Merge branch 'v1.4.x' into test_under_slurm

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 100
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 100
+    groups:
+      actions-dependencies:
+        patterns:
+          - "*"

.github/workflows/CodeQL.yml

@@ -0,0 +1,48 @@
+name: CodeQL
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: 0 7 1 * *
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: /language:${{matrix.language}}
+
+  # Use this job for branch protection rules
+  report-codeql-status:
+    name: Report CodeQL Status
+    if: always()
+    needs: analyze
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check build status
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

.github/workflows/PackagePublish.yml

@@ -31,6 +31,12 @@ jobs:
             environment: publish-pypi
 
     steps:
+<<<<<<< HEAD
+=======
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+>>>>>>> v0.4.x
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
@@ -41,6 +47,7 @@ jobs:
         with:
           virtualenvs-create: false
 
+<<<<<<< HEAD
       - name: Checkout source
         uses: actions/checkout@v3
 
@@ -50,14 +57,26 @@ jobs:
         run: |
           release_tag=${{github.ref}}
           poetry version "${release_tag:11}"
+=======
+      # Get the new package version from the release tag
+      # Git release tags are expected to start with "refs/tags/v"
+      - name: Set package version
+        run: |
+          release_tag=${{github.ref}}
+          poetry version "${release_tag#refs/tags/v}"
+>>>>>>> v0.4.x
 
       - name: Build package
         run: poetry build -v
 
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
+<<<<<<< HEAD
           verbose: true
+=======
+          print-hash: true
+>>>>>>> v0.4.x
           repository-url: ${{ matrix.host }}
           user: ${{ secrets.REPO_USER }}
           password: ${{ secrets.REPO_PASSWORD }}

.github/workflows/PackageTest.yml

@@ -4,6 +4,11 @@ on:
   workflow_dispatch:
   workflow_call:
   push:
+<<<<<<< HEAD
+=======
+  schedule:
+    - cron: 0 7 1,15 * *
+>>>>>>> v0.4.x
 
 jobs:
   run-tests:
@@ -12,6 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+<<<<<<< HEAD
         slurm_version:
           - 20.02.5.1
           - 20.11.9.1
@@ -37,6 +43,23 @@ jobs:
         run: |
           pip install poetry
           poetry env use python${{ matrix.python_version }}
+=======
+        python-version: [ "3.8", "3.9", "3.10", "3.11" ]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: false
+>>>>>>> v0.4.x
 
       - name: Install dependencies
         run: poetry install --with tests
@@ -50,7 +73,10 @@ jobs:
       # Report partial coverage results to codacy for the current python version
       - name: Report partial coverage results
         if: github.event_name != 'release'
+<<<<<<< HEAD
         shell: bash
+=======
+>>>>>>> v0.4.x
         run: bash <(curl -Ls https://coverage.codacy.com/get.sh) report --partial -l Python -r coverage.xml
         env:
           CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
@@ -63,7 +89,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Finish reporting coverage
+<<<<<<< HEAD
         shell: bash
+=======
+>>>>>>> v0.4.x
         run: bash <(curl -Ls https://coverage.codacy.com/get.sh) final
         env:
           CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}

pyproject.toml

@@ -3,7 +3,10 @@ requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
-name = "shinigami"
+name = "crc-shinigami"
+packages = [
+    { include = "shinigami" },
+]
 version = "0.0.0"  # Version is set dynamically by the CI tool on publication
 authors = ["Pitt Center for Research Computing"]
 readme = "README.md"
@@ -28,7 +31,7 @@ shinigami = "shinigami.cli:Application.execute"
 python = ">=3.8"
 pydantic = "^2.0.3"
 pydantic-settings = "^2.0.2"
-asyncssh = {extras = ["bcrypt", "fido2"], version = "^2.13.2"}
+asyncssh = { extras = ["bcrypt", "fido2"], version = "^2.13.2" }
 pandas = "1.5.3"  # Newer versions are incompatible with Python 3.8
 
 [tool.poetry.group.tests]

shinigami/__init__.py

@@ -10,7 +10,7 @@
 import importlib.metadata
 
 try:
-    __version__ = importlib.metadata.version('shinigami')
+    __version__ = importlib.metadata.version('crc-shinigami')
 
 except importlib.metadata.PackageNotFoundError:  # pragma: no cover
     __version__ = '0.0.0'