Merge pull request #50 from climbfuji/feature/update_jcsda_emc_spack_…

…stack_from_authoritative_20220404

Update jcsda emc spack stack from authoritative 20220404

.github/ISSUE_TEMPLATE/build_error.yml

@@ -16,19 +16,29 @@ body:
     attributes:
       label: Steps to reproduce the issue
       description: |
-        Fill in the exact spec you are trying to build and the relevant part of the error message
-      placeholder: |
+        Fill in the console output from the exact spec you are trying to build.
+      value: |
         ```console
-        $ spack install <spec>
+        $ spack spec -I <spec>
         ...
         ```
+  - type: textarea
+    id: error
+    attributes:
+      label: Error message
+      description: |
+        Please post the error message from spack inside the `<details>` tag below:
+      value: |
+        <details><summary>Error message</summary><pre>
+        ...
+        </pre></details>
     validations:
       required: true
   - type: textarea
     id: information
     attributes:
       label: Information on your system
-      description: Please include the output of `spack debug report`
+      description: Please include the output of `spack debug report`.
     validations:
       required: true
   - type: markdown

.github/workflows/bootstrap.yml

@@ -31,7 +31,7 @@ jobs:
               bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch unzip which xz python3 python3-devel tree \
               cmake bison bison-devel libstdc++-static
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -61,7 +61,7 @@ jobs:
               bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
               make patch unzip xz-utils python3 python3-dev tree \
               cmake bison
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -90,7 +90,7 @@ jobs:
           apt-get install -y \
               bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
               make patch unzip xz-utils python3 python3-dev tree
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -118,7 +118,7 @@ jobs:
               bzip2 curl file gcc-c++ gcc gcc-fortran tar git gpg2 gzip \
               make patch unzip which xz python3 python3-devel tree \
               cmake bison
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -138,7 +138,7 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake [email protected] tree
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       - name: Bootstrap clingo
         run: |
           source share/spack/setup-env.sh
@@ -157,8 +157,8 @@ jobs:
       - name: Install dependencies
         run: |
           brew install tree
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-      - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+      - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Bootstrap clingo
@@ -174,8 +174,8 @@ jobs:
       matrix:
         python-version: ['2.7', '3.5', '3.6', '3.7', '3.8', '3.9']
     steps:
-      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-      - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+      - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Setup repo and non-root user
@@ -202,7 +202,7 @@ jobs:
           apt-get install -y \
               bzip2 curl file g++ gcc patchelf gfortran git gzip \
               make patch unzip xz-utils python3 python3-dev tree
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -231,7 +231,7 @@ jobs:
               bzip2 curl file g++ gcc patchelf gfortran git gzip \
               make patch unzip xz-utils python3 python3-dev tree \
               gawk
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -256,7 +256,7 @@ jobs:
           brew install tree
           # Remove GnuPG since we want to bootstrap it
           sudo rm -rf /usr/local/bin/gpg
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846
       - name: Bootstrap GnuPG
         run: |
           source share/spack/setup-env.sh
@@ -272,7 +272,7 @@ jobs:
           brew install gawk tree
           # Remove GnuPG since we want to bootstrap it
           sudo rm -rf /usr/local/bin/gpg
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846
       - name: Bootstrap GnuPG
         run: |
           source share/spack/setup-env.sh

.github/workflows/build-containers.yml

@@ -37,7 +37,7 @@ jobs:
     name: Build ${{ matrix.dockerfile[0] }}
     steps:
       - name: Checkout
-        uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+        uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
 
       - name: Set Container Tag Normal (Nightly)
         run: |
@@ -67,21 +67,21 @@ jobs:
         uses: docker/setup-buildx-action@94ab11c41e45d028884a99163086648e898eed25 # @v1
 
       - name: Log in to GitHub Container Registry
-        uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7 # @v1
+        uses: docker/login-action@dd4fa0671be5250ee6f50aedf4cb05514abda2c7 # @v1
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Log in to DockerHub
         if: ${{ github.event_name != 'pull_request' }}
-        uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7 # @v1
+        uses: docker/login-action@dd4fa0671be5250ee6f50aedf4cb05514abda2c7 # @v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build & Deploy ${{ matrix.dockerfile[1] }}
-        uses: docker/build-push-action@7f9d37fa544684fb73bfe4835ed7214c255ce02b # @v2
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a # @v2
         with:
           file: share/spack/docker/${{matrix.dockerfile[1]}}
           platforms: ${{ matrix.dockerfile[2] }}

.github/workflows/execute_installer.ps1

@@ -0,0 +1,7 @@
+$ proc = Start-Process  ${{ env.spack_installer }}\spack.exe "/install /quiet" -Passthru
+$handle = $proc.Handle # cache proc.Handle
+$proc.WaitForExit();
+
+if ($proc.ExitCode -ne 0) {
+    Write-Warning "$_ exited with status code $($proc.ExitCode)"
+}

.github/workflows/macos_python.yml

@@ -24,8 +24,8 @@ jobs:
     name: gcc with clang
     runs-on: macos-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: spack install
@@ -39,8 +39,8 @@ jobs:
     runs-on: macos-latest
     timeout-minutes: 700
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: spack install
@@ -52,8 +52,8 @@ jobs:
     name: scipy, mpl, pd
     runs-on: macos-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: spack install

.github/workflows/setup_git.ps1

@@ -0,0 +1,11 @@
+# (c) 2021 Lawrence Livermore National Laboratory
+
+Set-Location spack
+
+git config --global user.email "[email protected]"
+git config --global user.name "Test User"
+
+if ($(git branch --show-current) -ne "develop")
+{
+    git branch develop origin/develop
+}

.github/workflows/system_shortcut_check.ps1

@@ -0,0 +1,4 @@
+param ($systemFolder, $shortcut)
+
+$start = [System.Environment]::GetFolderPath("$systemFolder")
+Invoke-Item "$start\Programs\Spack\$shortcut"

.github/workflows/unit_tests.yaml

@@ -15,8 +15,8 @@ jobs:
   validate:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: Install Python Packages
@@ -31,10 +31,10 @@ jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: Install Python packages
@@ -57,7 +57,7 @@ jobs:
       packages: ${{ steps.filter.outputs.packages }}
       with_coverage: ${{ steps.coverage.outputs.with_coverage }}
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       if: ${{ github.event_name == 'push' }}
       with:
         fetch-depth: 0
@@ -106,10 +106,10 @@ jobs:
         - python-version: 3.9
           concretizer: original
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install System packages
@@ -127,6 +127,10 @@ jobs:
           if python -c 'import sys; sys.exit(not sys.version_info >= (3, 6))'; then
               pip install --upgrade flake8 isort>=4.3.5 mypy>=0.900 black
           fi
+    - name: Pin pathlib for Python 2.7
+      if: ${{ matrix.python-version == 2.7 }}
+      run: |
+          pip install -U pathlib2==2.3.6
     - name: Setup git configuration
       run: |
           # Need this for the git tests to succeed.
@@ -167,10 +171,10 @@ jobs:
     needs: [ validate, style, changes ]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: Install System packages
@@ -214,7 +218,7 @@ jobs:
           dnf install -y \
               bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
     - name: Setup repo and non-root user
       run: |
           git --version
@@ -233,10 +237,10 @@ jobs:
     needs: [ validate, style, changes ]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: Install System packages
@@ -282,10 +286,10 @@ jobs:
       matrix:
         python-version: [3.8]
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python packages
@@ -327,8 +331,8 @@ jobs:
     needs: [ validate, style, changes ]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # @v2
+    - uses: actions/setup-python@9c644ca2ab8e57ea0a487b5ec2f8290740378bfd # @v2
       with:
         python-version: 3.9
     - name: Install Python packages