[WIP] Update of Perlmutter build script

.github/pull_request_template.md

@@ -1,15 +1,28 @@
-Please review the [developer documentation](https://github.com/QMCPACK/qmcpack/wiki/Development-workflow)
-on the wiki of this project that contains help and requirements.
+<!--
+Please review the developer documentation on the wiki of this project that contains help and requirements.
 
-Please also follow the [GitHub Pull Request guidance](https://qmcpack.readthedocs.io/en/develop/developing.html#github-pull-request-guidance). As much as possible, try to avoid the ["Don't"s](https://qmcpack.readthedocs.io/en/develop/developing.html#don-t) to help maintain a high development velocity.
+https://github.com/QMCPACK/qmcpack/wiki/Development-workflow
 
-## Proposed changes
+Please also follow the GitHub Pull Request guidance.
+
+https://qmcpack.readthedocs.io/en/develop/developing.html#github-pull-request-guidance
 
+As much as possible, try to avoid the "Don't"s to help maintain a high development velocity.
+
+https://qmcpack.readthedocs.io/en/develop/developing.html#don-t
+-->
+## Proposed changes
+<!--
 Describe what this PR changes and why.  If it closes an issue, link to it here
-with [a supported keyword](https://help.github.com/en/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword).
+with a supported keyword.
+
+https://help.github.com/en/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword
+-->
+
+
 
 ## What type(s) of changes does this code introduce?
-_Delete the items that do not apply_
+<!-- Delete the items that do not apply -->
 
 - Bugfix
 - New feature
@@ -21,16 +34,29 @@ _Delete the items that do not apply_
 - Other (please describe):
 
 ### Does this introduce a breaking change?
-
+<!-- Delete one. If you are unsure, you can put "Maybe" or "Possibly" -->
 - Yes
 - No
 
 ## What systems has this change been tested on?
+<!--
+You can be brief here, but it is strongly recommended to provide some information.
 
-## Checklist
+For example, if you are changing code in Nexus, list at least the following:
+
+- Python w/ version (run `python --version`)
+- NumPy w/ version (run `python -c "import numpy; print(numpy.__version__)"`)
+- Pytest w/ version (run `pytest --version`)
+-->
 
-_Update the following with an [x] where the items apply. If you're unsure about any of them, don't hesitate to ask.  This is
-simply a reminder of what we are going to look for before merging your code._
+
+
+## Checklist
+<!--
+Update the following with an [x] where the items apply.
+If you're unsure about any of them, don't hesitate to ask. 
+This is simply a reminder of what we are going to look for before merging your code.
+-->
 
 * * [ ] I have read the pull request guidance and develop docs
 * * [ ] This PR is up to date with the current state of 'develop'

.github/workflows/ci-github-actions-nexus.yaml

@@ -21,28 +21,30 @@ jobs:
 
     steps:
     - name: Checkout Action
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Setup Graphviz
       run: sudo apt-get install graphviz
 
     - name: Install uv and Setup Python ${{ matrix.python-version }}
-      uses: astral-sh/setup-uv@v7
+      uses: astral-sh/setup-uv@v8.3.0
       with:
-        version: "0.11.6"
+        version: "0.11.26"
         python-version: ${{ matrix.python-version }}
 
     - name: Install Project and All Dependencies
       run: uv sync --locked --all-extras --dev
       working-directory: ./nexus
 
-    - name: Use Numpy 1.22.0 (Python 3.10 only)
+    - name: Downgrade to Minimum Versions (Python 3.10 only)
       if: contains(matrix.python-version, '3.10')
-      run: uv pip install numpy==1.22.0
+      run: uv pip install numpy==1.22.0 scipy==1.8.0 h5py==3.6.0 matplotlib==3.3.0 spglib==1.16.0 cif2cell==2.1.0 pydot==2.0.0 seekpath==2.0.0
       working-directory: ./nexus
 
     - name: Run Nexus Tests
-      run: uv run pytest nexus/tests/
+      run: |
+        source .venv/bin/activate
+        pytest nexus/tests/
       working-directory: ./nexus
 
   macos:
@@ -54,26 +56,28 @@ jobs:
 
     steps:
     - name: Checkout Action
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Setup Graphviz
       run: brew install graphviz
 
     - name: Install uv and Setup Python ${{ matrix.python-version }}
-      uses: astral-sh/setup-uv@v7
+      uses: astral-sh/setup-uv@v8.3.0
       with:
-        version: "0.11.6"
+        version: "0.11.26"
         python-version: ${{ matrix.python-version }}
 
     - name: Install Project and All Dependencies
       run: uv sync --locked --all-extras --dev
       working-directory: ./nexus
 
-    - name: Use Numpy 1.22.0 (Python 3.10 only)
+    - name: Downgrade to Minimum Versions (Python 3.10 only)
       if: contains(matrix.python-version, '3.10')
-      run: uv pip install numpy==1.22.0
+      run: uv pip install numpy==1.22.0 scipy==1.8.0 spglib==1.16.0 cif2cell==2.1.0 pydot==2.0.0 seekpath==2.0.0 matplotlib==3.8.4
       working-directory: ./nexus
 
     - name: Run Nexus Tests
-      run: uv run pytest nexus/tests/
+      run: |
+        source .venv/bin/activate
+        pytest nexus/tests/
       working-directory: ./nexus

.github/workflows/ci-github-actions-self-hosted.yaml

@@ -71,7 +71,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
@@ -170,7 +170,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
@@ -266,7 +266,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
@@ -362,7 +362,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}

.github/workflows/ci-github-actions-static.yaml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Configure
         run: tests/test_automation/github-actions/ci/run_step_static.sh configure

.github/workflows/ci-github-actions.yaml

@@ -36,6 +36,7 @@ jobs:
             Clang14-NoMPI-ASan-Real,
             Clang14-NoMPI-ASan-Complex,
             Clang14-NoMPI-UBSan-Real,
+            Clang14-NoMPI-Sandbox-ASan-Real,
             Clang16-NoMPI-Offload-Real,
             Clang16-NoMPI-Offload-Complex,
           ]
@@ -105,6 +106,11 @@ jobs:
               image: ghcr.io/qmcpack/ubuntu22-openmpi:latest
               options: -u 1001
 
+          - jobname: Clang14-NoMPI-Sandbox-ASan-Real
+            container:
+              image: ghcr.io/qmcpack/ubuntu22-openmpi:latest
+              options: -u 1001
+
           - jobname: Clang14-NoMPI-UBSan-Real
             container:
               image: ghcr.io/qmcpack/ubuntu22-openmpi:latest
@@ -122,7 +128,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Configure
         run: tests/test_automation/github-actions/ci/run_step.sh configure
@@ -149,19 +155,19 @@ jobs:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   macos:
-    runs-on: macos-14
+    runs-on: macos-26
     env:
       GH_JOBNAME: ${{ matrix.jobname }}
       GH_OS: macOS
 
     strategy:
       fail-fast: false
       matrix:
-        jobname: [macOS-GCC14-NoMPI-Real]
+        jobname: [macOS-GCC16-NoMPI-Real]
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Set Python Version
         uses: actions/setup-python@v6
@@ -171,7 +177,7 @@ jobs:
       - name: Setup Dependencies
         run: |
           brew upgrade || brew link --overwrite [email protected]
-          brew install gcc@14 ninja hdf5 fftw boost
+          brew install gcc@16 ninja hdf5 fftw boost
           python3 -m pip install numpy h5py pytest pytest-cov pytest-order
 
       - name: Configure
@@ -223,7 +229,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Echo Debug
         run: |

.github/workflows/close-inactive-issues-prs.yaml

@@ -0,0 +1,30 @@
+name: Close inactive issues
+on:
+  schedule:
+    - cron: "45 13 * * 3"
+      timezone: "America/New_York"
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    env:
+      stale-issue-time: 365 # 1 year
+      stale-pr-time: 365 # 1 year
+      close-time: 28   # 4 weeks
+    steps:
+      - uses: actions/[email protected]
+        with:
+          operations-per-run: 10
+          days-before-issue-stale: ${{ env.stale-issue-time }}
+          days-before-issue-close: ${{ env.close-time }}
+          stale-issue-label: "stale"
+          stale-issue-message: "This issue is stale because it has been open for ${{ env.stale-issue-time }} days with no activity. It will be closed in ${{ env.close-time }} days if there is no fresh activity. Please comment within ${{ env.close-time }} days if this issue is still important to you and it should be kept open."
+          close-issue-message: "This issue was closed because it has been inactive for ${{ env.close-time }} days since being marked as stale."
+          days-before-pr-stale: ${{ env.stale-pr-time }}
+          days-before-pr-close: ${{ env.close-time }}
+          stale-pr-label: "stale"
+          stale-pr-message: "This pull request is stale because it has been open for ${{ env.stale-pr-time }} days with no activity. It will be closed in ${{ env.close-time }} days if there is no fresh activity. Please comment within ${{ env.close-time }} days if this pull request is still important to you and it should be kept open."
+          close-pr-message: "This pull request was closed because it has been inactive for ${{ env.close-time }} days since being marked as stale."
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ghcr-develop.yaml

@@ -19,7 +19,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-centos10.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu22-clang.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu22-openmpi.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu22-serial.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu24-openmpi.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4