Merge pull request #29 from MannLabs/development

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MannLabs · Aug 2, 2022 · 820ce5d · 820ce5d
2 parents 80aaf73 + 31500b9
commit 820ce5d
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diff --git a/HISTORY.md b/HISTORY.md
@@ -1,5 +1,8 @@
 ## Changelog
 
+### 1.1.15
+* FIX: Allow to use multiple modifications for the prediction of peptide properties.
+
 ### 1.1.14
 * FIX: Fix the m/z fragment calculation for the modified peptides.
 * FIX: Fix the extraction of the protein names and sequences for the protein groups in DIA-NN.

diff --git a/README.md b/README.md
@@ -152,7 +152,7 @@ In case of issues, check out the following:
 ---
 ## Citations
 
-A manuscript is currently in preparation.
+Pre-print published online: bioRxiv (2022), doi: 10.1101/2022.07.12.499676v1.
 
 ---
 ## How to contribute

diff --git a/alphaviz/__init__.py b/alphaviz/__init__.py
@@ -1,7 +1,7 @@
 #!python
 
 __project__ = "alphaviz"
-__version__ = "1.1.14"
+__version__ = "1.1.15"
 __license__ = "Apache"
 __description__ = "A interactive Dashboard to explore mass spectrometry data."
 __author__ = "Eugenia Voytik"

diff --git a/alphaviz/gui.py b/alphaviz/gui.py
@@ -2380,7 +2380,7 @@ def run_prediction(self, *args):
                     df[col] = df[col].astype('str')
                 except:
                     print(f'cannot convert the column {col}')
-            df.mod_sites = df.mod_sites.astype('int').astype('str')
+            df.mod_sites = df.mod_sites.astype('str')
             df.mod_sites.replace('0', '', inplace=True)
             df['nce'] = 30
             df['instrument'] = 'Lumos'

diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.14
+current_version = 1.1.15
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control
@@ -1,5 +1,5 @@
 Package: alphaviz
-Version: 1.1.14
+Version: 1.1.15
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: alphaviz

diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/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/alphaviz-1.1.14-py3-none-any.whl[stable,gui-stable]"
+pip install "../../dist/alphaviz-1.1.15-py3-none-any.whl[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10

diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist
@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphaviz.1.1.14</string>
+	<string>alphaviz.1.1.15</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.1.14</string>
+	<string>1.1.15</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/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/alphaviz-1.1.14-py3-none-any.whl[stable,gui-stable]"
+pip install "../../dist/alphaviz-1.1.15-py3-none-any.whl[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10
@@ -40,5 +40,5 @@ cp ../../LICENSE.txt Resources/LICENSE.txt
 cp ../logos/alpha_logo.png Resources/alpha_logo.png
 chmod 777 scripts/*
 
-pkgbuild --root dist/alphaviz --identifier de.mpg.biochem.alphaviz.app --version 1.1.14 --install-location /Applications/alphaviz.app --scripts scripts alphaviz.pkg
+pkgbuild --root dist/alphaviz --identifier de.mpg.biochem.alphaviz.app --version 1.1.15 --install-location /Applications/alphaviz.app --scripts scripts alphaviz.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path alphaviz.pkg dist/alphaviz_gui_installer_macos.pkg
diff --git a/release/one_click_macos_gui/distribution.xml b/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>alphaviz 1.1.14</title>
+    <title>alphaviz 1.1.15</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" />

diff --git a/release/one_click_windows_gui/alphaviz_innoinstaller.iss b/release/one_click_windows_gui/alphaviz_innoinstaller.iss
@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "alphaviz"
-#define MyAppVersion "1.1.14"
+#define MyAppVersion "1.1.15"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphaviz"
 #define MyAppExeName "alphaviz_gui.exe"

diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/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/alphaviz-1.1.14-py3-none-any.whl[stable,gui-stable]"
+pip install "../../dist/alphaviz-1.1.15-py3-none-any.whl[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10