Merge remote-tracking branch 'origin/dev' into ipynb-benchmarking

.github/workflows/codeql.yml

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+# 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:
+ pull_request:
+ # The branches below must be a subset of the branches above
+ branches: [ "master", "dev", "release/*" ]
+
+jobs:
+ code_ql:
+ name: CodeQL Analysis
+ runs-on: ubuntu-latest
+ permissions:
+ actions: read
+ contents: read
+ security-events: write
+
+ strategy:
+ fail-fast: false
+ matrix:
+ language: [ 'python' ]
+ # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+ # Use only 'java' to analyze code written in Java, Kotlin or both
+ # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+ # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@v3
+
+ # Initializes the CodeQL tools for scanning.
+ - name: Initialize CodeQL
+ uses: github/codeql-action/init@v2
+ with:
+ languages: ${{ matrix.language }}
+ # If you wish to specify custom queries, you can do so here or in a config file.
+ # By default, queries listed here will override any specified in a config file.
+ # Prefix the list here with "+" to use these queries and those in the config file.
+
+ # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+ # queries: security-extended,security-and-quality
+
+
+ # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java).
+ # If this step fails, then you should remove it and run the build manually (see below)
+ # - name: Autobuild
+ # uses: github/codeql-action/autobuild@v2
+
+ # ℹ️ Command-line programs to run using the OS shell.
+ # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+ # If the Autobuild fails above, remove it and uncomment the following three lines.
+ # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+ # - run: |
+ # echo "Run, Build Application using script"
+ # ./location_of_script_within_repo/buildscript.sh
+
+ - name: Perform CodeQL Analysis
+ uses: github/codeql-action/analyze@v2
+ with:
+ category: "/language:${{matrix.language}}"

.github/workflows/coverage.yml

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+name: Coverage
+
+on:
+ push:
+ pull_request:
+ paths:
+ - prog_models
+
+jobs:
+ coverage:
+ timeout-minutes: 30
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: ['3.10']
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies cache
+ uses: actions/cache@v2
+ with:
+ path: ~/.cache/pip
+ key: pip-cache
+ - name: Install additional dependencies
+ run: |
+ pip install coverage
+ pip install importlib_metadata
+ - name: Update
+ run: pip install --upgrade --upgrade-strategy eager -e .
+ - name: Run coverage
+ run: |
+ coverage run -m tests.test_base_models
+ coverage run -a -m tests.test_battery
+ coverage run -a -m tests.test_calc_error
+ coverage run -a -m tests.test_centrifugal_pump
+ coverage run -a -m tests.test_composite
+ coverage run -a -m tests.test_datasets
+ coverage run -a -m tests.test_dict_like_matrix_wrapper
+ coverage run -a -m tests.test_direct
+ coverage run -a -m tests.test_estimate_params
+ coverage run -a -m tests.test_ensemble
+ coverage run -a -m tests.test_linear_model
+ coverage run -a -m tests.test_pneumatic_valve
+ coverage run -a -m tests.test_powertrain
+ coverage run -a -m tests.test_serialization
+ coverage run -a -m tests.test_sim_result
+ coverage run -a -m tests.test_uav_model
+ coverage xml -i
+ - name: "Upload coverage to Codecov"
+ uses: codecov/codecov-action@v3

.github/workflows/greetings.yml

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+name: Greetings
+
+on: [pull_request_target]
+
+jobs:
+ greeting:
+ runs-on: ubuntu-latest
+ permissions:
+ issues: write
+ pull-requests: write
+ steps:
+ - uses: actions/first-interaction@v1
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+ pr-message: "Thank you for your contributions. If you haven't already, please send a signed Contributor License Agreement (CLA) to Christopher Teubert (christopher.a.teubert@nasa.gov). CLAs can be found here: https://github.com/nasa/prog_models/tree/master/forms. Also, make sure you're familiar with the developer notes and contributing sections of our developers guide, https://nasa.github.io/progpy/dev_guide.html#notes-for-developers"

.github/workflows/pr-messages.yml

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+name: Print PR Message - Non Release
+
+on: 
+ pull_request:
+ branches:
+ - 'dev'
+ types: [opened]
+
+jobs:
+ pr_msg: 
+ timeout-minutes: 5
+ runs-on: ubuntu-latest
+ steps:
+ - name: Auto Comment
+ uses: wow-actions/auto-comment@v1
+ with:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ pullRequestOpened: >
+ Thank you for opening this PR. Each PR into dev requires a code review. For the code review, look at the following:
+
+ - [ ] Reviewer (someone other than author) should look for bugs, efficiency, readability, testing, and coverage in examples (if relevant).
+
+ - [ ] Ensure that each PR adding a new feature should include a test verifying that feature.
+
+ - [ ] All errors from static analysis must be resolved.
+ 
+ - [ ] Review the test coverage reports (if there is a change) - will be added as comment on PR if there is a change
+
+ - [ ] Review the software benchmarking results (if there is a change) - will be added as comment on PR
+
+ - [ ] Any added dependencies are included in requirements.txt, setup.py, and dev_guide.rst (this document)
+
+ - [ ] All warnings from static analysis must be reviewed and resolved - if deemed appropriate.

.github/workflows/print-benchmarking.yml

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+name: Print Benchmarking
+
+on: pull_request
+
+jobs:
+ benchmark_branch: 
+ timeout-minutes: 20
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: ['3.9']
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v2
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install -e .
+ - name: benchmark
+ id: bench
+ shell: bash
+ run: |
+ bench=$(python -m tests.benchmarking)
+ # V To support multiline strings V
+ bench="${bench//'%'/'%25'}"
+ bench="${bench//$'\n'/'%0A'}"
+ bench="${bench//$'\r'/'%0D'}"
+ echo "::set-output name=bench::$bench"
+ - name: Clone prog_models
+ uses: actions/checkout@v2
+ with:
+ repository: nasa/prog_models
+ ref: ${{ github.event.pull_request.base.ref }}
+ path: prog_models_target
+ - name: Downgrade
+ run: |
+ python -m pip uninstall -y prog_models
+ python -m pip install -e ./prog_models_target
+ cd prog_models_target
+ - name: benchmark-pre
+ id: bench-pre
+ shell: bash
+ run: |
+ bench=$(python -m tests.benchmarking)
+ # V To support multiline strings V
+ bench="${bench//'%'/'%25'}"
+ bench="${bench//$'\n'/'%0A'}"
+ bench="${bench//$'\r'/'%0D'}"
+ echo "::set-output name=bench::$bench"
+ - name: Auto Comment
+ uses: wow-actions/auto-comment@v1
+ with:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ pullRequestOpened: >
+ Benchmarking Results
+
+ From:
+
+ ${{steps.bench-pre.outputs.bench}}
+ 
+ To:
+
+ ${{steps.bench.outputs.bench}}
+
+ pullRequestSynchronize: > 
+ Benchmarking Results [Update]
+
+ From:
+
+ ${{steps.bench-pre.outputs.bench}}
+
+ 
+ To:
+
+
+ ${{steps.bench.outputs.bench}}