Open testing with python3.13

meteor/counter.py

@@ -85,7 +85,7 @@ def launch_mapping(self) -> None:
             )
             mapping_process.execute()
 
-    def write_table(self, cramfile: Path, outfile: Path) -> None:
+    def write_table(self, cramfile: Path, outfile: Path) -> int:
         """Function that create a count table using pysam. First index the cram file,
         then count reads using the function idxstats from pysam, and output a count
         table.
@@ -351,7 +351,7 @@ def compute_abs(self, unique_dict: dict, multiple_dict: dict) -> dict:
             genes: unique_dict[genes] + multiple_dict[genes] for genes in unique_dict
         }
 
-    def write_stat(self, output: Path, abundance_dict: dict, database: dict) -> None:
+    def write_stat(self, output: Path, abundance_dict: dict, database: dict) -> int:
         """Write count table.
 
         :param output: [STRING] = output filename

meteor/session.py

@@ -34,7 +34,7 @@ class Component:
     DEFAULT_GAP_CHAR: ClassVar[str] = "N"
     DEFAULT_CORE_SIZE: ClassVar[int] = 100
 
-    threads: int | None
+    threads: int
     fastq_dir: Path = field(default_factory=Path)
     mapping_dir: Path = field(default_factory=Path)
     profile_dir: Path = field(default_factory=Path)

pyproject.toml

@@ -23,7 +23,7 @@ packages = [
 meteor = "meteor.meteor:main"
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.13"
+python = "^3.10"
 pandas = "^2.1.2"
 pysam = "^0.22.0"
 packaging = "^23.2"