Upgrade to psm_utils v0.9, which now uses Pydantic v2

compomics · May 2, 2024 · 2a947ee · 2a947ee
1 parent 37ba9db
commit 2a947ee
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Showing 2 changed files with 1 addition and 6 deletions.
diff --git a/ms2rescore/parse_psms.py b/ms2rescore/parse_psms.py
@@ -70,10 +70,6 @@ def parse_psms(config: Dict, psm_list: Union[PSMList, None]) -> PSMList:
         new_ids = [_match_psm_ids(old_id, pattern) for old_id in psm_list["spectrum_id"]]
         psm_list["spectrum_id"] = new_ids
 
-    # TODO: Temporary fix until implemented in psm_utils
-    # Ensure that spectrum IDs are strings (Pydantic 2.0 does not coerce int to str)
-    psm_list["spectrum_id"] = [str(spec_id) for spec_id in psm_list["spectrum_id"]]
-
     return psm_list
 
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -47,8 +47,7 @@ dependencies = [
     "numpy>=1.16.0; python_version != '3.11'",
     "pandas>=1.0",
     "plotly>=5",
-    "psm_utils>=0.8",
-    "pydantic>=1.8.2,<2",                      # Fix compatibility with v2 in psm_utils
+    "psm_utils>=0.9",
     "pyteomics>=4.1.0, <4.7",
     "rich>=12",
     "tomli>=2; python_version < '3.11'",