From d8e90ce2c2dab6cd72eb33a6e48acb7e6dfb5fce Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Tue, 21 May 2024 11:04:08 +0200
Subject: [PATCH] FIX alphabase noqa

---
 alpharaw/viz/df_utils.py            | 6 +++---
 extra_requirements/development.txt  | 2 ++
 nbs_tests/test_viz_multinotch.ipynb | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/alpharaw/viz/df_utils.py b/alpharaw/viz/df_utils.py
index d1c9efc..f947c44 100644
--- a/alpharaw/viz/df_utils.py
+++ b/alpharaw/viz/df_utils.py
@@ -6,7 +6,7 @@
 from alpharaw.match.match_utils import match_closest_peaks, match_highest_peaks
 
 from alphabase.peptide.precursor import (
-    calc_precursor_mz,
+    update_precursor_mz,
     calc_precursor_isotope_intensity,
 )
 
@@ -368,7 +368,7 @@ def translate_frag_df_to_plot_df(
         for iso in isotope_names:
             fragment_df[f"precursor_{iso}"] = precursor_df[iso].values[0]
         if len(isotope_names) > 0:
-            fragment_df[f"precursor_mono_idx"] = precursor_df.mono_isotope_idx.values[0]
+            fragment_df["precursor_mono_idx"] = precursor_df.mono_isotope_idx.values[0]
 
     return fragment_df
 
@@ -386,7 +386,7 @@ def make_precursor_fragment_df(
     precursor_df = pd.DataFrame(
         dict(sequence=[sequence], mods=[mods], mod_sites=[mod_sites], charge=charge)
     )
-    calc_precursor_mz(precursor_df)
+    update_precursor_mz(precursor_df)
     if include_precursor_isotopes:
         calc_precursor_isotope_intensity(precursor_df, max_isotope=max_isotope)
     if include_fragments:
diff --git a/extra_requirements/development.txt b/extra_requirements/development.txt
index 7351420..6b8c7e8 100644
--- a/extra_requirements/development.txt
+++ b/extra_requirements/development.txt
@@ -25,4 +25,6 @@ furo
 alphabase>=1.1.0
 alphatims
 
+pytest
 pre-commit==3.7.0
+nbmake==1.5.3
diff --git a/nbs_tests/test_viz_multinotch.ipynb b/nbs_tests/test_viz_multinotch.ipynb
index c9861a7..2e0e4d1 100644
--- a/nbs_tests/test_viz_multinotch.ipynb
+++ b/nbs_tests/test_viz_multinotch.ipynb
@@ -237,7 +237,7 @@
     "    \"mod_sites\": [\"\",\"9\"],\n",
     "    \"rt\": [4.3,4.3],\n",
     "})\n",
-    "precursur_func.calc_precursor_mz(psm_df)\n",
+    "precursur_func.update_precursor_mz(psm_df)\n",
     "precursur_func.calc_precursor_isotope(psm_df)"
    ]
   },