Merge pull request #375 from theGreatHerrLebert/feature/intensity-variation-timsim-dda

Feature/intensity variation timsim dda

Author: theGreatHerrLebert

imspy/imspy/simulation/timsim/simulator.py

@@ -1,4 +1,5 @@
 import os
+import sys
 import platform
 import argparse
 import time
@@ -77,7 +78,7 @@ def build_arg_parser() -> argparse.ArgumentParser:
     Builds and returns the command line argument parser.
     """
     parser = argparse.ArgumentParser(
-        description='🦀💻 TIMSIM 🔬🐍 - Run a proteomics experiment simulation with PASEF-like acquisition '
+        description='TIMSIM - Run a proteomics experiment simulation with PASEF-like acquisition '
                     'on a BRUKER TimsTOF.'
     )
 
@@ -368,16 +369,23 @@ def check_required_args(args: argparse.Namespace, parser: argparse.ArgumentParse
             parser.error("sigma_lower_rt must be less than sigma_upper_rt")
     if args.k_lower_rt >= args.k_upper_rt:
         parser.error("k_lower_rt must be less than k_upper_rt")
-    
+
+
+def banner(use_unicode=True):
+    if use_unicode:
+        return "🦀💻 TIMSIM 🔬🐍 - Proteomics Simulation Engine"
+    else:
+        return "TIMSIM - Proteomics Simulation Engine"
+
 
 # ----------------------------------------------------------------------
 # Main Execution
 # ----------------------------------------------------------------------
-
 def main():
 
-    print("🦀💻 TIMSIM 🔬🐍 - Run a proteomics experiment simulation with PASEF-like acquisition on a BRUKER TimsTOF.")
-    print("Version: 0.3.20")
+    print(banner(sys.stdout.isatty()))
+
+    print("Version: 0.3.21")
     print("Author: David Teschner, JGU Mainz, GitHub: @theGreatHerrLebert")
     print("License: MIT")
 
@@ -851,4 +859,4 @@ def main():
     )
 
 if __name__ == '__main__':
-    main()
+    main()

imspy/imspy/timstof/dbsearch/imspy_dda.py

@@ -86,7 +86,7 @@ def main():
     check_memory(limit_in_gb=16)
 
     # use argparse to parse command line arguments
-    parser = argparse.ArgumentParser(description='🦀💻 IMSPY - timsTOF DDA 🔬🐍 - PROTEOMICS IMS DDA data analysis '
+    parser = argparse.ArgumentParser(description='IMSPY - timsTOF DDA - PROTEOMICS IMS DDA data analysis '
                                                  'using imspy and sagepy.')
 
     # Required string argument for path of bruker raw data

imspy/imspy/timstof/dbsearch/utility.py

@@ -27,7 +27,7 @@
 
 def check_memory(
         limit_in_gb: int = 16,
-        msg: str = "⚠️ Warning: System has only {total_ram_gb:.2f}GB of RAM, which is below the recommended {limit_in_gb}GB."):
+        msg: str = "Warning: System has only {total_ram_gb:.2f}GB of RAM, which is below the recommended {limit_in_gb}GB."):
 
     if hasattr(os, "sysconf"):
         total_ram_bytes = os.sysconf("SC_PAGE_SIZE") * os.sysconf("SC_PHYS_PAGES")
@@ -36,7 +36,7 @@ def check_memory(
             msg = msg.format(total_ram_gb=total_ram_gb, limit_in_gb=limit_in_gb)
             warnings.warn(msg)
     else:
-        warnings.warn("⚠️ Unable to determine system memory.")
+        warnings.warn("Unable to determine system memory.")
 
 # Run the check
 check_memory()

imspy/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "imspy"
-version = "0.3.20"
+version = "0.3.21"
 description = "A Python package for analyzing timsTOF ion mobility spectrometry data, including tools for raw data acccess and simulation."
 authors = [
     { name = "theGreatHerrLebert", email = "davidteschner@googlemail.com" }
@@ -19,7 +19,7 @@ dependencies = [
     "wandb>=0.12.1",
     "mokapot>=0.10.0",
     "sagepy>=0.3.12",
-    "imspy-connector>=0.3.20",
+    "imspy-connector>=0.3.21",
     "scipy>=1.7.1",
     "tqdm>=4.66",
     "pyarrow>=13.0",

imspy_connector/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "imspy-connector"
-version = "0.3.20"
+version = "0.3.21"
 edition = "2021"
 
 [lib]

imspy_connector/pyproject.toml

@@ -7,7 +7,7 @@ name = "imspy_connector"
 dependencies = [
     "opentims-bruker-bridge>=1.1.0",
 ]
-version = "0.3.20"
+version = "0.3.21"
 requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Rust",