diff --git a/.github/actions/setup_lfs/action.yml b/.github/actions/setup_lfs/action.yml
index fe8156a1cd0..e65045956ca 100644
--- a/.github/actions/setup_lfs/action.yml
+++ b/.github/actions/setup_lfs/action.yml
@@ -27,7 +27,7 @@ runs:
       shell: bash
 
     - name: Restore LFS cache
-      uses: actions/cache/restore@v3
+      uses: actions/cache/restore@v4
       id: lfs-cache-refdata
       with:
         path: tardis-refdata/.git/lfs
@@ -49,7 +49,7 @@ runs:
       # 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
+      uses: actions/cache/save@v4
       id: lfs-cache-refdata-save
       with:
         path: tardis-refdata/.git/lfs
@@ -67,7 +67,7 @@ runs:
       shell: bash
 
     - name: Restore LFS cache
-      uses: actions/cache/restore@v3
+      uses: actions/cache/restore@v4
       id: lfs-cache-regression-data
       with:
         path: tardis-regression-data/.git/lfs
@@ -89,7 +89,7 @@ runs:
       # 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
+      uses: actions/cache/save@v4
       id: lfs-cache-regression-data-save
       with:
         path: tardis-regression-data/.git/lfs
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 5088149cd78..627a144ae84 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.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 }}
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index fefb7048d2f..7fc44e742e2 100644
--- a/.github/workflows/build-docs.yml
+++ b/.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 }}
diff --git a/.github/workflows/clean-docs.yml b/.github/workflows/clean-docs.yml
index 8126ab7cb23..cbbed1b1b53 100644
--- a/.github/workflows/clean-docs.yml
+++ b/.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: |
diff --git a/.github/workflows/codestyle.yml b/.github/workflows/codestyle.yml
index 3f59212bd56..82bba3de516 100644
--- a/.github/workflows/codestyle.yml
+++ b/.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
 
diff --git a/.github/workflows/docstr-cov.yml b/.github/workflows/docstr-cov.yml
index 645d285bffd..6ebe1fd1e24 100644
--- a/.github/workflows/docstr-cov.yml
+++ b/.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
diff --git a/.github/workflows/mailmap.yml b/.github/workflows/mailmap.yml
index 13e977060e6..4ca95d7a198 100644
--- a/.github/workflows/mailmap.yml
+++ b/.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
diff --git a/.github/workflows/post-release.yml b/.github/workflows/post-release.yml
index 5216453b00e..1f86be25591 100644
--- a/.github/workflows/post-release.yml
+++ b/.github/workflows/post-release.yml
@@ -8,13 +8,13 @@ on:
   release:
     types: [published]
 
-  workflow_dispatch:  # manual trigger
+  workflow_dispatch: # manual trigger
 
 jobs:
   changelog:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           repository: tardis-sn/tardis
           token: ${{ secrets.BOT_TOKEN }}
@@ -26,7 +26,7 @@ jobs:
       - name: Update changelog
         run: github-changes -o tardis-sn -r tardis --only-pulls --use-commit-body -f CHANGELOG.md -k ${{ secrets.BOT_TOKEN }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: changelog
           path: CHANGELOG.md
@@ -34,15 +34,15 @@ jobs:
   citation:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Wait for Zenodo webhook
         run: sleep 180
 
       - name: Setup Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.x'
+          python-version: "3.x"
 
       - name: Install doi2cff
         run: pip install git+https://github.com/citation-file-format/doi2cff
@@ -52,7 +52,7 @@ jobs:
           rm CITATION.cff
           doi2cff init 10.5281/zenodo.592480
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: citation
           path: CITATION.cff
@@ -60,23 +60,23 @@ jobs:
   credits:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Wait for Zenodo webhook
         run: sleep 180
 
       - name: Setup Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.x'
+          python-version: "3.x"
 
-      - name: Install rst-include 
+      - name: Install rst-include
         run: pip install rst-include==2.1.2.2 requests==2.27.1
 
       - name: Update README.rst
         run: python .ci-helpers/update_credits.py
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: credits
           path: |
@@ -87,9 +87,9 @@ jobs:
     needs: [changelog, citation, credits]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           path: /tmp
 
diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
index 51cb50333de..69268254ed0 100644
--- a/.github/workflows/pre-release.yml
+++ b/.github/workflows/pre-release.yml
@@ -6,8 +6,8 @@ name: pre-release
 
 on:
   schedule:
-    - cron: '0 0 * * 0'
-  workflow_dispatch:  # manual trigger
+    - cron: "0 0 * * 0"
+  workflow_dispatch: # manual trigger
 
 defaults:
   run:
@@ -17,7 +17,7 @@ jobs:
   zenodo:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           repository: tardis-sn/tardis_zenodo
           token: ${{ secrets.BOT_TOKEN }}
@@ -28,14 +28,14 @@ jobs:
           KEY_SECRET_JSON: ${{ secrets.ZENODO_KEY_SECRET_JSON }}
 
       - name: Download Lock File
-        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-        
+        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
@@ -52,7 +52,7 @@ jobs:
         run: jupyter nbconvert gather_data.ipynb --to html --execute --ExecutePreprocessor.timeout=6000 --allow-errors
         if: failure()
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: zenodo_json
           path: .zenodo.json
@@ -61,9 +61,9 @@ jobs:
     needs: zenodo
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           path: /tmp
 
@@ -137,4 +137,4 @@ jobs:
         if: steps.create-pr.outputs.pull-request-operation == 'created'
 
   compare_refdata:
-      uses: tardis-sn/tardis-refdata/.github/workflows/compare-refdata.yml@master
+    uses: tardis-sn/tardis-refdata/.github/workflows/compare-refdata.yml@master
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index c02b21fcbc1..be32edfaa4d 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -9,23 +9,23 @@ on:
     branches: [master]
     types: [closed]
 
-  workflow_dispatch:  # manual trigger
+  workflow_dispatch: # manual trigger
 
 jobs:
   create:
     if: github.event_name == 'workflow_dispatch' ||
-        (startsWith(github.head_ref, 'pre-release-20') && github.event.pull_request.merged == true)
+      (startsWith(github.head_ref, 'pre-release-20') && github.event.pull_request.merged == true)
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.x'
+          python-version: "3.x"
 
       - name: Install setuptools_scm
         run: pip install 'setuptools_scm<7'
@@ -34,7 +34,7 @@ jobs:
         run: python .ci-helpers/get_current_version.py
 
       - name: Get next version
-        run:  |
+        run: |
           python .ci-helpers/get_next_version.py
           echo "NEW_TAG=$(python .ci-helpers/get_next_version.py)" >> $GITHUB_ENV
 
diff --git a/.github/workflows/update-refdata.yml b/.github/workflows/update-refdata.yml
index f70a22eab70..467c2c300e6 100644
--- a/.github/workflows/update-refdata.yml
+++ b/.github/workflows/update-refdata.yml
@@ -9,8 +9,8 @@ on:
     types: [update-refdata-command]
 
 env:
-  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-regression-data=${{ github.workspace }}/tardis-regression-data --generate-reference 
-  CACHE_NUMBER: 1  # increase to reset cache manually
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-regression-data=${{ github.workspace }}/tardis-regression-data --generate-reference
+  CACHE_NUMBER: 1 # increase to reset cache manually
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
@@ -25,22 +25,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout pull/${{ github.event.client_payload.pull_request.number }}
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.client_payload.pull_request.head.sha }}
-          
+
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
-  
+
       - name: Download Lock File
-        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-      
+        run: wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
+
       - name: Generate Cache Key
-        run: | 
+        run: |
           file_hash=$(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
@@ -79,7 +79,7 @@ jobs:
 
             These are the changes made by https://github.com/tardis-sn/tardis/pull/${{ github.event.client_payload.pull_request.number }}, please be careful before merging this pull request.
         id: create-pr
-      
+
       - name: Create pull request regression data
         uses: peter-evans/create-pull-request@v4
         with:
@@ -111,7 +111,7 @@ jobs:
       - name: Post comment (success)
         uses: peter-evans/create-or-update-comment@v2
         with:
-          token:  ${{ secrets.BOT_TOKEN }}
+          token: ${{ secrets.BOT_TOKEN }}
           issue-number: ${{ github.event.client_payload.pull_request.number }}
           comment-id: ${{ steps.fc.outputs.comment-id }}
           edit-mode: replace
@@ -127,13 +127,13 @@ jobs:
         env:
           REFDATA_URL: https://github.com/tardis-sn/tardis-refdata/pulls
           REGDATA_URL: https://github.com/tardis-sn/tardis-regression-data/pulls
-          
+
         if: success()
 
       - name: Post comment (failure)
         uses: peter-evans/create-or-update-comment@v2
         with:
-          token:  ${{ secrets.BOT_TOKEN }}
+          token: ${{ secrets.BOT_TOKEN }}
           issue-number: ${{ github.event.client_payload.pull_request.number }}
           comment-id: ${{ steps.fc.outputs.comment-id }}
           edit-mode: replace