perf: fix 120k-frame OOM in compute_rmsd_matrix and speed up cluster_… #167

	name: CI

	on:
	pull_request:
	push:
	branches: [main]
	workflow_dispatch:

	permissions:
	contents: read

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	ci:
	name: CI (py${{ matrix.python-version }})
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.12", "3.13"]
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@v6

	- name: Setup Conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: mdpp
	auto-activate: true
	channels: conda-forge,defaults
	channel-priority: strict
	python-version: ${{ matrix.python-version }}
	use-mamba: true

	- name: Install dependencies
	run: bash setup.sh

	- name: Run pre-commit hooks
	run: pre-commit run --all-files --show-diff-on-failure

	- name: Run tests
	run: pytest -n auto

	- name: Build docs
	run: mkdocs build --strict

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