improve type hints based on mypy analysis #571

Workflow file for this run

	name: Build and test
	on:
	push:
	branches:
	- "**"
	pull_request:
	jobs:
	gfortran:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	version: [9, 10, 11, 12]
	os: [ubuntu-latest]
	include:
	#- version: 4.8
	# os: ubuntu-18.04
	# cmake_args: -DFABM_USE_IEEE_ARITHMETIC=OFF
	#- version: 5
	# os: ubuntu-18.04
	#- version: 6
	# os: ubuntu-18.04
	- version: 7
	os: ubuntu-20.04
	- version: 8
	os: ubuntu-20.04
	cmake_args: -DFABM_USE_CONTIGUOUS=OFF
	- version: 13
	os: ubuntu-24.04
	- version: 14
	os: ubuntu-24.04
	fail-fast: false
	runs-on: ${{ matrix.os }}
	env:
	FFLAGS: -fcheck=all
	steps:
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ">=3.7"
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip pyyaml
	- name: Install compiler
	run: \|
	sudo apt-get update
	sudo apt-get install gfortran-${{ matrix.version }}
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Run all test cases with host emulators
	run: python3 util/developers/run_all_testcases.py harness --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }}
	- name: Run all test cases with pyfabm
	run: python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }}
	ifort:
	# for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	include:
	- version: "2021.1.2.62"
	url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508"
	# - version: "2022.2.1.16992"
	# url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998"
	# - version: "2023.2.0.49254"
	# url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/237236c4-434b-4576-96ac-020ceeb22619"
	- version: "2024.2.0.426"
	url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181"
	fail-fast: false
	runs-on: ubuntu-latest
	env:
	FFLAGS: -check all
	steps:
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ">=3.7"
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip pyyaml
	- name: Install compiler
	run: \|
	wget --no-verbose ${{ matrix.url_dir }}/l_fortran-compiler_p_${{ matrix.version }}_offline.sh
	/bin/sh l_fortran-compiler_p_${{ matrix.version }}_offline.sh -a --silent --cli --install-dir ${HOME}/intel --eula accept
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Run all test cases with host emulators
	run: \|
	source ${HOME}/intel/setvars.sh
	python3 util/developers/run_all_testcases.py harness --show_logs --compiler ifort
	- name: Run all test cases with pyfabm
	run: \|
	source ${HOME}/intel/setvars.sh
	python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifort
	env:
	FFLAGS: ${{ env.FFLAGS }} -fp-model precise -fp-model source
	ifx:
	# for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	include:
	- version: "2023.2.0.49254"
	url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/237236c4-434b-4576-96ac-020ceeb22619"
	fflags: -check all,nouninit,nocontiguous
	# nouninit because https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-missing-clang-rt-msan-to-link-Fortran-program-in-debug-build/m-p/1536555
	# nocontiguous because spurious errors occur when assigning null() to contiguous pointers, see https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-2024-0-2-runtime-error-about-non-contiguous-target/m-p/1583909
	#- version: "2024.0.2.28"
	# url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/41df6814-ec4b-4698-a14d-421ee2b02aa7"
	- version: "2024.2.0.426"
	url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181"
	fflags: -check all,nouninit,nocontiguous
	# memory sanitizer (uninit) still seems broken, as it reports errors in libc.so (it should be auto-linked to sanitized libc, but apparently not)
	# contiguous check still broken, to be fixed in 2025.x as per https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-2024-0-2-runtime-error-about-non-contiguous-target/m-p/1583909
	fail-fast: false
	runs-on: ubuntu-latest
	steps:
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ">=3.7"
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip pyyaml
	- name: Install compiler
	run: \|
	wget --no-verbose ${{ matrix.url_dir }}/l_fortran-compiler_p_${{ matrix.version }}_offline.sh
	/bin/sh l_fortran-compiler_p_${{ matrix.version }}_offline.sh -a --silent --cli --install-dir ${HOME}/intel --eula accept
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Run all test cases with host emulators
	run: \|
	source ${HOME}/intel/setvars.sh
	python3 util/developers/run_all_testcases.py harness --show_logs --compiler ifx
	env:
	FFLAGS: ${{ matrix.fflags }}
	- name: Run all test cases with pyfabm
	run: \|
	source ${HOME}/intel/setvars.sh
	python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifx
	env:
	FFLAGS: ${{ matrix.fflags }} -fp-model=precise
	nvfortran:
	# for available versions, see https://developer.nvidia.com/nvidia-hpc-sdk-releases
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	include:
	- version: "20.7" # released 2020-08
	exe: nvhpc_2020_207_Linux_x86_64_cuda_11.0
	# - version: "20.9" # released 2020-10
	# exe: nvhpc_2020_209_Linux_x86_64_cuda_11.0
	# - version: "22.9" # released 2022-10
	# exe: nvhpc_2022_229_Linux_x86_64_cuda_11.7
	# - version: "23.7" # released 2023-07
	# exe: nvhpc_2023_237_Linux_x86_64_cuda_12.2
	- version: "24.5" # released 2024-05
	exe: nvhpc_2024_245_Linux_x86_64_cuda_12.4
	fail-fast: false
	runs-on: ubuntu-latest
	env:
	FFLAGS: -Mbounds -Mchkptr
	steps:
	- name: Free up disk space
	run: \|
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf "$AGENT_TOOLSDIRECTORY"
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ">=3.7"
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip pyyaml
	- name: Install compiler
	run: \|
	wget --no-verbose https://developer.download.nvidia.com/hpc-sdk/${{ matrix.version }}/${{ matrix.exe }}.tar.gz
	tar xpzf ${{ matrix.exe }}.tar.gz
	rm ${{ matrix.exe }}.tar.gz
	${{ matrix.exe }}/install
	env:
	NVHPC_SILENT: true
	NVHPC_INSTALL_DIR: /home/runner/nvhpc
	NVHPC_INSTALL_TYPE: single
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Run all test cases with host emulators
	run: python3 util/developers/run_all_testcases.py harness --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
	- name: Run all test cases with pyfabm
	run: python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
	aocc:
	# for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/aocc/package.py
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	include:
	- version: "3.2.0" # released 2021-12-02 (LLVM 13.0)
	pyfabm_cmake_args: -DCMAKE_Fortran_FLAGS_DEBUG= # skip -g as that triggers segfault
	url_dir: https://download.amd.com/developer/eula/aocc-compiler
	# - version: "4.0.0" # released 2022-11-10 (LLVM 14.0.6)
	# url_dir: https://download.amd.com/developer/eula/aocc-compiler
	# - version: "4.1.0" # released 2023-08-04 (LLVM 16.0.3)
	# url_dir: https://download.amd.com/developer/eula/aocc/aocc-4-1
	- version: "4.2.0" # released 2024-02-27 (LLVM 16.0.3)
	url_dir: https://download.amd.com/developer/eula/aocc/aocc-4-2
	fail-fast: false
	runs-on: ubuntu-latest
	steps:
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ">=3.7"
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip pyyaml
	- name: Install compiler
	run: \|
	cd /home/runner
	wget --no-verbose ${{ matrix.url_dir }}/aocc-compiler-${{ matrix.version }}.tar
	tar xpf aocc-compiler-${{ matrix.version }}.tar
	rm aocc-compiler-${{ matrix.version }}.tar
	./aocc-compiler-${{ matrix.version }}/install.sh
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Run all test cases with host emulators
	run: \|
	source /home/runner/setenv_AOCC.sh
	python3 util/developers/run_all_testcases.py harness --show_logs --compiler flang
	- name: Run all test cases with pyfabm
	run: \|
	source /home/runner/setenv_AOCC.sh
	python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler flang ${{ matrix.pyfabm_cmake_args }}
	flang-new:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	os: [windows-latest]
	fail-fast: false
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: cmd /C call {0}
	env:
	CMAKE_GENERATOR: Ninja
	steps:
	- uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	- name: Install Python dependencies
	run: conda install -c conda-forge pyyaml flang>=19.0 ninja c-compiler
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Run all test cases with host emulators
	run: \|
	set CMAKE_GENERATOR_PLATFORM=
	set CMAKE_GENERATOR_TOOLSET=
	python util/developers/run_all_testcases.py harness --show_logs --compiler flang-new
	- name: Run all test cases with pyfabm
	run: \|
	set CMAKE_GENERATOR_PLATFORM=
	set CMAKE_GENERATOR_TOOLSET=
	python util/developers/run_all_testcases.py pyfabm --show_logs --compiler flang-new -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE
	pyfabm:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
	fail-fast: false
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Set up Python ${{ matrix.python-version }} with conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	channels: conda-forge
	- name: Install dependencies
	run: conda install pip python-build
	- name: Build distribution
	run: python -m build
	- name: Install
	run: python -m pip install -v .
	- name: Test
	run: \|
	python -c "import pyfabm;print('pyfabm version =', getattr(pyfabm, '__version__', None))"
	for f in testcases/*.yaml; do fabm_describe_model $f; done
	for f in testcases/*.yaml; do fabm_complete_yaml --add_missing $f; done
	- name: Run notebooks
	if: matrix.python-version != '3.7' # due to https://github.com/conda-forge/webcolors-feedstock/issues/26
	run: \|
	conda install ipython jupyterlab ipympl matplotlib scipy
	cd testcases/python
	for f in *.ipynb; do ipython --gui qt -c "%run $f"; done
	- name: Type checking with mypy
	if: matrix.python-version != '3.7'
	run: \|
	conda install mypy pyyaml
	mypy src/pyfabm
	- name: Install with customization via command line arguments
	run: \|
	rm -rf build
	python -m pip install -v -C--build-option=build_ext -C--build-option="--cmake-opts=-DFABM_INSTITUTES=examples" .
	- name: Install with customization via setup.cfg
	run: \|
	rm -rf build
	echo "[build_ext]" > setup.cfg
	echo "cmake_opts=-DFABM_INSTITUTES=examples" >> setup.cfg
	python -m pip install -v .
	fabm0d:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	runs-on: ubuntu-latest
	steps:
	- name: Install NetCDF
	run: \|
	sudo apt-get update
	sudo apt-get install libnetcdff-dev
	- name: Clone FABM
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Clone GOTM
	uses: actions/checkout@v4
	with:
	repository: gotm-model/code
	ref: v6.0
	path: gotm
	submodules: recursive
	- name: Build
	run: \|
	cmake -S src/drivers/0d -B build -DGOTM_BASE=gotm
	cmake --build build --target install
	stat ~/local/fabm/0d/bin/fabm0d
	cmake:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	strategy:
	matrix:
	cmake-version: ["3.13"]
	runs-on: ubuntu-latest
	steps:
	- name: Clone FABM
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Download and extract cmake
	run: \|
	wget --no-verbose https://cmake.org/files/v${{ matrix.cmake-version }}/cmake-${{ matrix.cmake-version }}.0-Linux-x86_64.tar.gz
	tar -xvf cmake-${{ matrix.cmake-version }}.0-Linux-x86_64.tar.gz
	- name: Build
	run: \|
	cmake-${{ matrix.cmake-version }}.0-Linux-x86_64/bin/cmake -S . -B build
	cmake-${{ matrix.cmake-version }}.0-Linux-x86_64/bin/cmake --build build --target install
	ninja:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	runs-on: ubuntu-latest
	steps:
	- name: Clone FABM
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Install Ninja
	run: \|
	sudo apt-get update
	sudo apt-get install ninja-build
	- name: Build
	run: \|
	cmake -S . -B build -G Ninja
	cmake --build build --target install
	binder:
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name != github.repository
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- name: Clone repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Set up Python with conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	environment-file: .binder/environment.yml
	activate-environment: fabm
	- name: Install
	run: .binder/postBuild
	env:
	REPO_DIR: .

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improve type hints based on mypy analysis #571

Workflow file

improve type hints based on mypy analysis #571

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