minute change

.github/workflows/bridge.yml

@@ -1,13 +1,13 @@
 name: tardis-carsus-bridge
 
-on: 
+on:
   workflow_call: # to be called by save_atomic_files workflow
     outputs:
       ref-check-trig:
         value: ${{ jobs.tardis-build.outputs.step-ref-check-trig}}
   workflow_dispatch: # for running manually
 
-        
+
 env:
   XUVTOP: /tmp/chianti
   CHIANTI_DL_URL: https://download.chiantidatabase.org
@@ -17,9 +17,9 @@ env:
   CMFGEN_DB_VER: atomic_data_15nov16.tar.gz
   # original reference data
   REF1_PATH: ${{ github.workspace }}/tardis-refdata/unit_test_data_org.h5
-  # generated reference data using the new atomic file 
+  # generated reference data using the new atomic file
   REF2_PATH: ${{ github.workspace }}/tardis-refdata/unit_test_data.h5
-  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata 
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata
                 --generate-reference
   CACHE_NUMBER: 1
 
@@ -34,7 +34,7 @@ jobs:
       - uses: actions/checkout@v2
         with:
           path: carsus/
-        
+
       - uses: actions/cache@v3
         with:
           path: ${{ env.XUVTOP }}
@@ -47,7 +47,7 @@ jobs:
             wget -q ${{ env.CHIANTI_DL_URL }}/${{ env.CHIANTI_DB_VER }} -O ${{ env.XUVTOP }}/chianti.tar.gz
             tar -zxf ${{ env.XUVTOP }}/chianti.tar.gz -C ${{ env.XUVTOP }}
         if: steps.chianti-cache.outputs.cache-hit != 'true'
-      
+
       - uses: actions/cache@v3
         with:
           path: /tmp/atomic
@@ -65,7 +65,7 @@ jobs:
           environment-file: conda-lock.yml
           init-shell: bash
           cache-environment: true
-          cache-downloads: true 
+          cache-downloads: true
           environment-name: carsus
 
       - name: Install package
@@ -76,13 +76,13 @@ jobs:
           jupyter nbconvert ${{ env.NBCONVERT_FLAGS }} carsus/docs/tardis_atomdata_ref.ipynb
         env:
           CARSUS_REFDATA: ${{ github.workspace }}/carsus-refdata
-        
+
       - name: Upload Atom Data
         uses: actions/upload-artifact@v2
         with:
           name: atom-data
           path: carsus/docs/kurucz_cd23_chianti_H_He.h5
-  
+
   tardis-build:
     needs: carsus-build
     runs-on: ubuntu-latest
@@ -93,10 +93,10 @@ jobs:
       - uses: actions/checkout@v2
         with:
           repository: tardis-sn/tardis
-        
+
       - name: Download refdata_compare notebook
         run: wget https://raw.githubusercontent.com/tardis-sn/tardis-refdata/master/notebooks/ref_data_compare_from_paths.ipynb
-        
+
       - name: Clone tardis-sn/tardis-refdata
         uses: actions/checkout@v2
         with:
@@ -109,6 +109,7 @@ jobs:
 
       - name: Restore LFS cache
         uses: actions/cache@v3
+        id: lfs-cache
         with:
           path: tardis-refdata/.git/lfs
           key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v${{ env.CACHE_NUMBER }}
@@ -139,32 +140,32 @@ jobs:
 
       - name: Install package
         run: pip install -e .
-        
+
       - name: Download atom data
         uses: actions/[email protected]
         with:
           name: atom-data
           path: carsus/docs/kurucz_cd23_chianti_H_He.h5
-      
+
       - name: Replace Atomic Data
         run: cp carsus/docs/kurucz_cd23_chianti_H_He.h5/kurucz_cd23_chianti_H_He.h5 tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
-      
+
       - name: Generate Reference Data Copy
-        run: cp tardis-refdata/unit_test_data.h5 tardis-refdata/unit_test_data_org.h5 
+        run: cp tardis-refdata/unit_test_data.h5 tardis-refdata/unit_test_data_org.h5
 
       - name: Generate New Reference Data
         run:  pytest tardis ${{ env.PYTEST_FLAGS }}
 
       - name: Compare Reference Data
         run: |
             jupyter nbconvert ${{ env.NBCONVERT_FLAGS }} ref_data_compare_from_paths.ipynb
-      
+
       - name: Upload comparison notebook
         uses: actions/upload-artifact@v2
         with:
           name: Comparison Notebook
           path: ref_data_compare_from_paths.html
-      
+
       - name: Check if reference data are equal
         id: ref-equal-check
         continue-on-error: true
@@ -173,7 +174,7 @@ jobs:
       # continue-on-error check would display a green tick even when the step passes
       # but is necessary for other steps to run
       # if the workflow was called by save-atomic-files workflow(the only other option)
-      # and refdata comparison failed this workflow would pass but the 
+      # and refdata comparison failed this workflow would pass but the
       # bridge-ref-check job in save-atomic-files about refdata comparison would fail
       - name: Fail the workflow if reference data check fails
         if: github.event_name == 'workflow_dispatch' && steps.ref-equal-check.outcome == 'failure'

.github/workflows/carsus-data-repos-config.yml

@@ -1,8 +1,8 @@
 name: carsus-data-repos-config
 
-on: 
-  workflow_dispatch: 
-        
+on:
+  workflow_dispatch:
+
 env:
   NBCONVERT_FLAGS: --execute --ExecutePreprocessor.timeout=600 --to html
 
@@ -35,14 +35,14 @@ jobs:
         with:
           path: carsus-data-nist
           key: ${{ runner.os }}-cache-${{ hashFiles('carsus-data-nist/**/*.lock') }}
-        
+
       - run: |
           for repo in carsus-data-cmfgen carsus-data-kurucz carsus-data-nist; do
             repo_path="$repo"
-       
+
             if [ ! -d $repo_path ] ; then
-              git clone https://github.com/tardis-sn/$repo $repo_path     
-            else                               
+              git clone https://github.com/tardis-sn/$repo $repo_path
+            else
               cd $repo_path
               git fetch
               git checkout origin/main
@@ -55,20 +55,20 @@ jobs:
           environment-file: conda-lock.yml
           init-shell: bash
           cache-environment: true
-          cache-downloads: true 
+          cache-downloads: true
           environment-name: carsus
 
       - name: Install package
         run: pip install -e carsus/
-          
+
       - name: Run notebooks
         run: |
           jupyter nbconvert ${{ env.NBCONVERT_FLAGS }} carsus/docs/tardis_atomdata_ref.ipynb
         env:
           CARSUS_REFDATA: ${{ github.workspace }}/carsus-refdata
-        
+
       - name: Upload Atom Data
         uses: actions/upload-artifact@v3
         with:
           name: atom-data
-          path: carsus/docs/kurucz_cd23_cmfgen_H_Si.h5
+          path: carsus/docs/kurucz_cd23_cmfgen_H_Si.h5

.github/workflows/codestyle.yml

@@ -14,7 +14,7 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  ruff: 
+  ruff:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -31,13 +31,13 @@ jobs:
 
       - name: Download Lock File
         run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-        
+
       - 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
-            
+
       - uses: mamba-org/setup-micromamba@v1
         with:
            environment-file: conda-linux-64.lock
@@ -46,19 +46,19 @@ jobs:
            environment-name: tardis
            cache-environment: true
            cache-downloads: true
-      
+
       - name: Show statistics pull request
         if: github.event_name == 'pull_request_target'
         run: ruff check --statistics  --show-fixes $(git --no-pager diff --name-only origin/master HEAD --) | tee ruff_stats.txt
-      
+
       - name: Show entire output pull request
         if: github.event_name == 'pull_request_target'
         run: ruff check --output-format=concise $(git --no-pager diff --name-only origin/master HEAD --) | tee ruff_full.txt
 
       - name: Show statistics push
         if: github.event_name == 'push'
         run: ruff check --statistics  --show-fixes . | tee ruff_stats.txt
-      
+
       - name: Show entire output push
         if: github.event_name == 'push'
         run: ruff check --output-format=concise . | tee ruff_full.txt
@@ -70,19 +70,19 @@ jobs:
           path: ruff_stats.txt
 
       - name: Entire output read
-        id: ruff_complete 
+        id: ruff_complete
         uses: juliangruber/[email protected]
         with:
           path: ruff_full.txt
-      
+
       - name: Find Comment
         if: always() && github.event_name == 'pull_request_target'
         uses: peter-evans/find-comment@v1
         id: fc
         with:
           issue-number: ${{ github.event.number }}
           body-includes: I ran ruff on the latest commit
-      
+
       - name: Post comment
         if: github.event_name == 'pull_request_target'
         uses: peter-evans/create-or-update-comment@v2
@@ -93,10 +93,10 @@ jobs:
           edit-mode: replace
           body: |
             *\*beep\* \*bop\**
-            Hi human, 
-            I ran ruff on the latest commit (${{ github.event.pull_request.head.sha }}). 
+            Hi human,
+            I ran ruff on the latest commit (${{ github.event.pull_request.head.sha }}).
             Here are the outputs produced.
-            Results can also be downloaded as artifacts [**here**](${{ env.URL }}). 
+            Results can also be downloaded as artifacts [**here**](${{ env.URL }}).
             Summarised output:
             <details>
 
@@ -112,16 +112,16 @@ jobs:
               ```diff
               ${{ steps.ruff_complete.outputs.content }}
               ```
-              
+
             </details>
         env:
           URL: https://github.com/${{ github.repository_owner }}/${{ github.event.repository.name }}/actions/runs/${{ github.run_id }}?check_suite_focus=true
-          
+
       - name: Save results artifact
         uses: actions/upload-artifact@v4
         if: always()
         with:
           name: ruff-results
           path: |
             ruff_full.txt
-            ruff_stats.txt
+            ruff_stats.txt

.github/workflows/docs-build.yml

@@ -117,7 +117,7 @@ jobs:
           environment-file: conda-lock.yml
           init-shell: bash
           cache-environment: true
-          cache-downloads: true 
+          cache-downloads: true
           environment-name: carsus
 
       - name: Install package

.github/workflows/save_atomic_files.yml

@@ -1,14 +1,14 @@
 name: save-atomic-files
 
-on: 
+on:
   workflow_dispatch:
   schedule:
     - cron: '0 0 * * 0' # run at midnight every Sunday
 
 jobs:
   create-artifacts:
     uses: ./.github/workflows/bridge.yml
-  
+
   zip_artifacts:
     needs: create-artifacts
     runs-on: ubuntu-latest
@@ -34,13 +34,13 @@ jobs:
           password: ${{ secrets.GH_DROPOFF_PASSWORD }}
           source: '*_*_*.zip'
           target: "/storage/github_dropoffs/tardis/"
-  
+
   bridge-ref-check:
     needs: create-artifacts
     runs-on: ubuntu-latest
     if: needs.create-artifacts.outputs.ref-check-trig == 'failure'
     # fails if refdata comparison failed in the bridge
-    # continue-on-error wouldn't put a red cross 
+    # continue-on-error wouldn't put a red cross
     # even if the bridge passes on refdata compare step
     steps:
-      - run: exit 1
+      - run: exit 1