From 5f925f93bd71a9efecdeedf744b2c1a1da624a9c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 8 Feb 2026 04:12:54 +0000 Subject: [PATCH] Bump urllib3 from 2.5.0 to 2.6.3 Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.5.0 to 2.6.3. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.5.0...2.6.3) --- updated-dependencies: - dependency-name: urllib3 dependency-version: 2.6.3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- uv.lock | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/uv.lock b/uv.lock index d254c0b..58edf78 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,5 @@ version = 1 -revision = 2 +revision = 3 requires-python = ">=3.9" resolution-markers = [ "python_full_version >= '3.12'", @@ -883,22 +883,24 @@ name = "kalign" version = "3.4.5" source = { editable = "." } dependencies = [ - { name = "biopython" }, - { name = "matplotlib", version = "3.9.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "matplotlib", version = "3.10.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, { name = "numpy", version = "2.3.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, - { name = "pandas" }, - { name = "rich" }, - { name = "scikit-bio" }, ] [package.optional-dependencies] all = [ { name = "biopython" }, + { name = "matplotlib", version = "3.9.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, + { name = "matplotlib", version = "3.10.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "pandas" }, { name = "scikit-bio" }, ] +analysis = [ + { name = "matplotlib", version = "3.9.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, + { name = "matplotlib", version = "3.10.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "pandas" }, +] biopython = [ { name = "biopython" }, ] @@ -947,7 +949,6 @@ dev = [ [package.metadata] requires-dist = [ - { name = "biopython", specifier = ">=1.85" }, { name = "biopython", marker = "extra == 'all'", specifier = ">=1.85" }, { name = "biopython", marker = "extra == 'biopython'", specifier = ">=1.85" }, { name = "biopython", marker = "extra == 'dev'", specifier = ">=1.85" }, @@ -955,11 +956,13 @@ requires-dist = [ { name = "black", marker = "extra == 'dev'" }, { name = "build", marker = "extra == 'dev'" }, { name = "flake8", marker = "extra == 'dev'" }, - { name = "matplotlib", specifier = ">=3.9.4" }, + { name = "matplotlib", marker = "extra == 'all'", specifier = ">=3.9.4" }, + { name = "matplotlib", marker = "extra == 'analysis'", specifier = ">=3.9.4" }, { name = "mypy", marker = "extra == 'dev'" }, { name = "myst-parser", marker = "extra == 'docs'" }, { name = "numpy", specifier = ">=1.19.0" }, - { name = "pandas", specifier = ">=2.3.0" }, + { name = "pandas", marker = "extra == 'all'", specifier = ">=2.3.0" }, + { name = "pandas", marker = "extra == 'analysis'", specifier = ">=2.3.0" }, { name = "pytest", marker = "extra == 'dev'", specifier = ">=6.0" }, { name = "pytest", marker = "extra == 'test'", specifier = ">=6.0" }, { name = "pytest-benchmark", marker = "extra == 'dev'" }, @@ -968,10 +971,8 @@ requires-dist = [ { name = "pytest-cov", marker = "extra == 'test'" }, { name = "pytest-xdist", marker = "extra == 'dev'" }, { name = "pytest-xdist", marker = "extra == 'test'" }, - { name = "rich", specifier = ">=14.0.0" }, { name = "rich", marker = "extra == 'dev'" }, { name = "rich", marker = "extra == 'test'" }, - { name = "scikit-bio", specifier = ">=0.6.3" }, { name = "scikit-bio", marker = "extra == 'all'", specifier = ">=0.6.3" }, { name = "scikit-bio", marker = "extra == 'dev'", specifier = ">=0.6.3" }, { name = "scikit-bio", marker = "extra == 'skbio'", specifier = ">=0.6.3" }, @@ -979,7 +980,7 @@ requires-dist = [ { name = "sphinx-rtd-theme", marker = "extra == 'docs'" }, { name = "twine", marker = "extra == 'dev'" }, ] -provides-extras = ["biopython", "skbio", "io", "all", "dev", "test", "docs"] +provides-extras = ["biopython", "skbio", "io", "analysis", "all", "dev", "test", "docs"] [package.metadata.requires-dev] dev = [ @@ -2765,11 +2766,11 @@ wheels = [ [[package]] name = "urllib3" -version = "2.5.0" +version = "2.6.3" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/15/22/9ee70a2574a4f4599c47dd506532914ce044817c7752a79b6a51286319bc/urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760", size = 393185, upload-time = "2025-06-18T14:07:41.644Z" } +sdist = { url = "https://files.pythonhosted.org/packages/c7/24/5f1b3bdffd70275f6661c76461e25f024d5a38a46f04aaca912426a2b1d3/urllib3-2.6.3.tar.gz", hash = "sha256:1b62b6884944a57dbe321509ab94fd4d3b307075e0c2eae991ac71ee15ad38ed", size = 435556, upload-time = "2026-01-07T16:24:43.925Z" } wheels = [ - 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