mhcflow 0.2.2__tar.gz → 0.2.3__tar.gz

{mhcflow-0.2.2 → mhcflow-0.2.3}/.gitignore

@@ -24,3 +24,6 @@ wheels/
 .tox/
 
 _version.py
+
+## documentation
+site/

{mhcflow-0.2.2 → mhcflow-0.2.3}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.3
 Name: mhcflow
-Version: 0.2.2
+Version: 0.2.3
 Summary: MHC Class I and II workflow with fisher, realigner and typer.
 Project-URL: Source, https://github.com/svm-zhang/mhcflow
 Project-URL: Documentation, https://svm-zhang.github.io/mhcflow/
 Project-URL: Issues, https://github.com/svm-zhang/mhcflow/issues
-Author-email: simo <svm.zhang@gmail.com>
-Maintainer-email: Simo Zhang <svm.zhang@gmail.com>
+Author-email: simo <me@simovz.me>
+Maintainer-email: Simo Zhang <me@simovz.me>
 License: MIT
 Keywords: bioinformatics, genomics, sequencing, HLA typing
 Classifier: Development Status :: 4 - Beta
@@ -18,6 +18,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries
 Requires-Python: >=3.10
@@ -31,7 +32,6 @@ Description-Content-Type: text/markdown
 
 [![PyPI version](https://img.shields.io/pypi/v/mhcflow)](https://pypi.org/project/mhcflow/)
 ![Python versions](https://img.shields.io/pypi/pyversions/mhcflow)
-[![PyPI Downloads](https://img.shields.io/pypi/dm/mhcflow)](https://pypistats.org/packages/mhcflow)
 ![License](https://img.shields.io/pypi/l/mhcflow)
 
 MHC class I and II typing workflow including fishing, realigning, and typing that

{mhcflow-0.2.2 → mhcflow-0.2.3}/README.md

@@ -2,7 +2,6 @@
 
 [![PyPI version](https://img.shields.io/pypi/v/mhcflow)](https://pypi.org/project/mhcflow/)
 ![Python versions](https://img.shields.io/pypi/pyversions/mhcflow)
-[![PyPI Downloads](https://img.shields.io/pypi/dm/mhcflow)](https://pypistats.org/packages/mhcflow)
 ![License](https://img.shields.io/pypi/l/mhcflow)
 
 MHC class I and II typing workflow including fishing, realigning, and typing that

{mhcflow-0.2.2 → mhcflow-0.2.3}/pyproject.toml

@@ -10,7 +10,7 @@ description = "MHC Class I and II workflow with fisher, realigner and typer."
 readme = {file="README.md", content-type = "text/markdown"}
 keywords = ["bioinformatics, genomics, sequencing, HLA typing"]
 authors = [
-    { name = "simo", email = "svm.zhang@gmail.com" }
+    { name = "simo", email = "me@simovz.me" }
 ]
 classifiers = [
   "Development Status :: 4 - Beta",
@@ -22,6 +22,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
   "Topic :: Software Development :: Libraries"
 ]
@@ -36,7 +37,7 @@ urls.Documentation = "https://svm-zhang.github.io/mhcflow/"
 urls.Issues = "https://github.com/svm-zhang/mhcflow/issues"
 license = "MIT"
 maintainers = [
-    { name = "Simo Zhang", email = "svm.zhang@gmail.com" }
+    { name = "Simo Zhang", email = "me@simovz.me" }
 ]
 dynamic = ["version"]
 requires-python = ">= 3.10"
@@ -44,11 +45,10 @@ requires-python = ">= 3.10"
 [project.scripts]
 mhcflow = "mhcflow:run_mhcflow"
 
-[tool.rye]
-managed = true
-dev-dependencies = [
-    "tox>=4.24.2",
+[dependency-groups]
+dev = [
     "mypy>=1.15.0",
+    "zensical>=0.0.23",
 ]
 
 [tool.hatch]
@@ -56,7 +56,6 @@ metadata.allow-direct-references = true
 build.targets.sdist.include = [
   "/src",
   "/tests",
-  "/tox.ini"
 ]
 build.targets.wheel.packages = ["src/mhcflow"]
 build.hooks.vcs.version-file = "src/mhcflow/_version.py"

mhcflow-0.2.3/src/mhcflow/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.2.3'
+__version_tuple__ = version_tuple = (0, 2, 3)
+
+__commit_id__ = commit_id = None

{mhcflow-0.2.2 → mhcflow-0.2.3}/src/mhcflow/dumper.py

@@ -55,7 +55,7 @@ def _bam2fq_from_idx(
     # each idx file will be input to samtools view -N
     qnames = idx_df["qnames"].unique().to_numpy()
     qnames_batches = np.array_split(qnames, nproc)
-    idxs = []
+    idxs: list[_PathLike] = []
     for i in range(len(qnames_batches)):
         qname_batch_fspath = outdir / f"{sm}.fisher.idxs.{i}.txt"
         pl.DataFrame({"qnames": qnames_batches[i]}).write_csv(

{mhcflow-0.2.2 → mhcflow-0.2.3}/src/mhcflow/helper.py

@@ -3,34 +3,34 @@ import json
 import sys
 from collections.abc import Sequence
 from dataclasses import dataclass, field
+from pathlib import Path
+from typing import TypeAlias
 
 from tinyscibio import BAMetadata, _PathLike, parse_path
 
 from .logger import logger
 
+_PathOrPaths: TypeAlias = _PathLike | list[_PathLike]
+
 
 @dataclass
 class FileManifest:
-    _inputs: dict[str, _PathLike | Sequence[_PathLike]] = field(
-        default_factory=dict, init=False
-    )
-    _outputs: dict[str, _PathLike | Sequence[_PathLike]] = field(
-        default_factory=dict, init=False
-    )
+    _inputs: dict[str, _PathOrPaths] = field(default_factory=dict, init=False)
+    _outputs: dict[str, _PathOrPaths] = field(default_factory=dict, init=False)
     _aux: dict[str, _PathLike] = field(default_factory=dict, init=False)
-    _intermediates: dict[str, _PathLike | Sequence[_PathLike]] = field(
+    _intermediates: dict[str, _PathOrPaths] = field(
         default_factory=dict, init=False
     )
-    _intermediate_aux: dict[str, _PathLike | Sequence[_PathLike]] = field(
+    _intermediate_aux: dict[str, _PathOrPaths] = field(
         default_factory=dict, init=False
     )
 
     @property
-    def inputs(self) -> dict[str, _PathLike | Sequence[_PathLike]]:
+    def inputs(self) -> dict[str, _PathOrPaths]:
         return self._inputs
 
     @property
-    def outputs(self) -> dict[str, _PathLike | Sequence[_PathLike]]:
+    def outputs(self) -> dict[str, _PathOrPaths]:
         return self._outputs
 
     @property
@@ -38,34 +38,26 @@ class FileManifest:
         return self._aux
 
     @property
-    def intermediate_aux(self) -> dict[str, _PathLike | Sequence[_PathLike]]:
+    def intermediate_aux(self) -> dict[str, _PathOrPaths]:
         return self._intermediate_aux
 
     @property
-    def intermediates(self) -> dict[str, _PathLike | Sequence[_PathLike]]:
+    def intermediates(self) -> dict[str, _PathOrPaths]:
         return self._intermediates
 
-    def _register_inputs(
-        self, **kwargs: _PathLike | Sequence[_PathLike]
-    ) -> None:
+    def _register_inputs(self, **kwargs: _PathOrPaths) -> None:
         self._inputs.update(**kwargs)
 
-    def _register_outputs(
-        self, **kwargs: _PathLike | Sequence[_PathLike]
-    ) -> None:
+    def _register_outputs(self, **kwargs: _PathOrPaths) -> None:
         self._outputs.update(**kwargs)
 
     def _register_aux(self, **kwargs: _PathLike) -> None:
         self._aux.update(**kwargs)
 
-    def _register_intermediate(
-        self, **kwargs: _PathLike | Sequence[_PathLike]
-    ) -> None:
+    def _register_intermediate(self, **kwargs: _PathOrPaths) -> None:
         self._intermediates.update(**kwargs)
 
-    def _register_intermediate_aux(
-        self, **kwargs: _PathLike | Sequence[_PathLike]
-    ) -> None:
+    def _register_intermediate_aux(self, **kwargs: _PathOrPaths) -> None:
         self._intermediate_aux.update(**kwargs)
 
     @classmethod
@@ -162,11 +154,14 @@ def _verify_prev_run(fm: FileManifest, overwrite: bool = False) -> bool:
 
     logger.info("Verify manifest from previous run.")
     done = parse_path(fm.aux.get("done", ""))
-    intermediate_dones = []
+    intermediate_dones: list[_PathLike] = []
     for k, v in fm.intermediate_aux.items():
         if not k.endswith("done") and not k.endswith("dones"):
             continue
-        intermediate_dones += v if isinstance(v, list) else [v]
+        if isinstance(v, list):
+            intermediate_dones.extend(v)
+        else:
+            intermediate_dones.append(v)
     not_exists = [
         str(f) for f in intermediate_dones if not parse_path(f).exists()
     ]

mhcflow-0.2.2/src/mhcflow/_version.py

@@ -1,21 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '0.2.2'
-__version_tuple__ = version_tuple = (0, 2, 2)

mhcflow-0.2.2/tox.ini

@@ -1,20 +0,0 @@
-[tox]
-requires =
-  tox>=4
-env_list = type
-skip_missing_interpreters = true
-
-[gh-actions]
-python =
-  3.10: type
-  3.11: type
-  3.12: type
-  3.13: type
-
-
-[testenv:type]
-description = "Run type checker on code base"
-deps =
-  mypy>=1.11
-  types-requests>=2.32
-commands = mypy "src{/}mhcflow"