Merge branch 'master' into mc-refactor

.github/actions/setup_lfs/action.yml

@@ -1,97 +1,96 @@
-name: 'Setup LFS'
-description: 'Pull LFS repositories and caches them'
+name: "Setup LFS"
+description: "Pull LFS repositories and caches them"
 
 inputs:
   refdata-repo:
     description: "tardis refdata repository"
     required: false
-    default: 'tardis-sn/tardis-refdata'
-  regression-data-repo: 
+    default: "tardis-sn/tardis-refdata"
+  regression-data-repo:
     description: "tardis regression data repository"
     required: false
-    default: 'tardis-sn/tardis-regression-data'
+    default: "tardis-sn/tardis-regression-data"
 
 runs:
-    using: "composite"
-    steps:
-      - uses: actions/checkout@v4
-      - name: Clone Refdata Repo
-        uses: actions/checkout@v4
-        with:
-          repository: ${{ inputs.refdata-repo }}
-          path: tardis-refdata
-          lfs: false
+  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: 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@v3
-        id: lfs-cache-refdata
-        with:
-          path: tardis-refdata/.git/lfs
-          key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
+    - 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'  && always() || false }}
-        uses: actions/cache/save@v3
-        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:
-          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
-        shell: bash
+    - name: Git LFS Pull
+      run: git lfs pull
+      working-directory: tardis-refdata
+      if: steps.lfs-cache-refdata.outputs.cache-hit != 'true'
+      shell: bash
 
-      - name: Restore LFS cache
-        uses: actions/cache/restore@v3
-        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'  && always() || false }}
-        uses: actions/cache/save@v3
-        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: 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'  && 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:
+        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
+      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'  && 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/benchmarks.yml

@@ -33,20 +33,20 @@ jobs:
       contains(github.event.pull_request.labels.*.name, 'benchmarks')))
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         if: github.event_name != 'pull_request_target'
         with:
           fetch-depth: 0
 
       - name: Checkout pull/${{ github.event.number }}
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.sha }}
           fetch-depth: 0
         if: github.event_name == 'pull_request_target'
 
       - name: Restore Atom Data
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         id: atom-data-restore
         with:
           path: benchmarks/data/kurucz_cd23_chianti_H_He.h5
@@ -59,7 +59,7 @@ jobs:
           wget -q "$REPO_URL/items?path=atom_data/kurucz_cd23_chianti_H_He.h5&versionType=branch&version=master&resolveLfs=true" -O benchmarks/data/kurucz_cd23_chianti_H_He.h5
 
       - name: Save Atom Data
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         if: ${{ steps.atom-data-restore.outputs.cache-hit != 'true'  && always() || false }}
         id: atom-data-cache-save
         with:
@@ -186,7 +186,7 @@ jobs:
           URL: https://github.com/${{ github.repository_owner }}/${{ github.event.repository.name }}/actions/runs/${{ github.run_id }}?check_suite_focus=true
 
       - name: Save results artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

.github/workflows/build-docs.yml

@@ -157,7 +157,7 @@ jobs:
           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 }}

.github/workflows/clean-docs.yml

@@ -5,26 +5,24 @@
 name: clean-docs
 
 on:
-
   delete:
-    branches:                           # remove deleted branches
-      - '*'
+    branches: # remove deleted branches
+      - "*"
 
-  pull_request_target:                  # remove closed or merged pull requests
+  pull_request_target: # remove closed or merged pull requests
     branches:
-      - '*'
+      - "*"
     types:
       - closed
 
 env:
-  DEPLOY_BRANCH: gh-pages               #  deployed docs branch
+  DEPLOY_BRANCH: gh-pages #  deployed docs branch
 
 jobs:
   clean:
     runs-on: ubuntu-latest
     steps:
-
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set folder to delete
         run: |

.github/workflows/codestyle.yml

@@ -17,10 +17,10 @@ jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.x
 

.github/workflows/docstr-cov.yml

@@ -1,4 +1,4 @@
-# Log in to jsonbin.org with tardis-bot GitHub account to get an API key and 
+# Log in to jsonbin.org with tardis-bot GitHub account to get an API key and
 # store it as a repository secret.
 
 # Updated badge will be available at:
@@ -9,11 +9,11 @@ name: docstr-cov
 on:
   push:
     branches:
-    - master
+      - master
 
   pull_request:
     branches:
-    - master
+      - master
 
 env:
   THRESHOLD: 0.05
@@ -25,13 +25,12 @@ jobs:
   check:
     runs-on: ubuntu-latest
     steps:
-
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.x
 
@@ -47,7 +46,7 @@ jobs:
           elif [[ ${{ github.event_name }} == 'pull_request' ]]; then
             echo "BASE=${{ github.event.pull_request.base.sha }}" >> $GITHUB_ENV
             echo "HEAD=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV
-          
+
           else
             echo "Unexpected event trigger"
             exit 1

.github/workflows/mailmap.yml

@@ -12,7 +12,7 @@ jobs:
   check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           fetch-depth: 0