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ci-inference.yml
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# Lingfei Wang, 2022. All rights reserved.
name: Network inference tests
on:
push:
branches:
- master
- dev
paths:
- 'setup.py'
- 'src/**'
- 'bin/**'
- '.github/workflows/ci-inference.yml'
- '.github/actions/install-bash/**'
- '.github/actions/zenodo-url-translate/**'
- '.github/actions/inference-test-dataset/**'
- '.github/scripts/inference-test-dataset.py'
jobs:
test-skin1:
name: Skin static network end-to-end tests
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9","3.10"]
steps:
- uses: actions/checkout@v4
- name: Install
uses: ./.github/actions/install-bash
with:
python-version: ${{ matrix.python-version }}
- name: Get dataset URL
id: zenodo-url-translate
uses: ./.github/actions/zenodo-url-translate
with:
url: https://zenodo.org/records/6858494/files/inference-skin1.tar.xz?download=1
- name: Test dataset
uses: ./.github/actions/inference-test-dataset
with:
url: ${{ steps.zenodo-url-translate.outputs.url }}
test-path: ci_testspace
makefile: static.mk
expected-folder: test/tmp_static_expected
actual-folder: tmp_static
expected-h5: test/output/static_expected.h5
actual-h5: output/static.h5
makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "mm", "JOINT": "1", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}'
exclusions: 'footprints.bed net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz net_nweight.tsv.gz net_iweight.tsv.gz net_inweight.tsv.gz'
test-blood1:
name: Blood static network unit tests
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9","3.10"]
steps:
- uses: actions/checkout@v4
- name: Install
uses: ./.github/actions/install-bash
with:
python-version: ${{ matrix.python-version }}
- name: Get dataset URL
id: zenodo-url-translate
uses: ./.github/actions/zenodo-url-translate
with:
url: https://zenodo.org/records/6858494/files/inference-blood1.tar.xz?download=1
- name: Test dataset
uses: ./.github/actions/inference-test-dataset
with:
url: ${{ steps.zenodo-url-translate.outputs.url }}
test-path: ci_testspace
makefile: test_static.mk
expected-folder: test/tmp_static_expected
actual-folder: test/tmp_static
expected-h5: test/output/static_expected.h5
actual-h5: test/output/static.h5
makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}'
exclusions: 'reads.bam reads.bai net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz'
test-blood2:
name: Blood dynamic network unit tests
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9","3.10"]
steps:
- uses: actions/checkout@v4
- name: Install
uses: ./.github/actions/install-bash
with:
python-version: ${{ matrix.python-version }}
- name: Get dataset URL
id: zenodo-url-translate
uses: ./.github/actions/zenodo-url-translate
with:
url: https://zenodo.org/records/6858494/files/inference-blood2.tar.xz?download=1
- name: Test dataset
uses: ./.github/actions/inference-test-dataset
with:
url: ${{ steps.zenodo-url-translate.outputs.url }}
test-path: ci_testspace
makefile: test_dynamic.mk
expected-folder: test/tmp_dynamic_expected
actual-folder: test/tmp_dynamic
expected-h5: test/output/dynamic_expected.h5
actual-h5: test/output/dynamic.h5
makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3", "PARAMS-DYNAMIC-SUBSETS_RNA": "1000 10 10"}'
exclusions: 'reads.bam reads.bai net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz'