[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.ci-helpers/get_current_version.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import sys
+
 from setuptools_scm import version_from_scm
 
 version = version_from_scm(".").tag.public

.ci-helpers/get_min_docstr_cov.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+
 from parse import *
 
 input = sys.stdin.readline()

.ci-helpers/get_next_version.py

@@ -2,6 +2,7 @@
 
 import sys
 from datetime import date
+
 from setuptools_scm import version_from_scm
 from setuptools_scm.version import guess_next_date_ver
 

.ci-helpers/update_credits.py

@@ -43,7 +43,7 @@ def generate_zenodo():
         )
 
         not_found_msg = """
-                        Couldn"t retrieve the TARDIS software citation from Zenodo. Get it 
+                        Couldn"t retrieve the TARDIS software citation from Zenodo. Get it
                         directly from `this link <https://zenodo.org/record/{CONCEPT_DOI}>`_    .
                         """
 

.coveragerc

@@ -28,7 +28,7 @@ omit =
 
     tardis/gui/*
     tardis/stats/*
-   
+
 ignore_errors = True
 
 [html]

.github/actions/setup_env/action.yml

@@ -14,14 +14,14 @@ runs:
         run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ inputs.os-label }}.lock
         if: matrix.pip == true
         shell: bash
-      
+
       - name: Generate Cache Key
-        run: | 
+        run: |
           file_hash=$(cat conda-${{ inputs.os-label }}.lock | shasum -a 256 | cut -d' ' -f1)
           echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
         id: cache-environment-key
         shell: bash
-        
+
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: conda-${{ inputs.os-label }}.lock

.github/workflows/archive/update-refdata.yml

@@ -34,7 +34,7 @@ jobs:
 
       - name: Setup environment
         uses: ./.github/actions/setup_env
-        with: 
+        with:
           os-label: linux-64
 
       - name: Install package

.github/workflows/benchmarks.yml

@@ -16,7 +16,7 @@ on:
       - labeled # benchmarks label required
   workflow_dispatch:
 
-env: 
+env:
   DEPLOY_BRANCH: main
 
 concurrency:
@@ -76,8 +76,8 @@ jobs:
         if: github.event_name != 'pull_request_target'
         run: |
           git log -n 4  --pretty=format:"%H" >> tag_commits.txt
-          asv run -a repeat=1 -a rounds=1 HASHFILE:tag_commits.txt | tee asv-output.log  
-          if grep -q failed asv-output.log; then 
+          asv run -a repeat=1 -a rounds=1 HASHFILE:tag_commits.txt | tee asv-output.log
+          if grep -q failed asv-output.log; then
             echo "Some benchmarks have failed!"
             exit 1
           fi
@@ -107,8 +107,8 @@ jobs:
         run: |
           echo $(git rev-parse HEAD) > commit_hashes.txt
           echo $(git rev-parse master) >> commit_hashes.txt
-          asv run -a repeat=2 -a rounds=1 HASHFILE:commit_hashes.txt | tee asv-output-PR.log  
-            if grep -q failed asv-output-PR.log; then 
+          asv run -a repeat=2 -a rounds=1 HASHFILE:commit_hashes.txt | tee asv-output-PR.log
+            if grep -q failed asv-output-PR.log; then
               echo "Some benchmarks have failed!"
               exit 1
             fi
@@ -195,7 +195,7 @@ jobs:
           external_repository: tardis-sn/tardis-benchmarks
           user_name: "TARDIS Bot"
           user_email: "[email protected]"
-      
+
       - name: Find Comment
         if: always() && github.event_name == 'pull_request_target'
         uses: peter-evans/find-comment@v1
@@ -214,10 +214,10 @@ jobs:
           edit-mode: replace
           body: |
             *\*beep\* \*bop\**
-            Hi human, 
-            I ran benchmarks as you asked comparing master (${{ github.event.pull_request.base.sha }}) and the latest commit (${{ github.event.pull_request.head.sha }}). 
+            Hi human,
+            I ran benchmarks as you asked comparing master (${{ github.event.pull_request.base.sha }}) and the latest commit (${{ github.event.pull_request.head.sha }}).
             Here are the logs produced by ASV.
-            Results can also be downloaded as artifacts [**here**](${{ env.URL }}). 
+            Results can also be downloaded as artifacts [**here**](${{ env.URL }}).
 
             Significantly changed benchmarks:
             <details>
@@ -234,7 +234,7 @@ jobs:
               ```diff
               ${{ steps.asv_pr_vs_master.outputs.content }}
               ```
-              
+
             </details>
 
             If you want to see the graph of the results, you can check it [**here**](${{ env.URL_PAGES }})

.github/workflows/build-docs.yml

@@ -90,10 +90,10 @@ jobs:
 
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
-      
+
       - name: Setup environment
         uses: ./.github/actions/setup_env
-        with: 
+        with:
           os-label: linux-64
 
       - name: Copy atom_data

.github/workflows/codestyle.yml

@@ -33,20 +33,20 @@ jobs:
 
       - name: Run Black
         run: black --check tardis
-  ruff: 
+  ruff:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
       - 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
@@ -55,23 +55,23 @@ jobs:
           environment-name: tardis
           cache-environment: true
           cache-downloads: true
-      
+
       - name: Show statistics
         run: ruff check  --statistics  --show-fixes . | tee ruff_stats.txt
         id: ruff_stats
-      
+
       - name: Show entire output
         run: ruff check . --output-format=full | tee ruff_full.txt
         id: ruff_complete
-      
+
       - name: Find Comment
         if: always() && github.event_name == 'pull_request_target'
         uses: peter-evans/find-comment@v1
         id: fc
         with:
           issue-number: ${{ github.event.number }}
           body-includes: I ran ruff on the latest commit
-      
+
       - name: Post comment
         if: github.event_name == 'pull_request_target'
         uses: peter-evans/create-or-update-comment@v2
@@ -82,10 +82,10 @@ jobs:
           edit-mode: replace
           body: |
             *\*beep\* \*bop\**
-            Hi human, 
-            I ran ruff on the latest commit (${{ 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>
 
@@ -101,11 +101,11 @@ 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()
@@ -114,5 +114,3 @@ jobs:
           path: |
             ruff_full.txt
             ruff_stats.txt
-
-            

.github/workflows/post-release.yml

@@ -121,7 +121,7 @@ jobs:
 
             These are the changes required after the latest TARDIS release.
 
-            > :warning: **Warning:** 
+            > :warning: **Warning:**
             >
             > The `post_release` workflow waits for a webhook and then updates the citation files. If the file is not modified by this pull request, please check the latest release on [Zenodo's website](https://zenodo.org/record/592480), close this pull request, and [manually run the workflow](https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow).
             >

.github/workflows/pre-release.yml

@@ -30,14 +30,14 @@ jobs:
       - name: Download Lock File
         run:  wget -q https://raw.githubusercontent.com/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
@@ -95,7 +95,7 @@ jobs:
 
             <br>
 
-            > :warning: **WARNING:** 
+            > :warning: **WARNING:**
             >
             > This pull request should be auto-merged. **Do not merge manually if any check fails**.
             >
@@ -140,7 +140,7 @@ jobs:
 
   compare_refdata:
     uses: tardis-sn/tardis-refdata/.github/workflows/compare-refdata.yml@master
-  
+
   pip_tests:
     uses: ./.github/workflows/tests.yml
     with:

.github/workflows/stardis-tests.yml

@@ -14,7 +14,7 @@ on:
 defaults:
   run:
     shell: bash -l {0}
- 
+
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
 
@@ -34,7 +34,7 @@ jobs:
 
     name: ${{ matrix.label }}
     runs-on: ${{ matrix.os }}
-    steps:     
+    steps:
       - uses: actions/checkout@v4
         with:
           repository: tardis-sn/stardis
@@ -46,29 +46,29 @@ jobs:
           miniforge-version: latest
           activate-environment: stardis
           use-mamba: true
-  
+
       - name: Cache lockfile
         uses: actions/cache@v4
         with:
           path: ${{ matrix.prefix }}
           key: conda-${{ matrix.label }}-${{ hashFiles(format('conda-{0}.lock', matrix.label)) }}-${{ env.CACHE_NUMBER }}
         id: cache-conda
-  
+
       - name: Update Conda Environment
         id: update-env
         run: |
           mamba update -n stardis --file conda-${{ matrix.label }}.lock
         if: steps.cache-conda.outputs.cache-hit != 'true'
-        
+
       - name: Install tardis
         id: install-tardis
         run: |
           pip install git+https://github.com/tardis-sn/tardis.git@${{ github.sha }}
-          
+
       - name: Install stardis
         id: install-stardis
         run: |
           pip install -e .[test]
 
-      - name: Run stardis tests  
-        run: pytest
+      - name: Run stardis tests
+        run: pytest