update development dependencies

.github/workflows/lints.yaml

@@ -20,4 +20,4 @@ jobs:
           enable-cache: true
 
       - name: nox (lints and style)
-        run: uv run --with nox nox -s lints style
+        run: uv run nox -s lints style

pyproject.toml

@@ -1,12 +1,18 @@
 [build-system]
-requires = ["hatchling"]
+requires = [
+    "hatchling",
+]
 build-backend = "hatchling.build"
 
 [project]
 name = "paleomix"
-dynamic = ["version"]
+dynamic = [
+    "version",
+]
 
-authors = [{ name = "Mikkel Schubert", email = "MikkelSch@gmail.com" }]
+authors = [
+    { name = "Mikkel Schubert", email = "MikkelSch@gmail.com" },
+]
 license = { file = "LICENSE" }
 description = "Bioinformatics pipelines for HTS data"
 readme = { file = "README.rst", content-type = "text/x-rst" }
@@ -23,7 +29,12 @@ dependencies = [
     "typing_extensions>=4.0",
 ]
 
-keywords = ["pipeline", "bioinformatics", "hts", "bam"]
+keywords = [
+    "pipeline",
+    "bioinformatics",
+    "hts",
+    "bam",
+]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
@@ -52,13 +63,13 @@ nox = [
 ]
 
 testing = [
-    "coverage[toml]~=7.6",
-    "pytest~=8.3",
-    "pytest-cov~=6.0",
+    "coverage[toml]~=7.15",
+    "pytest~=9.1",
+    "pytest-cov~=7.1",
 ]
 
 linting = [
-    "ruff==0.9.3",
+    "ruff==0.15.22",
 ]
 
 typing = [
@@ -87,7 +98,7 @@ show_missing = true
 precision = 1
 
 exclude_also = [
-    # Exclude code-blocks that are only used during (pyright) type-checking
+    # Exclude code-blocks that are only used during type-checking
     "^if TYPE_CHECKING:",
 ]
 
@@ -99,7 +110,12 @@ profile = "black"
 
 [tool.pyright]
 # Used since `strict = [...]` prevents individual `reportX` settings:
-include = ["src", "tests", "typings", "noxfile.py"]
+include = [
+    "src",
+    "tests",
+    "typings",
+    "noxfile.py",
+]
 # typeCheckingMode = "strict"
 
 # Location of custom stub files
@@ -111,16 +127,22 @@ reportUnnecessaryIsInstance = "none"
 reportUnusedCallResult = "none"
 
 [tool.pytest.ini_options]
-markers = ["slow"]
+markers = [
+    "slow",
+]
 
 [tool.ruff]
 target-version = "py39"
 output-format = "concise"
 
-exclude = ["docs/**"]
+exclude = [
+    "docs/**",
+]
 
 [tool.ruff.lint]
-select = ["ALL"]
+select = [
+    "ALL",
+]
 
 ignore = [
     # Rules either deemed too burdensome to implement or not useful
@@ -169,10 +191,20 @@ ignore = [
 ]
 
 # flake8-annotations - pending rework using typesafe framework
-"src/paleomix/pipelines/*/makefile.py" = ["ANN"]
-"src/paleomix/pipelines/*/pipeline.py" = ["ANN"]
-"src/paleomix/pipelines/*/project.py" = ["ANN"]
-"src/paleomix/pipelines/zonkey/**.py" = ["ANN"]
+"src/paleomix/pipelines/*/makefile.py" = [
+    "ANN",
+]
+"src/paleomix/pipelines/*/pipeline.py" = [
+    "ANN",
+]
+"src/paleomix/pipelines/*/project.py" = [
+    "ANN",
+]
+"src/paleomix/pipelines/zonkey/**.py" = [
+    "ANN",
+]
 
 [tool.uv]
-reinstall-package = ["paleomix"]
+reinstall-package = [
+    "paleomix",
+]

src/paleomix/__main__.py

@@ -77,7 +77,7 @@ def main(argv: list[str] | None = None) -> int:
     if not argv or argv[0] in ("-h", "--help", "help"):
         print(_HELP.format(version=paleomix.__version__))
         return 0
-    elif argv[0] in ("--version",):
+    elif argv[0] == "--version":
         print(f"paleomix v{paleomix.__version__}")
         return 0
 

src/paleomix/common/fileutils.py

@@ -168,7 +168,7 @@ def open_rb(filename: PathTypes) -> IO[bytes]:
         header = handle.peek(2)
 
         if header.startswith(b"\x1f\x8b"):
-            return cast(IO[bytes], _GzipFile(mode="rb", fileobj=handle))
+            return cast("IO[bytes]", _GzipFile(mode="rb", fileobj=handle))
         elif header.startswith(b"BZ"):
             return _BZ2File(handle, "rb")
         else:

src/paleomix/common/formats/bed.py

@@ -126,6 +126,11 @@ def __lt__(self, obj: object) -> bool:
 
         return bed_1 < bed_2
 
+    def __hash__(self) -> int:
+        return hash(
+            (self.contig, self.start, self.end, self.name, self.score, self.strand)
+        )
+
 
 def read_bed_file(
     filename: str,

src/paleomix/common/procs.py

@@ -29,7 +29,7 @@ def quote_args(args: object) -> str:
     objects: Iterable[object]
     if isinstance(args, os.PathLike):
         # WORKAROUND for pyright warning about "partially unknown" types
-        objects = [cast(object, args)]
+        objects = [cast("object", args)]
     elif isinstance(args, (str, bytes)) or not isinstance(args, Iterable):
         objects = [args]
     else:
@@ -38,7 +38,7 @@ def quote_args(args: object) -> str:
     values: list[str] = []
     for value in objects:
         if isinstance(value, os.PathLike):
-            value = os.fsdecode(cast(Any, value))
+            value = os.fsdecode(cast("Any", value))
 
         if isinstance(value, bytes):
             value = value.decode("utf-8", errors="replace")

src/paleomix/common/utilities.py

@@ -177,3 +177,6 @@ def __gt__(self, other: object) -> bool:
         if not isinstance(other, type(self)):
             return NotImplemented
         return other < self
+
+    def __hash__(self) -> int:
+        raise NotImplementedError

src/paleomix/common/versions.py

@@ -56,7 +56,7 @@ def __init__(
     def call(self) -> tuple[str, ...]:
         call = self._call
         if call[0] == "%(PYTHON)s":
-            return (sys.executable,) + call[1:]
+            return (sys.executable, *call[1:])
 
         return call
 

src/paleomix/pipelines/bam/main.py

@@ -23,7 +23,7 @@ def main(argv: list[str], pipeline: str = "bam") -> int:
     args = parser.parse_args(argv)
     if args.command in ("new", "makefile", "mkfile"):
         return _main_template()
-    elif args.command in ("example",):
+    elif args.command == "example":
         return _main_copy_example(args.destination)
 
     if args.command.startswith("dry") and args.pipeline_mode == "run":

src/paleomix/pipelines/bam/makefile.py

@@ -629,7 +629,7 @@ def _validate_prefixes(makefiles, pipeline_variant):
             except (OSError, ValueError) as error:
                 if pipeline_variant == "bam":
                     raise MakefileError(f"Error reading/indexing FASTA: {error}")
-                logging.warning("Error reading/indexing FASTA: %s", error)
+                logger.warning("Error reading/indexing FASTA: %s", error)
             else:
                 if max(contigs.values()) > _BAM_MAX_SEQUENCE_LENGTH:
                     logger.warning(

src/paleomix/pipelines/bam/pipeline.py

@@ -528,7 +528,7 @@ def run_mapdamage(layout: Layout, genome, records):
             dependencies=(extra_task,),
         )
 
-    if run_type in ("rescale",):
+    if run_type == "rescale":
         # Rescales BAM quality scores using model built above
         assert extra_task is not None
         task = MapDamageRescaleNode(

src/paleomix/pipelines/zonkey/build_mito.py

@@ -173,17 +173,15 @@ def main(argv):
     with open(args.output_prefix + ".summary", "w") as handle:
         stats["filename"] = os.path.abspath(args.bam)
 
-        for key, value in sorted(stats.items()):
-            handle.write(f"{key}: {value}\n")
+        handle.writelines(f"{key}: {value}\n" for key, value in sorted(stats.items()))
 
     with open(args.output_prefix + ".phy", "w") as handle:
         handle.write(interleaved_phy(sequences_to_msa(sequences)))
 
     with open(args.output_prefix + ".fasta", "w") as handle:
         for key, record in sorted(sequences.items()):
             handle.write(f">{key}\n")
-            for line in fragment(60, record.sequence):
-                handle.write(f"{line}\n")
+            handle.writelines(f"{line}\n" for line in fragment(60, record.sequence))
 
         return 0
 

src/paleomix/pipelines/zonkey/build_tped.py

@@ -227,8 +227,10 @@ def write_summary(args, filename, statistics):
         handle.write(f"name: {args.name}\n")
         handle.write(f"filename: {os.path.abspath(args.bam)}\n")
 
-        for key in ("n_reads", "n_reads_used", "n_sites_incl_ts", "n_sites_excl_ts"):
-            handle.write("{}: {}\n".format(key, statistics.get(key, "MISSING")))
+        handle.writelines(
+            "{}: {}\n".format(key, statistics.get(key, "MISSING"))
+            for key in ("n_reads", "n_reads_used", "n_sites_incl_ts", "n_sites_excl_ts")
+        )
 
 
 def process_bam(args, data, bam_handle, mapping):

src/paleomix/pipelines/zonkey/parts/nuclear.py

@@ -390,8 +390,7 @@ def _setup(self, temp: fileutils.PathTypes) -> None:
             samples = [line.split(None, 1)[0] for line in in_handle]
 
         with open(os.path.join(temp, "samples.clust"), "w") as handle:
-            for sample in samples:
-                handle.write(f"{sample} {sample} {sample}\n")
+            handle.writelines(f"{sample} {sample} {sample}\n" for sample in samples)
 
     def _teardown(self, temp: fileutils.PathTypes) -> None:
         for ext in ("log", "nosex"):
@@ -524,9 +523,7 @@ def _setup(self, temp: fileutils.PathTypes) -> None:
         if self._k_file is not None:
             stats = read_summary(self._k_file)
             n_sites = float(stats[self._k_field])
-            k = max(
-                1, int(math.ceil(self._snp_distance / (self._genome_size / n_sites)))
-            )
+            k = max(1, math.ceil(self._snp_distance / (self._genome_size / n_sites)))
 
             self._param_k = k
             assert isinstance(self._command, AtomicCmd)
@@ -758,7 +755,7 @@ def _setup(self, temp: fileutils.PathTypes) -> None:
                 if not line:
                     continue
 
-                name, size, hits, _ = line.split("\t")
+                name, _, hits, _ = line.split("\t")
                 name = self._mapping.get(name, name)
                 if name not in self._contigs:
                     # Excluding contigs is allowed

src/paleomix/tools/rmdup_collapsed.py

@@ -64,7 +64,7 @@ def copy_number(read: AlignedSegment) -> int:
     if read.has_tag("XP"):
         value, tag_type = read.get_tag("XP", with_value_type=True)
         if tag_type == "i":
-            return cast(int, value)
+            return cast("int", value)
 
     return 0
 

tests/common_tests/command_test/command_test.py

@@ -82,7 +82,7 @@ def test_atomicfile__valid_paths() -> None:
 def test_atomiccmd__paths__invalid_values(
     cls: type[IOFileTypes], value: object
 ) -> None:
-    with pytest.raises(TypeError, match="expected str, bytes or os.PathLike object"):
+    with pytest.raises(TypeError, match=r"expected str, bytes or os.PathLike object"):
         cls(value)  # pyright: ignore[reportArgumentType]
 
 

tests/common_tests/makefile_test.py

@@ -1005,17 +1005,20 @@ def test_fastq_path__path_must_meet_spec() -> None:
     assert accept_any(_DUMMY_PATH, se_reads) == se_reads
     assert accept_any(_DUMMY_PATH, pe_reads) == pe_reads
 
-    with pytest.raises(MakefileError, match="Expected value: a path without a {pair}"):
+    with pytest.raises(MakefileError, match=r"Expected value: a path without a {pair}"):
         accept_se(_DUMMY_PATH, pe_reads)
 
-    with pytest.raises(MakefileError, match="Expected value: a path with a {pair} key"):
+    with pytest.raises(
+        MakefileError,
+        match=r"Expected value: a path with a {pair} key",
+    ):
         accept_pe(_DUMMY_PATH, se_reads)
 
 
 @pytest.mark.parametrize("value", _common_invalid_values(extra=(1,)))
 def test_fastq_path__rejects_non_strings(value: object) -> None:
     spec = FASTQPath()
-    with pytest.raises(MakefileError, match="Expected value: a path without a {pair}"):
+    with pytest.raises(MakefileError, match=r"Expected value: a path without a {pair}"):
         spec(_DUMMY_PATH, value)
 
 

tests/common_tests/sequences_test.py

@@ -21,7 +21,7 @@
 _REF_DST = "TGCAKYWSRMBDHVNX"
 
 
-@pytest.mark.parametrize(("src", "dst"), zip(_REF_SRC, _REF_DST))
+@pytest.mark.parametrize(("src", "dst"), tuple(zip(_REF_SRC, _REF_DST)))
 def test_complement__single_nt(src: str, dst: str) -> None:
     assert complement(src) == dst
     assert complement(src.lower()) == dst.lower()
@@ -72,7 +72,7 @@ def test_reverse_complement() -> None:
 _IUB_DST = "ACGTMRWSYKVHDB"
 
 
-@pytest.mark.parametrize(("src", "dst"), zip(_IUB_SRC, _IUB_DST))
+@pytest.mark.parametrize(("src", "dst"), tuple(zip(_IUB_SRC, _IUB_DST)))
 def test_genotype__permutations(src: str, dst: str) -> None:
     for seq in itertools.permutations(src):
         assert encode_genotype("".join(seq)) == dst

tests/common_tests/versions_test.py

@@ -119,7 +119,7 @@ def test_requirement__version__command_not_found() -> None:
 def test_requirement__version__command_not_executable() -> None:
     obj = Requirement(call=("./README.rst",), regexp=r"v(\d+\.\d+)")
 
-    with pytest.raises(RequirementError, match="[Errno 13]"):
+    with pytest.raises(RequirementError, match=r"[Errno 13]"):
         obj.version()
 
 

tests/pipelines/bam/makefile_test.py

@@ -184,7 +184,7 @@ def test_genomes__simple_genome(tmp_path: Path) -> None:
 def test_genomes__bad_wildcard_in_name(tmp_path: Path) -> None:
     filepath = _write_genome_yaml(tmp_path, {"T*est": "/path/to/genome.fasta"})
 
-    with pytest.raises(MakefileError, match="'*' is not allowed in Genome names"):
+    with pytest.raises(MakefileError, match=r"'*' is not allowed in Genome names"):
         _read_makefile(filepath)
 
 
@@ -727,5 +727,8 @@ def test_makefile__validation__paired_must_have_key(tmp_path: Path) -> None:
     """,
     )
 
-    with pytest.raises(MakefileError, match="Expected value: a path with a {pair} key"):
+    with pytest.raises(
+        MakefileError,
+        match=r"Expected value: a path with a {pair} key",
+    ):
         _read_makefile(filepath)