Merge branch 'main' into hexPitch

.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-22.04
-        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:
@@ -10,9 +13,15 @@ on:
     paths-ignore:
       - 'doc/**'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    # 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 }}
       COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
@@ -24,16 +33,19 @@ jobs:
           python-version: '3.11'
       - name: Update package index
         run: sudo apt-get update
-      - name: Install mpi libs
-        run: sudo apt-get -y install libopenmpi-dev
-      - name: Install Tox and any other packages
-        run: pip install tox
-      - name: Run Coverage Part 1
-        run: tox -e cov1
-      - name: Run Coverage Part 2
-        run: tox -e cov2 || true
+      - name: Install ARMI and MPI
+        run: |
+          sudo apt-get -y install libopenmpi-dev
+          pip install -e .[memprof,mpi,test]
+      - name: Run Coverage
+        run: |
+          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
       - 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

@@ -5,9 +5,14 @@ on:
     branches:
       - main
 
+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:
@@ -22,14 +27,17 @@ jobs:
         run: sudo apt-get -y install libopenmpi-dev
       - name: Install Pandoc
         run: sudo apt-get -y install pandoc
-      - name: Install Tox and any other packages
-        run: pip install tox
       - name: Setup Graphviz
-        uses: ts-graphviz/setup-graphviz@v1
+        uses: ts-graphviz/setup-graphviz@v2.0.2
       - name: Make HTML Docs
-        run: tox -e doc
+        run: |
+          pip install -e .[memprof,mpi,test,docs]
+          cd doc
+          git submodule init
+          git submodule update
+          make html
       - name: deploy
-        uses: JamesIves/github-pages-deploy-action@4.1.5
+        uses: JamesIves/github-pages-deploy-action@v4.6.1
         with:
           token: ${{ secrets.ACCESS_TOKEN }}
           repository-name: ${{ github.repository_owner }}/terrapower.github.io

.github/workflows/find_test_crumbs.py

@@ -26,6 +26,8 @@
     "armi/logs/armiRun.mpi.log",
     "armi/tests/tutorials/case-suite/",
     "armi/tests/tutorials/logs/",
+    "armiRun.h5",
+    "logs/",
 ]
 
 

.github/workflows/licensechecker.yaml

@@ -1,8 +1,13 @@
 name: Check License Lines
+
+permissions:
+  contents: read
+
 on: [push, pull_request]
+
 jobs:
   check-license-lines:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
     - uses: actions/checkout@master
     - name: Check License Lines

.github/workflows/linting.yaml

@@ -1,11 +1,14 @@
 name: Linting
 
+permissions:
+  contents: read
+
 on: [push, pull_request]
 
 jobs:
   build:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v2
@@ -15,7 +18,7 @@ jobs:
           python-version: '3.9'
       - name: Update package index
         run: sudo apt-get update
-      - name: Install Tox and any other packages
-        run: pip install tox
       - name: Run Linter
-        run: tox -e lint
+        run:  |
+          pip install -e .[test]
+          ruff check .

.github/workflows/mac_tests.yaml

@@ -0,0 +1,37 @@
+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:
+
+    runs-on: macos-14
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.11'
+      - name: Upgrade PIP
+        run: python -m pip install --upgrade pip
+      - name: Run Unit Tests on MacOS
+        run: |
+          brew install openmpi
+          pip install -e .[memprof,mpi,test]
+          pytest -n 4 armi

.github/workflows/stale.yaml

@@ -0,0 +1,27 @@
+# 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:
+    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:
@@ -8,13 +11,17 @@ on:
     paths-ignore:
       - 'doc/**'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python: [3.9, '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v2
@@ -26,7 +33,10 @@ jobs:
         run: sudo apt-get update
       - name: Install mpi libs
         run: sudo apt-get -y install libopenmpi-dev
-      - name: Install Tox and any other packages
-        run: pip install tox
-      - name: Run Tox
-        run: tox -e test,mpitest
+      - name: Run Tests
+        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 coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --ignore=venv armi/utils/tests/test_directoryChangersMpi.py || true

.github/workflows/validatemanifest.yaml

@@ -1,19 +1,22 @@
 name: Validate Manifest
 
+permissions:
+  contents: read
+
 on: [push, pull_request]
 
 jobs:
   build:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v2
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
           python-version: '3.11'
-      - name: Install Tox and any other packages
-        run: pip install tox
-      - name: Run Tox
-        run: tox -e manifest
+      - name: Validate Manifest
+        run: |
+          pip install toml
+          python .github/workflows/validatemanifest.py

.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:
 
@@ -21,9 +30,10 @@ jobs:
           python-version: '3.11'
       - name: Upgrade PIP
         run: python -m pip install --upgrade pip
-      - name: Install deps
-        run: python -m pip install tox tox-gh-actions
-      - name: Run Tox
-        run: tox -e test
+      - name: Run Unit Tests on Windows
+        run: |
+          pip install mpi4py==3.1.6
+          pip install -e .[memprof,mpi,test]
+          pytest -n 4 armi
       - name: Find Test Crumbs
         run: python .github/workflows/find_test_crumbs.py