Develop

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pmotools"
-version = "v1.2.0"
+version = "v1.2.1"
 description = "Tools for building and analyzing PMO files"
 readme = "README.md"
 authors = [

src/pmotools/pmo_engine/pmo_exporter.py

@@ -11,7 +11,7 @@
 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 @@ def extract_alleles_per_sample_table(
             "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:

src/pmotools/pmo_engine/pmo_reader.py

@@ -7,6 +7,7 @@
 import sys
 from collections import defaultdict
 from pmotools import __version__ as __pmotools_version__
+from pmotools import __schema_version__
 
 
 class PMOReader:
@@ -66,7 +67,7 @@ def combine_multiple_pmos(pmos: list[dict]):
         # 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",

src/pmotools/scripts/pmo_to_tables/extract_allele_table.py

@@ -11,7 +11,7 @@
 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,

src/pmotools/scripts/pmo_utils/validate_pmo.py

@@ -7,7 +7,7 @@
 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)",

tests/test_default_schema_version.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+import inspect
+import os
+import unittest
+
+from pmotools import __schema_version__
+from pmotools.pmo_engine.pmo_exporter import PMOExporter
+from pmotools.scripts.pmo_to_tables import extract_allele_table
+from pmotools.scripts.pmo_utils import validate_pmo
+
+
+class TestDefaultSchemaVersion(unittest.TestCase):
+    """The default schema must follow the schema version, not the package version."""
+
+    def setUp(self):
+        self.expected_schema_fname = (
+            f"portable_microhaplotype_object_v{__schema_version__}.schema.json"
+        )
+
+    def assert_default_schema(self, fnp):
+        self.assertEqual(os.path.basename(fnp), self.expected_schema_fname)
+        self.assertTrue(os.path.exists(fnp), f"{fnp} does not exist")
+
+    def test_extract_alleles_per_sample_table_default_schema(self):
+        default = (
+            inspect.signature(PMOExporter.extract_alleles_per_sample_table)
+            .parameters["jsonschema_fnp"]
+            .default
+        )
+        self.assert_default_schema(default)
+
+    def test_extract_allele_table_cli_default_schema(self):
+        self.assert_default_schema(
+            extract_allele_table.get_parser().get_default("jsonschema")
+        )
+
+    def test_validate_pmo_cli_default_schema_version(self):
+        self.assertEqual(
+            validate_pmo.get_parser_validate_pmo().get_default("jsonschema_version"),
+            __schema_version__,
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_pmo_engine/test_pmo_reader.py

@@ -3,6 +3,7 @@
 import os
 import unittest
 
+from pmotools import __schema_version__, __version__
 from pmotools.pmo_engine.pmo_reader import PMOReader
 from pmotools.pmo_engine.pmo_checker import PMOChecker, load_schema
 
@@ -121,6 +122,11 @@ def test_combine_multiple_pmos_v1_1_0(self):
         )
         checker = PMOChecker(pmo_jsonschema_data)
         checker.validate_pmo_json(combined_pmo)
+        self.assertEqual(combined_pmo["pmo_header"]["pmo_version"], __schema_version__)
+        self.assertEqual(
+            combined_pmo["pmo_header"]["generation_method"]["program_version"],
+            __version__,
+        )
         # check against expected
         with open(
             os.path.join(