varcode 11.3.0__tar.gz → 11.3.2__tar.gz

{varcode-11.3.0 → varcode-11.3.2}/CHANGELOG.md

@@ -1,5 +1,17 @@
 # Change Log
 
+## v11.3.2
+
+- Type VCF compression as the literal values pandas accepts, and pin
+  pandas-stubs in the lint extra so mypy checks pandas calls the same way in
+  every environment.
+
+## v11.3.1
+
+- Stop renaming MAF columns in place, which pandas has deprecated for removal.
+- Replace deprecated pytest generator parameters and instance-method
+  class-scoped fixtures in the test suite.
+
 ## v11.3.0
 
 - Add opt-in bounded discovery of newly created initiation codons over paired

{varcode-11.3.0/varcode.egg-info → varcode-11.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 11.3.0
+Version: 11.3.2
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode
@@ -34,6 +34,7 @@ Requires-Dist: biopython>=1.85; extra == "test-data"
 Provides-Extra: lint
 Requires-Dist: ruff; extra == "lint"
 Requires-Dist: mypy==2.4.0; extra == "lint"
+Requires-Dist: pandas-stubs==3.0.5.260914; extra == "lint"
 Dynamic: license-file
 
 [![Tests](https://github.com/openvax/varcode/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/varcode/actions/workflows/tests.yml)

{varcode-11.3.0 → varcode-11.3.2}/pyproject.toml

@@ -39,7 +39,7 @@ orf = ["orfdata>=0.43.0,<1"]
 uorf = ["orfdata>=0.43.0,<1"]
 rna = ["pysam>=0.21"]
 test-data = ["osteosarc>=0.14.4,<0.16", "biopython>=1.85"]
-lint = ["ruff", "mypy==2.4.0"]
+lint = ["ruff", "mypy==2.4.0", "pandas-stubs==3.0.5.260914"]
 
 [project.scripts]
 varcode-genes = "varcode.cli.genes_script:main"

{varcode-11.3.0 → varcode-11.3.2}/tests/test_dbnsfp_validation.py

@@ -61,7 +61,7 @@ def generate_dbnsfp_validation_set():
         'dna_ref',
         'dna_alt',
         'aa_pos',
-        'aa_alt'], generate_dbnsfp_validation_set())
+        'aa_alt'], list(generate_dbnsfp_validation_set()))
 def test_dbnsfp_validation_set_transcript_mutation(
         ensembl_transcript_id,
         chrom,

{varcode-11.3.0 → varcode-11.3.2}/tests/test_effect_classes.py

@@ -505,7 +505,7 @@ def generate_silent_stop_codon_effects():
             transcript_id,
             Silent)
 
-@pytest.mark.parametrize(['variant', 'transcript_id', 'effect_class'], generate_silent_stop_codon_effects())
+@pytest.mark.parametrize(['variant', 'transcript_id', 'effect_class'], list(generate_silent_stop_codon_effects()))
 def test_silent_stop_codons(variant, transcript_id, effect_class):
     expect_effect(
         variant,

{varcode-11.3.0 → varcode-11.3.2}/tests/test_reference.py

@@ -50,7 +50,7 @@ def generate_reference_name_aliases():
                     assembly_name
                 )
 
-@pytest.mark.parametrize(['candidate', 'assembly_name'], generate_reference_name_aliases())
+@pytest.mark.parametrize(['candidate', 'assembly_name'], list(generate_reference_name_aliases()))
 def test_infer_reference_name_aliases(candidate, assembly_name):
     eq_(infer_reference_name(candidate), assembly_name)
     
@@ -64,7 +64,7 @@ def generate_reference_name_fasta_filenames():
                     assembly_name
                 )
 
-@pytest.mark.parametrize(['candidate', 'assembly_name'], generate_reference_name_fasta_filenames())
+@pytest.mark.parametrize(['candidate', 'assembly_name'], list(generate_reference_name_fasta_filenames()))
 def test_reference_name_fasta_filenames(candidate, assembly_name):
     eq_(infer_reference_name(candidate), assembly_name)
 

{varcode-11.3.0 → varcode-11.3.2}/tests/test_vcf_parsing.py

@@ -295,7 +295,8 @@ class TestGetMetadata:
     examples of both shapes."""
 
     @pytest.fixture(scope="class")
-    def header(self):
+    @classmethod
+    def header(cls):
         path = os.path.join(
             DATA_DIR, "real_callers", "mutect2_example.vcf")
         return VCFHeader.from_path(path)

{varcode-11.3.0 → varcode-11.3.2}/tests/test_vcf_spec_examples.py

@@ -264,7 +264,8 @@ class TestTrioEndToEndExpectedShapes:
     """
 
     @pytest.fixture(scope="class")
-    def parsed_rows(self):
+    @classmethod
+    def parsed_rows(cls):
         h = VCFHeader.from_path(TRIO_PATH)
         rows = []
         with open(TRIO_PATH) as fh:

{varcode-11.3.0 → varcode-11.3.2}/varcode/maf.py

@@ -103,7 +103,7 @@ def load_maf_dataframe(
             # MAFs in the wild have capitalization differences in their
             # column names, normalize them to always use the names above
             if expected.lower() == actual.lower():
-                df.rename(columns={actual: expected}, inplace=True)
+                df = df.rename(columns={actual: expected})
             else:
                 error_message = (
                     "Expected column %s but got %s" % (expected, actual))

{varcode-11.3.0 → varcode-11.3.2}/varcode/vcf.py

@@ -17,6 +17,7 @@ import urllib.parse
 import urllib.request
 import logging
 from collections import OrderedDict
+from typing import Literal
 from warnings import warn
 
 import pandas
@@ -535,7 +536,7 @@ def read_vcf_into_dataframe(
     else:
         raise NotImplementedError("Only local files are supported.")
 
-    compression = None
+    compression: Literal["gzip", "bz2"] | None = None
     if path.endswith(".gz"):
         compression = "gzip"
     elif path.endswith(".bz2"):

varcode-11.3.2/varcode/version.py

@@ -0,0 +1 @@
+__version__ = "11.3.2"

{varcode-11.3.0 → varcode-11.3.2/varcode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 11.3.0
+Version: 11.3.2
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode
@@ -34,6 +34,7 @@ Requires-Dist: biopython>=1.85; extra == "test-data"
 Provides-Extra: lint
 Requires-Dist: ruff; extra == "lint"
 Requires-Dist: mypy==2.4.0; extra == "lint"
+Requires-Dist: pandas-stubs==3.0.5.260914; extra == "lint"
 Dynamic: license-file
 
 [![Tests](https://github.com/openvax/varcode/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/varcode/actions/workflows/tests.yml)

{varcode-11.3.0 → varcode-11.3.2}/varcode.egg-info/requires.txt

@@ -9,6 +9,7 @@ sercol>=1.0.3
 [lint]
 ruff
 mypy==2.4.0
+pandas-stubs==3.0.5.260914
 
 [orf]
 orfdata<1,>=0.43.0

varcode-11.3.0/varcode/version.py

@@ -1 +0,0 @@
-__version__ = "11.3.0"