From bfda297ef993a28871931aba32ade675c09e5fcc Mon Sep 17 00:00:00 2001 From: Florian Plaza Onate Date: Fri, 29 Mar 2024 13:59:08 +0000 Subject: [PATCH] Fix tests --- meteor/merging.py | 8 ++++---- meteor/tests/test_merging.py | 2 ++ meteor/tests/test_profiler.py | 1 + 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/meteor/merging.py b/meteor/merging.py index 9ffa028..b95d102 100644 --- a/meteor/merging.py +++ b/meteor/merging.py @@ -39,11 +39,11 @@ class Merging(Session): prefix: str min_msp_abundance: float min_msp_occurrence: int - remove_sample_with_no_msp: bool = True - output_mpa: bool = False + remove_sample_with_no_msp: bool + output_mpa: bool mpa_taxonomic_level: str - output_biom: bool = False - output_gene_matrix: bool = False + output_biom: bool + output_gene_matrix: bool ranks: dict[str, str] = field( default_factory=lambda: { "superkingdom": "k__", diff --git a/meteor/tests/test_merging.py b/meteor/tests/test_merging.py index 902fa38..8a6a88f 100644 --- a/meteor/tests/test_merging.py +++ b/meteor/tests/test_merging.py @@ -34,6 +34,7 @@ def merging_profiles(datadir: Path, tmp_path: Path) -> Merging: min_msp_occurrence=0, remove_sample_with_no_msp=False, output_mpa=False, + mpa_taxonomic_level=None, output_biom=False, output_gene_matrix=True, ) @@ -59,6 +60,7 @@ def merging_fast(datadir: Path, tmp_path: Path) -> Merging: min_msp_occurrence=0, remove_sample_with_no_msp=False, output_mpa=False, + mpa_taxonomic_level=None, output_biom=False, output_gene_matrix=False, ) diff --git a/meteor/tests/test_profiler.py b/meteor/tests/test_profiler.py index b4b991b..f375cc6 100644 --- a/meteor/tests/test_profiler.py +++ b/meteor/tests/test_profiler.py @@ -30,6 +30,7 @@ def profiler_standard(datadir: Path, tmp_path: Path) -> Profiler: meteor=meteor, rarefaction_level=-1, seed=12345, + coverage_factor=100.0, normalization="", core_size=4, msp_filter=0.5,