Fix stubgen #54
Workflow file for this run
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# Copyright (C) 2024 Roberto Rossini (roberros@uio.no) | |
# SPDX-License-Identifier: MIT | |
name: Run fuzzy tests | |
on: | |
push: | |
branches: [main] | |
paths: | |
- ".github/workflows/fuzzy-testing.yml" | |
- "cmake/**" | |
- "src/**" | |
- "test/scripts/fuzzer.py" | |
- "utils/devel/stubgen.py" | |
- "utils/devel/symlink_pyarrow_libs.py" | |
- "CMakeLists.txt" | |
- "conanfile.py" | |
- "pyproject.toml" | |
pull_request: | |
paths: | |
- "cmake/**" | |
- "src/**" | |
- "test/scripts/fuzzer.py" | |
- "utils/devel/stubgen.py" | |
- "utils/devel/symlink_pyarrow_libs.py" | |
- "CMakeLists.txt" | |
- "conanfile.py" | |
- "pyproject.toml" | |
schedule: | |
# Run weekly | |
- cron: "15 3 * * 0" | |
workflow_dispatch: | |
inputs: | |
duration: | |
description: "Test duration in seconds" | |
required: true | |
default: "600" | |
type: string | |
resolution: | |
description: "Matrix resolution to use for testing" | |
required: true | |
default: "random" | |
type: string | |
# https://stackoverflow.com/a/72408109 | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
defaults: | |
run: | |
shell: bash | |
jobs: | |
build-project: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
include: | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "NONE", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "weight", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "VC", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "NONE", | |
bin-type: "variable", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic8", | |
normalization: "NONE", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic8", | |
normalization: "KR", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic9", | |
normalization: "NONE", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic9", | |
normalization: "VC", | |
bin-type: "fixed", | |
} | |
container: | |
image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19 | |
options: "--user=root" | |
env: | |
CCACHE_DISABLE: "1" | |
CONAN_HOME: "/opt/conan/" | |
HICTK_CI: "1" | |
steps: | |
- name: Clone hictkpy | |
uses: actions/checkout@v4 | |
- name: Fix permissions | |
run: | | |
chown -R $(id -u):$(id -g) $PWD | |
- name: Generate cache key | |
id: cache-key | |
run: | | |
hash="${{ hashFiles('conanfile.py') }}" | |
echo "key=fuzzer-$hash" >> $GITHUB_OUTPUT | |
- name: Install Python | |
run: | | |
apt-get update | |
apt-get install -y python3.12 python3.12-dev | |
- name: Restore Conan cache | |
id: cache-conan | |
uses: actions/cache/restore@v4 | |
with: | |
key: conan-${{ steps.cache-key.outputs.key }} | |
path: ${{ env.CONAN_HOME }}/p | |
- name: Clean Conan cache (pre-build) | |
if: steps.cache-conan.outputs.cache-hit != 'true' | |
run: | | |
conan cache clean "*" --build | |
conan cache clean "*" --download | |
conan cache clean "*" --source | |
conan remove --confirm "*" | |
- name: Build and install | |
run: pip install --verbose '.[all]' | |
- name: Clean Conan cache (post-build) | |
if: steps.cache-conan.outputs.cache-hit != 'true' | |
run: | | |
conan cache clean "*" --build | |
conan cache clean "*" --download | |
conan cache clean "*" --source | |
- name: Save Conan cache | |
uses: actions/cache/save@v4 | |
if: steps.cache-conan.outputs.cache-hit != 'true' | |
with: | |
key: conan-${{ steps.cache-key.outputs.key }} | |
path: ${{ env.CONAN_HOME }}/p | |
- name: Install test dependencies | |
run: | | |
pip install --no-cache-dir 'cooler==0.10.*' 'numpy<2' | |
- name: Detect CI type | |
id: ci-type | |
run: | | |
if git log --format=%B -n 1 ${{ github.event.after }} | grep -qF '[ci full]'; then | |
echo "type=full" >> $GITHUB_OUTPUT | |
else | |
echo "type=short" >> $GITHUB_OUTPUT | |
fi | |
- name: Prepare for test | |
id: test-params | |
run: | | |
duration=120 | |
if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
duration='${{ inputs.duration }}' | |
elif [[ '${{ steps.ci-type.outputs.type }}' == 'full' ]]; then | |
duration=3600 | |
fi | |
resolution=50000 | |
if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
if [[ '${{ inputs.resolution }}' == 'random' ]]; then | |
resolution="$( | |
python3 -c 'import random; import sys; print(random.choice([int(x) for x in sys.argv[1:]]))' \ | |
1000 5000 10000 50000 100000 500000 | |
)" | |
else | |
resolution='${{ inputs.resolution }}' | |
fi | |
fi | |
if [[ '${{ matrix.bin-type }}' == variable ]]; then | |
resolution=0 | |
fi | |
2>&1 echo "Duration: ${duration}" | |
2>&1 echo "Resolution: ${resolution}" | |
echo "duration=$duration" | tee -a "$GITHUB_OUTPUT" | |
echo "resolution=$resolution" | tee -a "$GITHUB_OUTPUT" | |
- name: Clone hictk | |
uses: actions/checkout@v4 | |
with: | |
repository: "paulsengroup/hictk" | |
path: hictk | |
- name: Download test datasets | |
run: | | |
hictk/test/fuzzer/scripts/download_test_datasets.py \ | |
hictk/test/fuzzer/test_files.json \ | |
. \ | |
--format cool "${{ matrix.format }}" \ | |
--resolution "${{ steps.test-params.outputs.resolution }}" \ | |
--dataset "${{ matrix.dataset }}" \ | |
--nproc 2 | |
- name: Run test (df) | |
run: | | |
test/scripts/fuzzer.py \ | |
--resolution ${{ steps.test-params.outputs.resolution }} \ | |
--duration '${{ steps.test-params.outputs.duration }}' \ | |
--normalization ${{ matrix.normalization }} \ | |
--nproc $(nproc) \ | |
--format df \ | |
*".${{ matrix.format }}" \ | |
*.cool | |
- name: Run test (numpy) | |
run: | | |
test/scripts/fuzzer.py \ | |
--resolution ${{ steps.test-params.outputs.resolution }} \ | |
--duration '${{ steps.test-params.outputs.duration }}' \ | |
--normalization ${{ matrix.normalization }} \ | |
--nproc $(nproc) \ | |
--format numpy \ | |
*".${{ matrix.format }}" \ | |
*.cool | |
- name: Run test (coo) | |
run: | | |
test/scripts/fuzzer.py \ | |
--resolution ${{ steps.test-params.outputs.resolution }} \ | |
--duration '${{ steps.test-params.outputs.duration }}' \ | |
--normalization ${{ matrix.normalization }} \ | |
--nproc $(nproc) \ | |
--format csr \ | |
*".${{ matrix.format }}" \ | |
*.cool | |
fuzzy-testing-status-check: | |
name: Status Check (fuzzy-testing) | |
if: ${{ always() }} | |
runs-on: ubuntu-latest | |
needs: | |
- build-project | |
steps: | |
- name: Collect job results | |
if: needs.build-project.result != 'success' | |
run: exit 1 |