Merge branch 'main' into customIsotopicsStrawman

.github/workflows/black.yaml

@@ -2,17 +2,20 @@ name: black
 
 on: [push, pull_request]
 
+permissions:
+  contents: read
+
 # use workaround due to: https://github.com/psf/black/issues/2079#issuecomment-812359146
 jobs:
-    check-formatting:
-        runs-on: ubuntu-24.04
-        steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python 3.11
-              uses: actions/setup-python@v2
-              with:
-                python-version: '3.11'
-            - name: Install Black
-              run: pip install 'black==22.6.0'
-            - name: Run black --check .
-              run: black --check .
+  check-formatting:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.11'
+      - name: Install Black
+        run: pip install 'black==22.6.0'
+      - name: Run black --check .
+        run: black --check .

.github/workflows/coverage.yaml

@@ -1,5 +1,8 @@
 name: Coverage
 
+permissions:
+  contents: read
+
 on:
   push:
     branches:
@@ -10,8 +13,14 @@ on:
     paths-ignore:
       - 'doc/**'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
+    # Deploying coverage to coveralls.io should not happen on forks
+    if: github.repository == 'terrapower/armi'
     runs-on: ubuntu-24.04
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -33,9 +42,11 @@ jobs:
           coverage run --rcfile=pyproject.toml -m pytest -n 4 --cov=armi --cov-config=pyproject.toml --cov-report=lcov --ignore=venv armi
           mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --cov-report=lcov --cov-append --ignore=venv armi/tests/test_mpiFeatures.py || true
           mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --cov-report=lcov --cov-append --ignore=venv armi/tests/test_mpiParameters.py || true
+          mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --cov-report=lcov --cov-append --ignore=venv armi/tests/test_mpiDirectoryChangers.py || true
           coverage combine --rcfile=pyproject.toml --keep -a
+          coverage report --rcfile=pyproject.toml -i --skip-empty --skip-covered --sort=cover --fail-under=90
       - name: Publish to coveralls.io
-        uses: coverallsapp/github-action@v1.1.2
+        uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: coverage.lcov
+          file: coverage.lcov

.github/workflows/docs.yaml

@@ -4,10 +4,16 @@ on:
   push:
     branches:
       - main
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build:
-
+    # Building and deploying docs is broken on forked repos
+    if: github.repository == 'terrapower/armi'
     runs-on: ubuntu-22.04
 
     steps:
@@ -32,10 +38,18 @@ jobs:
           git submodule update
           make html
       - name: deploy
+        if: github.ref == 'refs/heads/main'
         uses: JamesIves/[email protected]
         with:
           token: ${{ secrets.ACCESS_TOKEN }}
           repository-name: ${{ github.repository_owner }}/terrapower.github.io
           branch: main
           folder: doc/_build/html
           target-folder: armi
+      - name: Archive Docs from PR
+        if: github.ref != 'refs/heads/main'
+        uses: actions/upload-artifact@v4
+        with:
+          name: pr-docs
+          path: doc/_build/html
+          retention-days: 5

.github/workflows/licensechecker.yaml

@@ -1,5 +1,10 @@
 name: Check License Lines
+
+permissions:
+  contents: read
+
 on: [push, pull_request]
+
 jobs:
   check-license-lines:
     runs-on: ubuntu-24.04

.github/workflows/linting.yaml

@@ -1,5 +1,8 @@
 name: Linting
 
+permissions:
+  contents: read
+
 on: [push, pull_request]
 
 jobs:

.github/workflows/mac_tests.yaml

@@ -1,13 +1,22 @@
 name: ARMI MacOS Tests
 
+permissions:
+  contents: read
+
 on:
   push:
+    branches:
+      - main
     paths-ignore:
       - 'doc/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 

.github/workflows/stale.yaml

@@ -0,0 +1,29 @@
+# This workflow warns and then closes PRs that have had no activity for a specified amount of time.
+#
+# You can adjust the behavior by modifying this file.
+# For more information, see: https://github.com/actions/stale
+name: Mark Stale PRs
+
+on:
+  schedule:
+  # once a day at 3:14 AM
+  - cron: '14 3 * * *'
+
+permissions:
+  pull-requests: write
+
+jobs:
+  stale:
+    # This workflow is not designed to make sense on forks
+    if: github.repository == 'terrapower/armi'
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/stale@v8
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          stale-pr-message: "This pull request has been automatically marked as stale because it has not had any activity in the last 100 days. It will be closed in 7 days if no further activity occurs. Thank you for your contributions."
+          stale-pr-label: "stale"
+          days-before-pr-stale: 100
+          days-before-pr-close: 7
+          days-before-issue-stale: -1
+          operations-per-run: 100

.github/workflows/unittests.yaml

@@ -1,5 +1,8 @@
 name: ARMI unit tests
 
+permissions:
+  contents: read
+
 on:
   push:
     paths-ignore:
@@ -8,20 +11,25 @@ on:
     paths-ignore:
       - 'doc/**'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 
     runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python: [3.9, '3.10', '3.11']
+        python: [3.9, '3.10', '3.11', '3.12', '3.13']
 
     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: ${{ matrix.python }}
+          allow-prereleases: true
       - name: Update package index
         run: sudo apt-get update
       - name: Install mpi libs
@@ -30,5 +38,6 @@ jobs:
         run: |
           pip install -e .[memprof,mpi,test]
           pytest -n 4 armi
-          mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --ignore=venv armi/tests/test_mpiFeatures.py || true
-          mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --ignore=venv armi/tests/test_mpiParameters.py || true
+          mpiexec -n 2 --use-hwthread-cpus pytest armi/tests/test_mpiFeatures.py
+          mpiexec -n 2 --use-hwthread-cpus pytest armi/tests/test_mpiParameters.py
+          mpiexec -n 2 --use-hwthread-cpus pytest armi/utils/tests/test_directoryChangersMpi.py

.github/workflows/validatemanifest.yaml

@@ -1,5 +1,8 @@
 name: Validate Manifest
 
+permissions:
+  contents: read
+
 on: [push, pull_request]
 
 jobs:

.github/workflows/wintests.yaml

@@ -1,13 +1,22 @@
 name: ARMI Windows tests
 
+permissions:
+  contents: read
+
 on:
   push:
+    branches:
+      - main
     paths-ignore:
       - 'doc/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 

.gitignore

@@ -1,81 +1,81 @@
-# No non-source python resources.
+# No non-source python resources
 *.pyc
-*.pyo
 *.pyd
+*.pyo
 *.pyx
 
 # No build artifacts
-build
-wheelhouse
-*.lib
 *.dll
-bin/*
+*.lib
+.apidocs/
 /bin
-dist/
+armi/tests/tutorials/case-suite
+bin/*
+build
+coverage.lcov
+coverage.xml
+coverage_results.*
 dist-*/
+dist/
 doc/_build
-doc/user/tutorials
-doc/tutorials/anl-afci-177*
-doc/tutorials/case-suite
-armi/tests/tutorials/case-suite
-.apidocs/
+doc/anl-afci-177
 doc/gallery
 doc/gallery-src/framework/*.yaml
-.coverage
-coverage.xml
-coverage.lcov
-coverage_results.*
+doc/tutorials/anl-afci-177*
+doc/tutorials/case-suite
+doc/user/tutorials
 htmlcov/
 monkeytype.*
+wheelhouse
 
-# No workspace crumbs.
-*~
-.*.swp
-.settings
-.vscode
-.project
-.metadata
-.idea/
-.pydevproject
+# No workspace crumbs
+**/.coverage*
+**/__pycache__
+**/logs/*
+*.ascii
+*.egg-info/
 *.sublime-project
 *.sublime-workspace
-*.egg-info/
-phabricator-lint.txt
-temp-*
-tags
 *.temp
-.externalToolBuilders/
+*~
+.*.swp
 .cache/
+.coverage
+.DS_Store
+.externalToolBuilders/
+.hypothesis/
+.idea/
+.ipynb_checkpoints
+.metadata
+.mypy_cache/
+.project
+.pydevproject
 .pytest_cache/
-pytestdebug.log
-dump-temp-*
-dump-tests*
+.ruff_cache/
+.settings
+.tox
 .vim-bookmarks
+.vscode
 armi-venv/*
+dump-temp-*
+dump-tests*
+phabricator-lint.txt
+pytestdebug.log
+reportsOutputFiles/
+tags
+temp-*
 venv*/
-.mypy_cache/
-**/__pycache__
-**/.coverage*
-**/logs/*
-*.ascii
 
-# Misc. exclusions
-*.html
-*.diff
+# Ignore common data files
 *.avi
-*.ppm
-*.mp4
+*.diff
 *.h5
+*.html
+*.mp4
+*.ppm
 *.txt
 
-# metadata file specific to MacOS
-.DS_Store
-
 # vis files
-*.vtu
 *.vtd
+*.vtu
 *.xdmf
-
-# fixtures
-.ipynb_checkpoints
-.tox