Merge remote-tracking branch 'upstream/master' into restructure/assem…

…ble_plasma_cleanup

.github/workflows/benchmarks.yml

@@ -14,6 +14,7 @@ on:
       - reopened
       - synchronize
       - labeled # benchmarks label required
+      - ready_for_review
   workflow_dispatch:
 
 env: 
@@ -31,6 +32,7 @@ jobs:
   build:
     if: github.repository_owner == 'tardis-sn' &&
       (github.event_name == 'push' ||
+      (!github.event.pull_request.draft) ||
       github.event_name == 'workflow_dispatch' ||
       (github.event_name == 'pull_request_target' &&
       contains(github.event.pull_request.labels.*.name, 'benchmarks')))
@@ -72,11 +74,11 @@ jobs:
       - name: Accept all asv questions
         run: asv machine --yes
 
-      - name: Run benchmarks for last 5 commits if not PR
+      - name: Run benchmarks for last 4 commits if not PR
         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  
+          asv run -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
@@ -107,17 +109,17 @@ 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  
+          asv run -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
 
       - name: Compare Master and PR head
-        run: asv compare origin/master HEAD --config asv.conf.json | tee asv-compare-output.log
+        run: asv compare origin/master HEAD --factor 1.1 --split --sort ratio | tee asv-compare-output.log
 
       - name: Compare Master and PR head but only show changed results
-        run: asv compare origin/master HEAD --only-changed --config asv.conf.json | tee asv-compare-changed-output.log
+        run: asv compare origin/master HEAD --only-changed --factor 1.1 --split --sort ratio | tee asv-compare-changed-output.log
 
       - name: Benchmarks compare output
         id: asv_pr_vs_master

.github/workflows/build-docs.yml

@@ -18,6 +18,7 @@ on:
       - reopened
       - synchronize
       - labeled # requires the `build-docs` label
+      - ready_for_review
 
   workflow_dispatch: # manual trigger
 
@@ -37,6 +38,7 @@ defaults:
 jobs:
   check-for-changes:
     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 }}

.github/workflows/codestyle.yml

@@ -7,8 +7,7 @@ name: codestyle
 on:
   push:
     branches:
-      - "*"
-
+      - master
   pull_request_target:
     branches:
       - master
@@ -37,6 +36,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Download Lock File
         run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
@@ -57,12 +58,22 @@ jobs:
           cache-downloads: true
 
       - name: Show statistics
-        run: ruff check  --statistics  --show-fixes . | tee ruff_stats.txt
-        id: ruff_stats
+        run: ruff check  --statistics  --show-fixes $(git --no-pager diff --name-only ${{ github.event.pull_request.base.sha }}  ${{ github.event.pull_request.head.sha }} --) | tee ruff_stats.txt
 
       - name: Show entire output
-        run: ruff check . --output-format=full | tee ruff_full.txt
-        id: ruff_complete
+        run: ruff check --output-format=concise $(git --no-pager diff --name-only ${{ github.event.pull_request.base.sha }}  ${{ github.event.pull_request.head.sha }} --) | tee ruff_full.txt
+
+      - name: Statistics output read
+        id: ruff_stats
+        uses: juliangruber/[email protected]
+        with:
+          path: ruff_stats.txt
+
+      - name: Entire output read
+        id: ruff_complete 
+        uses: juliangruber/[email protected]
+        with:
+          path: ruff_full.txt
 
       - name: Find Comment
         if: always() && github.event_name == 'pull_request_target'

.github/workflows/pre-release.yml

@@ -143,5 +143,6 @@ jobs:
 
   pip_tests:
     uses: ./.github/workflows/tests.yml
+    secrets: inherit
     with:
       pip_git: true

.github/workflows/stardis-tests.yml

@@ -3,12 +3,17 @@ name: stardis-tests
 on:
   push:
     branches:
-    - '*'
+    - master
 
   pull_request:
     branches:
     - '*'
 
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
   workflow_dispatch:
 
 defaults:
@@ -22,18 +27,15 @@ jobs:
   build:
     strategy:
       matrix:
-        label: [osx-64, linux-64]
+        label: [linux-64]
         include:
           - os: ubuntu-latest
             label: linux-64
             prefix: /usr/share/miniconda3/envs/stardis
 
-          - os: macos-latest
-            label: osx-64
-            prefix: /Users/runner/miniconda3/envs/stardis
-
     name: ${{ matrix.label }}
     runs-on: ${{ matrix.os }}
+    if: ${{ !github.event.pull_request.draft }}
     steps:     
       - uses: actions/checkout@v4
         with:

.zenodo.json

@@ -154,17 +154,20 @@
       "name": "Holas, Alexander"
     },
     {
-      "name": "Reinecke, Martin"
+      "name": "Eweis, Youssef"
     },
     {
-      "name": "Eweis, Youssef"
+      "name": "Reinecke, Martin"
     },
     {
       "name": "Bylund, Tomas"
     },
     {
       "name": "Black, William"
     },
+    {
+      "name": "Gupta, Sumit"
+    },
     {
       "name": "Bentil, Laud"
     },
@@ -176,41 +179,38 @@
       "name": "Kumar, Ansh"
     },
     {
-      "name": "Gupta, Sumit"
+      "name": "Alam, Arib"
     },
     {
-      "name": "Alam, Arib"
+      "name": "Kumar, Asish"
     },
     {
       "name": "Bartnik, Matthew"
     },
     {
-      "name": "Varma Buddaraju, Rohith"
+      "name": "Magee, Mark"
     },
     {
-      "name": "Magee, Mark"
+      "name": "Dutta, Anirban"
     },
     {
-      "name": "Lu, Jing"
+      "name": "Varma Buddaraju, Rohith"
     },
     {
-      "name": "Visser, Erin"
+      "name": "Livneh, Ran"
     },
     {
-      "name": "Dutta, Anirban"
+      "name": "Lu, Jing"
     },
     {
-      "name": "Kumar, Asish"
+      "name": "Visser, Erin"
     },
     {
       "name": "Daksh, Ayushi"
     },
     {
       "name": "Kambham, Satwik"
     },
-    {
-      "name": "Livneh, Ran"
-    },
     {
       "name": "Bhakar, Jayant"
     },
@@ -228,49 +228,49 @@
       "name": "Srivastava, Sarthak"
     },
     {
-      "name": "Actions, GitHub"
+      "name": "Reichenbach, John"
     },
     {
       "name": "Jain, Rinkle"
     },
     {
-      "name": "Reichenbach, John"
+      "name": "Floers, Andreas"
     },
     {
-      "name": "Floers, Andreas"
+      "name": "Actions, GitHub"
     },
     {
-      "name": "Gupta, Harshul"
+      "name": "Chaumal, Aarya"
     },
     {
-      "name": "Brar, Antreev"
+      "name": "Gupta, Harshul"
     },
     {
-      "name": "Chaumal, Aarya"
+      "name": "Brar, Antreev"
     },
     {
       "name": "Singh, Sourav"
     },
     {
-      "name": "Selsing, Jonatan"
+      "name": "Kumar, Aman"
     },
     {
-      "name": "Matsumura, Yuki"
+      "name": "Sofiatti, Caroline"
     },
     {
       "name": "Kowalski, Nathan"
     },
     {
-      "name": "Sofiatti, Caroline"
+      "name": "Selsing, Jonatan"
     },
     {
-      "name": "Patidar, Abhishek"
+      "name": "Talegaonkar, Chinmay"
     },
     {
-      "name": "Kumar, Aman"
+      "name": "Matsumura, Yuki"
     },
     {
-      "name": "Talegaonkar, Chinmay"
+      "name": "Patidar, Abhishek"
     },
     {
       "name": "Venkat, Shashank"
@@ -339,10 +339,10 @@
       "name": "PATIDAR, ABHISHEK"
     },
     {
-      "name": "Kharkar, Atharwa"
+      "name": "Nayak U, Ashwin"
     },
     {
-      "name": "Nayak U, Ashwin"
+      "name": "Kharkar, Atharwa"
     },
     {
       "name": "Kumar, Atul"