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feat(pandas): Flopy pandas support #1194

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feat(pandas): Flopy pandas support

feat(pandas): Flopy pandas support #1194

Workflow file for this run

.github/workflows/commit.yml at d906939
name: FloPy continuous integration
on:
push:
branches:
- master
- develop
- ci-diagnose*
- notebooks
pull_request:
branches:
- master
- develop
jobs:
build:
name: Build
runs-on: ubuntu-latest
defaults:
run:
shell: bash
timeout-minutes: 10
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: 3.8
cache: 'pip'
cache-dependency-path: pyproject.toml
- name: Install Python dependencies
run: |
pip install --upgrade pip
pip install build twine
pip install .
python -c "import flopy; print(f'{flopy.__version__}')"
- name: Build package
run: |
python -m build
- name: Check package
run: |
twine check --strict dist/*
lint:
name: Lint
runs-on: ubuntu-latest
defaults:
run:
shell: bash
timeout-minutes: 10
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: 3.8
cache: 'pip'
cache-dependency-path: pyproject.toml
- name: Install Python dependencies
run: |
pip install .
pip install ".[lint]"
- name: Run isort
run: |
echo "if isort check fails update isort using"
echo " pip install isort --upgrade"
echo "and run"
echo " isort ./flopy"
echo "and then commit the changes."
isort --check --diff ./flopy
- name: Run black
run: |
echo "if black check fails update black using"
echo " pip install black --upgrade"
echo "and run"
echo " black ./flopy"
echo "and then commit the changes."
black --check --diff ./flopy
- name: Run flake8
run: |
flake8 --count --show-source --exit-zero ./flopy
- name: Run pylint
run: |
pylint --jobs=2 --errors-only --exit-zero ./flopy
- name: Check CITATION.cff
run: |
cffconvert --validate
cffconvert -f apalike
cffconvert -f bibtex
smoke:
name: Smoke test
runs-on: ubuntu-latest
defaults:
run:
shell: bash
timeout-minutes: 10
env:
PYTHON_VERSION: 3.8
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION }}
cache: 'pip'
cache-dependency-path: pyproject.toml
- name: Install Python dependencies
run: |
pip install --upgrade pip
pip install .
pip install ".[test,optional]"
- name: Install Modflow executables
uses: modflowpy/install-modflow-action@v1
- name: Smoke test
working-directory: autotest
run: pytest -v -n=auto --smoke --color=yes --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Upload failed test outputs
uses: actions/upload-artifact@v3
if: failure()
with:
name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }}
path: ./autotest/.failed/**
- name: Upload coverage
if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
uses: codecov/codecov-action@v3
with:
files: ./autotest/coverage.xml
test:
name: Test
needs: smoke
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ ubuntu-latest, macos-latest, windows-latest ]
python-version: [ 3.8, 3.9, "3.10", "3.11" ]
exclude:
# avoid shutil.copytree infinite recursion bug
# https://github.com/python/cpython/pull/17098
- python-version: '3.8.0'
defaults:
run:
shell: bash
timeout-minutes: 45
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Setup Python
if: runner.os != 'Windows'
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
cache: 'pip'
cache-dependency-path: pyproject.toml
- name: Install Python dependencies
if: runner.os != 'Windows'
run: |
pip install --upgrade pip
pip install .
pip install ".[test, optional]"
- name: Setup Micromamba
if: runner.os == 'Windows'
uses: mamba-org/setup-micromamba@v1
with:
environment-file: etc/environment.yml
cache-environment: true
cache-downloads: true
create-args: >-
python=${{ matrix.python-version }}
init-shell: >-
bash
powershell
- name: Install Python dependencies
shell: bash -l {0}
if: runner.os == 'Windows'
run: |
pip install xmipy
pip install .
- name: Install Modflow-related executables
uses: modflowpy/install-modflow-action@v1
- name: Install Modflow dev build executables
uses: modflowpy/install-modflow-action@v1
with:
repo: modflow6-nightly-build
- name: Update FloPy packages
if: runner.os != 'Windows'
run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
- name: Update FloPy packages
if: runner.os == 'Windows'
shell: bash -l {0}
run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
- name: Run tests
if: runner.os != 'Windows'
working-directory: ./autotest
run: |
pytest -v -m="not example and not regression" -n=auto --color=yes --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
coverage report
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Run tests
if: runner.os == 'Windows'
shell: bash -l {0}
working-directory: ./autotest
run: |
pytest -v -m="not example and not regression" -n=auto --color=yes --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
coverage report
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Upload failed test outputs
uses: actions/upload-artifact@v3
if: failure()
with:
name: failed-${{ matrix.os }}-${{ matrix.python-version }}
path: |
./autotest/.failed/**
- name: Upload coverage
if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
uses: codecov/codecov-action@v3
with:
files: ./autotest/coverage.xml