Add method to ED1d for calculating membrane resistance as a function of ion concentration #8961

Workflow file for this run

.github/workflows/checks.yml at 1206178

	# 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 )'

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Add method to ED1d for calculating membrane resistance as a function of ion concentration #8961

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Add method to ED1d for calculating membrane resistance as a function of ion concentration #8961

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Workflow file for this run