Fix tests

metagenopolis · Mar 29, 2024 · bfda297 · bfda297
1 parent d827bb9
commit bfda297
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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,