From 9605ca5e344ed0bad07b6a73d8b99cb126fd5f79 Mon Sep 17 00:00:00 2001 From: tfenne Date: Tue, 21 Jan 2025 15:39:17 -0700 Subject: [PATCH] Fixup after pinning new fgpyo version. --- poetry.lock | 62 +++++++++++++++++++++++++++---------------- pyproject.toml | 4 +-- tests/test_variant.py | 3 --- 3 files changed, 40 insertions(+), 29 deletions(-) diff --git a/poetry.lock b/poetry.lock index 100fa2b..9f4946f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "attrs" @@ -611,35 +611,39 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc [[package]] name = "fgpyo" -version = "0.8.0" +version = "0.8.1-dev" description = "Python bioinformatics and genomics library" optional = false -python-versions = "<4.0,>=3.8.0" -files = [ - {file = "fgpyo-0.8.0-py3-none-any.whl", hash = "sha256:d08c7bc21f39ca41216e6611613f2ee8fe5ccb5f52c43e5de2def95697cdf33d"}, - {file = "fgpyo-0.8.0.tar.gz", hash = "sha256:07f58af40f867b6d8cbe6417c9e9b077dd7067ca3cc57d3eca97a4c1432195fd"}, -] +python-versions = ">=3.9.0,<4.0" +files = [] +develop = false [package.dependencies] attrs = ">=19.3.0" -numpy = {version = ">=1.26.4,<2.0.0", markers = "python_version >= \"3.12\""} +numpy = {version = "^1.26.4", markers = "python_version >= \"3.12\""} pysam = ">=0.22.1" -strenum = ">=0.4.15,<0.5.0" +strenum = "^0.4.15" + +[package.source] +type = "git" +url = "https://github.com/fulcrumgenomics/fgpyo" +reference = "c5eb469a4fbe4f2e600e17f929cc89379c661e7a" +resolved_reference = "c5eb469a4fbe4f2e600e17f929cc89379c661e7a" [[package]] name = "filelock" -version = "3.16.1" +version = "3.17.0" description = "A platform independent file lock." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - 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{file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"}, - {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"}, + {file = "tzdata-2025.1-py2.py3-none-any.whl", hash = "sha256:7e127113816800496f027041c570f50bcd464a020098a3b6b199517772303639"}, + {file = "tzdata-2025.1.tar.gz", hash = "sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694"}, ] [[package]] @@ -2432,4 +2448,4 @@ test = ["pytest"] [metadata] lock-version = "2.0" python-versions = "^3.12" -content-hash = "c401a1d5773fb02e2c3603ff3aa18d7509bd4da6b31e5a67386feaf12607f1db" +content-hash = "9c57ee0dd9c5e94f5639b4ab66f7efbd8a60e8638eafe1fcf800efba02ca13e0" diff --git a/pyproject.toml b/pyproject.toml index a07daaa..6710eb6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,7 @@ python = "^3.12" pyproject_hooks= "^1.0.0,!=1.1.0" pybedlite = "^1.0.0" strenum = "^0.4.15" -fgpyo = "^0.8.0" +fgpyo = {git ="https://github.com/fulcrumgenomics/fgpyo" , rev= "c5eb469a4fbe4f2e600e17f929cc89379c661e7a" } pysam = "^0.22.1" ordered-set = "^4.1.0" primer3-py = "^2.0.3" @@ -141,8 +141,6 @@ addopts = [ "--cov", "--cov-report=xml", "--cov-branch", - "--mypy", - "--ruff", "--doctest-plus", "--doctest-modules", "-v" diff --git a/tests/test_variant.py b/tests/test_variant.py index 8445445..9018203 100644 --- a/tests/test_variant.py +++ b/tests/test_variant.py @@ -1,6 +1,5 @@ from pathlib import Path -import pysam import pytest from fgpyo.vcf.builder import VariantBuilder from fgpyo.vcf.builder import VcfFieldNumber @@ -123,7 +122,6 @@ def test_variant_lookup_filtering(tmp_path: Path, builder: VariantBuilder) -> No builder.add("chr1", pos=1020, ref="A", alts="C") vcf = tmp_path / "test.vcf.gz" builder.to_path(vcf) - pysam.tabix_index(str(vcf), preset="vcf") lookup = VariantLookup([vcf], min_maf=0.1, include_missing_mafs=False) variants = lookup.query("chr1", 1000, 1020) @@ -150,7 +148,6 @@ def test_variant_lookup_masking(tmp_path: Path, builder: VariantBuilder) -> None builder.add("chr1", pos=1030, ref="AA", alts="CG", info={"AF": 0.1}) vcf = tmp_path / "test.vcf.gz" builder.to_path(vcf) - pysam.tabix_index(str(vcf), preset="vcf") lookup = VariantLookup([vcf], min_maf=0.1, include_missing_mafs=False) # 0 1 2 3 4 5