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.github/actions/setup_env/action.yml

@@ -21,12 +21,16 @@ runs:
           echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
         id: cache-environment-key
         shell: bash
-        
-      - uses: mamba-org/setup-micromamba@v1
+
+      - uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: conda-${{ inputs.os-label }}.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+          init-shell: bash
+          create-args: conda-lock
+          environment-name: tardis-base
+
+      - name: Install packages
+        run: |
+          mkdir micromamba_tardis
+          conda-lock install --prefix micromamba_tardis conda-${{ inputs.os-label }}.lock
+          micromamba activate ./micromamba_tardis
+        shell: bash -el {0}

.github/actions/setup_lfs/action.yml

@@ -1,5 +1,5 @@
 name: "Setup LFS"
-description: "Pull LFS repositories and caches them"
+description: "Downloads and extracts regression data from Zenodo"
 
 
 inputs:
@@ -11,42 +11,43 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - name: Clone tardis-sn/tardis-regression-data
-      uses: actions/checkout@v4
-      with:
-        repository: ${{ inputs.regression-data-repo }}
-        path: tardis-regression-data
-
-    - name: Create LFS file list
-      run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
-      working-directory: tardis-regression-data
+    - name: Download regression data from Zenodo
+      run: |
+        wget --show-progress --progress=bar:force https://sandbox.zenodo.org/records/156229/files/tardis-regression-np.zip
+        mkdir -p tardis-regression-data
+        unzip -q tardis-regression-np.zip -d tardis-regression-data
       shell: bash
 
-    - name: Restore LFS cache
-      uses: actions/cache/restore@v4
-      id: lfs-cache-regression-data
-      with:
-        path: tardis-regression-data/.git/lfs
-        key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-regression-data/.lfs-assets-id') }}-v1
-
-    - name: Git LFS Pull
-      run: git lfs pull
-      working-directory: tardis-regression-data
-      if: steps.lfs-cache-regression-data.outputs.cache-hit != 'true'
-      shell: bash
-
-    - name: Git LFS Checkout
-      run: git lfs checkout
-      working-directory: tardis-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: tardis-regression-data/.git/lfs
-        key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-regression-data/.lfs-assets-id') }}-v1
+    # - name: Create LFS file list
+    #   run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+    #   working-directory: tardis-regression-data
+    #   shell: bash
+
+    # - name: Restore LFS cache
+    #   uses: actions/cache/restore@v4
+    #   id: lfs-cache-regression-data
+    #   with:
+    #     path: tardis-regression-data/.git/lfs
+    #     key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-regression-data/.lfs-assets-id') }}-v1
+
+    # - name: Git LFS Pull
+    #   run: git lfs pull
+    #   working-directory: tardis-regression-data
+    #   if: steps.lfs-cache-regression-data.outputs.cache-hit != 'true'
+    #   shell: bash
+
+    # - name: Git LFS Checkout
+    #   run: git lfs checkout
+    #   working-directory: tardis-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: tardis-regression-data/.git/lfs
+    #     key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-regression-data/.lfs-assets-id') }}-v1

.github/workflows/build-docs.yml

@@ -7,18 +7,19 @@ name: docs
 on:
   push:
     branches:
-      - master
+      - '*'
+
+  # pull_request_target:
+  #   branches:
+  #     - master
 
-  pull_request_target:
-    branches:
-      - master
 
-    types:
-      - opened
-      - reopened
-      - synchronize
-      - labeled # requires the `build-docs` label
-      - ready_for_review
+    # types:
+    #   - opened
+    #   - reopened
+    #   - synchronize
+    #   - labeled # requires the `build-docs` label
+    #   - ready_for_review
 
   workflow_dispatch: # manual trigger
 
@@ -38,7 +39,7 @@ defaults:
 jobs:
   check-for-changes:
     runs-on: ubuntu-latest
-    if: ${{ !github.event.pull_request.draft }}
+    # if: ${{ !github.event.pull_request.draft }}  # Commented out to allow running on forks
     outputs:
       trigger-check-outcome: ${{ steps.trigger_check.outcome }}
       docs-check-outcome: ${{ steps.docs_check.outcome }}
@@ -77,8 +78,10 @@ jobs:
 
   build-docs:
     runs-on: ubuntu-latest
-    needs: check-for-changes
-    if: needs.check-for-changes.outputs.trigger-check-outcome == 'success' || needs.check-for-changes.outputs.docs-check-outcome == 'success'
+    # needs: check-for-changes 
+    # if: needs.check-for-changes.outputs.trigger-check-outcome == 'success' || needs.check-for-changes.outputs.docs-check-outcome == 'success' 
+    permissions:
+      contents: write  # Add permissions for deployment
     steps:
       - uses: actions/checkout@v4
         if: github.event_name != 'pull_request_target'
@@ -108,14 +111,19 @@ jobs:
           mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-regression-data/atom_data/. ~/Downloads/tardis-data
 
       - name: Install package
-        run: pip install -e .
+        run: |
+          micromamba activate ./micromamba_tardis
+          pip install -e .
 
       - name: Install Sphinx extensions
         run: |
+          micromamba activate ./micromamba_tardis
           pip install sphinxcontrib-googleanalytics
 
       - name: Build documentation
-        run: cd docs/ && make html NCORES=auto
+        run: |
+          micromamba activate ./micromamba_tardis
+          cd docs/ && make html NCORES=auto
 
       - name: Set destination directory
         run: |
@@ -160,14 +168,15 @@ jobs:
       - name: Deploy ${{ env.DEST_DIR }}
         uses: peaceiris/actions-gh-pages@v4
         with:
-          github_token: ${{ secrets.BOT_TOKEN }}
+          # github_token: ${{ secrets.BOT_TOKEN }}  # Comment out bot token
+          github_token: ${{ github.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: "GitHub Actions" # change back to TARDIS Bot
+          user_email: "github-actions[bot]@users.noreply.github.com"  # change back to TARDIS email
 
       - name: Find comment
         uses: peter-evans/find-comment@v1

.github/workflows/tests.yml

@@ -58,34 +58,41 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup LFS
-        uses: ./.github/actions/setup_lfs
-
       - name: Setup environment
         uses: ./.github/actions/setup_env
         with:
           os-label: ${{ matrix.label }}
 
+      - name: Setup LFS
+        uses: ./.github/actions/setup_lfs
+
       - name: Install package editable
         if: ${{ !inputs.pip_git }}
         run: |
+          micromamba activate ./micromamba_tardis
           pip install -e . --user
 
       - name: Install package git
         if: ${{ inputs.pip_git }}
         run: |
+          micromamba activate ./micromamba_tardis
           pip install git+https://github.com/tardis-sn/tardis.git@master
 
       - name: Install qgridnext
         if: ${{ !inputs.pip_git }}
         run: |
+          micromamba activate ./micromamba_tardis
           pip install qgridnext
 
       - name: Run tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ matrix.continuum }} continuum"
+        run: |
+          micromamba activate ./micromamba_tardis
+          pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ matrix.continuum }} continuum"
 
       - name: Regression Data Generation tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum"
+        run: |
+          micromamba activate ./micromamba_tardis
+          pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum"
         if: contains(github.event.pull_request.labels.*.name, 'run-generation-tests') || github.ref == 'refs/heads/master'
 
       - run: mv .coverage .coverage.${{ strategy.job-index }}

asv.conf.json

@@ -17,7 +17,7 @@
         "origin/master",
         "HEAD"
     ],
-    "environment_type": "mamba",
+    "environment_type": "conda",
     "show_commit_url": "https://github.com/tardis-sn/tardis/commit/",
     "conda_environment_file": "tardis_env3.yml",
     "benchmark_dir": "benchmarks",