From c6205bba5b24d8b2dda18d3610c64068f8d1b358 Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Fri, 5 Jun 2026 11:05:52 +0200
Subject: [PATCH 1/3] Pin dependency version bounds for all main dependencies

Add lower and upper bounds to all core dependencies to prevent
incompatible major versions from being pulled in. Most notably,
pin pyteomics to < 5 to avoid breaking changes in downstream packages.
---
 pyproject.toml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7c08247..89f9ca9 100644
--- a/pyproject.toml
+++ b/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, < 3",
+    "psims >= 1, < 2",
+    "pyarrow >= 11",
+    "pydantic >= 2, < 3",
+    "pyteomics >= 4, < 5",
+    "rich >= 12, < 16",
+    "sqlalchemy >= 2, < 3",
 ]
 
 [project.optional-dependencies]

From b8d77148110242ecffaeb5bbe06a4aa886c06251 Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Fri, 5 Jun 2026 11:21:29 +0200
Subject: [PATCH 2/3] Set pandas upper bound to < 4: compatible with pandas 3.x

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 89f9ca9..e435104 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ dependencies = [
     "click >= 8, < 9",
     "lxml >= 4, < 7",
     "numpy >= 1.23, < 3",
-    "pandas >= 1.5, < 3",
+    "pandas >= 1.5, < 4",
     "psims >= 1, < 2",
     "pyarrow >= 11",
     "pydantic >= 2, < 3",

From 05be2f174c354c96ada11346505cd42035a5d0dd Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Fri, 5 Jun 2026 11:27:27 +0200
Subject: [PATCH 3/3] Bump version to 1.5.5

---
 CHANGELOG.md          | 6 ++++++
 psm_utils/__init__.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1ecebad..faa356c 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/psm_utils/__init__.py b/psm_utils/__init__.py
index 0a83a31..5454f0c 100644
--- a/psm_utils/__init__.py
+++ b/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