Merge pull request #19571 from nsoranzo/release_24.0_fix_annot

[24.0] Fix type annotations for pysam 0.23.0
galaxyproject · Feb 10, 2025 · bdcf09c · bdcf09c
2 parents 1dcfdec + 318aa57
commit bdcf09c
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Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -570,7 +570,7 @@ def merge(split_files: List[str], output_file: str) -> None:
         :param split_files: List of bam file paths to merge
         :param output_file: Write merged bam file to this location
         """
-        pysam.merge("-O", "BAM", output_file, *split_files)  # type: ignore[attr-defined]
+        pysam.merge("-O", "BAM", output_file, *split_files)  # type: ignore[attr-defined, unused-ignore]
 
     def init_meta(self, dataset: HasMetadata, copy_from: Optional[HasMetadata] = None) -> None:
         Binary.init_meta(self, dataset, copy_from=copy_from)
@@ -638,7 +638,7 @@ def groom_dataset_content(self, file_name: str) -> None:
             [f"-@{slots}", file_name, "-T", tmp_sorted_dataset_file_name_prefix, "-O", "BAM", "-o", sorted_file_name]
         )
         try:
-            pysam.sort(*sort_args)  # type: ignore[attr-defined]
+            pysam.sort(*sort_args)  # type: ignore[attr-defined, unused-ignore]
         except Exception:
             shutil.rmtree(tmp_dir, ignore_errors=True)
             raise
@@ -835,9 +835,9 @@ def set_meta(
             )
         if index_flag == "-b":
             # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
-            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]
+            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]
         else:
-            pysam.index(index_flag, "-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]
+            pysam.index(index_flag, "-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]
         dataset.metadata.bam_index = index_file
 
     def sniff(self, filename: str) -> bool:
@@ -1028,7 +1028,7 @@ def get_cram_version(self, filename: str) -> Tuple[int, int]:
 
     def set_index_file(self, dataset: HasFileName, index_file) -> bool:
         try:
-            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]
+            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]
             return True
         except Exception as exc:
             log.warning("%s, set_index_file Exception: %s", self, exc)

diff --git a/test/unit/data/datatypes/test_bam.py b/test/unit/data/datatypes/test_bam.py
@@ -1,6 +1,6 @@
 import json
 
-from pysam import (  # type: ignore[attr-defined]
+from pysam import (  # type: ignore[attr-defined, unused-ignore]
     AlignmentFile,
     view,
 )
@@ -16,8 +16,12 @@
 def test_merge_bam():
     with get_input_files("1.bam", "1.bam") as input_files, get_tmp_path() as outpath:
         Bam.merge(input_files, outpath)
-        alignment_count_output = int(view("-c", outpath).strip())
-        alignment_count_input = int(view("-c", input_files[0]).strip()) * 2
+        ret = view("-c", outpath)
+        assert isinstance(ret, str)
+        alignment_count_output = int(ret.strip())
+        ret = view("-c", input_files[0])
+        assert isinstance(ret, str)
+        alignment_count_input = int(ret.strip()) * 2
         assert alignment_count_input == alignment_count_output