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jdhughes-devjdhughes-dev
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ci(linting): Initial GitHub actions for linting (#954)
Reformat code using black with 79 character line length. Initial GitHub action uses miniconda and has first cut at running autotests on GitHub actions.
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‎.flake8

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

‎.github/workflows/ci.yml

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

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