From a711aff65659688e5c3831456c4cd744b41ed806 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 15 Nov 2024 09:51:23 +0100
Subject: [PATCH] add again what was lost by the failed merge commit
 97613f1336eca33fd74309d2bdbdd60f8b6e926d

---
 .bumpversion.cfg                        |  2 +-
 alphabase/__init__.py                   |  2 +-
 alphabase/psm_reader/maxquant_reader.py | 18 ++++++++++++++++++
 docs/conf.py                            |  2 +-
 4 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index b55048b4..37587c45 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.0
+current_version = 1.4.1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
diff --git a/alphabase/__init__.py b/alphabase/__init__.py
index 006941da..86008ce9 100644
--- a/alphabase/__init__.py
+++ b/alphabase/__init__.py
@@ -2,7 +2,7 @@
 
 
 __project__ = "alphabase"
-__version__ = "1.4.0"
+__version__ = "1.4.1"
 __license__ = "Apache"
 __description__ = "An infrastructure Python package of the AlphaX ecosystem"
 __author__ = "Mann Labs"
diff --git a/alphabase/psm_reader/maxquant_reader.py b/alphabase/psm_reader/maxquant_reader.py
index 1a62c392..87da6bda 100644
--- a/alphabase/psm_reader/maxquant_reader.py
+++ b/alphabase/psm_reader/maxquant_reader.py
@@ -1,4 +1,5 @@
 import copy
+import warnings
 from typing import Optional
 
 import numba
@@ -13,6 +14,9 @@
     psm_reader_yaml,
 )
 
+# make sure all warnings are shown
+warnings.filterwarnings("always")
+
 mod_to_unimod_dict = {}
 for mod_name, unimod_id in MOD_DF[["mod_name", "unimod_id"]].values:
     unimod_id = int(unimod_id)
@@ -249,6 +253,20 @@ def _load_file(self, filename):
         self._find_mod_seq_column(df)
         df = df[~pd.isna(df["Retention time"])]
         df.fillna("", inplace=True)
+
+        # remove MBR PSMs as they are currently not supported and will crash import
+        mapped_columns = self._find_mapped_columns(df)
+        if "scan_num" in mapped_columns:
+            scan_num_col = mapped_columns["scan_num"]
+            no_ms2_mask = df[scan_num_col] == ""
+            if (num_no_ms2_mask := np.sum(no_ms2_mask)) > 0:
+                warnings.warn(
+                    f"Maxquant psm file contains {num_no_ms2_mask} MBR PSMs without MS2 scan. This is not yet supported and rows containing MBR PSMs will be removed."
+                )
+                df = df[~no_ms2_mask]
+                df.reset_index(drop=True, inplace=True)
+        df[scan_num_col] = df[scan_num_col].astype(int)
+
         # if 'K0' in df.columns:
         #     df['Mobility'] = df['K0'] # Bug in MaxQuant? It should be 1/K0
         # min_rt = df['Retention time'].min()
diff --git a/docs/conf.py b/docs/conf.py
index 8cd3bdfa..687c35f7 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -24,7 +24,7 @@
 copyright = "2022, Mann Labs, MPIB"
 author = "Mann Labs, MPIB"
 
-release = "1.4.0"
+release = "1.4.1"
 
 # -- General configuration ---------------------------------------------------