pmotools 1.2.0__tar.gz → 1.2.2__tar.gz

{pmotools-1.2.0 → pmotools-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pmotools
-Version: 1.2.0
+Version: 1.2.2
 Summary: Tools for building and analyzing PMO files
 Author: Nicholas Hathaway, Kathryn Murie
 Author-email: Nicholas Hathaway <nickjhathaway@gmail.com>, Kathryn Murie <kathryn.murie@ucsf.edu>
@@ -681,7 +681,6 @@ License:                     GNU GENERAL PUBLIC LICENSE
 Requires-Dist: pandas>=2.2.2
 Requires-Dist: biopython>=1.83
 Requires-Dist: jsonschema>=4.23.0
-Requires-Dist: pre-commit
 Requires-Dist: openpyxl>=3.1.5
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

{pmotools-1.2.0 → pmotools-1.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pmotools"
-version = "v1.2.0"
+version = "v1.2.2"
 description = "Tools for building and analyzing PMO files"
 readme = "README.md"
 authors = [
@@ -13,7 +13,6 @@ dependencies = [
     "pandas>=2.2.2",
     "biopython>=1.83",
     "jsonschema>=4.23.0",
-    "pre-commit",
     "openpyxl>=3.1.5",
 ]
 
@@ -26,6 +25,7 @@ build-backend = "uv_build"
 
 [dependency-groups]
 dev = [
+    "pre-commit",
     "pytest>=8.4.1",
 ]
 

{pmotools-1.2.0 → pmotools-1.2.2}/src/pmotools/pmo_engine/pmo_exporter.py

@@ -11,7 +11,7 @@ from dataclasses import dataclass
 from pmotools.pmo_engine.pmo_checker import PMOChecker
 from pmotools.pmo_engine.pmo_processor import PMOProcessor
 
-from pmotools import __version__ as __pmotools_version__
+from pmotools import __schema_version__
 
 
 class BedLoc(NamedTuple):
@@ -627,11 +627,9 @@ class PMOExporter(object):
             "seq",
         ],
         jsonschema_fnp=os.path.join(
-            os.path.dirname(
-                os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-            ),
+            os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
             "schemas/",
-            f"portable_microhaplotype_object_v{__pmotools_version__}.schema.json",
+            f"portable_microhaplotype_object_v{__schema_version__}.schema.json",
         ),
         validate_pmo: bool = False,
     ) -> pd.DataFrame:

{pmotools-1.2.0 → pmotools-1.2.2}/src/pmotools/pmo_engine/pmo_reader.py

@@ -7,6 +7,7 @@ import os
 import sys
 from collections import defaultdict
 from pmotools import __version__ as __pmotools_version__
+from pmotools import __schema_version__
 
 
 class PMOReader:
@@ -66,7 +67,7 @@ class PMOReader:
         # currently losing all info about previous header info,
         # consider coming up with something in standard that might preserve this info if needed
         pmo_out["pmo_header"] = {
-            "pmo_version": __pmotools_version__,
+            "pmo_version": __schema_version__,
             "creation_date": datetime.datetime.now().strftime("%Y-%m-%d"),
             "generation_method": {
                 "program_name": "pmotools-python.PMOReader.combine_multiple_pmos",

{pmotools-1.2.0 → pmotools-1.2.2}/src/pmotools/scripts/pmo_to_tables/extract_allele_table.py

@@ -11,7 +11,7 @@ from pmotools.pmo_engine.pmo_checker import PMOChecker
 from pmotools.pmo_engine.pmo_processor import PMOProcessor
 from pmotools.pmo_engine.pmo_exporter import PMOExporter
 
-from pmotools import __version__ as __pmotools_version__
+from pmotools import __schema_version__
 
 
 def get_parser() -> argparse.ArgumentParser:
@@ -36,7 +36,7 @@ def get_parser() -> argparse.ArgumentParser:
                 os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
             ),
             "schemas/",
-            f"portable_microhaplotype_object_v{__pmotools_version__}.schema.json",
+            f"portable_microhaplotype_object_v{__schema_version__}.schema.json",
         ),
         type=str,
         required=False,

{pmotools-1.2.0 → pmotools-1.2.2}/src/pmotools/scripts/pmo_utils/validate_pmo.py

@@ -7,7 +7,7 @@ import json
 from pmotools.pmo_engine.pmo_reader import PMOReader
 from pmotools.pmo_engine.pmo_checker import PMOChecker
 from pmotools.utils.small_utils import Utils
-from pmotools import __version__ as __pmotools_version__
+from pmotools import __schema_version__
 
 
 def get_parser_validate_pmo() -> argparse.ArgumentParser:
@@ -18,7 +18,7 @@ def get_parser_validate_pmo() -> argparse.ArgumentParser:
     parser.add_argument("--pmo", type=str, required=True, help="a pmo file to validate")
     parser.add_argument(
         "--jsonschema_version",
-        default=__pmotools_version__,
+        default=__schema_version__,
         type=str,
         required=False,
         help="version of the jsonschema to validate against (default: %(default)s)",