ci(linting): Initial GitHub actions for linting

.flake8

@@ -15,6 +15,7 @@ ignore =
     E126, # continuation line over-indented for hanging indent
     E127, # continuation line over-indented for visual indent
     E128, # continuation line under-indented for visual indent
+    E203, # whitespace before
     E221, # multiple spaces before operator
     E222, # multiple spaces after operator
     E226, # missing whitespace around arithmetic operator
@@ -24,10 +25,13 @@ ignore =
     E501, # line too long (> 79 characters)
     E502, # backslash is redundant between brackets
     E722, # do not use bare 'except'
+    E741, # ambiguous variable name
     W291, # trailing whitespace
     W292, # no newline at end of file
     W293, # blank line contains whitespace
     W391, # blank line at end of file
     W503, # line break before binary operator
-    W504  # line break after binary operator
+    W504, # line break after binary operator
+    W605  # invalid escape sequence
+
 statistics = True

.github/workflows/ci.yml

@@ -0,0 +1,189 @@
+name: flopy continuous integration
+
+on:
+  push:
+  pull_request:
+
+jobs:
+
+  flopy_lint:
+    name: linting
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+
+    # check out repo
+    - name: Checkout flopy repo
+      uses: actions/checkout@v2
+
+    # Standard python fails on windows without GDAL installation. Using
+    # standard python here since only linting on linux.
+    # Use standard bash shell with standard python
+    - name: Setup Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Print python version
+      shell: bash
+      run: |
+        python --version
+
+    - name: Install Python 3.8 packages
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.pip.txt
+
+    - name: Run black
+      shell: bash
+      run: |
+        echo "if black check fails run"
+        echo "  black --line-length 79 ./flopy"
+        echo "and then commit the changes."
+        black --check --line-length 79 ./flopy
+
+    - name: Run flake8
+      shell: bash
+      run: |
+        flake8 --count --show-source --exit-zero ./flopy
+
+    - name: Run pylint
+      shell: bash
+      run: |
+        pylint --jobs=2 --errors-only --exit-zero ./flopy
+
+  flopyScriptNotebookCI:
+    name: additional tests
+    needs: flopy_lint
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        test-file: [autotest_notebooks.py, autotest_scripts.py]
+    steps:
+    # check out repo
+    - name: Checkout flopy repo
+      uses: actions/checkout@v2
+
+    # Standard python fails on windows without GDAL installation
+    # Using custom bash shell ("shell: bash -l {0}") with Miniconda
+    - name: Setup Miniconda
+      uses: goanpeca/setup-miniconda@v1.6.0
+      with:
+        python-version: 3.8
+        activate-environment: flopy
+        auto-update-conda: true
+        environment-file: environment.yml
+
+    - name: Determine python environment
+      shell: bash -l {0}
+      run: |
+        conda info
+        conda list
+
+    - name: Install additional Python 3.8 packages
+      if: matrix.test-file == 'autotest_notebooks.py'
+      shell: bash -l {0}
+      run: |
+        conda install nbconvert jupyter
+
+    - name: Install xmipy, pymake, and flopy
+      shell: bash -l {0}
+      run: |
+        pip install xmipy
+        pip install .
+        pip install https://github.com/modflowpy/pymake/zipball/master
+
+    - name: Download executables needed for tests
+      shell: bash -l {0}
+      run: |
+        python ./autotest/get_exes.py
+
+    - name: Add executables directory to path
+      shell: bash
+      run: |
+        echo "::add-path::$HOME/.local/bin"
+
+    - name: Run ${{ matrix.test-file }} CI
+      shell: bash -l {0}
+      run: |
+        coverage run -m nose -v ${{ matrix.test-file }} --with-id --with-timer \
+        --with-coverage --cover-package=flopy --cover-xml \
+        --cover-xml-file=../coverage.xml -w ./autotest
+
+    - name: List files in the root directory
+      shell: bash
+      run: |
+        ls -l
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1.0.12
+      with:
+        file: ./coverage.xml
+
+  flopyCI:
+    name: autotests
+    needs: flopy_lint
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8, 3.7, 3.6]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+    # check out repo
+    - name: Checkout flopy repo
+      uses: actions/checkout@v2
+
+    # Standard python fails on windows without GDAL installation
+    # Using custom bash shell ("shell: bash -l {0}") with Miniconda
+    - name: Setup Miniconda
+      uses: goanpeca/setup-miniconda@v1.6.0
+      with:
+        python-version: ${{ matrix.python-version }}
+        activate-environment: flopy
+        auto-update-conda: true
+        environment-file: environment.yml
+
+    - name: Determine python environment
+      shell: bash -l {0}
+      run: |
+        conda info
+        conda list
+
+    - name: Install xmipy, pymake, and flopy
+      shell: bash -l {0}
+      run: |
+        pip install xmipy
+        pip install .
+        pip install https://github.com/modflowpy/pymake/zipball/master
+
+    - name: Download executables needed for tests
+      shell: bash -l {0}
+      run: |
+        python ./autotest/get_exes.py
+
+    - name: Add executables directory to path
+      shell: bash
+      run: |
+        echo "::add-path::$HOME/.local/bin"
+
+    - name: Run nosetests
+      shell: bash -l {0}
+      run: |
+        coverage run -m nose -v --with-id --with-timer \
+        --with-coverage --cover-package=flopy --cover-xml \
+        --cover-xml-file=../coverage.xml -w ./autotest
+
+    - name: List files in the root directory
+      shell: bash
+      run: |
+        ls -l
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1.0.12
+      with:
+        file: ./coverage.xml