Merge pull request #10 from MannLabs/development

Add _check_if_all_dataframes_have_the_same_columns method to Loader class for validating dataframe consistency. Enhanced data handling by logging missing columns and removing them from MS1 and MS2 dataframes as needed.

Author: vuductung

.gitignore

@@ -142,4 +142,5 @@ nbs/directlfq/
 weights
 nbs/
 pkl
-models
+models
+submission

.vscode/settings.json

@@ -4,7 +4,7 @@
         "-s",
         "./tests",
         "-p",
-        "*test*.py"
+        "test*.py"
     ],
     "python.testing.pytestEnabled": false,
     "python.testing.unittestEnabled": true,

README.md

@@ -1,12 +1,12 @@
 #!python
 
-__project__ = "selectlfq"
+__project__ = "fragselect"
 __version__ = "0.0.1"
 __license__ = "Apache"
 __description__ = "An open-source Python package of the AlphaPept ecosystem"
 __author__ = "Mann Labs"
 __author_email__ = "opensource@alphapept.com"
-__github__ = "https://github.com/MannLabs/selectlfq"
+__github__ = "https://github.com/MannLabs/fragselect"
 __keywords__ = [
     "bioinformatics",
     "software",
@@ -28,7 +28,7 @@
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 __console_scripts__ = [
-    "selectlfq=selectlfq.cli:run",
+    "fragselect=fragselect.cli:run",
 ]
 __urls__ = {
     "Mann Labs at MPIB": "https://www.biochem.mpg.de/mann",

fragselect.png

@@ -5,7 +5,7 @@
 import click
 
 # local
-import selectlfq
+import fragselect
 
 
 @click.group(
@@ -15,18 +15,11 @@
     invoke_without_command=True,
 )
 @click.pass_context
-@click.version_option(selectlfq.__version__, "-v", "--version")
+@click.version_option(fragselect.__version__, "-v", "--version")
 def run(ctx, **kwargs):
-    name = f"selectLFQ {selectlfq.__version__}"
+    name = f"fragselect {fragselect.__version__}"
     click.echo("*" * (len(name) + 4))
     click.echo(f"* {name} *")
     click.echo("*" * (len(name) + 4))
     if ctx.invoked_subcommand is None:
         click.echo(run.get_help(ctx))
-
-
-@run.command("gui", help="Start graphical user interface.")
-def gui():
-    import selectlfq.gui
-
-    selectlfq.gui.run()