pywombat 1.2.0__tar.gz → 1.2.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pywombat-1.2.0 → pywombat-1.2.1}/CHANGELOG.md +9 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/PKG-INFO +2 -1
- {pywombat-1.2.0 → pywombat-1.2.1}/pyproject.toml +8 -2
- {pywombat-1.2.0 → pywombat-1.2.1}/uv.lock +46 -1
- {pywombat-1.2.0 → pywombat-1.2.1}/.github/copilot-instructions.md +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/.github/workflows/publish.yml +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/.gitignore +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/.python-version +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/QUICKSTART.md +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/README.md +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/examples/README.md +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/examples/de_novo_mutations.yml +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/examples/rare_variants_high_impact.yml +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/src/pywombat/__init__.py +0 -0
- {pywombat-1.2.0 → pywombat-1.2.1}/src/pywombat/cli.py +0 -0
|
@@ -5,6 +5,15 @@ All notable changes to PyWombat will be documented in this file.
|
|
|
5
5
|
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
|
|
6
6
|
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
|
|
7
7
|
|
|
8
|
+
## [1.2.1] - 2026-02-05
|
|
9
|
+
|
|
10
|
+
### Fixed
|
|
11
|
+
|
|
12
|
+
- **Missing Dependency**: Added `pyarrow>=14.0.0` as an explicit dependency
|
|
13
|
+
- Required for Parquet file operations (`scan_parquet`, `write_parquet`)
|
|
14
|
+
- Previously was an implicit dependency through Polars
|
|
15
|
+
- Ensures proper installation on all systems
|
|
16
|
+
|
|
8
17
|
## [1.2.0] - 2026-02-05
|
|
9
18
|
|
|
10
19
|
### Added
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: pywombat
|
|
3
|
-
Version: 1.2.
|
|
3
|
+
Version: 1.2.1
|
|
4
4
|
Summary: A CLI tool for processing and filtering bcftools tabulated TSV files with pedigree support
|
|
5
5
|
Project-URL: Homepage, https://github.com/bourgeron-lab/pywombat
|
|
6
6
|
Project-URL: Repository, https://github.com/bourgeron-lab/pywombat
|
|
@@ -16,6 +16,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
|
|
|
16
16
|
Requires-Python: >=3.12
|
|
17
17
|
Requires-Dist: click>=8.1.0
|
|
18
18
|
Requires-Dist: polars>=0.19.0
|
|
19
|
+
Requires-Dist: pyarrow>=14.0.0
|
|
19
20
|
Requires-Dist: pyyaml>=6.0
|
|
20
21
|
Requires-Dist: tqdm>=4.67.1
|
|
21
22
|
Provides-Extra: dev
|
|
@@ -1,11 +1,17 @@
|
|
|
1
1
|
[project]
|
|
2
2
|
name = "pywombat"
|
|
3
|
-
version = "1.2.
|
|
3
|
+
version = "1.2.1"
|
|
4
4
|
description = "A CLI tool for processing and filtering bcftools tabulated TSV files with pedigree support"
|
|
5
5
|
readme = "README.md"
|
|
6
6
|
authors = [{ name = "Freddy Cliquet", email = "fcliquet@pasteur.fr" }]
|
|
7
7
|
requires-python = ">=3.12"
|
|
8
|
-
dependencies = [
|
|
8
|
+
dependencies = [
|
|
9
|
+
"polars>=0.19.0",
|
|
10
|
+
"pyarrow>=14.0.0",
|
|
11
|
+
"click>=8.1.0",
|
|
12
|
+
"pyyaml>=6.0",
|
|
13
|
+
"tqdm>=4.67.1",
|
|
14
|
+
]
|
|
9
15
|
license = { text = "MIT" }
|
|
10
16
|
keywords = ["vcf", "bioinformatics", "genomics", "pedigree", "variant-calling"]
|
|
11
17
|
classifiers = [
|
|
@@ -150,6 +150,49 @@ wheels = [
|
|
|
150
150
|
{ url = "https://files.pythonhosted.org/packages/f4/d1/8d1b28d007da43c750367c8bf5cb0f22758c16b1104b2b73b9acadb2d17a/polars_runtime_32-1.35.2-cp39-abi3-win_arm64.whl", hash = "sha256:6861145aa321a44eda7cc6694fb7751cb7aa0f21026df51b5faa52e64f9dc39b", size = 36955684, upload-time = "2025-11-09T13:19:15.666Z" },
|
|
151
151
|
]
|
|
152
152
|
|
|
153
|
+
[[package]]
|
|
154
|
+
name = "pyarrow"
|
|
155
|
+
version = "23.0.0"
|
|
156
|
+
source = { registry = "https://pypi.org/simple" }
|
|
157
|
+
sdist = { url = "https://files.pythonhosted.org/packages/01/33/ffd9c3eb087fa41dd79c3cf20c4c0ae3cdb877c4f8e1107a446006344924/pyarrow-23.0.0.tar.gz", hash = "sha256:180e3150e7edfcd182d3d9afba72f7cf19839a497cc76555a8dce998a8f67615", size = 1167185, upload-time = "2026-01-18T16:19:42.218Z" }
|
|
158
|
+
wheels = [
|
|
159
|
+
{ url = "https://files.pythonhosted.org/packages/3d/bd/c861d020831ee57609b73ea721a617985ece817684dc82415b0bc3e03ac3/pyarrow-23.0.0-cp312-cp312-macosx_12_0_arm64.whl", hash = "sha256:5961a9f646c232697c24f54d3419e69b4261ba8a8b66b0ac54a1851faffcbab8", size = 34189116, upload-time = "2026-01-18T16:15:28.054Z" },
|
|
160
|
+
{ url = "https://files.pythonhosted.org/packages/8c/23/7725ad6cdcbaf6346221391e7b3eecd113684c805b0a95f32014e6fa0736/pyarrow-23.0.0-cp312-cp312-macosx_12_0_x86_64.whl", hash = "sha256:632b3e7c3d232f41d64e1a4a043fb82d44f8a349f339a1188c6a0dd9d2d47d8a", size = 35803831, upload-time = "2026-01-18T16:15:33.798Z" },
|
|
161
|
+
{ url = "https://files.pythonhosted.org/packages/57/06/684a421543455cdc2944d6a0c2cc3425b028a4c6b90e34b35580c4899743/pyarrow-23.0.0-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:76242c846db1411f1d6c2cc3823be6b86b40567ee24493344f8226ba34a81333", size = 44436452, upload-time = "2026-01-18T16:15:41.598Z" },
|
|
162
|
+
{ url = "https://files.pythonhosted.org/packages/c6/6f/8f9eb40c2328d66e8b097777ddcf38494115ff9f1b5bc9754ba46991191e/pyarrow-23.0.0-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:b73519f8b52ae28127000986bf228fda781e81d3095cd2d3ece76eb5cf760e1b", size = 47557396, upload-time = "2026-01-18T16:15:51.252Z" },
|
|
163
|
+
{ url = "https://files.pythonhosted.org/packages/10/6e/f08075f1472e5159553501fde2cc7bc6700944bdabe49a03f8a035ee6ccd/pyarrow-23.0.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:068701f6823449b1b6469120f399a1239766b117d211c5d2519d4ed5861f75de", size = 48147129, upload-time = "2026-01-18T16:16:00.299Z" },
|
|
164
|
+
{ url = "https://files.pythonhosted.org/packages/7d/82/d5a680cd507deed62d141cc7f07f7944a6766fc51019f7f118e4d8ad0fb8/pyarrow-23.0.0-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:1801ba947015d10e23bca9dd6ef5d0e9064a81569a89b6e9a63b59224fd060df", size = 50596642, upload-time = "2026-01-18T16:16:08.502Z" },
|
|
165
|
+
{ url = "https://files.pythonhosted.org/packages/a9/26/4f29c61b3dce9fa7780303b86895ec6a0917c9af927101daaaf118fbe462/pyarrow-23.0.0-cp312-cp312-win_amd64.whl", hash = "sha256:52265266201ec25b6839bf6bd4ea918ca6d50f31d13e1cf200b4261cd11dc25c", size = 27660628, upload-time = "2026-01-18T16:16:15.28Z" },
|
|
166
|
+
{ url = "https://files.pythonhosted.org/packages/66/34/564db447d083ec7ff93e0a883a597d2f214e552823bfc178a2d0b1f2c257/pyarrow-23.0.0-cp313-cp313-macosx_12_0_arm64.whl", hash = "sha256:ad96a597547af7827342ffb3c503c8316e5043bb09b47a84885ce39394c96e00", size = 34184630, upload-time = "2026-01-18T16:16:22.141Z" },
|
|
167
|
+
{ url = "https://files.pythonhosted.org/packages/aa/3a/3999daebcb5e6119690c92a621c4d78eef2ffba7a0a1b56386d2875fcd77/pyarrow-23.0.0-cp313-cp313-macosx_12_0_x86_64.whl", hash = "sha256:b9edf990df77c2901e79608f08c13fbde60202334a4fcadb15c1f57bf7afee43", size = 35796820, upload-time = "2026-01-18T16:16:29.441Z" },
|
|
168
|
+
{ url = "https://files.pythonhosted.org/packages/ec/ee/39195233056c6a8d0976d7d1ac1cd4fe21fb0ec534eca76bc23ef3f60e11/pyarrow-23.0.0-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:36d1b5bc6ddcaff0083ceec7e2561ed61a51f49cce8be079ee8ed406acb6fdef", size = 44438735, upload-time = "2026-01-18T16:16:38.79Z" },
|
|
169
|
+
{ url = "https://files.pythonhosted.org/packages/2c/41/6a7328ee493527e7afc0c88d105ecca69a3580e29f2faaeac29308369fd7/pyarrow-23.0.0-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:4292b889cd224f403304ddda8b63a36e60f92911f89927ec8d98021845ea21be", size = 47557263, upload-time = "2026-01-18T16:16:46.248Z" },
|
|
170
|
+
{ url = "https://files.pythonhosted.org/packages/c6/ee/34e95b21ee84db494eae60083ddb4383477b31fb1fd19fd866d794881696/pyarrow-23.0.0-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:dfd9e133e60eaa847fd80530a1b89a052f09f695d0b9c34c235ea6b2e0924cf7", size = 48153529, upload-time = "2026-01-18T16:16:53.412Z" },
|
|
171
|
+
{ url = "https://files.pythonhosted.org/packages/52/88/8a8d83cea30f4563efa1b7bf51d241331ee5cd1b185a7e063f5634eca415/pyarrow-23.0.0-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:832141cc09fac6aab1cd3719951d23301396968de87080c57c9a7634e0ecd068", size = 50598851, upload-time = "2026-01-18T16:17:01.133Z" },
|
|
172
|
+
{ url = "https://files.pythonhosted.org/packages/c6/4c/2929c4be88723ba025e7b3453047dc67e491c9422965c141d24bab6b5962/pyarrow-23.0.0-cp313-cp313-win_amd64.whl", hash = "sha256:7a7d067c9a88faca655c71bcc30ee2782038d59c802d57950826a07f60d83c4c", size = 27577747, upload-time = "2026-01-18T16:18:02.413Z" },
|
|
173
|
+
{ url = "https://files.pythonhosted.org/packages/64/52/564a61b0b82d72bd68ec3aef1adda1e3eba776f89134b9ebcb5af4b13cb6/pyarrow-23.0.0-cp313-cp313t-macosx_12_0_arm64.whl", hash = "sha256:ce9486e0535a843cf85d990e2ec5820a47918235183a5c7b8b97ed7e92c2d47d", size = 34446038, upload-time = "2026-01-18T16:17:07.861Z" },
|
|
174
|
+
{ url = "https://files.pythonhosted.org/packages/cc/c9/232d4f9855fd1de0067c8a7808a363230d223c83aeee75e0fe6eab851ba9/pyarrow-23.0.0-cp313-cp313t-macosx_12_0_x86_64.whl", hash = "sha256:075c29aeaa685fd1182992a9ed2499c66f084ee54eea47da3eb76e125e06064c", size = 35921142, upload-time = "2026-01-18T16:17:15.401Z" },
|
|
175
|
+
{ url = "https://files.pythonhosted.org/packages/96/f2/60af606a3748367b906bb82d41f0032e059f075444445d47e32a7ff1df62/pyarrow-23.0.0-cp313-cp313t-manylinux_2_28_aarch64.whl", hash = "sha256:799965a5379589510d888be3094c2296efd186a17ca1cef5b77703d4d5121f53", size = 44490374, upload-time = "2026-01-18T16:17:23.93Z" },
|
|
176
|
+
{ url = "https://files.pythonhosted.org/packages/ff/2d/7731543050a678ea3a413955a2d5d80d2a642f270aa57a3cb7d5a86e3f46/pyarrow-23.0.0-cp313-cp313t-manylinux_2_28_x86_64.whl", hash = "sha256:ef7cac8fe6fccd8b9e7617bfac785b0371a7fe26af59463074e4882747145d40", size = 47527896, upload-time = "2026-01-18T16:17:33.393Z" },
|
|
177
|
+
{ url = "https://files.pythonhosted.org/packages/5a/90/f3342553b7ac9879413aed46500f1637296f3c8222107523a43a1c08b42a/pyarrow-23.0.0-cp313-cp313t-musllinux_1_2_aarch64.whl", hash = "sha256:15a414f710dc927132dd67c361f78c194447479555af57317066ee5116b90e9e", size = 48210401, upload-time = "2026-01-18T16:17:42.012Z" },
|
|
178
|
+
{ url = "https://files.pythonhosted.org/packages/f3/da/9862ade205ecc46c172b6ce5038a74b5151c7401e36255f15975a45878b2/pyarrow-23.0.0-cp313-cp313t-musllinux_1_2_x86_64.whl", hash = "sha256:3e0d2e6915eca7d786be6a77bf227fbc06d825a75b5b5fe9bcbef121dec32685", size = 50579677, upload-time = "2026-01-18T16:17:50.241Z" },
|
|
179
|
+
{ url = "https://files.pythonhosted.org/packages/c2/4c/f11f371f5d4740a5dafc2e11c76bcf42d03dfdb2d68696da97de420b6963/pyarrow-23.0.0-cp313-cp313t-win_amd64.whl", hash = "sha256:4b317ea6e800b5704e5e5929acb6e2dc13e9276b708ea97a39eb8b345aa2658b", size = 27631889, upload-time = "2026-01-18T16:17:56.55Z" },
|
|
180
|
+
{ url = "https://files.pythonhosted.org/packages/97/bb/15aec78bcf43a0c004067bd33eb5352836a29a49db8581fc56f2b6ca88b7/pyarrow-23.0.0-cp314-cp314-macosx_12_0_arm64.whl", hash = "sha256:20b187ed9550d233a872074159f765f52f9d92973191cd4b93f293a19efbe377", size = 34213265, upload-time = "2026-01-18T16:18:07.904Z" },
|
|
181
|
+
{ url = "https://files.pythonhosted.org/packages/f6/6c/deb2c594bbba41c37c5d9aa82f510376998352aa69dfcb886cb4b18ad80f/pyarrow-23.0.0-cp314-cp314-macosx_12_0_x86_64.whl", hash = "sha256:18ec84e839b493c3886b9b5e06861962ab4adfaeb79b81c76afbd8d84c7d5fda", size = 35819211, upload-time = "2026-01-18T16:18:13.94Z" },
|
|
182
|
+
{ url = "https://files.pythonhosted.org/packages/e0/e5/ee82af693cb7b5b2b74f6524cdfede0e6ace779d7720ebca24d68b57c36b/pyarrow-23.0.0-cp314-cp314-manylinux_2_28_aarch64.whl", hash = "sha256:e438dd3f33894e34fd02b26bd12a32d30d006f5852315f611aa4add6c7fab4bc", size = 44502313, upload-time = "2026-01-18T16:18:20.367Z" },
|
|
183
|
+
{ url = "https://files.pythonhosted.org/packages/9c/86/95c61ad82236495f3c31987e85135926ba3ec7f3819296b70a68d8066b49/pyarrow-23.0.0-cp314-cp314-manylinux_2_28_x86_64.whl", hash = "sha256:a244279f240c81f135631be91146d7fa0e9e840e1dfed2aba8483eba25cd98e6", size = 47585886, upload-time = "2026-01-18T16:18:27.544Z" },
|
|
184
|
+
{ url = "https://files.pythonhosted.org/packages/bb/6e/a72d901f305201802f016d015de1e05def7706fff68a1dedefef5dc7eff7/pyarrow-23.0.0-cp314-cp314-musllinux_1_2_aarch64.whl", hash = "sha256:c4692e83e42438dba512a570c6eaa42be2f8b6c0f492aea27dec54bdc495103a", size = 48207055, upload-time = "2026-01-18T16:18:35.425Z" },
|
|
185
|
+
{ url = "https://files.pythonhosted.org/packages/f9/e5/5de029c537630ca18828db45c30e2a78da03675a70ac6c3528203c416fe3/pyarrow-23.0.0-cp314-cp314-musllinux_1_2_x86_64.whl", hash = "sha256:ae7f30f898dfe44ea69654a35c93e8da4cef6606dc4c72394068fd95f8e9f54a", size = 50619812, upload-time = "2026-01-18T16:18:43.553Z" },
|
|
186
|
+
{ url = "https://files.pythonhosted.org/packages/59/8d/2af846cd2412e67a087f5bda4a8e23dfd4ebd570f777db2e8686615dafc1/pyarrow-23.0.0-cp314-cp314-win_amd64.whl", hash = "sha256:5b86bb649e4112fb0614294b7d0a175c7513738876b89655605ebb87c804f861", size = 28263851, upload-time = "2026-01-18T16:19:38.567Z" },
|
|
187
|
+
{ url = "https://files.pythonhosted.org/packages/7b/7f/caab863e587041156f6786c52e64151b7386742c8c27140f637176e9230e/pyarrow-23.0.0-cp314-cp314t-macosx_12_0_arm64.whl", hash = "sha256:ebc017d765d71d80a3f8584ca0566b53e40464586585ac64176115baa0ada7d3", size = 34463240, upload-time = "2026-01-18T16:18:49.755Z" },
|
|
188
|
+
{ url = "https://files.pythonhosted.org/packages/c9/fa/3a5b8c86c958e83622b40865e11af0857c48ec763c11d472c87cd518283d/pyarrow-23.0.0-cp314-cp314t-macosx_12_0_x86_64.whl", hash = "sha256:0800cc58a6d17d159df823f87ad66cefebf105b982493d4bad03ee7fab84b993", size = 35935712, upload-time = "2026-01-18T16:18:55.626Z" },
|
|
189
|
+
{ url = "https://files.pythonhosted.org/packages/c5/08/17a62078fc1a53decb34a9aa79cf9009efc74d63d2422e5ade9fed2f99e3/pyarrow-23.0.0-cp314-cp314t-manylinux_2_28_aarch64.whl", hash = "sha256:3a7c68c722da9bb5b0f8c10e3eae71d9825a4b429b40b32709df5d1fa55beb3d", size = 44503523, upload-time = "2026-01-18T16:19:03.958Z" },
|
|
190
|
+
{ url = "https://files.pythonhosted.org/packages/cc/70/84d45c74341e798aae0323d33b7c39194e23b1abc439ceaf60a68a7a969a/pyarrow-23.0.0-cp314-cp314t-manylinux_2_28_x86_64.whl", hash = "sha256:bd5556c24622df90551063ea41f559b714aa63ca953db884cfb958559087a14e", size = 47542490, upload-time = "2026-01-18T16:19:11.208Z" },
|
|
191
|
+
{ url = "https://files.pythonhosted.org/packages/61/d9/d1274b0e6f19e235de17441e53224f4716574b2ca837022d55702f24d71d/pyarrow-23.0.0-cp314-cp314t-musllinux_1_2_aarch64.whl", hash = "sha256:54810f6e6afc4ffee7c2e0051b61722fbea9a4961b46192dcfae8ea12fa09059", size = 48233605, upload-time = "2026-01-18T16:19:19.544Z" },
|
|
192
|
+
{ url = "https://files.pythonhosted.org/packages/39/07/e4e2d568cb57543d84482f61e510732820cddb0f47c4bb7df629abfed852/pyarrow-23.0.0-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:14de7d48052cf4b0ed174533eafa3cfe0711b8076ad70bede32cf59f744f0d7c", size = 50603979, upload-time = "2026-01-18T16:19:26.717Z" },
|
|
193
|
+
{ url = "https://files.pythonhosted.org/packages/72/9c/47693463894b610f8439b2e970b82ef81e9599c757bf2049365e40ff963c/pyarrow-23.0.0-cp314-cp314t-win_amd64.whl", hash = "sha256:427deac1f535830a744a4f04a6ac183a64fcac4341b3f618e693c41b7b98d2b0", size = 28338905, upload-time = "2026-01-18T16:19:32.93Z" },
|
|
194
|
+
]
|
|
195
|
+
|
|
153
196
|
[[package]]
|
|
154
197
|
name = "pygments"
|
|
155
198
|
version = "2.19.2"
|
|
@@ -191,11 +234,12 @@ wheels = [
|
|
|
191
234
|
|
|
192
235
|
[[package]]
|
|
193
236
|
name = "pywombat"
|
|
194
|
-
version = "1.
|
|
237
|
+
version = "1.2.0"
|
|
195
238
|
source = { editable = "." }
|
|
196
239
|
dependencies = [
|
|
197
240
|
{ name = "click" },
|
|
198
241
|
{ name = "polars" },
|
|
242
|
+
{ name = "pyarrow" },
|
|
199
243
|
{ name = "pyyaml" },
|
|
200
244
|
{ name = "tqdm" },
|
|
201
245
|
]
|
|
@@ -210,6 +254,7 @@ dev = [
|
|
|
210
254
|
requires-dist = [
|
|
211
255
|
{ name = "click", specifier = ">=8.1.0" },
|
|
212
256
|
{ name = "polars", specifier = ">=0.19.0" },
|
|
257
|
+
{ name = "pyarrow", specifier = ">=14.0.0" },
|
|
213
258
|
{ name = "pytest", marker = "extra == 'dev'", specifier = ">=7.0.0" },
|
|
214
259
|
{ name = "pytest-cov", marker = "extra == 'dev'", specifier = ">=4.0.0" },
|
|
215
260
|
{ name = "pyyaml", specifier = ">=6.0" },
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|