Merge pull request #128 from MannLabs/development

Development

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.2
+current_version = 1.1.3
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

docs/conf.py

@@ -23,7 +23,7 @@
 copyright = '2022, Mann Labs, MPIB'
 author = 'Mann Labs, MPIB'
 
-release = "1.1.2"
+release = "1.1.3"
 
 # -- General configuration ---------------------------------------------------
 

peptdeep/__init__.py

@@ -11,7 +11,7 @@
 #     pass
 
 __project__ = "peptdeep"
-__version__ = "1.1.2"
+__version__ = "1.1.3"
 __license__ = "Apache 2.0"
 __description__ = "The AlphaX deep learning framework for Proteomics"
 __author__ = "Mann Labs"

peptdeep/pipeline_api.py

@@ -18,7 +18,7 @@
 )
 
 from peptdeep.spec_lib.translate import mod_to_unimod_dict
-from peptdeep.settings import global_settings
+from peptdeep.settings import global_settings, add_user_defined_modifications
 from peptdeep.utils import (
     logging, set_logger, 
     show_platform_info, show_python_info
@@ -267,6 +267,7 @@ def transfer_learn(verbose=True):
         Any kinds of exception if the pipeline fails.
     """
     try:
+        add_user_defined_modifications()
         mgr_settings = global_settings['model_mgr']
         mgr_settings['transfer']['verbose'] = verbose
 
@@ -303,7 +304,11 @@ def transfer_learn(verbose=True):
             dfs = []
             frag_inten_dfs = []
             for psm_file in mgr_settings['transfer']['psm_files']:
-                _lib = LibraryReaderBase()
+                _lib = LibraryReaderBase(
+                    modification_mapping=mgr_settings[
+                        'transfer']['psm_modification_mapping'
+                    ]
+                )
                 if not _check_is_file(psm_file): continue
                 dfs.append(_lib.import_file(psm_file))
                 frag_inten_dfs.append(_lib.fragment_intensity_df)
@@ -369,6 +374,7 @@ def generate_library():
         Any kinds of exception if the pipeline fails.
     """
     try:
+        add_user_defined_modifications()
         lib_settings = global_settings['library']
         output_folder = os.path.expanduser(
             lib_settings['output_folder']

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: peptdeep
-Version: 1.1.2
+Version: 1.1.3
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 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-1.1.2-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.1.3-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.1.1.2</string>
+	<string>peptdeep.1.1.3</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.1.2</string>
+	<string>1.1.3</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-1.1.2-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.1.3-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 1.1.2 --install-location /Applications/peptdeep.app --scripts scripts peptdeep.pkg
+pkgbuild --root dist/peptdeep --identifier de.mpg.biochem.peptdeep.app --version 1.1.3 --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 1.1.2</title>
+    <title>peptdeep 1.1.3</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-1.1.2-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.1.3-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 "1.1.2"
+#define MyAppVersion "1.1.3"
 #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"

settings.ini

@@ -5,7 +5,7 @@
 ### Python library ###
 repo = alphapeptdeep
 lib_name = peptdeep
-version = 1.1.2
+version = 1.1.3
 min_python = 3.7
 license = apache2