fix(benchmark-report): drop task cost fallback #430

Workflow file for this run

	# This workflow runs the pipeline tests and benchmark-report checks
	name: Pipeline CI
	on:
	pull_request:
	release:
	types: [published]
	merge_group:
	types:
	- checks_requested
	branches:
	- master
	- dev

	env:
	NXF_ANSI_LOG: false
	NFT_VER: "0.9.2"
	NFT_WORKDIR: "~"
	NFT_DIFF: "pdiff"
	NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
	TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}

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

	jobs:
	changes:
	name: Check for changes
	runs-on: ubuntu-latest
	outputs:
	nf_test_files: ${{ steps.list.outputs.components }}
	benchmark_pytest: ${{ steps.benchmark.outputs.benchmark_pytest }}
	benchmark_smoke: ${{ steps.benchmark.outputs.benchmark_smoke }}
	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0

	- name: List nf-test files
	id: list
	uses: adamrtalbot/detect-nf-test-changes@v0.0.3
	with:
	head: ${{ github.sha }}
	base: ${{ github.event.pull_request.base.sha \|\| github.event.merge_group.base_sha \|\| github.sha }}
	include: .github/include.yaml

	- name: print list of nf-test files
	run: \|
	echo ${{ steps.list.outputs.components }}

	- name: Detect benchmark report changes
	id: benchmark
	shell: bash
	env:
	EVENT_NAME: ${{ github.event_name }}
	PR_BASE_SHA: ${{ github.event.pull_request.base.sha }}
	MERGE_GROUP_BASE_SHA: ${{ github.event.merge_group.base_sha }}
	HEAD_SHA: ${{ github.sha }}
	run: \|
	if [[ "$EVENT_NAME" == "pull_request" ]]; then
	BASE_SHA="$PR_BASE_SHA"
	elif [[ "$EVENT_NAME" == "merge_group" ]]; then
	BASE_SHA="$MERGE_GROUP_BASE_SHA"
	else
	echo "benchmark_pytest=false" >> "$GITHUB_OUTPUT"
	echo "benchmark_smoke=false" >> "$GITHUB_OUTPUT"
	echo "Benchmark report checks are disabled for event: $EVENT_NAME"
	exit 0
	fi

	echo "Comparing benchmark-report surfaces between $BASE_SHA and $HEAD_SHA"
	CHANGED_FILES="$(git diff --name-only "$BASE_SHA" "$HEAD_SHA")"
	export CHANGED_FILES GITHUB_OUTPUT

	python <<'PY'
	import fnmatch
	import os

	changed = [line.strip() for line in os.environ.get("CHANGED_FILES", "").splitlines() if line.strip()]
	pytest_patterns = [
	".github/workflows/ci.yml",
	".github/include.yaml",
	"bin/aggregate_benchmark_report_data.py",
	"bin/benchmark_report.py",
	"bin/benchmark_report_aggregate.py",
	"bin/benchmark_report_normalize.py",
	"bin/benchmark_report_render.py",
	"bin/benchmark_report_template.html",
	"bin/normalize_benchmark_jsonl.py",
	"bin/render_benchmark_report.py",
	"bin/test_benchmark_report_fetch.py",
	"conftest.py",
	"modules/local/aggregate_benchmark_report_data/**",
	"modules/local/normalize_benchmark_jsonl/**",
	"modules/local/render_benchmark_report/**",
	"scripts/build_filtered_cost_sidecar.py",
	"tests/pipeline_benchmark_/*",
	"workflows/nf_aggregate/assets/log_dirs/**",
	"workflows/nf_aggregate/assets/logs/**",
	"workflows/nf_aggregate/assets/realworld_log_dirs/**",
	"workflows/nf_aggregate/assets/test_benchmark*.csv",
	"workflows/nf_aggregate/assets/test_benchmark*.parquet",
	]
	smoke_patterns = pytest_patterns + [
	"assets/brand.yml",
	"assets/schema_input.json",
	"main.nf",
	"modules/local/extract_tarball/**",
	"nextflow.config",
	"nextflow_schema.json",
	"workflows/nf_aggregate/main.nf",
	"workflows/nf_aggregate/nextflow.config",
	]

	def matched_files(patterns):
	return sorted({
	path for path in changed
	if any(fnmatch.fnmatch(path, pattern) for pattern in patterns)
	})

	pytest_matches = matched_files(pytest_patterns)
	smoke_matches = matched_files(smoke_patterns)

	print("Benchmark-report pytest matches:")
	if pytest_matches:
	for path in pytest_matches:
	print(f" - {path}")
	else:
	print(" (none)")

	print("Benchmark-report smoke matches:")
	if smoke_matches:
	for path in smoke_matches:
	print(f" - {path}")
	else:
	print(" (none)")

	with open(os.environ["GITHUB_OUTPUT"], "a", encoding="utf-8") as fh:
	fh.write(f"benchmark_pytest={'true' if pytest_matches else 'false'}\n")
	fh.write(f"benchmark_smoke={'true' if smoke_matches else 'false'}\n")
	PY

	test:
	name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
	needs: [changes]
	if: needs.changes.outputs.nf_test_files != '[]'
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	NXF_VER:
	- "latest-everything"
	nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
	profile:
	- "docker"

	steps:
	- name: Check out pipeline code
	uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v2
	with:
	version: "${{ matrix.NXF_VER }}"

	- uses: actions/setup-python@v4
	with:
	python-version: "3.11"
	architecture: "x64"

	- name: Install pdiff to see diff between nf-test snapshots
	run: \|
	python -m pip install --upgrade pip
	pip install pdiff

	- name: Cache nf-test installation
	id: cache-software
	uses: actions/cache@v3
	with:
	path: \|
	/usr/local/bin/nf-test
	/home/runner/.nf-test/nf-test.jar
	key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest

	- name: Install nf-test
	if: steps.cache-software.outputs.cache-hit != 'true'
	run: \|
	wget -qO- https://code.askimed.com/install/nf-test \| bash
	sudo mv nf-test /usr/local/bin/

	- name: Run nf-test
	run: \|
	nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap

	- uses: pcolby/tap-summary@v1
	with:
	path: >-
	test.tap

	- name: Output log on failure
	if: failure()
	run: \|
	sudo apt install bat > /dev/null
	batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log

	- name: Publish Test Report
	uses: mikepenz/action-junit-report@v3
	if: always() # always run even if the previous step fails
	with:
	report_paths: test.xml

	benchmark-report-pytest:
	name: Benchmark report pytest
	needs: [changes]
	if: needs.changes.outputs.benchmark_pytest == 'true'
	runs-on: ubuntu-latest
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1

	- uses: actions/setup-python@v4
	with:
	python-version: "3.12"
	architecture: "x64"

	- name: Install uv
	run: \|
	python -m pip install --upgrade pip
	pip install uv

	- name: Run benchmark report pytest suites
	run: \|
	uv run --with typer --with pyyaml --with jinja2 --with pyarrow --with pytest --with httpx pytest -v modules/local/aggregate_benchmark_report_data/tests/test_aggregate.py modules/local/normalize_benchmark_jsonl/tests/test_normalize.py modules/local/render_benchmark_report/tests/test_render.py bin/test_benchmark_report_fetch.py

	benchmark-report-smoke:
	name: Benchmark report smoke test
	needs: [changes]
	if: needs.changes.outputs.benchmark_smoke == 'true'
	runs-on: ubuntu-latest
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v2
	with:
	version: "latest-everything"

	- name: Run offline benchmark smoke test
	run: \|
	cat > benchmark-smoke-params.json <<'JSON'
	{
	"input": "workflows/nf_aggregate/assets/test_benchmark.csv",
	"generate_benchmark_report": true,
	"outdir": "benchmark-smoke-results"
	}
	JSON
	nextflow run . -params-file benchmark-smoke-params.json -profile docker

	confirm-pass:
	runs-on: ubuntu-latest
	needs:
	- changes
	- test
	- benchmark-report-pytest
	- benchmark-report-smoke
	if: always()
	steps:
	- name: All tests ok
	if: ${{ !contains(needs.*.result, 'failure') }}
	run: exit 0
	- name: One or more tests failed
	if: ${{ contains(needs.*.result, 'failure') }}
	run: exit 1

	- name: debug-print
	if: always()
	run: \|
	echo "toJSON(needs) = ${{ toJSON(needs) }}"
	echo "toJSON(needs..result) = ${{ toJSON(needs..result) }}"

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fix(benchmark-report): drop task cost fallback #430

Workflow file

fix(benchmark-report): drop task cost fallback #430

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Workflow file for this run