Implement pure Braginskii closure in diffusive processes, fix bugs in conductivity, add more sheath diagnostics #1237

	name: Tests
	on: [push, pull_request]

	defaults:
	run:
	shell: bash

	jobs:
	cmake_tests:
	name: ${{ matrix.config.name }}
	runs-on: ${{ matrix.config.os }}
	env:
	OMP_NUM_THREADS: ${{ matrix.config.omp_num_threads }}
	PYTHONPATH: ${{ github.workspace }}/tools/pylib
	OMPI_MCA_rmaps_base_oversubscribe: yes
	MPIRUN: mpiexec -np
	strategy:
	fail-fast: false
	matrix:
	config:
	- name: "CMake default options"
	os: ubuntu-22.04
	configure_options: "-DPACKAGE_TESTS=OFF"

	steps:
	- name: Job information
	run: \|
	echo Build: ${{ matrix.config.name }}, ${{ matrix.config.os }}
	echo Configure options: ${{ matrix.config.configure_options }}

	- name: Install dependencies
	run: sudo apt update &&
	sudo apt install -y
	libfftw3-dev
	libnetcdf-dev
	libnetcdf-c++4-dev
	netcdf-bin
	python3
	python3-pip
	python3-pytest
	python3-numpy
	python3-scipy
	openmpi-bin
	libopenmpi-dev
	liblapack-dev
	libparpack2-dev

	- uses: actions/checkout@v2
	with:
	submodules: true

	- name: Install pip packages
	run: \|
	./.pip_install_for_tests.sh 'netcdf4~=1.5' boutdata boututils
	# Add the pip install location to the runner's PATH
	echo ~/.local/bin >> $GITHUB_PATH
	- name: Build and run tests
	run: cmake . -B build $BOUT_CONFIGURE_OPTIONS &&
	cmake --build build &&
	cd build &&
	ctest --output-on-failure --timeout 300
	env:
	LD_LIBRARY_PATH: /home/runner/local/lib:$LD_LIBRARY_PATH
	BOUT_CONFIGURE_OPTIONS: ${{ matrix.config.configure_options }}

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