From cf2b0e2f1b6acddfe59e4279f545a477d26735d2 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 12:36:36 +0100
Subject: [PATCH 1/3] fix bug in get_frame_indices

---
 alphadia/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/alphadia/utils.py b/alphadia/utils.py
index 7281f4d9..3c61708a 100644
--- a/alphadia/utils.py
+++ b/alphadia/utils.py
@@ -745,7 +745,7 @@ def get_frame_indices(
         optimal_cycle_limits[0] = precursor_cycle_max_index - optimal_len
 
         if optimal_cycle_limits[0] < 0:
-            optimal_cycle_limits[0] = 0
+            optimal_cycle_limits[0] = 0 if precursor_cycle_max_index % 2 == 0 else 1
 
     # Convert back to frame indices
     frame_limits = optimal_cycle_limits * cycle_len + zeroth_frame

From 2bfbfbbe919eb21f5f3e883c7bb8e141ecc702a2 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 17:48:19 +0100
Subject: [PATCH 2/3] adapt tests

---
 tests/unit_tests/test_data.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_data.py b/tests/unit_tests/test_data.py
index ba3e972f..c6ba5143 100644
--- a/tests/unit_tests/test_data.py
+++ b/tests/unit_tests/test_data.py
@@ -367,7 +367,7 @@ def test_get_frame_indices_optimization_left_min_size_overflow(mock_alpha_raw_ji
     optimize_size = 4
     min_size = 1000
     rt_values = np.array([90.0, 95.0], dtype=np.float32)
-    expected_indices = np.array([[0, 95, 1]], dtype=np.int64)
+    expected_indices = np.array([[5, 95, 1]], dtype=np.int64)
 
     # when
     frame_indices = mock_alpha_raw_jit.get_frame_indices(

From a83a958e8ef1a950543840faf6737e842f0e05ec Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 17:48:41 +0100
Subject: [PATCH 3/3] upgrade alphabase to 1.4.2

---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index 31f893c9..c421c4e8 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -5,7 +5,7 @@ numba==0.59.1
 argparse==1.4.0
 alpharaw==0.4.5
 alphatims==1.0.8
-alphabase==1.4.0 # test: tolerate_version
+alphabase==1.4.2 # test: tolerate_version
 peptdeep==1.3.0 # test: tolerate_version
 progressbar==2.5
 neptune==1.10.4