Update Workflows

.github/actions/setup_env/action.yml

@@ -11,13 +11,13 @@ runs:
   using: "composite"
   steps:
       - name: Download Lock File
-        run:  wget -q https://raw.githubusercontent.com/tardis-sn/stardis/main/conda-${{ inputs.os-label }}.lock
+        run:  wget -q https://raw.githubusercontent.com/stardis-sn/stardis/main/conda-${{ inputs.os-label }}.lock
         shell: bash
 
       - name: Generate Cache Key
         run: | 
           file_hash=$(cat conda-${{ inputs.os-label }}.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
+          echo "file_hash=stardis-conda-env-${{ inputs.os-label }}-${file_hash}-v1" >> "${GITHUB_OUTPUT}"
         id: cache-environment-key
         shell: bash
 

.github/actions/setup_lfs/action.yml

@@ -1,52 +1,38 @@
 name: "Setup LFS"
-description: "Pull LFS repositories and caches them"
-
+description: "Sets up Git LFS, retrieves LFS cache and fails if cache is not available"
 
 inputs:
   regression-data-repo:
-    description: "stardis regression data repository"
+    description: "Repository containing regression data (format: owner/repo)"
     required: false
-    default: "tardis-sn/stardis-regression-data"
+    default: "stardis-sn/stardis-regression-data"
 
 runs:
   using: "composite"
   steps:
-    - name: Clone tardis-sn/stardis-regression-data
+    - name: Clone stardis-sn/stardis-regression-data
       uses: actions/checkout@v4
       with:
         repository: ${{ inputs.regression-data-repo }}
         path: stardis-regression-data
+        lfs: false
 
     - name: Create LFS file list
-      run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+      run: |
+        git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-files-list
       working-directory: stardis-regression-data
       shell: bash
-
+    
     - name: Restore LFS cache
       uses: actions/cache/restore@v4
       id: lfs-cache-regression-data
       with:
         path: stardis-regression-data/.git/lfs
-        key: ${{ runner.os }}-lfs-${{ hashFiles('stardis-regression-data/.lfs-assets-id') }}-v1
-
-    - name: Git LFS Pull
-      run: git lfs pull
-      working-directory: stardis-regression-data
-      if: steps.lfs-cache-regression-data.outputs.cache-hit != 'true'
-      shell: bash
+        key: stardis-regression-full-data-${{ hashFiles('stardis-regression-data/.lfs-files-list') }}-${{ inputs.regression-data-repo }}-v1
+        fail-on-cache-miss: true
 
     - name: Git LFS Checkout
+      if: steps.lfs-cache-regression-data.outputs.cache-hit == 'true'
       run: git lfs checkout
       working-directory: stardis-regression-data
-      if: steps.lfs-cache-regression-data.outputs.cache-hit == 'true'
       shell: bash
-
-    - name: Save LFS cache if not found
-      # uses fake ternary
-      # for reference: https://github.com/orgs/community/discussions/26738#discussioncomment-3253176
-      if: ${{ steps.lfs-cache-regression-data.outputs.cache-hit != 'true' && !contains(github.ref, 'merge') && always() || false }}
-      uses: actions/cache/save@v4
-      id: lfs-cache-regression-data-save
-      with:
-        path: stardis-regression-data/.git/lfs
-        key: ${{ runner.os }}-lfs-${{ hashFiles('stardis-regression-data/.lfs-assets-id') }}-v1

.github/workflows/build-docs.yml

@@ -1,46 +1,97 @@
 name: build-docs
 on:
   push:
-  workflow_dispatch:
+    branches:
+      - main
 
+  pull_request_target:
+    branches:
+      - main
+
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - labeled # requires the `build-docs` label
+      - ready_for_review
+
+  workflow_dispatch: # manual trigger
 env:
-  CACHE_NUMBER: 0
-  DEPLOY_BRANCH: gh-pages               # deployed docs branch
+  CACHE_NUMBER: 0 # increase to reset cache manually
+  DEPLOY_BRANCH: gh-pages # deployed docs branch
+  HDF5_USE_FILE_LOCKING: "FALSE" # disable file locking
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
 
 defaults:
   run:
     shell: bash -le {0}
+
 jobs:
+  check-for-changes:
+    runs-on: ubuntu-latest
+    if: ${{ !github.event.pull_request.draft }}
+    outputs:
+      trigger-check-outcome: ${{ steps.trigger_check.outcome }}
+      docs-check-outcome: ${{ steps.docs_check.outcome }}
+    steps:
+      - uses: actions/checkout@v4
+        if: github.event_name != 'pull_request_target'
+
+      - name: Checkout pull/${{ github.event.number }}
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.sha }}
+        if: github.event_name == 'pull_request_target'
+
+      - name: Check for trigger by push event, manual dispatch, build-docs label on a PR
+        id: trigger_check
+        if: github.event_name == 'push' || github.event_name == 'workflow_dispatch' || github.event_name == 'pull_request_target' && contains(github.event.pull_request.labels.*.name, 'build-docs')
+        run: |
+          echo "Building docs as a test."
+          exit 0
+        continue-on-error: true
+
+      - name: Check for changes in documentation
+        run: |
+          if git diff origin/main..."$(git rev-parse --abbrev-ref HEAD)" --name-only | cat | grep '^docs/' | grep -q .; then
+              num_files=$(git diff --name-only origin/main...HEAD | grep '^docs/' | wc -l)
+              echo "Changes found in documentation files: $num_files"
+              exit 0
+          else
+              echo "No changes found in documentation files - will stop running the pipeline."
+              exit 1
+          fi
+        id: docs_check
+        if: steps.trigger_check.outcome != 'success'
+        continue-on-error: true
+
+
   build-sphinx-html:
-    if: ((github.repository == 'tardis-sn/stardis') && (${{ github.head_ref || github.ref_name}} == 'main')) || (github.repository_owner != 'tardis-sn')
+    if: (github.repository == 'tardis-sn/stardis' && (github.head_ref || github.ref_name) == 'main') || github.repository_owner != 'tardis-sn'
     # The above line makes this action run if it is either not on the upstream/main or the main branch of upstream/main.
     # If there is a better way to implement this, I'd like someone to please share.
     # The context to get the branch name is from https://stackoverflow.com/a/71158878
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v4
+        if: github.event_name != 'pull_request_target'
 
-      - uses: actions/checkout@v2
-
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Checkout pull/${{ github.event.number }}
+        uses: actions/checkout@v4
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: stardis
-          use-mamba: true
-
-      - name: Cache Environment Lockfile
-        id: cache-env-lockfile
-        uses: actions/cache@v3
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.sha }}
+        if: github.event_name == 'pull_request_target'
+
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
         with:
-          path: /usr/share/miniconda3/envs/stardis
-          key: conda-linux-64-${{ hashFiles('conda-linux-64.lock') }}-${{ env.CACHE_NUMBER }}
-
-      - name: Update Conda Environment
-        id: update-env
-        run: |
-          mamba update -n stardis --file conda-linux-64.lock
-        if: steps.cache-env-lockfile.outputs.cache-hit != 'true'
+          os-label: linux-64
 
       - name: Install TARDIS
         id: install-tardis
@@ -58,7 +109,7 @@ jobs:
         id: make-sphinx-html
         run: |
           make -C docs html
-          
+
       - name: Set destination directory
         run: |
           BRANCH=$(echo ${GITHUB_REF#refs/heads/})
@@ -72,7 +123,7 @@ jobs:
 
           elif [[ $EVENT == pull_request_target ]]; then
             echo "DEST_DIR=pull/$PR" >> $GITHUB_ENV
-            
+
           else
             echo "Unexpected event trigger $EVENT"
             exit 1
@@ -85,17 +136,31 @@ jobs:
           EVENT: ${{ github.event_name }}
           PR: ${{ github.event.number }}
 
+      - name: Set clean branch option
+        run: |
+          if [[ $EVENT == workflow_dispatch ]]; then
+            echo "CLEAN_BRANCH=true" >> $GITHUB_ENV
+
+          else
+            echo "CLEAN_BRANCH=false" >> $GITHUB_ENV
+
+          fi
+
+          cat $GITHUB_ENV
+        env:
+          EVENT: ${{ github.event_name }}
+
       - name: Deploy ${{ env.DEST_DIR }}
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.BOT_TOKEN }}
           publish_branch: ${{ env.DEPLOY_BRANCH }}
           publish_dir: ./docs/_build/html
           destination_dir: ${{ env.DEST_DIR }}
           keep_files: true
           force_orphan: ${{ env.CLEAN_BRANCH }}
-          user_name: 'TARDIS Bot'
-          user_email: 'tardis.sn.bot@gmail.com'
+          user_name: "TARDIS Bot"
+          user_email: "tardis.sn.bot@gmail.com"
 
       - name: Find comment
         uses: peter-evans/find-comment@v1
@@ -108,7 +173,7 @@ jobs:
       - name: Post comment (success)
         uses: peter-evans/create-or-update-comment@v1
         with:
-          token:  ${{ secrets.BOT_TOKEN }}
+          token: ${{ secrets.BOT_TOKEN }}
           issue-number: ${{ github.event.number }}
           comment-id: ${{ steps.fc.outputs.comment-id }}
           edit-mode: replace
@@ -118,7 +183,7 @@ jobs:
             Hi, human.
 
             The **`${{ github.workflow }}`** workflow has **succeeded** :heavy_check_mark:
-            
+
             [**Click here**](${{ env.URL }}) to see your results.
         env:
           URL: https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/pull/${{ github.event.number }}/index.html
@@ -127,7 +192,7 @@ jobs:
       - name: Post comment (failure)
         uses: peter-evans/create-or-update-comment@v1
         with:
-          token:  ${{ secrets.BOT_TOKEN }}
+          token: ${{ secrets.BOT_TOKEN }}
           issue-number: ${{ github.event.number }}
           comment-id: ${{ steps.fc.outputs.comment-id }}
           edit-mode: replace
@@ -137,7 +202,7 @@ jobs:
             Hi, human.
 
             The **`${{ github.workflow }}`** workflow has **failed** :x:
-            
+
             [**Click here**](${{ env.URL }}) to see the build log.
         env:
           URL: https://github.com/${{ github.repository_owner }}/${{ github.event.repository.name }}/actions/runs/${{ github.run_id }}?check_suite_focus=true

.github/workflows/lfs-cache.yml

@@ -0,0 +1,75 @@
+name: Save LFS Cache
+
+on:
+  workflow_call:
+    inputs:
+      regression-data-repo:
+        description: "Repository containing regression data (format: owner/repo)"
+        required: false
+        default: "stardis-sn/stardis-regression-data"
+        type: string
+      allow_lfs_pull:
+        description: "If true, allows LFS pull operations"
+        required: false
+        default: false
+        type: boolean
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+concurrency:
+  # Only one workflow can run at a time
+  # the workflow group is a unique identifier and contains the workflow name, pull request number, and regression data repo
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ inputs.regression-data-repo }}
+  cancel-in-progress: true
+
+
+jobs:
+  lfs-cache:
+    if: github.repository_owner == 'tardis-sn'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ inputs.regression-data-repo }}
+          path: stardis-regression-data
+
+      - name: Create LFS file list
+        run: |
+          git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-files-list
+        working-directory: stardis-regression-data
+
+      - name: Test cache availability
+        uses: actions/cache/restore@v4
+        id: test-lfs-cache-regression-data
+        with:
+          path: stardis-regression-data/.git/lfs
+          key: stardis-regression-full-data-${{ hashFiles('stardis-regression-data/.lfs-files-list') }}-${{ inputs.regression-data-repo }}-v1
+          lookup-only: true
+
+      - name: Fail if LFS pull is needed but not allowed
+        if: |
+          steps.test-lfs-cache-regression-data.outputs.cache-hit != 'true' && 
+          inputs.allow_lfs_pull != true
+        run: |
+          echo "Error: LFS pull is required but not allowed (allow_lfs_pull is false)"
+          exit 1
+
+      - name: Git LFS Pull
+        if: |
+          steps.test-lfs-cache-regression-data.outputs.cache-hit != 'true' && 
+          inputs.allow_lfs_pull == true
+        run: git lfs pull
+        working-directory: stardis-regression-data
+
+      - name: Git LFS Checkout
+        run: git lfs checkout
+        working-directory: stardis-regression-data
+
+      - name: Save LFS cache if not found
+        uses: actions/cache/save@v4
+        if: ${{ steps.test-lfs-cache-regression-data.outputs.cache-hit != 'true' && !contains(github.ref, 'merge') }}
+        with:
+          path: stardis-regression-data/.git/lfs
+          key: stardis-regression-full-data-${{ hashFiles('stardis-regression-data/.lfs-files-list') }}-${{ inputs.regression-data-repo }}-v1

.github/workflows/tests.yml

@@ -19,17 +19,21 @@ defaults:
     shell: bash -l {0}
 
 jobs:
+  lfs-cache:
+    uses: ./.github/workflows/lfs-cache.yml
+    with:
+      regression-data-repo: tardis-sn/tardis-regression-data
+      allow_lfs_pull: ${{ github.ref == 'refs/heads/main' || contains(github.event.pull_request.labels.*.name, 'git-lfs-pull') }}
+
   build:
+    needs: lfs-cache
     if: github.repository_owner == 'tardis-sn'
     strategy:
       matrix:
         include:
         - os: ubuntu-latest
           label: linux-64
           prefix: /usr/share/miniconda3/envs/stardis
-        # - os: ubuntu-latest
-        #   label: linux-64-cuda
-        #   prefix: /usr/share/miniconda3/envs/stardis
         - os: macos-latest
           label: osx-64
           prefix: /Users/runner/miniconda3/envs/stardis