From 913b6a0952fded67d7e07372dac6c30891f0f5af Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 18:41:05 +0100
Subject: [PATCH 1/4] log whole environment

---
 alphadia/planning.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/alphadia/planning.py b/alphadia/planning.py
index c8dc429f..8bc1370c 100644
--- a/alphadia/planning.py
+++ b/alphadia/planning.py
@@ -3,6 +3,7 @@
 import os
 import socket
 from datetime import datetime
+from importlib import metadata
 from pathlib import Path
 
 import alphabase
@@ -166,6 +167,14 @@ def log_environment(self):
         logger.progress(f"{'directlfq':<15} : {directlfq.__version__}")
         logger.progress("===================================================")
 
+        logger.progress("================= Pip Environment =================")
+        pip_env = [
+            f"{dist.metadata['Name']}=={dist.version}"
+            for dist in metadata.distributions()
+        ]
+        logger.progress(" ".join(pip_env))
+        logger.progress("===================================================")
+
     def init_alphabase(self):
         """Init alphabase by registering custom modifications."""
 

From 527fc84af79c8d0dffd3f62cb9c02ae893e06c7a Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 18:41:44 +0100
Subject: [PATCH 2/4] remove obsolete property and setter for raw_path_list

---
 alphadia/planning.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/alphadia/planning.py b/alphadia/planning.py
index 8bc1370c..40f0513d 100644
--- a/alphadia/planning.py
+++ b/alphadia/planning.py
@@ -131,15 +131,6 @@ def __init__(
 
         torch.set_num_threads(self.config["general"]["thread_count"])
 
-    @property
-    def raw_path_list(self) -> list[str]:
-        """List of input files locations."""
-        return self._raw_path_list
-
-    @raw_path_list.setter
-    def raw_path_list(self, raw_path_list: list[str]):
-        self._raw_path_list = raw_path_list
-
     @property
     def config(self) -> Config:
         """Dict with all configuration parameters for the extraction."""

From 0c970a9703ed10a16b798c5d93782795e6da2ef0 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 18:42:09 +0100
Subject: [PATCH 3/4] docstrings

---
 alphadia/planning.py | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/alphadia/planning.py b/alphadia/planning.py
index 40f0513d..ab1d1574 100644
--- a/alphadia/planning.py
+++ b/alphadia/planning.py
@@ -49,16 +49,23 @@ def __init__(
 
         Parameters
         ----------
-        raw_data : list
+
+        output_folder : str
+            output folder to save the results
+
+        raw_path_list : list
             list of input file locations
 
-        config_path : str, optional
-            yaml file containing the default config.
+        library_path : str, optional
+            path to the spectral library file. If not provided, the library is built from fasta files
 
-        config_update_path : str, optional
-           yaml file to update the default config.
+        fasta_path_list : list, optional
+            list of fasta file locations to build the library from
+
+        config_base_path : str, optional
+            yaml file containing the default config.
 
-        config_update : dict, optional
+        config : dict, optional
             dict to update the default config. Can be used for debugging purposes etc.
 
         quant_path : str, optional
@@ -97,7 +104,7 @@ def __init__(
         # print environment
         self.log_environment()
 
-        # 1. default config path is not defined in the function definition to account for for different path separators on different OS
+        # 1. default config path is not defined in the function definition to account for different path separators on different OS
         if config_base_path is None:
             # default yaml config location under /misc/config/config.yaml
             config_base_path = os.path.join(
@@ -114,7 +121,7 @@ def __init__(
             update_config = Config("user defined")
             update_config.from_dict(config)
         else:
-            update_config = config
+            update_config = config  # TODO what is it in this case?
 
         self.config.update([update_config], print_modifications=True)
 
@@ -150,7 +157,7 @@ def spectral_library(self, spectral_library: SpecLibFlat) -> None:
         self._spectral_library = spectral_library
 
     def log_environment(self):
-        logger.progress("=================== Environment ===================")
+        logger.progress("================ AlphaX Environment ===============")
         logger.progress(f"{'alphatims':<15} : {alphatims.__version__:}")
         logger.progress(f"{'alpharaw':<15} : {alpharaw.__version__}")
         logger.progress(f"{'alphabase':<15} : {alphabase.__version__}")

From c0d7a8ddcec2d0e91e39af5d653ba7360df88e7c Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 27 Nov 2024 18:42:25 +0100
Subject: [PATCH 4/4] make speclib file removal safe

---
 alphadia/planning.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/alphadia/planning.py b/alphadia/planning.py
index ab1d1574..cd34dd39 100644
--- a/alphadia/planning.py
+++ b/alphadia/planning.py
@@ -400,7 +400,10 @@ def run(
 
     def clean(self):
         if not self.config["general"]["save_library"]:
-            os.remove(os.path.join(self.output_folder, "speclib.hdf"))
+            try:
+                os.remove(os.path.join(self.output_folder, "speclib.hdf"))
+            except Exception as e:
+                logger.exception(f"Error deleting library: {e}")
 
 
 def _log_exception_event(