bio2zarr 0.1.5__py3-none-any.whl → 0.1.6__py3-none-any.whl

bio2zarr/{vcf2zarr/verification.py → vcz_verification.py}

@@ -1,12 +1,12 @@
-import cyvcf2
 import numpy as np
 import numpy.testing as nt
 import tqdm
 import zarr
 
+from bio2zarr import core
 from bio2zarr.zarr_utils import first_dim_iter
 
-from .. import constants
+from . import constants
 
 
 def assert_all_missing_float(a):
@@ -146,7 +146,10 @@ def assert_format_val_equal(vcf_val, zarr_val, vcf_type, vcf_number):
         nt.assert_equal(vcf_val, zarr_val)
 
 
+@core.requires_optional_dependency("cyvcf2", "vcf")
 def verify(vcf_path, zarr_path, show_progress=False):
+    import cyvcf2
+
     root = zarr.open(store=zarr_path, mode="r")
     pos = root["variant_position"][:]
     allele = root["variant_allele"][:]

{bio2zarr-0.1.5.dist-info → bio2zarr-0.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bio2zarr
-Version: 0.1.5
+Version: 0.1.6
 Summary: Convert bioinformatics data to Zarr
 Author-email: sgkit Developers <project@sgkit.dev>
 License:                                  Apache License
@@ -216,23 +216,24 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.26
 Requires-Dist: zarr<3,>=2.17
-Requires-Dist: click
+Requires-Dist: numcodecs[msgpack]!=0.14.0,!=0.14.1,<0.16
 Requires-Dist: tabulate
 Requires-Dist: tqdm
 Requires-Dist: humanfriendly
-Requires-Dist: cyvcf2
-Requires-Dist: bed_reader
+Requires-Dist: coloredlogs
+Requires-Dist: click
+Requires-Dist: pandas
 Provides-Extra: dev
+Requires-Dist: click>=8.2.0; extra == "dev"
 Requires-Dist: hypothesis-vcf; extra == "dev"
 Requires-Dist: msprime; extra == "dev"
 Requires-Dist: pysam; extra == "dev"
@@ -241,6 +242,16 @@ Requires-Dist: pytest-coverage; extra == "dev"
 Requires-Dist: pytest-xdist; extra == "dev"
 Requires-Dist: sgkit>=0.8.0; extra == "dev"
 Requires-Dist: tqdm; extra == "dev"
+Requires-Dist: tskit>=0.6.4; extra == "dev"
+Requires-Dist: bed_reader; extra == "dev"
+Requires-Dist: cyvcf2; extra == "dev"
+Provides-Extra: tskit
+Requires-Dist: tskit>=0.6.4; extra == "tskit"
+Provides-Extra: vcf
+Requires-Dist: cyvcf2; extra == "vcf"
+Provides-Extra: all
+Requires-Dist: tskit>=0.6.4; extra == "all"
+Requires-Dist: cyvcf2; extra == "all"
 Dynamic: license-file
 
 [![CI](https://github.com/sgkit-dev/bio2zarr/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/sgkit-dev/bio2zarr/actions/workflows/ci.yml)

bio2zarr-0.1.6.dist-info/RECORD

@@ -0,0 +1,21 @@
+bio2zarr/__init__.py,sha256=KiUGyya-9RHNcBldB8Lc1g3rP3CRjaL-5Olben0_6qA,49
+bio2zarr/__main__.py,sha256=4pF1IBO4CcswA_Fe7NmK_pqGOUHCwsd_8YU7dP92n9c,578
+bio2zarr/_version.py,sha256=ESbJO0YD7TYfOUv_WDIJJgWELGepEWsoyhqVifEcXPA,511
+bio2zarr/cli.py,sha256=WrLfUyV6VggqtDAcI3c1S5YN62ZVOent5f9JzSkX_vA,17570
+bio2zarr/constants.py,sha256=QjbtFeBUZ-XqG35ZFIFj8EYrta_EwUkC2B5VGRP7oQs,425
+bio2zarr/core.py,sha256=mYi2Vmh_YdNEd3weE0zZIPr7ToEUynq8nNCVvONVaqM,12140
+bio2zarr/plink.py,sha256=hkrgXKkxfExgOpgNkj0SszEh9qA8R3T6kXCd-4jsXO8,11498
+bio2zarr/provenance.py,sha256=c_Z__QbWkLS0Rfa8D7LgEhtStng_zRMJX8comaDXIkw,142
+bio2zarr/tskit.py,sha256=6YWbh8M3VJQtVpy2pD8x7Zf0jmc4HOIZwIlWcVaqjvU,10816
+bio2zarr/typing.py,sha256=HdXNwIBEqYtGNwKyeUDQv6-H-pKSwNZO0qD2_VxTXEY,48
+bio2zarr/vcf.py,sha256=_eQJm74YcKBfKDGM283ibhE40nUrkxO6Ee1giDfKjLg,60207
+bio2zarr/vcf_utils.py,sha256=xrsmxpu1xyXtl6FaYuU562WZP-iVUIaqzxD-11MHfAM,19541
+bio2zarr/vcz.py,sha256=yD2mvDZuzlAH73qPRVsUwqHSK-9HMdV4Vcif2JxfcCM,42610
+bio2zarr/vcz_verification.py,sha256=4YZZnAuMH-z9uPqAeBONdsZADz2MtY57D7RAbMa90yY,8119
+bio2zarr/zarr_utils.py,sha256=99J7ycaG92K_AcWRF2S9A4ec2_4cXL6kjYT99GBfli4,415
+bio2zarr-0.1.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+bio2zarr-0.1.6.dist-info/METADATA,sha256=Me_jLTDVz76lOtidDs1gVrXnwU_rm4ARBpEz_Ozmt6U,15405
+bio2zarr-0.1.6.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+bio2zarr-0.1.6.dist-info/entry_points.txt,sha256=bbIbR8fWMGruyLaoCxO1O22nKidWKUzMgYbTYdsN6YQ,181
+bio2zarr-0.1.6.dist-info/top_level.txt,sha256=ouAvp3u9N25eKrQbN8BCDLPcWWQLhtlgdHKu8AtEj5Q,9
+bio2zarr-0.1.6.dist-info/RECORD,,

{bio2zarr-0.1.5.dist-info → bio2zarr-0.1.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{bio2zarr-0.1.5.dist-info → bio2zarr-0.1.6.dist-info}/entry_points.txt

@@ -1,3 +1,5 @@
 [console_scripts]
+plink2zarr = bio2zarr.cli:plink2zarr_main
+tskit2zarr = bio2zarr.cli:tskit2zarr_main
 vcf2zarr = bio2zarr.cli:vcf2zarr_main
 vcfpartition = bio2zarr.cli:vcfpartition

bio2zarr/vcf2zarr/__init__.py

@@ -1,38 +0,0 @@
-from .icf import (
-    IntermediateColumnarFormat,
-    explode,
-    explode_finalise,
-    explode_init,
-    explode_partition,
-)
-from .vcz import (
-    VcfZarrSchema,
-    convert,
-    encode,
-    encode_finalise,
-    encode_init,
-    encode_partition,
-    inspect,
-    mkschema,
-)
-from .verification import verify
-
-# NOTE some of these aren't intended to be part of the external
-# interface (like IntermediateColumnarFormat), but putting
-# them into the list to keep the lint nagging under control
-__all__ = [
-    "IntermediateColumnarFormat",
-    "explode",
-    "explode_finalise",
-    "explode_init",
-    "explode_partition",
-    "VcfZarrSchema",
-    "convert",
-    "encode",
-    "encode_finalise",
-    "encode_init",
-    "encode_partition",
-    "inspect",
-    "mkschema",
-    "verify",
-]

bio2zarr-0.1.5.dist-info/RECORD

@@ -1,21 +0,0 @@
-bio2zarr/__init__.py,sha256=KiUGyya-9RHNcBldB8Lc1g3rP3CRjaL-5Olben0_6qA,49
-bio2zarr/__main__.py,sha256=wUKNNps8MAAEpMvLgVaI449eKyfr7Jpk2mMtYbNl4Ek,531
-bio2zarr/_version.py,sha256=Y4jy4bEMmwl_qNPCmiMFnlQ2ofMoqyG37hp8uwI3m10,511
-bio2zarr/cli.py,sha256=eyOSqU7hlZuvXEVB2g3qWPK6ys0A1C1gMahVz51hRqs,15999
-bio2zarr/constants.py,sha256=QjbtFeBUZ-XqG35ZFIFj8EYrta_EwUkC2B5VGRP7oQs,425
-bio2zarr/core.py,sha256=4xqNf3Txgyhcx23bzXZHq3GW0Jh24fPQwob7lKO7s0w,11668
-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=u1nkFRecY__IgkfV3N0Sr3AFIUSN8sYEF463K1HIgEE,19496
-bio2zarr/zarr_utils.py,sha256=99J7ycaG92K_AcWRF2S9A4ec2_4cXL6kjYT99GBfli4,415
-bio2zarr/vcf2zarr/__init__.py,sha256=0_of1iGzIDhvti49Gbcgd47oP63mKvouk9uLgKgiwoQ,791
-bio2zarr/vcf2zarr/icf.py,sha256=G70eC6LgrJUvGBHKYrcV83BA7Mm3D170zIsoXRZgoUA,42895
-bio2zarr/vcf2zarr/vcz.py,sha256=cfUCBsQW5dbhDu7NzXkd1Dalsev7UkFDXVOyChAHw8Q,49409
-bio2zarr/vcf2zarr/verification.py,sha256=uM-mg0yvUTBs-MvWBd4jxTS0zKCUbxEQpm4ALJADdMI,8037
-bio2zarr-0.1.5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-bio2zarr-0.1.5.dist-info/METADATA,sha256=rWYid_erOvB8gywz8N4TXBfR7ezSELuaF5Hyq3iV86w,15000
-bio2zarr-0.1.5.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-bio2zarr-0.1.5.dist-info/entry_points.txt,sha256=3adtRrClMpjatEbiYqK5bm9WHA2PaJN5hK-Cs_zkpaI,97
-bio2zarr-0.1.5.dist-info/top_level.txt,sha256=ouAvp3u9N25eKrQbN8BCDLPcWWQLhtlgdHKu8AtEj5Q,9
-bio2zarr-0.1.5.dist-info/RECORD,,