com/greenelab/greenelab.com
validations:
required: true

- type: input
id: version
attributes:
label: Version of Lab Website Template you are using
description: See your `CITATION.cff` file.
placeholder: ex. 1.0.0
validations:
required: true

- type: textarea
id: description
attributes:
label: Description
description: |
Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in?
placeholder: Description
validations:
required: true
35 changes: 35 additions & 0 deletions .github/DISCUSSION_TEMPLATE/q-a.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
body:
- type: checkboxes
attributes:
label: Checks
options:
- label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first.
required: true

- type: input
id: repo
attributes:
label: Link to your website repo
description: "In almost all cases, **we cannot help you if you don't provide this**."
placeholder: ex. https://github.com/greenelab/greenelab.com
validations:
required: true

- type: input
id: version
attributes:
label: Version of Lab Website Template you are using
description: See your `CITATION.cff` file.
placeholder: ex. 1.0.0
validations:
required: true

- type: textarea
id: description
attributes:
label: Description
description: |
Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in?
placeholder: Description
validations:
required: true
6 changes: 5 additions & 1 deletion .github/ISSUE_TEMPLATE/issue.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,19 @@ body:
id: repo
attributes:
label: Link to your website repo
description: "**Strongly recommended** so we can help troubleshoot your issue."
description: "In almost all cases, **we cannot help you if you don't provide this**."
placeholder: ex. https://github.com/greenelab/greenelab.com
validations:
required: true

- type: input
id: version
attributes:
label: Version of Lab Website Template you are using
description: See your `CITATION.cff` file.
placeholder: ex. 1.0.0
validations:
required: true

- type: textarea
id: description
Expand Down
19 changes: 10 additions & 9 deletions .github/workflows/build-preview.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -22,36 +22,37 @@ jobs:

steps:
# for debugging
- name: Print contexts
uses: crazy-max/ghaction-dump-context@v1
- uses: crazy-max/ghaction-dump-context@v2

- name: Checkout branch contents
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: ${{ github.event.pull_request.head.repo.full_name }}
ref: ${{ github.head_ref }}

- name: Install Ruby packages
if: github.event.action != 'closed'
uses: ruby/setup-ruby@v1
uses: ruby/setup-ruby@v1.172.0
with:
ruby-version: "3.0"
ruby-version: "3.1"
vincerubinetti marked this conversation as resolved.
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bundler-cache: true

- name: Get Pages url
if: github.event.action != 'closed'
id: pages
uses: actions/configure-pages@v2
with:
enablement: false
uses: actions/configure-pages@v4

# for debugging
- if: runner.debug == '1'
uses: mxschmitt/action-tmate@v3

- name: Build preview version of site
if: github.event.action != 'closed'
run: |
JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"

- name: Commit preview to Pages branch
uses: rossjrw/pr-preview-action@v1
uses: rossjrw/pr-preview-action@v1.4.7
with:
source-dir: _site
umbrella-dir: ${{ env.PREVIEWS_FOLDER }}
23 changes: 14 additions & 9 deletions .github/workflows/build-site.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,30 +21,35 @@ jobs:

steps:
# for debugging
- name: Print contexts
uses: crazy-max/ghaction-dump-context@v1
- uses: crazy-max/ghaction-dump-context@v2
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- name: Checkout branch contents
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Ruby packages
uses: ruby/setup-ruby@v1
uses: ruby/setup-ruby@v1.172.0
with:
ruby-version: "3.0"
ruby-version: "3.1"
bundler-cache: true

- name: Get Pages url
id: pages
uses: actions/configure-pages@v2
with:
enablement: false
uses: actions/configure-pages@v4

# for debugging
- if: runner.debug == '1'
uses: mxschmitt/action-tmate@v3

- name: Set root url
run: |
echo "\n\nurl: ${{ steps.pages.outputs.origin }}" >> _config.yaml

- name: Build live version of site
run: |
JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"

- name: Commit live site to Pages branch
uses: JamesIves/github-pages-deploy-action@v4
uses: JamesIves/github-pages-deploy-action@v4.5.0
with:
folder: _site
clean-exclude: ${{ env.PREVIEWS_FOLDER }}
Expand Down
26 changes: 15 additions & 11 deletions .github/workflows/first-time-setup.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -14,21 +14,24 @@ jobs:

steps:
# for debugging
- name: Print contexts
uses: crazy-max/ghaction-dump-context@v1
- uses: crazy-max/ghaction-dump-context@v2

- name: Create Pages branch
uses: peterjgrainger/action-create-branch@v2.4.0
uses: peterjgrainger/action-create-branch@v3.0.0
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
branch: "gh-pages"

- name: Checkout Pages branch
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
ref: gh-pages

# for debugging
- if: runner.debug == '1'
uses: mxschmitt/action-tmate@v3

# clean slate, as if starting from orphan branch
- name: Clear Pages branch
run: rm -rf * .github .docker .gitignore
Expand All @@ -41,26 +44,27 @@ jobs:
run: echo "Placeholder homepage" > index.html

- name: Commit changes to Pages branch
uses: stefanzweifel/git-auto-commit-action@v4
uses: stefanzweifel/git-auto-commit-action@v5
with:
branch: gh-pages
commit_message: "Clear branch"

- name: Checkout main branch
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Remove files user doesn't need
run: |
rm -rf \
CHANGELOG.md \
testbed.md \
.github/ISSUE_TEMPLATE \
.github/DISCUSSION_TEMPLATE \
.github/workflows/versioning.yaml \
.github/pull_request_template.md \

- name: Rename files
run: |
mv .github/user_pull_request_template.md .github/pull_request_template.md
mv -f .github/user_pull_request_template.md .github/pull_request_template.md

- name: Set vars for personalization
run: |
Expand All @@ -80,7 +84,7 @@ jobs:
" > README.md

- name: Personalize Jekyll config for user
uses: actions/github-script@v6
uses: actions/github-script@v7
with:
script: |
const { readFileSync, writeFileSync } = require("fs");
Expand All @@ -97,7 +101,7 @@ jobs:
writeFileSync(file, contents);

- name: Personalize homepage for user
uses: actions/github-script@v6
uses: actions/github-script@v7
with:
script: |
const { readFileSync, writeFileSync } = require("fs");
Expand All @@ -109,6 +113,6 @@ jobs:
writeFileSync(file, contents);

- name: Commit changed files
uses: stefanzweifel/git-auto-commit-action@v4
uses: stefanzweifel/git-auto-commit-action@v5
with:
commit_message: "Setup repo"
17 changes: 10 additions & 7 deletions .github/workflows/update-citations.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -29,17 +29,16 @@ jobs:

steps:
# for debugging
- name: Print contexts
uses: crazy-max/ghaction-dump-context@v1
- uses: crazy-max/ghaction-dump-context@v2

- name: Checkout branch contents
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: ${{ github.event.pull_request.head.repo.full_name }}
ref: ${{ github.head_ref }}

- name: Setup Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: "pip"
Expand All @@ -49,13 +48,17 @@ jobs:
run: |
python -m pip install --upgrade --requirement ./_cite/requirements.txt

# for debugging
- if: runner.debug == '1'
uses: mxschmitt/action-tmate@v3

- name: Build updated citations
run: python _cite/cite.py
timeout-minutes: 15

- name: Check if citations changed
id: changed
uses: tj-actions/verify-changed-files@v13
uses: tj-actions/verify-changed-files@v18
with:
files: |
_data/citations.yaml
Expand All @@ -64,15 +67,15 @@ jobs:
if: |
steps.changed.outputs.files_changed == 'true' &&
inputs.open-pr != true
uses: stefanzweifel/git-auto-commit-action@v4
uses: stefanzweifel/git-auto-commit-action@v5
with:
commit_message: "Update citations"

- name: Open pull request with updated citations
if: |
steps.changed.outputs.files_changed == 'true' &&
inputs.open-pr == true
uses: peter-evans/create-pull-request@v4
uses: peter-evans/create-pull-request@v6
with:
branch: citation-update
title: Periodic citation update
Expand Down
19 changes: 10 additions & 9 deletions .github/workflows/update-url.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -20,21 +20,22 @@ jobs:

steps:
# for debugging
- name: Print contexts
uses: crazy-max/ghaction-dump-context@v1
- uses: crazy-max/ghaction-dump-context@v2

- name: Get Pages url
id: pages
uses: actions/configure-pages@v2
with:
enablement: false
uses: actions/configure-pages@v4

- name: Checkout branch contents
uses: actions/checkout@v3
uses: actions/checkout@v4

# for debugging
- if: runner.debug == '1'
uses: mxschmitt/action-tmate@v3

# update link to site in readme
- name: Update readme
uses: actions/github-script@v6
uses: actions/github-script@v7
with:
script: |
const { readFileSync, writeFileSync } = require("fs");
Expand All @@ -53,14 +54,14 @@ jobs:

- name: Check if readme changed
id: changed
uses: tj-actions/verify-changed-files@v13
uses: tj-actions/verify-changed-files@v18
with:
files: |
README.md

- name: Commit changed files
if: steps.changed.outputs.files_changed == 'true'
uses: stefanzweifel/git-auto-commit-action@v4
uses: stefanzweifel/git-auto-commit-action@v5
with:
commit_message: "Update url"

Expand Down
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