Merge pull request #15 from MannLabs/development

Development

.gitignore

@@ -190,3 +190,5 @@ misc/bumpversion.sh
 figures/
 _docs/
 _proc/
+
+sandbox/

directlfq/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "directlfq"
-__version__ = "0.2.10"
+__version__ = "0.2.11"
 __license__ = "Apache"
 __description__ = "An open-source Python package of the AlphaPept ecosystem"
 __author__ = "Mann Labs"

directlfq/utils.py

@@ -433,8 +433,8 @@ def filter_input(filter_dict, input):
 def merge_protein_and_ion_cols(input_df, config_dict):
     protein_cols =  config_dict.get("protein_cols")
     ion_cols = config_dict.get("ion_cols")
-    input_df['protein'] = input_df.apply(lambda row : "_".join(row[protein_cols].astype('string')), axis = 1)
-    input_df['ion'] = input_df.apply(lambda row : "_".join(row[ion_cols].astype('string')), axis = 1)
+    input_df['protein'] = join_columns(input_df, protein_cols)
+    input_df['ion'] = join_columns(input_df, ion_cols)
 
     input_df = input_df.rename(columns = {config_dict.get('quant_ID') : "quant_val"})
     return input_df
@@ -458,7 +458,7 @@ def merge_protein_cols_and_ion_dict(input_df, config_dict):
 
     ion_dfs = []
     #concatenate multiple protein columns into one
-    input_df['protein'] = input_df.apply(lambda row: "_".join(row[protein_cols].astype('string')), axis=1)
+    input_df['protein'] = join_columns(input_df, protein_cols)
 
     input_df = input_df.drop(columns = [x for x in protein_cols if x!='protein'])
     for hierarchy_type in ion_hierarchy.keys():
@@ -483,6 +483,12 @@ def merge_protein_cols_and_ion_dict(input_df, config_dict):
     input_df = pd.concat(ion_dfs, ignore_index=True)
     return input_df
 
+def join_columns(df, columns, separator='_'):
+    if len(columns) == 1:
+        return df[columns[0]].fillna('nan').astype(str)
+    else:
+        return df[columns].fillna('nan').astype(str).agg(separator.join, axis=1)
+
 
 def get_quantitative_columns(input_df, hierarchy_type, config_dict, ion_headers_merged):
     naming_columns = ion_headers_merged + ['protein']

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.10
+current_version = 0.2.11
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: directlfq
-Version: 0.2.10
+Version: 0.2.11
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: directlfq

release/one_click_linux_gui/create_installer_linux.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_linux_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/directlfq-0.2.10-py3-none-any.whl[stable, gui]"
+pip install "../../dist/directlfq-0.2.11-py3-none-any.whl[stable, gui]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>directlfq.0.2.10</string>
+	<string>directlfq.0.2.11</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.2.10</string>
+	<string>0.2.11</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

release/one_click_macos_gui/create_installer_macos.sh

@@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel
 
 # Setting up the local package
 cd release/one_click_macos_gui
-pip install "../../dist/directlfq-0.2.10-py3-none-any.whl[stable, gui]"
+pip install "../../dist/directlfq-0.2.11-py3-none-any.whl[stable, gui]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10
@@ -40,5 +40,5 @@ cp ../../LICENSE Resources/LICENSE
 cp ../logos/alpha_logo.png Resources/alpha_logo.png
 chmod 777 scripts/*
 
-pkgbuild --root dist/directlfq --identifier de.mpg.biochem.directlfq.app --version 0.2.10 --install-location /Applications/directlfq.app --scripts scripts directlfq.pkg
+pkgbuild --root dist/directlfq --identifier de.mpg.biochem.directlfq.app --version 0.2.11 --install-location /Applications/directlfq.app --scripts scripts directlfq.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path directlfq.pkg dist/directlfq_gui_installer_macos.pkg

release/one_click_macos_gui/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>directlfq 0.2.10</title>
+    <title>directlfq 0.2.11</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

release/one_click_windows_gui/create_installer_windows.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_windows_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/directlfq-0.2.10-py3-none-any.whl[stable, gui]"
+pip install "../../dist/directlfq-0.2.11-py3-none-any.whl[stable, gui]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10

release/one_click_windows_gui/directlfq_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "directlfq"
-#define MyAppVersion "0.2.10"
+#define MyAppVersion "0.2.11"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/directlfq"
 #define MyAppExeName "directlfq_gui.exe"

settings.ini

@@ -13,7 +13,7 @@ author = Constantin Ammar
 author_email = constantin.ammar@gmail.com
 copyright = fast.ai
 branch = master
-version = 0.2.10
+version = 0.2.11
 min_python = 3.6
 audience = Developers
 language = English