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Fix stubgen

Fix stubgen #54

Workflow file for this run

# 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