Merge branch 'master' into lossy-compression

Signed-off-by: Greg Sjaardema <[email protected]>
sandialabs · Sep 11, 2024 · 00d68fc · 00d68fc
2 parents 89f1bf1 + 8aa86d2
commit 00d68fc
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Showing 52 changed files with 1,659 additions and 1,116 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: daily
+
+  - package-ecosystem: pip
+    directory: /cmake/tribits/doc/sphinx
+    schedule:
+      interval: daily
+
+  - package-ecosystem: docker
+    directory: /docker/exodus
+    schedule:
+      interval: daily
+
+  - package-ecosystem: docker
+    directory: /docker/seacas
+    schedule:
+      interval: daily
diff --git a/.github/workflows/build_external_lib.yml b/.github/workflows/build_external_lib.yml
@@ -13,6 +13,9 @@ concurrency:
   group: ${{ github.workflow}}-${{ github.head_ref }}  
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
 
   build-deps:
@@ -24,7 +27,12 @@ jobs:
         compiler: [ gnu, clang ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}

diff --git a/.github/workflows/build_netcdf_no_hdf5.yml b/.github/workflows/build_netcdf_no_hdf5.yml
@@ -14,6 +14,9 @@ concurrency:
   group: ${{ github.workflow}}-${{ github.head_ref }}  
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
 
   build-deps:
@@ -26,7 +29,12 @@ jobs:
         netcdf: [ 4.9.2 ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
@@ -37,7 +45,7 @@ jobs:
         ###
       - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.netcdf }}
         id: cache-TPL-mpi
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.netcdf }}
           key: TPL-v5-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.netcdf }}
@@ -84,15 +92,20 @@ jobs:
           }
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
         run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev
 
       - name: Fetch TPL Cache
         id: cache-TPL
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.config.compiler }}-${{ matrix.netcdf }}
           key: TPL-v5-${{ runner.os }}-${{ matrix.config.compiler }}-${{ matrix.netcdf }}

diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml
@@ -12,6 +12,9 @@ concurrency:
   group: ${{ github.workflow}}-${{ github.head_ref }}  
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
 
   build-deps:
@@ -26,7 +29,12 @@ jobs:
         cgns: [ 4.4.0 ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
@@ -37,7 +45,7 @@ jobs:
         ###
       - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         id: cache-TPL
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
           key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
@@ -67,15 +75,20 @@ jobs:
         cgns: [ 4.4.0 ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
         run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev
 
       - name: Fetch TPL Cache
         id: cache-TPL
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
           key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
@@ -88,7 +101,7 @@ jobs:
 # Configure and build
 ###
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: '3.11'
 

diff --git a/.github/workflows/build_variant.yml b/.github/workflows/build_variant.yml
@@ -14,6 +14,9 @@ concurrency:
   group: ${{ github.workflow}}-${{ github.head_ref }}  
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   build-deps:
 
@@ -27,7 +30,12 @@ jobs:
         cgns: [ 4.4.0 ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
@@ -38,7 +46,7 @@ jobs:
         ###
       - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         id: cache-TPL-mpi
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
           key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
@@ -372,15 +380,20 @@ jobs:
           }
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
         run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev libboost-all-dev
 
       - name: Fetch TPL Cache
         id: cache-TPL
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
           key: TPL-v2-${{ runner.os }}-${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}

diff --git a/.github/workflows/cla.yml b/.github/workflows/cla.yml
@@ -14,9 +14,14 @@ jobs:
   CLAAssistant:
     runs-on: ubuntu-latest
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
       - name: "CLA Assistant"
         if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target'
-        uses: contributor-assistant/github-action@v2.3.2
+        uses: contributor-assistant/github-action@f41946747f85d28e9a738f4f38dbcc74b69c7e0e # v2.5.1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # the below token should have repo scope and must be manually added by you in the repository's secret

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,78 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: ["master"]
+  schedule:
+    - cron: "0 0 * * 1"
+
+permissions:
+  contents: read
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ["cpp", "python"]
+        # CodeQL supports [ $supported-codeql-languages ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - name: Checkout repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@4dd16135b69a43b6c8efb853346f8437d92d3c93 # v3.26.6
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@4dd16135b69a43b6c8efb853346f8437d92d3c93 # v3.26.6
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+      #   If the Autobuild fails above, remove it and uncomment the following three lines.
+      #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+      # - run: |
+      #   echo "Run, Build Application using script"
+      #   ./location_of_script_within_repo/buildscript.sh
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@4dd16135b69a43b6c8efb853346f8437d92d3c93 # v3.26.6
+        with:
+          category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/coverity-scan.yml b/.github/workflows/coverity-scan.yml
@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - coverity
+permissions:
+  contents: read
+
 jobs:
 
   build-deps:
@@ -17,7 +20,12 @@ jobs:
         cgns: [ 4.4.0 ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
@@ -28,7 +36,7 @@ jobs:
         ###
       - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         id: cache-TPL
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
           key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
@@ -58,15 +66,20 @@ jobs:
         cgns: [ 4.4.0 ]
     steps:
 
-      - uses: actions/checkout@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@446798f8213ac2e75931c1b0769676d927801858 # v2.10.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Install System dependencies
         shell: bash -l {0}
         run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev
 
       - name: Fetch TPL Cache
         id: cache-TPL
-        uses: actions/cache@v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
           key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}