Add upper version bounds for all main dependencies

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.5.5] - 2026-06-05
+
+### Changed
+
+- Pin version bounds for all core dependencies. Most notably, `pyteomics` is now constrained to `< 5` to avoid breaking changes introduced in the upcoming major release.
+
 ## [1.5.4] - 2026-05-13
 
 ### Fixed

psm_utils/__init__.py

@@ -1,6 +1,6 @@
 """Common utilities for parsing and handling PSMs, and search engine results."""
 
-__version__ = "1.5.4"
+__version__ = "1.5.5"
 __all__ = ["Peptidoform", "PSM", "PSMList"]
 
 from warnings import filterwarnings

pyproject.toml

@@ -20,16 +20,16 @@ classifiers = [
 dynamic = ["version"]
 requires-python = ">=3.10"
 dependencies = [
-    "click",
-    "lxml",
-    "numpy",
-    "pandas",
-    "psims",
-    "pyarrow",
-    "pydantic >= 2",
-    "pyteomics >= 4",
-    "rich",
-    "sqlalchemy >= 2",
+    "click >= 8, < 9",
+    "lxml >= 4, < 7",
+    "numpy >= 1.23, < 3",
+    "pandas >= 1.5, < 4",
+    "psims >= 1, < 2",
+    "pyarrow >= 11",
+    "pydantic >= 2, < 3",
+    "pyteomics >= 4, < 5",
+    "rich >= 12, < 16",
+    "sqlalchemy >= 2, < 3",
 ]
 
 [project.optional-dependencies]