From 69f76745ccd21814d8720f9fe1af60bb257b55e3 Mon Sep 17 00:00:00 2001 From: "Arjan Draisma (wur)" <74908173+adraismawur@users.noreply.github.com> Date: Wed, 17 Jul 2024 15:08:42 +0200 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Cunliang Geng --- src/nplinker/data/nplinker.toml | 3 ++- tests/unit/genomics/test_runbigscape.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/nplinker/data/nplinker.toml b/src/nplinker/data/nplinker.toml index 4a24d812..d4238673 100644 --- a/src/nplinker/data/nplinker.toml +++ b/src/nplinker/data/nplinker.toml @@ -56,7 +56,8 @@ version = 1 parameters = "--mibig --clans-off --mix --include_singletons --cutoffs 0.30" # for version 2, use the following parameters string: # parameters = "--mibig_version 3.1 --include_singletons --gcf_cutoffs 0.30" -# Note that BiG-SCAPE v2 has subcommands. NPLinker requires the "cluster" subcommand to be used. +# Note that BiG-SCAPE v2 has subcommands. NPLinker requires the "cluster" subcommand and its parameters to be used. +NPLinker will automatically set the following parameters: `--pfam_path`, `--inputdir` and `--outputdir`. So, do not set them here. # BiG-SCPAPE v2 also runs a --mix analysis by default, and does not need this to be included. # Which bigscape cutoff to use for NPLinker analysis. # There might be multiple cutoffs in bigscape output. diff --git a/tests/unit/genomics/test_runbigscape.py b/tests/unit/genomics/test_runbigscape.py index d759d0f2..b10fa18f 100644 --- a/tests/unit/genomics/test_runbigscape.py +++ b/tests/unit/genomics/test_runbigscape.py @@ -17,9 +17,9 @@ def test_run_bigscape(tmp_path, version): assert result is True +@pytest.mark.skipif(os.getenv('GITHUB_ACTIONS') == 'true', reason="The test is time-consuming on CI") @pytest.mark.parametrize("version", [1, 2]) def test_run_bigscape_small_dataset(tmp_path, version): - pytest.skip("This test is too slow to run in CI") result = bigscape.run_bigscape( antismash_path=DATA_DIR / "bigscape" / "minimal_dataset", output_path=tmp_path,