bio2zarr 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl

bio2zarr/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# 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, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.2'
-__version_tuple__ = version_tuple = (0, 1, 2)
+__version__ = version = '0.1.4'
+__version_tuple__ = version_tuple = (0, 1, 4)

bio2zarr/vcf2zarr/icf.py

@@ -41,7 +41,7 @@ class VcfFieldSummary(core.JsonDataclass):
         return VcfFieldSummary(**d)
 
 
-@dataclasses.dataclass
+@dataclasses.dataclass(order=True)
 class VcfField:
     category: str
     name: str
@@ -192,6 +192,16 @@ class IcfMetadata(core.JsonDataclass):
         d["contigs"] = [Contig(**cd) for cd in d["contigs"]]
         return IcfMetadata(**d)
 
+    def __eq__(self, other):
+        if not isinstance(other, IcfMetadata):
+            return NotImplemented
+        return (
+            self.samples == other.samples
+            and self.contigs == other.contigs
+            and self.filters == other.filters
+            and sorted(self.fields) == sorted(other.fields)
+        )
+
 
 def fixed_vcf_field_definitions():
     def make_field_def(name, vcf_type, vcf_number):
@@ -1085,9 +1095,8 @@ class IntermediateColumnarFormatWriter:
                     for field in info_fields:
                         tcw.append(field.full_name, variant.INFO.get(field.name, None))
                     if has_gt:
-                        if variant.genotype is None:
-                            val = None
-                        else:
+                        val = None
+                        if "GT" in variant.FORMAT and variant.genotype is not None:
                             val = variant.genotype.array()
                         tcw.append("FORMAT/GT", val)
                     for field in format_fields:

bio2zarr/zarr_utils.py

@@ -1,9 +1,8 @@
 import zarr
-from packaging.version import Version
 
 
 def zarr_v3() -> bool:
-    return Version(zarr.__version__).major >= 3
+    return zarr.__version__ >= "3"
 
 
 if zarr_v3():

{bio2zarr-0.1.2.dist-info → bio2zarr-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bio2zarr
-Version: 0.1.2
+Version: 0.1.4
 Summary: Convert bioinformatics data to Zarr
 Author-email: sgkit Developers <project@sgkit.dev>
 License:                                  Apache License

{bio2zarr-0.1.2.dist-info → bio2zarr-0.1.4.dist-info}/RECORD

@@ -1,6 +1,6 @@
 bio2zarr/__init__.py,sha256=KiUGyya-9RHNcBldB8Lc1g3rP3CRjaL-5Olben0_6qA,49
 bio2zarr/__main__.py,sha256=wUKNNps8MAAEpMvLgVaI449eKyfr7Jpk2mMtYbNl4Ek,531
-bio2zarr/_version.py,sha256=SFCDdrYA67D1Je-jHgVVh4LOopkPvuV6NMtqSJ7Tfhg,411
+bio2zarr/_version.py,sha256=hcPkC9vIGgfrKK6ft7ysLT7iOCjpFmCBmyKLmXiaZ1g,511
 bio2zarr/cli.py,sha256=Iife89BfTR_AUarm-AIW0lAIYxd370OmP1KKePgFXzk,16008
 bio2zarr/constants.py,sha256=QjbtFeBUZ-XqG35ZFIFj8EYrta_EwUkC2B5VGRP7oQs,425
 bio2zarr/core.py,sha256=4xqNf3Txgyhcx23bzXZHq3GW0Jh24fPQwob7lKO7s0w,11668
@@ -8,14 +8,14 @@ bio2zarr/plink.py,sha256=Yr1meT4AgS2qnwM64-Nmthh4HbjaPXsddYiJdtfYWBg,6999
 bio2zarr/provenance.py,sha256=c_Z__QbWkLS0Rfa8D7LgEhtStng_zRMJX8comaDXIkw,142
 bio2zarr/typing.py,sha256=BYxhL16sKRoNxa6amf6AYxvt5Ke9qzv2np_kOT_zPJo,79
 bio2zarr/vcf_utils.py,sha256=tuPzuMiwGYgMlQA49L6EuIplw9DOVaOw1DTa03OJS7k,18268
-bio2zarr/zarr_utils.py,sha256=Ldt65YdyR8bxa0ZyVvMYqQ8z72vx1iPLbL7J2wx8No8,466
+bio2zarr/zarr_utils.py,sha256=99J7ycaG92K_AcWRF2S9A4ec2_4cXL6kjYT99GBfli4,415
 bio2zarr/vcf2zarr/__init__.py,sha256=0_of1iGzIDhvti49Gbcgd47oP63mKvouk9uLgKgiwoQ,791
-bio2zarr/vcf2zarr/icf.py,sha256=Lz5BeqP-d1G8xihZvua9911UJh-aszegCdj_7l32QV4,42074
+bio2zarr/vcf2zarr/icf.py,sha256=_gYCn4PBTB6MUmXoc7DROz0VaMdloY-Eeo3GPbSq28Q,42415
 bio2zarr/vcf2zarr/vcz.py,sha256=cfUCBsQW5dbhDu7NzXkd1Dalsev7UkFDXVOyChAHw8Q,49409
 bio2zarr/vcf2zarr/verification.py,sha256=uM-mg0yvUTBs-MvWBd4jxTS0zKCUbxEQpm4ALJADdMI,8037
-bio2zarr-0.1.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-bio2zarr-0.1.2.dist-info/METADATA,sha256=tG3yLpms9XBSyJKfyXOIYw59qRoYVyKpJFKTLDpbO2Q,14978
-bio2zarr-0.1.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-bio2zarr-0.1.2.dist-info/entry_points.txt,sha256=3adtRrClMpjatEbiYqK5bm9WHA2PaJN5hK-Cs_zkpaI,97
-bio2zarr-0.1.2.dist-info/top_level.txt,sha256=ouAvp3u9N25eKrQbN8BCDLPcWWQLhtlgdHKu8AtEj5Q,9
-bio2zarr-0.1.2.dist-info/RECORD,,
+bio2zarr-0.1.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+bio2zarr-0.1.4.dist-info/METADATA,sha256=goC7scfCITs1Uw_AWy42Eq3iOaL8uEZvwss2CcuAvos,14978
+bio2zarr-0.1.4.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+bio2zarr-0.1.4.dist-info/entry_points.txt,sha256=3adtRrClMpjatEbiYqK5bm9WHA2PaJN5hK-Cs_zkpaI,97
+bio2zarr-0.1.4.dist-info/top_level.txt,sha256=ouAvp3u9N25eKrQbN8BCDLPcWWQLhtlgdHKu8AtEj5Q,9
+bio2zarr-0.1.4.dist-info/RECORD,,

{bio2zarr-0.1.2.dist-info → bio2zarr-0.1.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any