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Updates to support numpy2 and github actions (sandialabs#84)
* bump action versions * update to use np.nan (all lowercase) * replace freq string H and S with lower case string * index into the series using iloc * update trapz to trapezoid * use raw string when docs contain math * updated build action for docs * bump version number * updated build action * update to combine files in coverage report * update build action
1 parent 72571b1 commit 9ca3afe

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-115
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‎.github/workflows/build_docs.yml

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@@ -5,7 +5,10 @@ name: docs
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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workflow_dispatch:
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jobs:
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build:
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name: Build the documentation with Sphinx
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- name: Build documentation
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run: sphinx-build documentation/ documentation/_build/html
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v1
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uses: actions/upload-pages-artifact@v3
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with:
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path: 'documentation/_build/html'
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deploy:
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name: Deploy documentation to GitHub Pages
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needs: build
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if: github.event_name == 'push'
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permissions:
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contents: read
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pages: write # to deploy to Pages
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uses: actions/configure-pages@v3
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v1
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uses: actions/deploy-pages@v4

‎.github/workflows/build_tests.yml

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@@ -13,16 +13,18 @@ on:
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jobs:
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build:
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build_wheels:
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name: Build wheels
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11', '3.12']
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os: [windows-latest, macOS-latest, ubuntu-latest]
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fail-fast: false
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python setup.py bdist_wheel
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ls dist/*
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- name: Save wheel
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uses: actions/upload-artifact@v3
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: pecos_${{ matrix.python-version }}_${{ matrix.os }}.whl
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path: dist/pecos*
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install_import:
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needs: build
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test_wheels:
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name: Test wheels
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needs: build_wheels
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11', '3.12']
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os: [windows-latest, macOS-latest, ubuntu-latest]
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os: [windows-latest, macOS-latest, ubuntu-latest]
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fail-fast: false
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steps:
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Download wheel
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pecos_${{ matrix.python-version }}_${{ matrix.os }}.whl
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- name: Install pecos
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run: |
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python -m pip install --upgrade pip
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pip install wheel numpy pandas jinja2 matplotlib pytest
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pip install --no-index --pre --find-links=. pecos
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- name: Usage of pecos
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- name: Import pecos
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run: |
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python -c "import pecos"
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pytest_coverage:
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run_coverage:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11', '3.12']
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os: [windows-latest, macOS-latest, ubuntu-latest]
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fail-fast: false
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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pip install -r requirements.txt
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python -m pip install -e .
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- name: Run Tests
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run: |
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run: |
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coverage erase
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coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" -m pytest --doctest-modules --doctest-glob="*.rst" pecos
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coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" --append -m pytest --doctest-glob="*.rst" documentation
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env:
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COVERAGE_FILE: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
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- name: Save coverage
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@v4
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with:
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name: coverage
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name: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
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path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
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include-hidden-files: true
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combine_reports:
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needs: [ pytest_coverage ]
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needs: [ run_coverage ]
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runs-on: ubuntu-latest
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steps:
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: 3.11
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- name: Install coverage
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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python -m pip install -e .
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pip install coveralls
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- name: Download coverage artifacts from test matrix
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uses: actions/download-artifact@v2
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uses: actions/download-artifact@v4
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with:
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name: coverage
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pattern: .coverage.*.ubuntu-latest # coverage from other OS cause problems
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- name: Setup coverage and combine reports
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run: coverage combine .coverage.*.ubuntu-latest
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- name: Create coverage report
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run: |
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echo "[paths]" > .coveragerc
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echo "source = " >> .coveragerc
@@ -124,55 +133,21 @@ jobs:
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echo " D:\\a\\pecos\\pecos\\pecos" >> .coveragerc
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echo " /home/runner/work/pecos/pecos/pecos" >> .coveragerc
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echo " /Users/runner/work/pecos/pecos/pecos" >> .coveragerc
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coverage combine
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- name: Create coverage report
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run: |
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echo " ${{ github.workspace }}/pecos" >> .coveragerc
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coverage report
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coverage json --pretty-print
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coverage html --show-contexts
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- name: Save coverage JSON
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@v4
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with:
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name: coverage
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name: coverage-json
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path: coverage.json
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- name: Save coverage html
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@v4
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with:
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name: coverage
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name: coverage-html
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path: htmlcov
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coveralls:
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needs: [ pytest_coverage ]
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runs-on: ubuntu-latest
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continue-on-error: true
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steps:
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: 3.11
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- uses: actions/checkout@v2
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- name: Install coverage
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run: |
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python -m pip install --upgrade pip
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pip install coveralls
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pip install -r requirements.txt
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python -m pip install -e .
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- name: Download coverage artifacts from test matrix
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uses: actions/download-artifact@v2
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with:
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name: coverage
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- name: Setup coverage and combine reports
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run: |
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echo "[paths]" > .coveragerc
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echo "source = " >> .coveragerc
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echo " pecos/" >> .coveragerc
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echo " pecos\\" >> .coveragerc
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echo " D:\\a\\pecos\\pecos\\pecos" >> .coveragerc
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echo " /home/runner/work/pecos/pecos/pecos" >> .coveragerc
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echo " /Users/runner/work/pecos/pecos/pecos" >> .coveragerc
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coverage combine
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- name: Push to coveralls
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run: |
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coveralls --service=github
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run: coveralls --service=github --rcfile=.coveragerc
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎documentation/composite_signal.rst

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@@ -36,7 +36,7 @@ the PerformanceMonitoring object.
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>>> import numpy as np
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>>> import pecos
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>>> pm = pecos.monitoring.PerformanceMonitoring()
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>>> index = pd.date_range('1/1/2017', periods=24, freq='H')
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>>> index = pd.date_range('1/1/2017', periods=24, freq='h')
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>>> data = {'A': np.arange(24)}
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>>> df = pd.DataFrame(data, index=index)
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>>> pm.add_dataframe(df)

‎documentation/metrics.rst

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@@ -31,7 +31,7 @@ To compute QCI,
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>>> import numpy as np
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>>> import pecos
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>>> pm = pecos.monitoring.PerformanceMonitoring()
34-
>>> index = pd.date_range('1/1/2017', periods=24, freq='H')
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>>> index = pd.date_range('1/1/2017', periods=24, freq='h')
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>>> data = {'A': np.arange(24)}
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>>> df = pd.DataFrame(data, index=index)
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>>> pm.add_dataframe(df)

‎documentation/timefilter.rst

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>>> import numpy as np
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>>> import pecos
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>>> pm = pecos.monitoring.PerformanceMonitoring()
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>>> index = pd.date_range('1/1/2017', periods=24, freq='H')
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>>> index = pd.date_range('1/1/2017', periods=24, freq='h')
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>>> data = {'A': np.arange(24)}
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>>> df = pd.DataFrame(data, index=index)
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>>> pm.add_dataframe(df)

‎documentation/whatsnew.rst

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Release Notes
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================
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.. include:: whatsnew/v1.0.0.rst
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.. include:: whatsnew/v0.3.1.rst
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.. include:: whatsnew/v0.3.0.rst
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.. include:: whatsnew/v0.2.0.rst

‎documentation/whatsnew/v0.3.0.rst

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.. _whatsnew_030:
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v0.3.0 (main)
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v0.3.0 (October 17, 2023)
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--------------------------
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* Bug fix in custom static and streaming quality control tests to use a specific column

‎documentation/whatsnew/v0.3.1.rst

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.. _whatsnew_031:
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v0.3.1 (October 27, 2023)
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--------------------------
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* Relaxed dtype check in tests
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* Fixed import fail due to pytest ModuleNotFoundError

‎documentation/whatsnew/v1.0.0.rst

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.. _whatsnew_100:
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Version 1.0.0 (main)
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--------------------------
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* Updates to support Numpy2
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‎examples/dashboard/dashboard_example_1.py

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# Populate the object with a dataframe and translation dictionary
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# In this example, fake data is generated using a sin wave function
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index = pd.date_range(analysis_date, periods=24, freq='H')
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index = pd.date_range(analysis_date, periods=24, freq='h')
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data=np.sin(np.random.rand(3,1)*np.arange(0,24,1))
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df = pd.DataFrame(data=data.transpose(), index=index, columns=['A', 'B', 'C'])
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pm.add_dataframe(df)

‎pecos/__init__.py

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from pecos import utils
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from pecos import pv
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__version__ = '0.3.1'
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__version__ = '1.0.0'
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__copyright__ = """Copyright 2016 National Technology & Engineering
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Solutions of Sandia, LLC (NTESS). Under the terms of Contract

‎pecos/graphics.py

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temp = np.append(temp[0],len(tfilter)-1)
158158
count = 0
159159
for i in range(len(temp)-1):
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if tfilter[temp[i]] == 0:
160+
if tfilter.iloc[temp[i]] == 0:
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if count == 0:
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ax.axvspan(data.index[temp[i]], data.index[temp[i+1]],
163163
facecolor='k', alpha=0.2, label='Time filter')
@@ -399,7 +399,7 @@ def plot_doy_heatmap(data, cmap='nipy_spectral', vmin=None, vmax=None,
399399
data.index.minute + \
400400
data.index.second/60 + \
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data.index.microsecond/(60*1000000.0)
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piv = pd.pivot_table(data,values=col_name,index=['Y'],columns=['X'],fill_value=np.NaN)
402+
piv = pd.pivot_table(data,values=col_name,index=['Y'],columns=['X'],fill_value=np.nan)
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# Create the heatmap
405405
plt.figure(figsize = figsize)

‎pecos/metrics.py

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logger = logging.getLogger(__name__)
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def qci(mask, tfilter=None):
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"""
12+
r"""
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Compute the quality control index (QCI) for each column, defined as:
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1515
:math:`QCI=\dfrac{\sum_{t\in T}X_{dt}}{|T|}`
@@ -42,7 +42,7 @@ def qci(mask, tfilter=None):
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return qci
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def rmse(data1, data2, tfilter=None):
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"""
45+
r"""
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Compute the root mean squared error (RMSE) for each column, defined as:
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:math:`RMSE=\sqrt{\dfrac{\sum{(data_1-data_2)^2}}{n}}`
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return rmse
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def time_integral(data, tfilter=None):
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"""
89+
r"""
9090
Compute the time integral (F) for each column, defined as:
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9292
:math:`F=\int{fdt}`
9393
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where
9595
:math:`f` is a column of data
9696
:math:`dt` is the time step between observations.
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The integral is computed using the trapezoidal rule from numpy.trapz.
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The integral is computed using the trapezoidal rule from numpy.trapezoid.
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Results are given in [original data units]*seconds.
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NaN values are set to 0 for integration.
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125125
F = {}
126126
for col in data.columns:
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F[col] = float(np.trapz(data.loc[:,col], tdelta))
127+
F[col] = float(np.trapezoid(data.loc[:,col], tdelta))
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129129
F = pd.Series(F)
130130

131131
return F
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133133
def time_derivative(data, tfilter=None):
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"""
134+
r"""
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Compute the derivative (f') of each column, defined as:
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:math:`f'=\dfrac{df}{dt}`
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return f
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def probability_of_detection(observed, actual, tfilter=None):
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"""
173+
r"""
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Compute probability of detection (PD) for each column, defined as:
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:math:`PD=\dfrac{TP}{TP+FN}`
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228228
return PD
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def false_alarm_rate(observed, actual, tfilter=None):
231-
"""
231+
r"""
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Compute false alarm rate (FAR) for each column, defined as:
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:math:`FAR=\dfrac{TN}{TN+FP}`

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