move all REMARKs parsing into read_metadata_from_remarks() #1109

Workflow file for this run

	name: CI

	on: [push, pull_request]

	jobs:
	macos14:
	name: "macOS 14"
	runs-on: macos-14
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	env:
	SKBUILD_CMAKE_ARGS: "-DEXTRA_WARNINGS=ON;-DFETCH_ZLIB_NG=ON"
	SKBUILD_CMAKE_TARGETS: "all;check"
	steps:
	- uses: actions/checkout@v4
	- name: Build wheel and install
	run: \|
	python3 -m venv pyenv
	source pyenv/bin/activate
	python3 -m pip install wheel
	python3 -m pip wheel -v .
	python3 -m pip install gemmi-*.whl
	- name: Python Tests
	run: \|
	source pyenv/bin/activate
	python3 -m unittest discover -v -s tests/
	python3 -m pip install sphinx
	cd docs
	sphinx-build -M doctest . _build -n -E
	- uses: actions/upload-artifact@v4
	with:
	name: gemmi-macos14
	path: \|
	./gemmi-*.whl
	retention-days: 14

	macos12:
	name: "macOS 12 (w/o python)"
	runs-on: macos-12
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	steps:
	- uses: actions/checkout@v4
	- name: mkdir build
	run: cmake -E make_directory ${{runner.workspace}}/build
	- name: CMake Build
	working-directory: ${{runner.workspace}}/build
	shell: bash
	run: \|
	cmake --version
	cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=MinSizeRel -DBUILD_SHARED_LIBS=OFF
	cmake --build . -j3
	cmake --build . --target check -j3
	- name: Install
	working-directory: ${{runner.workspace}}/build
	shell: bash
	run: sudo cmake --install .
	- name: Test
	run: \|
	ctest --output-on-failure
	python3 tests/test_prog.py
	- uses: actions/upload-artifact@v4
	with:
	name: gemmi-macos12
	path: \|
	${{runner.workspace}}/build/gemmi
	${{runner.workspace}}/build/libgemmi*
	retention-days: 14

	windows2022:
	name: "Windows 2022"
	runs-on: windows-2022
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	env:
	SKBUILD_CMAKE_ARGS: "-DFETCH_ZLIB_NG=ON"
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: "3.10"
	- name: build and test
	run: \|
	python -m pip install -v .
	python -m pip install numpy
	python -m unittest discover -v -s tests/
	- name: run doctest
	working-directory: ./docs
	run: \|
	python -m pip install sphinx
	sphinx-build -M doctest . _build -n -E

	ubuntu2404:
	name: "Ubuntu 24.04"
	runs-on: ubuntu-24.04
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	steps:
	- uses: actions/checkout@v4
	- name: apt-get
	run: \|
	sudo apt-get update
	sudo apt-get install python3-full g++ gfortran python3-numpy
	- name: build and test
	run: \|
	g++ --version
	python3 -m venv pyenv
	source pyenv/bin/activate
	export SKBUILD_CMAKE_ARGS='-DFETCH_ZLIB_NG=ON;-DCMAKE_BUILD_TYPE=None'
	python3 -m pip install -v .
	python3 -m unittest discover -v -s tests/
	- name: run doctest
	run: \|
	source pyenv/bin/activate
	python3 -m pip install -U sphinx
	cd docs
	sphinx-build -M doctest . _build -n -E

	ubuntu2204:
	name: "Ubuntu 22.04"
	runs-on: ubuntu-22.04
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	steps:
	- uses: actions/checkout@v4
	- name: apt-get
	run: \|
	sudo apt-get update
	sudo apt-get install libz-dev python3-pip g++ gfortran python3-numpy
	- name: install pybind11
	run: \|
	git clone --depth=1 https://github.com/pybind/pybind11.git
	#cd pybind11
	#cmake . -Wno-dev -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYBIND11_TEST=OFF
	#make
	#sudo make install
	- name: build and test
	run: \|
	g++ --version
	cmake --version
	mkdir build
	cd build
	cmake .. -DCMAKE_BUILD_TYPE=MinSizeRel -DUSE_FORTRAN=1 -DEXTRA_WARNINGS=1 -DUSE_PYTHON=1 -DPython_EXECUTABLE=/usr/bin/python3 -DBUILD_SHARED_LIBS=ON -DCMAKE_CXX_VISIBILITY_PRESET=hidden
	make -j2
	make -j2 check
	sudo make install
	python3 -m unittest discover -v -s ../tests/
	strip --strip-unneeded ./gemmi ./gemmi.cpython*.so
	- name: run doctest
	run: \|
	sudo python3 -m pip install -U sphinx
	export PYTHONPATH=$PWD/build
	cd docs
	sphinx-build -M doctest . _build -n -E

	ubuntu2004:
	name: "Ubuntu 20.04"
	runs-on: ubuntu-20.04
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	steps:
	- uses: actions/checkout@v4
	- name: apt-get
	run: \|
	sudo apt-get update
	sudo apt-get install libz-dev python3-pip g++ gfortran python3-numpy valgrind
	- name: install pybind11
	run: \|
	python3 -m pip install pybind11
	- name: build and test
	run: \|
	g++ --version
	cmake --version
	mkdir build
	cd build
	cmake .. -DCMAKE_BUILD_TYPE=Debug -DUSE_PYTHON=1 -DPython_EXECUTABLE=python3 -DBUILD_SHARED_LIBS=OFF
	cmake --build . --config Debug -j2
	cmake --build . --config Debug --target check -j2
	sudo cmake --install . --config Debug
	cd ..
	python3 -m unittest discover -v -s tests/
	- name: run doctest
	run: \|
	sudo pip3 install -U sphinx
	cd docs
	sphinx-build -M doctest . _build -n -E
	- name: run tests under valgrind
	run: PYTHONMALLOC=malloc valgrind python3 -m unittest discover -v -s tests/

	ubuntu2004_clang6:
	name: "Ubuntu 20.04 with Clang 6.0"
	runs-on: ubuntu-20.04
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	env:
	CC: clang-6.0
	CXX: clang++-6.0
	SKBUILD_CMAKE_ARGS: "-DCMAKE_CXX_STANDARD=11;-DEXTRA_WARNINGS=ON;-DSTANDALONE_PYTHON_MODULE=OFF"
	SKBUILD_CMAKE_TARGETS: "all;check"
	steps:
	- uses: actions/checkout@v4
	- run: sudo apt-get install clang-6.0 libz-dev python3-pip python3-numpy
	- name: install pybind11
	run: \|
	sudo /usr/bin/python3 -m pip install "pybind11[global]" build
	- name: build and test
	run: \|
	$CXX --version
	python3 -m build --sdist
	python3 -m pip install -v dist/gemmi-*.tar.gz
	python3 -m unittest discover -v -s tests/
	- name: run doctest
	run: \|
	python3 -m pip install -U sphinx
	cd docs
	sphinx-build -M doctest . _build -n -E

	almalinux:
	runs-on: ubuntu-latest
	name: "AlmaLinux 8"
	container: almalinux:8
	if: "!contains(github.event.head_commit.message, '[skip ci]')"
	steps:
	- uses: actions/checkout@v4
	- name: yum
	run: \|
	dnf update -y
	dnf install -y gcc-c++ cmake make git python38-devel python38-pip
	python3.8 -m pip install -U numpy
	g++ --version
	python3.8 --version
	cmake --version
	type python3.8
	- name: install pybind11
	run: \|
	git clone --branch stable --depth=1 https://github.com/pybind/pybind11.git
	cd pybind11
	cmake . -Wno-dev -DPYTHON_EXECUTABLE=/usr/bin/python3.8 -DPYBIND11_TEST=OFF
	make
	make install
	- name: build and test
	run: \|
	pwd
	cmake . -DUSE_PYTHON=1 -DPython_EXECUTABLE=/usr/bin/python3.8 -DFETCH_ZLIB_NG=ON
	make -j2
	make -j2 check
	make install
	python3.8 -m unittest discover -v -s ./tests/
	strip --strip-unneeded ./gemmi ./gemmi.cpython*.so
	- name: run doctest
	run: \|
	python3.8 -m pip install -U sphinx
	cd docs
	PYTHONPATH=.. sphinx-build -M doctest . _build -n -E
	- uses: actions/upload-artifact@v4
	with:
	name: gemmi-linux
	path: \|
	./gemmi
	./libgemmi_cpp.so
	./gemmi.cpython*.so
	retention-days: 14

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move all REMARKs parsing into read_metadata_from_remarks() #1109

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move all REMARKs parsing into read_metadata_from_remarks() #1109

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