Add Python 3.13 support (testing and builds); update dependency versions; bump version

Author: RalfG

.github/workflows/build_and_publish.yml

@@ -38,7 +38,7 @@ jobs:
         with:
           lfs: "true"
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.1
+        uses: pypa/cibuildwheel@v2.22.0
         with:
           output-dir: dist
       - uses: actions/upload-artifact@v4

.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
       max-parallel: 4
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

ms2pip/__init__.py

@@ -1,7 +1,7 @@
 # isort: skip_file
 """MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction."""
 
-__version__ = "4.0.0"
+__version__ = "4.1.0"
 
 from warnings import filterwarnings
 

pyproject.toml

@@ -40,13 +40,13 @@ dependencies = [
     "tomlkit>=0.5,<1",
     "sqlalchemy>=1.3,<2",
     "click>=7,<9",
-    "xgboost>=1.3",
+    "xgboost>=1.3,<3",
     "lxml>=4",
     "rich>=13",
     "pydantic>=2",
     "werkzeug>=2",
-    "psm_utils>=0.9",
-    "ms2rescore-rs",
+    "psm_utils>=1.0",
+    "ms2rescore-rs>=0.4,<2",
 ]
 
 [project.optional-dependencies]
@@ -91,7 +91,7 @@ target-version = 'py39'
 
 [tool.cibuildwheel]
 build = "cp3*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64"
-skip = "cp36-* cp37-* cp38-* cp313-*"                                               # No ms2rescore-rs for 3.13
+skip = "cp36-* cp37-* cp38-* cp39-*"
 test-command = "ms2pip --help"
 
 [tool.cibuildwheel.macos]