Fix mypy warnings

metagenopolis · Apr 3, 2024 · a9fc851 · a9fc851
1 parent 672921b
commit a9fc851
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/meteor/merging.py b/meteor/merging.py
@@ -41,7 +41,7 @@ class Merging(Session):
     min_msp_occurrence: int
     remove_sample_with_no_msp: bool
     output_mpa: bool
-    mpa_taxonomic_level: str
+    mpa_taxonomic_level: str|None
     output_biom: bool
     output_gene_matrix: bool
     ranks: dict[str, str] = field(

diff --git a/meteor/meteor.py b/meteor/meteor.py
@@ -783,7 +783,7 @@ def main() -> None:  # pragma: no cover
             args.min_msp_occurrence,
             args.remove_sample_with_no_msp,
             False,
-            "a",
+            None,
             #args.output_mpa,
             #args.taxonomic_level,
             args.output_biom,

diff --git a/meteor/profiler.py b/meteor/profiler.py
@@ -43,7 +43,7 @@ class Profiler(Session):
     meteor: type[Component]
     rarefaction_level: int
     seed: int
-    normalization: str
+    normalization: str|None
     core_size: int
     msp_filter: float
     completeness: float

diff --git a/meteor/tests/test_counter.py b/meteor/tests/test_counter.py
@@ -284,8 +284,8 @@ def test_save_cram(counter_unique: Counter, datadir: Path, tmp_path: Path) -> No
         reads, _ = counter_unique.filter_alignments(
             cramdesc
         )  # pylint: disable=unused-variable
-        read_list = list(chain(reads.values()))
-        merged_list = list(chain.from_iterable(read_list))
+        read_list = reads.values()
+        merged_list = chain.from_iterable(read_list)
         tmpcramfile = tmp_path / "test"
         counter_unique.save_cram_strain(tmpcramfile, cramdesc, merged_list, ref_json)
         assert tmpcramfile.exists()