Update sphinx-rtd-theme requirement from <3.0,>=1.0 to >=1.0,<4.0 #837

Workflow file for this run

	# 1.) Format and Lint code
	# 2.) Test code
	#
	# See:
	# https://docs.github.com/en/actions/guides/building-and-testing-python

	# Keep in sync with `test-skip.yml`.

	name: "Tests"

	on:
	push:
	branches:
	- "**"
	paths:
	- ".github/**"
	- "**.py"
	- "**.rst"
	- "docs/**"
	- ".flake8"
	- "pyproject.toml"
	- "*requirements.txt"
	tags:
	- "v[0-9]*"
	release:

	jobs:
	# TODO: The lint job can be removed in favor of pre-commit.ci when all
	# files are formatted with black and are compliant with flake8.
	lint:
	strategy:
	matrix:
	os:
	- "ubuntu-latest"
	python-version:
	- "3.9"
	runs-on: "${{ matrix.os }}"
	steps:
	- name: "Checkout repository"
	uses: "actions/checkout@v4"
	- name: "Set up Python ${{ matrix.python-version }}"
	uses: "actions/setup-python@v5"
	with:
	python-version: "${{ matrix.python-version }}"
	- name: "Export ${HOME}/.local/bin to ${PATH}"
	# Executable Python binaries are usually stored there.
	run: 'echo "${HOME}/.local/bin" >> ${GITHUB_PATH}'
	- name: "Get pip cache dir"
	# pip's cache path depends on the operating system. See
	# https://github.com/actions/cache/blob/main/examples.md#python---pip
	# This requires pip >=20.1.
	id: "pip-cache"
	run: \|
	python -m pip install --user --upgrade pip
	echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
	- name: "Create/Restore cache"
	uses: "actions/cache@v4"
	with:
	path: "${{ steps.pip-cache.outputs.dir }}/**"
	key: \|
	${{ runner.os }}-${{ matrix.python-version }}-${{ github.job }}
	restore-keys: \|
	${{ runner.os }}-${{ matrix.python-version }}
	${{ runner.os }}
	- name: "Install/Upgrade setuptools and wheel"
	run: "python -m pip install --user --upgrade setuptools wheel"
	- name: "Install/Upgrade packages in requirements-dev.txt"
	run: \|
	python -m pip install \
	--user \
	--upgrade \
	--requirement requirements-dev.txt
	- name: "Check code formatting with black"
	# TODO: The --include flag should be removed once all files are
	# formatted with black. But as long as this is not the case,
	# only check those files that are already formatted.
	run: \|
	python -m black ./ --check --diff --color \
	--include \
	docs/source/conf.py \
	misc/*.py \
	src/mdtools/__init__.py \
	src/mdtools/_metadata.py \
	src/mdtools/box.py \
	src/mdtools/dtrj.py \
	src/mdtools/file_handler.py \
	src/mdtools/functions.py \
	src/mdtools/numpy_helper_functions.py \
	src/mdtools/plot.py \
	src/mdtools/run_time_info.py \
	src/mdtools/scipy_helper_functions.py \
	src/mdtools/select.py \
	src/mdtools/statistics.py \
	src/mdtools/structure.py \
	src/mdtools/version.py \
	scripts/discretization/back_jump*.py \
	scripts/discretization/discrete_pos.py \
	scripts/discretization/kaplan_meier*.py \
	scripts/discretization/plot_*.py \
	scripts/discretization/state_lifetime* \
	scripts/dynamics/extract_renewal_events.py \
	scripts/dynamics/lifetime_autocorr*.py \
	scripts/dynamics/msd_layer*.py \
	scripts/dynamics/plot_msd_layer*.py \
	scripts/gmx/*.py \
	scripts/other/*.py \
	scripts/structure/densmap.py \
	scripts/structure/lig_change_at_pos_change_blocks.py \
	scripts/structure/subvolume_charge.py \
	scripts/structure/plot_gmx_densmap.py \
	scripts/structure/rmsd_vs_time.py \
	scripts/templates/*.py \
	*.py
	- name: "Lint code and docstrings with flake8"
	# Use setup.cfg to configure flake8
	# TODO: The --select flag should be removed once all files are
	# revised to be compliant with flake8. But as long as this is
	# not the case, select only those error codes that have been
	# fixed in all files.
	#
	# F821 ("undefined name name") gives false positives in
	# doctests, because it does not recognize `doctest_global_setup`
	# in the Sphinx configuration file `conf.py`.
	#
	# W504 ("line break after binary operator") is turned on in the
	# .flake config file but the error code isn't fixed in all
	# files, yet. So, ignore it in the CI workflow for now.
	#
	# The other ignored error codes are copied from the .flake8
	# config file.
	run: \|
	python -m flake8 ./ \
	--select=\
	E1,E2,E3,E4,E9,\
	F4,F7,F63,F82,\
	W1,W2,W3 \
	--extend-ignore=\
	S101,\
	D205,D400,\
	E203,W503,\
	S404,S603,\
	B028,\
	N806,N813,\
	W504,\
	F821

	test:
	strategy:
	matrix:
	# Tests must be run on all target platforms and Python versions.
	# Python <3.8 is not supported in the MacOS 14 runner.
	os:
	- "ubuntu-latest"
	- "macos-13"
	- "windows-latest"
	python-version:
	- "3.6"
	- "3.7"
	- "3.8"
	- "3.9"
	# Python 3.6 is not supported anymore in the Ubuntu 22.04 runner
	# https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
	exclude:
	- os: "ubuntu-latest"
	python-version: "3.6"
	include:
	- os: "ubuntu-20.04"
	python-version: "3.6"
	# Do not cancel in-progress jobs if any matrix job fails
	fail-fast: false
	runs-on: "${{ matrix.os }}"
	steps:
	- name: "Checkout repository"
	uses: "actions/checkout@v4"
	- name: "Set up Python ${{ matrix.python-version }}"
	uses: "actions/setup-python@v5"
	with:
	python-version: "${{ matrix.python-version }}"
	- name: "Export ${HOME}/.local/bin to ${PATH}"
	# Executable Python binaries are usually stored there.
	run: 'echo "${HOME}/.local/bin" >> ${GITHUB_PATH}'
	- name: "Get pip cache dir"
	# pip's cache path depends on the operating system. See
	# https://github.com/actions/cache/blob/main/examples.md#python---pip
	# This requires pip >=20.1.
	id: "pip-cache"
	run: \|
	python -m pip install --user --upgrade pip
	echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
	- name: "Create/Restore cache"
	uses: "actions/cache@v4"
	with:
	path: \|
	${{ steps.pip-cache.outputs.dir }}/**
	./docs/build/**
	key: \|
	${{ runner.os }}-${{ matrix.python-version }}-${{ github.job }}
	restore-keys: \|
	${{ runner.os }}-${{ matrix.python-version }}
	${{ runner.os }}
	- name: "Install/Upgrade setuptools and wheel"
	# MDAnalysis requires NumPy (>=1.19.2) for setup (see also
	# https://github.com/MDAnalysis/mdanalysis/issues/3374#issuecomment-889189979).
	# MDAnalysis <3.0 requires Cython <3.0 (see
	# https://github.com/MDAnalysis/mdanalysis/pull/4129 and
	# https://github.com/cython/cython/issues/3690).
	# Strangely, without `python-dev-tools` the installation of
	# MDAnalysis might fail while building the wheel.
	run: \|
	python -m pip install --user --upgrade setuptools wheel
	python -m pip install --user --upgrade python-dev-tools
	python -m pip install --user "Cython <3.0"
	python -m pip install --user "numpy >=1.19.2"
	- name: "Test installation of MDTools"
	run: \|
	python -m pip install --user .
	python -c "import mdtools"
	# Test import of all modules that must be loaded explicitly.
	python -c "import mdtools.plot"
	- name: "Install/Upgrade requirements to build the documentation"
	run: \|
	python -m pip install --user --upgrade -r docs/requirements-docs.txt
	- name: "Test build of the documentation"
	run: "make -C ./docs/ html"
	- name: "doctest"
	# Because the default dtypes of NumPy arrays are different on
	# Windows, doctest will detect false failures. See e.g.
	# https://stackoverflow.com/questions/36278590/numpy-array-dtype-is-coming-as-int32-by-default-in-a-windows-10-64-bit-machine
	if: "${{ runner.os != 'Windows' }}"
	run: "make -C ./docs/ doctest"
	- name: "linkcheck"
	if: "${{ runner.os == 'Linux' && matrix.python-version == '3.9' }}"
	run: "make -C ./docs/ linkcheck"
	- name: "Install/Upgrade PyTest"
	run: "python -m pip install --user --upgrade pytest"
	- name: "Test code with pytest"
	run: "python -m pytest ./"

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Update sphinx-rtd-theme requirement from <3.0,>=1.0 to >=1.0,<4.0 #837

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Update sphinx-rtd-theme requirement from <3.0,>=1.0 to >=1.0,<4.0 #837

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