Bump codecov/codecov-action from 5 to 6 #33

	# Run benchmarks on pull requests (fork-safe: no secrets needed)
	# Results are uploaded as artifacts and tracked by bench-pr-track.yaml
	name: Benchmarks (PR run)

	on:
	pull_request:
	types: [opened, reopened, synchronize]

	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	jobs:
	benchmark:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v6

	- name: Install Linux dependencies
	run: \|
	sudo apt-get update
	sudo apt-get -y install hdf5-tools libsz2 libaec-dev

	- name: Setup R and Bioconductor
	uses: grimbough/bioc-actions/setup-bioc@v1
	with:
	bioc-version: devel

	- name: Install R dependencies
	uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: \|
	any::bench
	any::devtools
	any::jsonlite
	any::reticulate

	- name: Setup Python
	uses: actions/setup-python@v6
	with:
	python-version: '3.x'

	- name: Install Python dependencies
	run: pip install anndata dummy-anndata

	- name: Configure reticulate
	run: echo "RETICULATE_PYTHON=$(which python)" >> $GITHUB_ENV

	- name: Run benchmarks
	run: Rscript benchmarks/run_benchmarks.R --output benchmark_results.json

	- name: Upload benchmark results
	uses: actions/upload-artifact@v7
	with:
	name: benchmark_results.json
	path: ./benchmark_results.json

	- name: Upload PR event
	uses: actions/upload-artifact@v7
	with:
	name: event.json
	path: ${{ github.event_path }}

Provide feedback