From ba4550d903f88d802ef8d5996fd5ef4ac8c5ad02 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 26 Jan 2026 12:29:08 +0000 Subject: [PATCH 1/2] Update pandas requirement from <3,>=1.4.0 to >=1.4.0,<4 Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.4.0...v3.0.0) --- updated-dependencies: - dependency-name: pandas dependency-version: 3.0.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f43b0ed8f..cfc05a9c6 100644 --- a/setup.py +++ b/setup.py @@ -63,7 +63,7 @@ "numpy >=1, <3", "packaging >=19.2", # Sync this with 'pandas-stubs' dev dependency - "pandas >=1.4.0, <3", + "pandas >=1.4.0, <4", "phylo-treetime >=0.11.2, <0.12", "pyfastx >=1.0.0, <3.0", "python_calamine >=0.2.0", From a0a21a7eccd24ddd6b0bc4ab030d31cd3df4813c Mon Sep 17 00:00:00 2001 From: Victor Lin Date: Wed, 28 Jan 2026 16:55:35 -0800 Subject: [PATCH 2/2] Update test matching for new Pandas error message A subtle difference from Pandas version 1 and 2 Can only use .str accessor with string values! to version 3 Can only use .str accessor with string values, not floating --- tests/functional/filter/cram/filter-query-numerical.t | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/functional/filter/cram/filter-query-numerical.t b/tests/functional/filter/cram/filter-query-numerical.t index 875c04802..dec1aac9e 100644 --- a/tests/functional/filter/cram/filter-query-numerical.t +++ b/tests/functional/filter/cram/filter-query-numerical.t @@ -42,7 +42,7 @@ string comparisons: > --query "coverage.str.endswith('.95')" \ > --output-strains filtered_strains.txt > /dev/null ERROR: Internal Pandas error when applying query: - Can only use .str accessor with string values! + \\tCan only use .str accessor with string values.* (re) Ensure the syntax is valid per . [2]