Pull in updates from development branch (#10)

Final initial import for release candidate 1 for v1.0.0. Includes libsansmic and sansmic modules. Includes tests and code coverage configuration. Includes sphinx documentation for UM and API docs, though github pages still needs to be configured. --------- Signed-off-by: David Hart <[email protected]>
sandialabs · Sep 14, 2024 · 8dc4f33 · 8dc4f33
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diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -6,19 +6,37 @@ coverage:
         target: auto
         threshold: 5
         base: auto
-        flags:
-          - "unit"
         paths:
           - "src/"
-          - "!tests/"
+          - "tests/"
         # advanced settings
-        # branches:
-        #   - main
+        branches:
+          - main
+          - dev
         if_ci_failed: error #success, failure, error, ignore
         informational: false
         only_pulls: false
-      tests:  # declare a new status context "tests"
-        target: 100%  # we always want 100% coverage here
-        paths:
-          - "tests/"  # only include coverage in "tests/" folder
-        only_pulls: true
+
+comment:
+  layout: "header, diff, components"  # show component info in the PR comment
+
+component_management:
+  default_rules:
+    statuses:
+      - type: project
+        target: auto
+        branches:
+          - "!main"
+  individual_components:
+    - component_id: module_python
+      name: python code
+      paths:
+        - src/python/**
+    - component_id: module_ext
+      name: C++ code
+      paths:
+        - src/ext_modules/**
+    - component_id: module_tests
+      name: tests
+      paths:
+        - tests/**
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,95 @@
+# 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 Advanced"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: '42 21 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: c-cpp
+          build-mode: manual
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        python -m pip install pybind11 setuptools
+        python setup.py build_ext
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
@@ -0,0 +1,82 @@
+name: Continuous Integration
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+
+      - name: Harden Runner
+        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
+        with:
+          egress-policy: audit
+
+      - name: Check out the commit
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ~${{ matrix.version }}
+
+      - name: Install development dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r requirements.txt
+          python3 -m pip install tomli
+
+      - name: Test install
+        run: python3 -m pip install .[tests]
+
+      - name: Test with pytest
+        run: python3 -m pytest --cov=sansmic --cov=tests examples/ tests/
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    #   - name: Check documentation coverage
+    #     run: |
+    #       make coverage
+    #       mv build/coverage/python.txt ../docs-coverage-report-${{ matrix.version }}.txt
+    #     working-directory: ./docs
+
+    #   - name: Archive documentation coverage results
+    #     uses: actions/upload-artifact@v3
+    #     with:
+    #       name: docs-coverage-report-${{ matrix.version }}
+    #       path: docs-coverage-report-${{ matrix.version }}.txt
+
+      - name: Test uninstall
+        run: python3 -m pip uninstall -y my-repository-name
+
+  # commits:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Harden Runner
+  #       uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
+  #       with:
+  #         egress-policy: audit
+
+  #     - name: Conventional Commits
+  #       uses: taskmedia/action-conventional-commits@9148865058f63a6cb560ff4bfd7d534505f43646 # v1.1.3
+  #       with:
+  #         types: >
+  #           build|chore|ci|docs|feat|fix|minor|patch|perf|style|refactor|test
diff --git a/.gitignore b/.gitignore
@@ -167,3 +167,4 @@ _local/
 
 docs/apidocs/pymodule/**
 docs/apidocs/clibrary/**
+DEPLOY.bat
Original file line number	Diff line number	Diff line change
Expand Up		@@ -167,3 +167,4 @@ _local/

		docs/apidocs/pymodule/**
		docs/apidocs/clibrary/**
		DEPLOY.bat