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Add method to ED1d for calculating membrane resistance as a function of ion concentration #8957

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Add method to ED1d for calculating membrane resistance as a function of ion concentration

Add method to ED1d for calculating membrane resistance as a function of ion concentration #8957

Workflow file for this run

.github/workflows/checks.yml at 09c9cb5
# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Checks
on:
push:
branches: [main]
pull_request:
branches: [main]
concurrency:
# NOTE: the value of `group` should be chosen carefully,
# otherwise we might end up over- or under-canceling workflow runs
# github.head_ref is only defined for pull request events
# so, if it's not present (i.e. event was triggered by push)
# we use github.ref instead
group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
cancel-in-progress: true
defaults:
run:
# important to make sure that all commands on Windows are run using Bash
# -l: login shell, needed when using Conda
shell: bash -l {0}
env:
# --color=yes needed for colorized output to be shown in GHA logs
# --pyargs watertap is needed to be able to define CLI options in watertap/conftest.py
PYTEST_ADDOPTS: "--color=yes"
PIP_PROGRESS_BAR: "off"
WATERTAP_KERNEL_NAME: watertap-dev
jobs:
code-formatting:
name: Check code is formatted (Black)
# OS and/or Python version don't make a difference, so we choose ubuntu and 3.8 as defaults
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install Black
# unlike the other jobs, we don't need to install WaterTAP and/or all the dev dependencies,
# but we still want to specify the Black version to use in requirements-dev.txt for local development
# so we extract the relevant line and pass it to a simple `pip install`
run: |
black_requirement="$(grep '^black==' requirements-dev.txt)"
pip --no-cache-dir install "$black_requirement"
- name: Run Black to verify that the committed code is formatted
run: |
black --check .
pylint:
name: Code linting (pylint)
runs-on: ubuntu-latest
needs: [code-formatting]
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install dev dependencies
run: |
pip install -r requirements-dev.txt
pip list
- name: Run pylint
run: |
pylint watertap
tests:
name: Tests (py${{ matrix.python-version }}/${{ matrix.os }})
runs-on: ${{ matrix.os-version }}
needs: [code-formatting]
strategy:
fail-fast: false
matrix:
python-version:
- '3.9'
- '3.10'
- '3.11'
os:
- linux
- win64
# - macos
include:
- os: linux
os-version: ubuntu-20.04
- os: win64
os-version: windows-2019
# - os: macos
# os-version: macos-10.15
- python-version: '3.10'
# limit uploading coverage report for a single Python version in the matrix
coverage: true
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: watertap-dev
python-version: ${{ matrix.python-version }}
miniforge-version: latest
- name: Install dependencies
run: |
echo '::group::Output of "conda install" commands'
conda install --quiet --yes pip setuptools wheel pandoc
echo '::endgroup::'
echo '::group::Output of "pip install" commands'
pip install -r requirements-dev.txt
echo '::endgroup::'
echo '::group::Output of "conda install -c conda-forge cyipopt" command'
conda install -c conda-forge cyipopt
echo '::endgroup::'
echo '::group::Display installed packages'
conda list
pip list
pip show idaes-pse
echo '::endgroup::'
echo '::group::Output of "idaes get-extensions" command'
idaes get-extensions --extra petsc --verbose
echo '::endgroup::'
- name: Add coverage report pytest options
if: matrix.coverage
run:
|
echo PYTEST_ADDOPTS="$PYTEST_ADDOPTS --cov-report=xml" >> $GITHUB_ENV
- name: Test with pytest
run: |
pytest --pyargs watertap
- name: Upload coverage report as job artifact
if: matrix.coverage
uses: actions/upload-artifact@v4
with:
name: coverage-report-${{ matrix.os }}
path: coverage.xml
if-no-files-found: error
- name: Test documentation code
run: |
make -C docs doctest -d
# TODO: this should be moved to a dedicated job/workflow
# until then, we can leave this here as a reminder
- name: Test documentation links
if: 'false'
run: |
make -C docs linkcheck -d
upload-coverage:
name: Upload coverage report (Codecov)
needs: [tests]
runs-on: ubuntu-latest
steps:
# the checkout step is needed to have access to codecov.yml
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
pattern: coverage-report-*
- name: Upload coverage report to Codecov
uses: codecov/codecov-action@v4
with:
fail_ci_if_error: true
verbose: true
# NOTE: secrets are not available for pull_request workflows
# However, as of 2024-02-10, Codecov is still allowing tokenless upload from PRs
# but does require token for other workflows e.g. merge to `main`
# see https://github.com/codecov/codecov-action/issues/1274#issuecomment-1934437359
token: ${{ secrets.CODECOV_TOKEN }}
# downgrading after v0.7.0 broke tokenless upload
# see codecov/codecov-action#1487
version: v0.6.0
user-mode-pytest:
name: pytest (user mode) (py${{ matrix.python-version }}/${{ matrix.os }})
runs-on: ${{ matrix.os-version }}
needs: [code-formatting]
strategy:
fail-fast: false
matrix:
python-version:
- '3.9'
- '3.11'
os:
- linux
- win64
include:
- os: linux
os-version: ubuntu-20.04
- os: win64
os-version: windows-2019
steps:
- name: Set up Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: watertap
python-version: ${{ matrix.python-version }}
- name: Define install URL (default)
env:
_repo_full_name: watertap-org/watertap
_ref_to_install: main
run: |
echo "_install_url=https://github.com/${_repo_full_name}/archive/${_ref_to_install}.zip" >> $GITHUB_ENV
- name: Define install URL (for PRs)
if: github.event.pull_request
env:
_repo_full_name: ${{ github.event.pull_request.head.repo.full_name }}
_ref_to_install: ${{ github.event.pull_request.head.sha }}
run:
echo "_install_url=https://github.com/${_repo_full_name}/archive/${_ref_to_install}.zip" >> $GITHUB_ENV
- name: Install watertap and testing dependencies
run: |
echo '::group::Output of "pip install" commands'
pip install "watertap @ ${_install_url}" pytest
echo '::endgroup::'
echo '::group::Display installed packages'
conda list
pip list
pip show idaes-pse
echo '::endgroup::'
echo '::group::Output of "idaes get-extensions" command'
idaes get-extensions --extra petsc --verbose
echo '::endgroup::'
- name: Run pytest
run: |
pytest --pyargs watertap
notebooks:
name: Test notebooks (py${{ matrix.python-version }}/${{ matrix.os }})
runs-on: ${{ matrix.os-version }}
needs: [code-formatting]
strategy:
fail-fast: false
matrix:
python-version:
- '3.9'
- '3.11'
os:
- linux
- win64
include:
- os: linux
os-version: ubuntu-20.04
- os: win64
os-version: windows-2019
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: watertap-dev
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
echo '::group::Output of "conda install" commands'
conda install --quiet --yes pip setuptools wheel pandoc
echo '::endgroup::'
echo '::group::Output of "pip install" commands'
pip install -r requirements-dev.txt
echo '::endgroup::'
echo '::group::Display installed packages'
conda list
pip list
pip show idaes-pse
echo '::endgroup::'
echo '::group::Output of "idaes get-extensions" command'
idaes get-extensions --extra petsc --verbose
echo '::endgroup::'
- name: Install Jupyter kernel
run: |
jupyter kernelspec list
python -m ipykernel install --user --name "${{ env.WATERTAP_KERNEL_NAME }}"
jupyter kernelspec list
- name: Run pytest with nbmake
run: |
pytest --nbmake --nbmake-kernel="${{ env.WATERTAP_KERNEL_NAME }}" **/*.ipynb
macos:
name: macOS setup (EXPERIMENTAL)
runs-on: macos-13
needs: [code-formatting]
strategy:
fail-fast: false
matrix:
python-version:
- '3.9'
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: watertap
python-version: ${{ matrix.python-version }}
- name: Install WaterTAP (dev) without idaes get-extensions
run: |
echo '::group::Output of "conda install" commands'
conda install --quiet --yes pip=21.1 wheel setuptools pandoc
echo '::endgroup::'
echo '::group::Output of "pip install" commands'
pip install -r requirements-dev.txt
echo '::endgroup::'
echo '::group::Display installed packages'
conda list
pip list
pip show pyomo idaes-pse
echo '::endgroup::'
- name: Install Ipopt from conda-forge
run:
conda install --quiet --yes -c conda-forge ipopt=3.14.11
- name: Build Pyomo extensions
run: |
conda install --quiet --yes cmake
# some failures are expected, but this should succeed as long as pynumero is built correctly
pyomo build-extensions || python -c "from pyomo.contrib.pynumero.asl import AmplInterface; exit(0) if AmplInterface.available() else exit(1)"
- name: Run pytest
run: |
pytest --pyargs watertap -k 'not (nf_dspmde.nf_ui or nf_dspmde.nf_with_bypass_ui or mvc.mvc_single_stage_ui or full_water_resource_recovery_facility.BSM2_P_extension_ui )'