new version of lwt (#138)

* merge changes * Update citations * initial fixes * rm example posts * fixes to lwt merge * fix merge errors * remove unneeded file --------- Co-authored-by: cgreene <[email protected]>
greenelab · Jan 28, 2025 · a08e1f5 · a08e1f5
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diff --git a/.github/workflows/build-preview.yaml b/.github/workflows/build-preview.yaml
@@ -21,8 +21,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
         uses: actions/checkout@v4
@@ -32,7 +32,7 @@ jobs:
 
       - name: Install Ruby packages
         if: github.event.action != 'closed'
-        uses: ruby/setup-ruby@v1.172.0
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: "3.1"
           bundler-cache: true
@@ -43,12 +43,13 @@ jobs:
         uses: actions/configure-pages@v4
 
       - uses: jwalton/gh-find-current-pr@master
+        if: github.event.action != 'closed'
         id: pr
         with:
           state: all
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       - name: Build preview version of site

diff --git a/.github/workflows/build-site.yaml b/.github/workflows/build-site.yaml
@@ -20,14 +20,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
         uses: actions/checkout@v4
 
       - name: Install Ruby packages
-        uses: ruby/setup-ruby@v1.172.0
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: "3.1"
           bundler-cache: true
@@ -36,8 +36,8 @@ jobs:
         id: pages
         uses: actions/configure-pages@v4
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       - name: Set root url

diff --git a/.github/workflows/first-time-setup.yaml b/.github/workflows/first-time-setup.yaml
@@ -13,8 +13,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Create Pages branch
         uses: peterjgrainger/[email protected]
@@ -28,8 +28,8 @@ jobs:
         with:
           ref: gh-pages
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       # clean slate, as if starting from orphan branch
@@ -70,17 +70,21 @@ jobs:
         run: |
           user="${{ github.repository_owner }}"
           description="An engaging 1-3 sentence description of your lab."
-          printf "USER=${user}" >> $GITHUB_ENV
-          printf "DESCRIPTION=${description}" >> $GITHUB_ENV
+          printf "\nUSER=${user}" >> $GITHUB_ENV
+          printf "\nDESCRIPTION=${description}" >> $GITHUB_ENV
 
       - name: Personalize readme for user
         run: |
           printf "
-          # ${{ env.USER }}'s Website
+            ![on-push](../../actions/workflows/on-push.yaml/badge.svg)
+            ![on-pull-request](../../actions/workflows/on-pull-request.yaml/badge.svg)
+            ![on-schedule](../../actions/workflows/on-schedule.yaml/badge.svg)
 
-          Visit **[website url](#)** 🚀
+            # ${{ env.USER }}'s Website
 
-          _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+            Visit **[website url](#)** 🚀
+
+            _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
           " > README.md
 
       - name: Personalize Jekyll config for user

diff --git a/.github/workflows/on-pull-request.yaml b/.github/workflows/on-pull-request.yaml
@@ -0,0 +1,22 @@
+name: on-pull-request
+run-name: on pull request activity
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-citations:
+    uses: ./.github/workflows/update-citations.yaml
+
+  build-preview:
+    needs: update-citations
+    uses: ./.github/workflows/build-preview.yaml
diff --git a/.github/workflows/on-push.yaml b/.github/workflows/on-push.yaml
@@ -0,0 +1,24 @@
+name: on-push
+run-name: on push to main
+
+on:
+  push:
+    branches:
+      - main
+
+  # run if user manually requests it
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-citations:
+    # skip first run because nothing enabled or setup yet
+    if: github.run_number != 1
+    uses: ./.github/workflows/update-citations.yaml
+
+  build-site:
+    needs: update-citations
+    uses: ./.github/workflows/build-site.yaml
diff --git a/.github/workflows/on-schedule.yaml b/.github/workflows/on-schedule.yaml
@@ -20,8 +20,3 @@ jobs:
     uses: ./.github/workflows/update-citations.yaml
     with:
       open-pr: true
-
-  build-preview:
-    needs: update-citations
-    if: needs.update-citations.outputs.changed == 'true'
-    uses: ./.github/workflows/build-preview.yaml
diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml
@@ -28,35 +28,47 @@ jobs:
     timeout-minutes: 15
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
+        if: github.event.action != 'closed'
         uses: actions/checkout@v4
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
 
       - name: Setup Python
+        if: github.event.action != 'closed'
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: "pip"
           cache-dependency-path: "**/requirements.txt"
 
       - name: Install Python packages
+        if: github.event.action != 'closed'
         run: |
           python -m pip install --upgrade --requirement ./_cite/requirements.txt
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       - name: Build updated citations
+        if: github.event.action != 'closed'
         run: python _cite/cite.py
         timeout-minutes: 15
 
+      - name: Commit cache
+        if: failure()
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          file_pattern: "**/.cache/**"
+          commit_message: "Commit cache"
+
       - name: Check if citations changed
+        if: github.event.action != 'closed'
         id: changed
         uses: tj-actions/verify-changed-files@v18
         with:
@@ -65,6 +77,7 @@ jobs:
 
       - name: Commit updated citations to branch
         if: |
+          github.event.action != 'closed' &&
           steps.changed.outputs.files_changed == 'true' &&
           inputs.open-pr != true
         uses: stefanzweifel/git-auto-commit-action@v5
@@ -73,12 +86,15 @@ jobs:
 
       - name: Open pull request with updated citations
         if: |
+          github.event.action != 'closed' &&
           steps.changed.outputs.files_changed == 'true' &&
           inputs.open-pr == true
         uses: peter-evans/create-pull-request@v6
         with:
           branch: citation-update
           title: Periodic citation update
+          body: |
+            To see a live preview of this PR, close (don't merge) and reopen it.
 
     outputs:
-      changed: ${{ steps.changed.outputs.files_changed }}
+      changed: ${{ steps.changed.outputs.files_changed || false }}
diff --git a/.github/workflows/update-url.yaml b/.github/workflows/update-url.yaml
@@ -19,8 +19,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Get Pages url
         id: pages
@@ -29,8 +29,8 @@ jobs:
       - name: Checkout branch contents
         uses: actions/checkout@v4
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       # update link to site in readme