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doc & skpkg: move `doc/manual` to `docs/` and update pre-commit config file #8

	name: Tests on PR

	on:
	pull_request:
	workflow_dispatch:

	jobs:
	tests-on-pr:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out libdiffpy
	uses: actions/checkout@v6
	with:
	fetch-depth: 0

	- name: Initialize miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: test
	channels: conda-forge
	conda-remove-defaults: "true"
	auto-update-conda: true
	auto-activate-base: false

	- name: Conda config
	run: >-
	conda config --set always_yes yes
	--set changeps1 no

	- name: Install requirements
	run: >-
	conda install
	--file requirements/build.txt
	--file requirements/conda.txt
	--file requirements/tests.txt

	- name: Configure SCons for the conda environment
	run: \|
	cat > sconscript.local <<'EOF'
	Import('env')
	import os
	prefix = os.environ['CONDA_PREFIX']
	env.Replace(CXX=os.path.join(prefix, 'bin', 'c++'))
	env.Prepend(CCFLAGS=['-isystem' + os.path.join(prefix, 'include')])
	env.Append(LIBPATH=os.path.join(prefix, 'lib'))
	env.Append(LINKFLAGS='-Wl,-rpath,' + os.path.join(prefix, 'lib'))
	EOF

	- name: Build and run C++ tests with coverage
	run: \|
	"$CONDA_PREFIX/bin/c++" --version
	scons build=coverage test

	- name: Generate coverage report
	run: >-
	gcovr --gcov-executable "$CONDA_PREFIX/bin/gcov"
	--root . --filter 'build/coverage-.*/diffpy/'
	--xml coverage.xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v5
	with:
	files: coverage.xml
	verbose: true
	fail_ci_if_error: true
	token: ${{ secrets.CODECOV_TOKEN }}