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

Author: kaklise

.github/workflows/build_docs.yml

@@ -5,7 +5,10 @@ name: docs
 on:
   push:
     branches: [main]
+  pull_request:
+    branches: [main]
   workflow_dispatch:
+
 jobs:
   build:
     name: Build the documentation with Sphinx
@@ -29,13 +32,14 @@ jobs:
       - name: Build documentation
         run: sphinx-build documentation/ documentation/_build/html
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
         with:
           path: 'documentation/_build/html'
 
   deploy:
     name: Deploy documentation to GitHub Pages
     needs: build
+    if: github.event_name == 'push'
     permissions:
       contents: read
       pages: write      # to deploy to Pages
@@ -49,4 +53,4 @@ jobs:
         uses: actions/configure-pages@v3
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v4

.github/workflows/build_tests.yml

@@ -13,16 +13,18 @@ on:
 
 jobs:
 
-  build:
+  build_wheels:
+    name: Build wheels
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
         os: [windows-latest, macOS-latest, ubuntu-latest]
+      fail-fast: false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -35,47 +37,50 @@ jobs:
       run: |
         python setup.py bdist_wheel
         ls dist/*
-    - name: Save wheel
-      uses: actions/upload-artifact@v3
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
       with:
         name: pecos_${{ matrix.python-version }}_${{ matrix.os }}.whl
         path: dist/pecos*
 
-  install_import:
-    needs: build
+  test_wheels:
+    name: Test wheels
+    needs: build_wheels
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
-        os: [windows-latest, macOS-latest, ubuntu-latest]    
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+      fail-fast: false
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Download wheel
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: pecos_${{ matrix.python-version }}_${{ matrix.os }}.whl
     - name: Install pecos
       run: |
         python -m pip install --upgrade pip
         pip install wheel numpy pandas jinja2 matplotlib pytest
         pip install --no-index --pre --find-links=. pecos
-    - name: Usage of pecos
+    - name: Import pecos
       run: |
         python -c "import pecos"
 
-  pytest_coverage:
+  run_coverage:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
         os: [windows-latest, macOS-latest, ubuntu-latest]
+      fail-fast: false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -85,37 +90,41 @@ jobs:
         pip install -r requirements.txt
         python -m pip install -e .
     - name: Run Tests
-      run: |
+      run: | 
         coverage erase
         coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" -m pytest --doctest-modules --doctest-glob="*.rst" pecos
         coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" --append -m pytest --doctest-glob="*.rst" documentation                                                                                                                                                                                                                                       
       env:
         COVERAGE_FILE: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
     - name: Save coverage
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: coverage
+        name: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
         path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+        include-hidden-files: true
 
   combine_reports:
-    needs: [ pytest_coverage ]
+    needs: [ run_coverage ]
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.11
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Install coverage
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
         python -m pip install -e .
+        pip install coveralls
     - name: Download coverage artifacts from test matrix
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
-        name: coverage
+        pattern: .coverage.*.ubuntu-latest # coverage from other OS cause problems
     - name: Setup coverage and combine reports
+      run: coverage combine .coverage.*.ubuntu-latest
+    - name: Create coverage report
       run: |
         echo "[paths]" > .coveragerc
         echo "source = " >> .coveragerc
@@ -124,55 +133,21 @@ jobs:
         echo "    D:\\a\\pecos\\pecos\\pecos" >> .coveragerc
         echo "    /home/runner/work/pecos/pecos/pecos" >> .coveragerc
         echo "    /Users/runner/work/pecos/pecos/pecos" >> .coveragerc
-        coverage combine
-    - name: Create coverage report
-      run: |
+        echo "    ${{ github.workspace }}/pecos" >> .coveragerc
         coverage report
         coverage json --pretty-print
         coverage html --show-contexts
     - name: Save coverage JSON
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: coverage
+        name: coverage-json
         path: coverage.json
     - name: Save coverage html
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: coverage
+        name: coverage-html
         path: htmlcov
-
-  coveralls:
-    needs: [ pytest_coverage ]
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-    - name: Set up Python 
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.11
-    - uses: actions/checkout@v2
-    - name: Install coverage
-      run: |
-        python -m pip install --upgrade pip
-        pip install coveralls
-        pip install -r requirements.txt
-        python -m pip install -e .
-    - name: Download coverage artifacts from test matrix
-      uses: actions/download-artifact@v2
-      with:
-        name: coverage
-    - name: Setup coverage and combine reports
-      run: |
-        echo "[paths]" > .coveragerc
-        echo "source = " >> .coveragerc
-        echo "    pecos/" >> .coveragerc
-        echo "    pecos\\" >> .coveragerc
-        echo "    D:\\a\\pecos\\pecos\\pecos" >> .coveragerc
-        echo "    /home/runner/work/pecos/pecos/pecos" >> .coveragerc
-        echo "    /Users/runner/work/pecos/pecos/pecos" >> .coveragerc
-        coverage combine
     - name: Push to coveralls
-      run: |
-        coveralls --service=github
+      run: coveralls --service=github --rcfile=.coveragerc
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

documentation/composite_signal.rst

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

documentation/metrics.rst

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

documentation/timefilter.rst

@@ -16,7 +16,7 @@ The following example defines a time filter between 3 AM and 9 PM,
     >>> import numpy as np
     >>> import pecos
     >>> pm = pecos.monitoring.PerformanceMonitoring()
-    >>> index = pd.date_range('1/1/2017', periods=24, freq='H')
+    >>> index = pd.date_range('1/1/2017', periods=24, freq='h')
     >>> data = {'A': np.arange(24)}
     >>> df = pd.DataFrame(data, index=index)
     >>> pm.add_dataframe(df)

documentation/whatsnew.rst

@@ -1,6 +1,10 @@
 Release Notes
 ================
 
+.. include:: whatsnew/v1.0.0.rst
+
+.. include:: whatsnew/v0.3.1.rst
+
 .. include:: whatsnew/v0.3.0.rst
 
 .. include:: whatsnew/v0.2.0.rst

documentation/whatsnew/v0.3.0.rst

@@ -1,6 +1,6 @@
 .. _whatsnew_030:
 
-v0.3.0 (main)
+v0.3.0 (October 17, 2023)
 --------------------------
 
 * Bug fix in custom static and streaming quality control tests to use a specific column

documentation/whatsnew/v0.3.1.rst

@@ -0,0 +1,7 @@
+.. _whatsnew_031:
+
+v0.3.1 (October 27, 2023)
+--------------------------
+
+* Relaxed dtype check in tests
+* Fixed import fail due to pytest ModuleNotFoundError

documentation/whatsnew/v1.0.0.rst

@@ -0,0 +1,7 @@
+.. _whatsnew_100:
+
+Version 1.0.0 (main)
+--------------------------
+
+* Updates to support Numpy2
+

examples/dashboard/dashboard_example_1.py

@@ -40,7 +40,7 @@
 
         # Populate the object with a dataframe and translation dictionary
         # In this example, fake data is generated using a sin wave function
-        index = pd.date_range(analysis_date, periods=24, freq='H')
+        index = pd.date_range(analysis_date, periods=24, freq='h')
         data=np.sin(np.random.rand(3,1)*np.arange(0,24,1))
         df = pd.DataFrame(data=data.transpose(), index=index, columns=['A', 'B', 'C'])
         pm.add_dataframe(df)