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numba>=0.58.1 + - numpy>=1.26.0 + - polars>=1.21.0,<2 + - pyranges>=0.1.3,<0.2 + - pandera>=0.31.1 + - pandas + - pyarrow + - natsort + - narwhals>=2.20.0 + - setuptools>=70 + - awkward>=2.5.0 + - polars-config-meta[polars]>=0.3.2 + - attrs + requires_python: '>=3.10' - pypi: https://files.pythonhosted.org/packages/e6/34/ebdc18bae6aa14fbee1a08b63c015c72b64868ff7dae68808ab500c492e2/tinycss2-1.4.0-py3-none-any.whl name: tinycss2 version: 1.4.0 @@ -17178,6 +17144,40 @@ packages: - pytest-cov ; extra == 'tests' - pytest-xdist ; extra == 'tests' requires_python: '>=3.8' +- pypi: https://files.pythonhosted.org/packages/e7/92/35dd3936a430c3f14bdd1a5b75f15f7ddccae79ef5e10087dc9e7a85089d/genoray-6.0.1-cp310-abi3-macosx_11_0_arm64.whl + name: genoray + version: 6.0.1 + sha256: 543b41fbebb2645e46ef54dbd0eb15b026baad14545a1ffe86fe780755af73b6 + requires_dist: + - seqpro>=0.21.1,<0.24 + - numpy>=1.26 + - pandas>=2.2.3 + - hirola>=0.3.0 + - pgenlib>=0.91.0 + - cyvcf2>=0.31.1 + - pysam>=0.22 + - polars>=1.37.1 + - polars-bio>=0.20.1,<0.34 + - rich>=13 + - typing-extensions>=4.14 + - pyarrow>=21 + - tqdm>=4.65 + - phantom-types>=3 + - more-itertools>=10 + - loguru>=0.7.0 + - attrs + - awkward + - numba + - cyclopts + - zstandard + - pydantic + - oxbow>=0.5.1,<0.6 + - joblib>=1.4.2,<2 + - joblib-progress>=1.0.6,<2 + - filelock>3,<4 + - scipy>=1.10 + - pooch>=1.7 + requires_python: '>=3.10,<3.15' - pypi: https://files.pythonhosted.org/packages/e7/e7/80988e32bf6f73919a113473a604f5a8f09094de312b9d52b79c2df7612b/jupyter_core-5.9.1-py3-none-any.whl name: jupyter-core version: 5.9.1 diff --git a/pixi.toml b/pixi.toml index 17715a7f..91261516 100644 --- a/pixi.toml +++ b/pixi.toml @@ -101,14 +101,14 @@ numba = "==0.59.1" [feature.py310.pypi-dependencies] pyarrow = ">=21" hirola = "==0.3" -seqpro = "==0.22.0" -# genoray >=5 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers +seqpro = "==0.23.0" +# genoray >=6 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers # py310-313 on both platforms. 5.0.0 carries # SparseVar2._find_ranges_chunked_sparse, the sparse chunked range API # _write_from_svar2 consumes (gvl#405), and the keyword-only, struct-grouped # _core pipeline entry points the test fixtures call (d-laub/genoray#153, #200). -# Mirrors the pyproject range. -genoray = ">=5,<6" +# 6.0.1 is the first release that allows seqpro 0.23. Mirrors the pyproject range. +genoray = ">=6.0.1,<7" polars = "==1.37.1" loguru = "*" natsort = "*" diff --git a/pyproject.toml b/pyproject.toml index df2878c4..c3405a77 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,14 +10,16 @@ readme = "README.md" license = { file = "LICENSE.txt" } requires-python = ">=3.10,<3.14" # >= 3.14 blocked by pyarrow/genoray dependencies = [ - "seqpro>=0.22", + "seqpro>=0.23", # >=5 carries SparseVar2._find_ranges_chunked_sparse, the sparse chunked # range API _write_from_svar2 consumes (gvl#405), and the keyword-only, # struct-grouped _core pipeline entry points the test fixtures call # (d-laub/genoray#153, #200). 5.0.0's breaking changes -- the GENORAY_* # environment variables, SparseVar2.from_vcf(reader_workers=) and - # resolve_log_level -- are all on APIs GVL never calls. - "genoray>=5,<6", + # resolve_log_level -- are all on APIs GVL never calls. 6.0.0's only + # breaking change drops the dense find_ranges_chunk path GVL no longer + # uses; >=6.0.1 is the first genoray that allows seqpro 0.23. + "genoray>=6.0.1,<7", "numpy", "loguru", "natsort",