From 626f839bc46d966d407c732e01f58ffe5db66f1a Mon Sep 17 00:00:00 2001 From: Lingfei Wang Date: Tue, 14 May 2024 18:25:38 -0400 Subject: [PATCH] Update tests in ci-inference.yml to include NTH=1 --- .github/workflows/ci-inference.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-inference.yml b/.github/workflows/ci-inference.yml index 2cee3c6..7371435 100644 --- a/.github/workflows/ci-inference.yml +++ b/.github/workflows/ci-inference.yml @@ -1,4 +1,4 @@ -# Lingfei Wang, 2022. All rights reserved. +# Lingfei Wang, 2022, 2024. All rights reserved. name: Network inference tests on: @@ -23,6 +23,7 @@ jobs: strategy: matrix: python-version: ["3.9","3.10"] + nth: ["2"] steps: - uses: actions/checkout@v4 - name: Install @@ -44,7 +45,7 @@ jobs: 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"}' + makefile-params: '{"ENVMODE": "none", "NTH": "${{ matrix.nth }}", "DEVICE": "cpu", "GENOME_MACS2": "mm", "JOINT": "1", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}' exclusions: 'footprints.bed net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz net_nweight.tsv.gz net_iweight.tsv.gz net_inweight.tsv.gz' test-blood1: @@ -53,6 +54,7 @@ jobs: strategy: matrix: python-version: ["3.9","3.10"] + nth: ["1","2"] steps: - uses: actions/checkout@v4 - name: Install @@ -74,7 +76,7 @@ jobs: actual-folder: test/tmp_static expected-h5: test/output/static_expected.h5 actual-h5: test/output/static.h5 - makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}' + makefile-params: '{"ENVMODE": "none", "NTH": "${{ matrix.nth }}", "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: @@ -83,6 +85,7 @@ jobs: strategy: matrix: python-version: ["3.9","3.10"] + nth: ["2"] steps: - uses: actions/checkout@v4 - name: Install @@ -104,5 +107,5 @@ jobs: 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"}' + makefile-params: '{"ENVMODE": "none", "NTH": "${{ matrix.nth }}", "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'