Merge pull request #71 from kaklise/master

Added GitHub actions
sandialabs · Jun 17, 2021 · d9f2a01 · d9f2a01
2 parents 39543fa + bad9312
commit d9f2a01
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diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
@@ -0,0 +1,241 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: build
+
+on:
+  push:
+    branches: [ master]
+  pull_request:
+    branches: [ master]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python --version
+        python -m pip install --upgrade pip
+        pip install wheel
+        pip install -r requirements.txt
+    - name: Build wheel
+      run: |
+        python setup.py bdist_wheel
+        ls dist/*
+    - name: Save wheel
+      uses: actions/upload-artifact@v2
+      with:
+        name: wheel
+        path: dist/pecos*.whl
+
+  test:
+    name: Import test
+    needs: build
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [windows-latest, macOS-latest, ubuntu-latest]    
+    steps:
+    - name: Set up Python 
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Download wheel
+      uses: actions/download-artifact@v2
+      with:
+        name: wheel
+    - name: Install pecos
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel
+        pip install --find-links=. pecos
+    - name: Import test
+      run: |
+        python -c "import pecos"
+
+  windows:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [windows-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python --version
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install coveralls
+        python setup.py develop
+    - name: Run Tests
+      run: |
+        coverage erase
+        coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" -m nose -v --nologcapture --with-doctest --traverse-namespace pecos
+      env:
+        COVERAGE_FILE: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+    - name: Save coverage
+      uses: actions/upload-artifact@v2
+      # if: ${{ matrix.os != 'windows-latest' }}
+      with:
+        name: coverage
+        path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+
+  macOS:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [macOS-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python --version
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install coveralls
+        python setup.py develop
+    - name: Run Tests
+      run: |
+        coverage erase
+        coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" -m nose -v --nologcapture --with-doctest --traverse-namespace --doctest-extension=.rst documentation/*.rst pecos
+      env:
+        COVERAGE_FILE: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+    - name: Save coverage
+      uses: actions/upload-artifact@v2
+      # if: ${{ matrix.os != 'windows-latest' }}
+      with:
+        name: coverage
+        path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+
+  linux:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [ubuntu-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        conda config --set always_yes yes --set changeps1 no
+        python --version
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install coveralls                                             
+        python setup.py develop
+    - name: Run Tests
+      run: |
+        coverage erase
+        coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" -m nose -v --nologcapture --with-doctest --doctest-extension=.rst --traverse-namespace documentation/*.rst pecos
+      env:
+        COVERAGE_FILE: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+    - name: Save coverage
+      uses: actions/upload-artifact@v2
+      # if: ${{ matrix.os != 'windows-latest' }}
+      with:
+        name: coverage
+        path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+
+  coverage:
+    needs: [ windows, macOS, linux ]
+    runs-on: windows-latest
+    steps:
+    - name: Set up Python 
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - uses: actions/checkout@v2
+    - name: Install coverage
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install coveralls
+        python setup.py develop
+    - 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: Create coverage report
+      run: |
+        coverage report
+        coverage json --pretty-print
+        coverage html --show-contexts
+    - name: Save coverage JSON
+      uses: actions/upload-artifact@v2
+      with:
+        name: coverage
+        path: coverage.json
+    - name: Save coverage html
+      uses: actions/upload-artifact@v2
+      with:
+        name: coverage
+        path: htmlcov
+
+  coveralls:
+    needs: [ windows, macOS, linux ]
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+    - name: Set up Python 
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - uses: actions/checkout@v2
+    - name: Install coverage
+      run: |
+        python -m pip install --upgrade pip
+        pip install coveralls
+        pip install -r requirements.txt
+        python setup.py develop
+    - 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
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/quick_check.yml b/.github/workflows/quick_check.yml
@@ -0,0 +1,31 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: quick-check
+
+on:
+  push:
+    branches: 
+    - '**'
+  pull_request:
+    branches:
+    - '**'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install packages
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install --upgrade coverage nose
+        python setup.py develop
+    - name: Run tests
+      run: |
+        nosetests -v --nologcapture --with-doctest --with-coverage --cover-package=pecos --cover-min-percentage=70 pecos
diff --git a/.travis.yml b/.travis.yml
@@ -26,6 +26,12 @@ matrix:
       services:
       - xvfb
       sudo: true
+    - python: 3.9
+      dist: xenial
+      env: CONDA_ENV=py39
+      services:
+      - xvfb
+      sudo: true
 
 addons:
     apt:

diff --git a/ci/requirements-py39.yml b/ci/requirements-py39.yml
@@ -0,0 +1,17 @@
+name: test_env
+channels:
+    - defaults
+    - http://conda.anaconda.org/pvlib
+dependencies:
+    - python=3.9
+    - pandas
+    - numpy
+    - jinja2
+    - matplotlib
+    - nose
+    - pvlib
+    - plotly
+    - ephem
+    - sqlalchemy
+    - pip:
+        - coveralls
diff --git a/documentation/conf.py b/documentation/conf.py
@@ -131,7 +131,7 @@
 #html_theme = 'sphinxdoc'
 
 def setup(app):
-  app.add_stylesheet( "pecos.css" )               
+  app.add_css_file( "pecos.css" )               
 
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 if not on_rtd:  # only import and set the theme if we're building docs locally

diff --git a/documentation/installation.rst b/documentation/installation.rst
@@ -1,7 +1,7 @@
 Installation
 ======================================
 
-Pecos requires Python (tested on 3.6, 3.7, and 3.8) along with several Python 
+Pecos requires Python (tested on 3.6, 3.7, 3.8, and 3.9) along with several Python 
 package dependencies.  Information on installing and using Python can be found at 
 https://www.python.org/.  Python distributions, such as Anaconda,
 are recommended to manage the Python interface.  

diff --git a/documentation/whatsnew.rst b/documentation/whatsnew.rst
@@ -1,6 +1,8 @@
 Release Notes
 ================
 
+.. include:: whatsnew/v0.2.1.rst
+
 .. include:: whatsnew/v0.2.0.rst
 
 .. include:: whatsnew/v0.1.9.rst

diff --git a/documentation/whatsnew/v0.2.0.rst b/documentation/whatsnew/v0.2.0.rst
@@ -1,6 +1,6 @@
 .. _whatsnew_020:
 
-v0.2.0 (master)
+v0.2.0 (March 5, 2021)
 --------------------------
 
 * Replaced the use of Excel files in examples/tests with CSV files.  The Excel files were causing test failures.

diff --git a/documentation/whatsnew/v0.2.1.rst b/documentation/whatsnew/v0.2.1.rst
@@ -0,0 +1,8 @@
+.. _whatsnew_021:
+
+v0.2.1 (master)
+--------------------------
+
+* Minor updates for testing and documentation
+* Added GitHub Actions and Python 3.9 tests
+
diff --git a/pecos/__init__.py b/pecos/__init__.py
@@ -6,7 +6,7 @@
 from pecos import utils
 from pecos import pv
 
-__version__ = '0.2.0'
+__version__ = '0.2.1'
 
 __copyright__ = """Copyright 2016 National Technology & Engineering 
     Solutions of Sandia, LLC (NTESS). Under the terms of Contract 

diff --git a/pecos/monitoring.py b/pecos/monitoring.py
@@ -853,7 +853,7 @@ def check_custom_streaming(self, quality_control_func, window, key=None,
         # still expects pandas DataFrames and Series in the user defined quality 
         # control function to keep data types consitent on the user side.
         np_mask = pd.DataFrame(True, index=self.df.index, columns=self.df.columns).values
-        np_data = df.values.astype('Float64')
+        np_data = df.values.astype('float64')
 
         ti = df.index.get_loc(df.index[0]+history_window)
 

diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,12 @@
+# Required
+pandas
+numpy
+jinja2
+matplotlib
+
+# Optional
+nose
+pvlib
+plotly
+ephem
+sqlalchemy