From 88f90ca29330456cc55d11e864a8232bfa1a0861 Mon Sep 17 00:00:00 2001 From: EugeniaVoytik Date: Tue, 2 Aug 2022 09:09:55 +0200 Subject: [PATCH 1/3] FIX: allow to use multiple modifications for the deep learning prediction --- alphaviz/gui.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/alphaviz/gui.py b/alphaviz/gui.py index de3a1e5..2e0f571 100644 --- 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' From 0eaa7596f272b78611fd75560f91a29e8a0074db Mon Sep 17 00:00:00 2001 From: EugeniaVoytik Date: Tue, 2 Aug 2022 09:10:18 +0200 Subject: [PATCH 2/3] docs: update the readme and history with new info --- HISTORY.md | 3 +++ README.md | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/HISTORY.md b/HISTORY.md index 2df5f39..09f4eb9 100644 --- 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 index 7f395d9..cf1a481 100644 --- 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 From 31500b9d5c0b81c850de99d7435ae6f86ba23333 Mon Sep 17 00:00:00 2001 From: EugeniaVoytik Date: Tue, 2 Aug 2022 09:10:47 +0200 Subject: [PATCH 3/3] =?UTF-8?q?Bump=20version:=201.1.14=20=E2=86=92=201.1.?= =?UTF-8?q?15?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- alphaviz/__init__.py | 2 +- misc/bumpversion.cfg | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 4 ++-- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/alphaviz_innoinstaller.iss | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- 9 files changed, 11 insertions(+), 11 deletions(-) diff --git a/alphaviz/__init__.py b/alphaviz/__init__.py index 7829a73..4ec0dd5 100644 --- 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/misc/bumpversion.cfg b/misc/bumpversion.cfg index 177ffc6..e1ebbc7 100644 --- 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\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 428f864..d800c4b 100644 --- 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 Description: alphaviz diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 708aa21..1c5ce45 100644 --- 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 index 601aa62..d353bcd 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - alphaviz.1.1.14 + alphaviz.1.1.15 CFBundleShortVersionString - 1.1.14 + 1.1.15 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 4eafd23..dc29bcc 100644 --- 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 index 43977d6..491d5b2 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - alphaviz 1.1.14 + alphaviz 1.1.15 diff --git a/release/one_click_windows_gui/alphaviz_innoinstaller.iss b/release/one_click_windows_gui/alphaviz_innoinstaller.iss index 49f670a..f21ca40 100644 --- 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 index 2dd5d76..8e2e3da 100644 --- 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