Merge pull request #175 from MannLabs/development

FIX use lumos model for Astral

Author: jalew188

.bumpversion.cfg

@@ -1,9 +1,9 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.2.1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
-serialize =
+serialize = 
 	{major}.{minor}.{patch}
 	{major}.{minor}.{patch}
 

.pre-commit-config.yaml

@@ -12,3 +12,5 @@ repos:
 #   hooks:
 #     - id: ruff-format
 #     - id: ruff
+
+exclude: .bumpversion.cfg

docs/conf.py

@@ -23,7 +23,7 @@
 copyright = '2022, Mann Labs, MPIB'
 author = 'Mann Labs, MPIB'
 
-release = "1.2.0"
+release = "1.2.1"
 
 # -- General configuration ---------------------------------------------------
 

peptdeep/__init__.py

@@ -11,7 +11,7 @@
 #     pass
 
 __project__ = "peptdeep"
-__version__ = "1.2.0"
+__version__ = "1.2.1"
 __license__ = "Apache 2.0"
 __description__ = "The AlphaX deep learning framework for Proteomics"
 __author__ = "Mann Labs"

peptdeep/constants/default_settings.yaml

@@ -81,7 +81,7 @@ model_mgr:
   use_predicted_charge_in_speclib: True # if True, it ignores min/max_precursor_charge in `library`
   instrument_group:
     ThermoTOF: ThermoTOF
-    Astral: ThermoTOF
+    Astral: Lumos
     Lumos: Lumos
     QE: QE
     timsTOF: timsTOF

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: peptdeep
-Version: 1.2.0
+Version: 1.2.1
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: peptdeep

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/peptdeep-1.2.0-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
 
 if [ "$1" == "CPU" ]; then
     pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>peptdeep.1.2.0</string>
+	<string>peptdeep.1.2.1</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.2.0</string>
+	<string>1.2.1</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/peptdeep-1.2.0-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller
@@ -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/peptdeep --identifier de.mpg.biochem.peptdeep.app --version 1.2.0 --install-location /Applications/peptdeep.app --scripts scripts peptdeep.pkg
+pkgbuild --root dist/peptdeep --identifier de.mpg.biochem.peptdeep.app --version 1.2.1 --install-location /Applications/peptdeep.app --scripts scripts peptdeep.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path peptdeep.pkg dist/peptdeep_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>peptdeep 1.2.0</title>
+    <title>peptdeep 1.2.1</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/peptdeep-1.2.0-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

release/one_click_windows_gui/peptdeep_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "peptdeep"
-#define MyAppVersion "1.2.0"
+#define MyAppVersion "1.2.1"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/peptdeep"
 #define MyAppExeName "peptdeep_gui.exe"