Merge pull request #65 from MannLabs/development

Development
MannLabs · Dec 27, 2022 · a12b0ab · a12b0ab
2 parents 0132e66 + 3ace28f
commit a12b0ab
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.3
+current_version = 0.3.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,13 +1,31 @@
-## Changelog
+# Changelog
 
-### 0.0.1
+Follow the changelog format from https://keepachangelog.com/en/1.0.0/.
 
-* FEAT: Initial creation of AlphaBase.
+## 1.0.0 - TODO Next Release
 
-### 0.2.0
+## 0.3.0 - 2022.12.27
+
+### Added
+
+- `alphabase.protein.fasta.SpecLibFasta.add_peptide_labeling()` supports mDIA.
+- `alphabase.spectral_library.flat.SpecLibFlat` class for flat spec_lib.
+- Move `alphabase.spectral_library.translate` module (.py) from alphapeptdeep to alphabase.
+- `alphabase.constants.modification.add_new_modifications()` to add user-defined modifications that are not in UniMod.
+- `alphabase.psm_reader.psm_reader.PSMReaderBase.add_modification_mapping()` to support arbitrary modifications of different search engines.
+- `alphabase.statistics.regression.LOESSRegression`
+- `alphabase.scoring` module added but not finished yet.
+
+### Changed
+
+- Use sphinx and readthedocs for documentation. nbdev is no longer for documentation, it is only used for unit testing (`nbdev_test`).
+- FastaLib to SpecLibFasta.
+- Protease: `trypsin`==`trypsin/p`, add `trypsin_not_p` will not cleave peptides before N-term of P.
+
+## 0.2.0
 
 First official release.
 
-### 0.2.1
+## 0.0.1
 
-Using Sphinx and readthedocs for documentation.
+FEAT: Initial creation of AlphaBase.
diff --git a/alphabase/__init__.py b/alphabase/__init__.py
@@ -2,16 +2,16 @@
 
 
 __project__ = "alphabase"
-__version__ = "0.2.3"
+__version__ = "0.3.0"
 __license__ = "Apache"
-__description__ = "An open-source Python package of the AlphaPept ecosystem"
+__description__ = "An infrastructure Python package of the AlphaX ecosystem"
 __author__ = "Mann Labs"
-__author_email__ = "opensource@alphapept.com"
+__author_email__ = "jalew188@gmail.com"
 __github__ = "https://github.com/MannLabs/alphabase"
 __keywords__ = [
     "bioinformatics",
     "software",
-    "AlphaPept ecosystem",
+    "AlphaX ecosystem",
 ]
 __python_version__ = ">=3.8,<3.10"
 __classifiers__ = [
@@ -35,9 +35,8 @@
     "Mann Labs at MPIB": "https://www.biochem.mpg.de/mann",
     "Mann Labs at CPR": "https://www.cpr.ku.dk/research/proteomics/mann/",
     "GitHub": __github__,
-    # "ReadTheDocs": None,
-    # "PyPi": None,
-    # "Scientific paper": None,
+    "Docs": "https://alphabase.readthedocs.io/en/latest/",
+    "PyPi": "https://pypi.org/project/alphabase/",
 }
 __extra_requirements__ = {
     "development": "requirements_development.txt",

diff --git a/alphabase/protein/fasta.py b/alphabase/protein/fasta.py
@@ -1175,7 +1175,8 @@ def add_peptide_labeling(self, labeling_channel_dict:dict=None):
             8: ['Dimethyl:2H(6)13C(2)@Any N-term','Dimethyl:2H(6)13C(2)@K'],
             }
             ```.
-            The key name could be int (recommended) or str, and the value must be 
+            The key name could be int (highly recommended or 
+            must be in the future) or str, and the value must be 
             a list of modification names (str) in alphabase format.
             It is set to `self.labeling_channels` if None.
             Defaults to None
@@ -1191,6 +1192,16 @@ def add_peptide_labeling(self, labeling_channel_dict:dict=None):
             df['labeling_channel'] = channel
             df_list.append(df)
         self._precursor_df = pd.concat(df_list, ignore_index=True)
+        try:
+            self._precursor_df[
+                'labeling_channel'
+            ] = self._precursor_df.labeling_channel.astype(np.int32)
+            if 'labeling_channel' not in self.key_numeric_columns:
+                self.key_numeric_columns.append('labeling_channel')
+        except:
+            if 'labeling_channel' in self.key_numeric_columns:
+                self.key_numeric_columns.remove('labeling_channel')
+
 
     def add_charge(self):
         """Add charge states

diff --git a/alphabase/spectral_library/base.py b/alphabase/spectral_library/base.py
@@ -38,7 +38,8 @@ class SpecLibBase(object):
         'miss_cleavage', 'mobility_pred',
         'nAA', 
         'precursor_mz', 
-        'rt_pred', 'rt_norm_pred'
+        'rt_pred', 'rt_norm_pred',
+        'labeling_channel',
     ]
     """
     list of str: Key numeric columns to be saved 

diff --git a/docs/conf.py b/docs/conf.py
@@ -23,7 +23,7 @@
 copyright = '2022, Mann Labs, MPIB'
 author = 'Mann Labs, MPIB'
 
-release = "0.2.3"
+release = "0.3.0"
 
 # -- General configuration ---------------------------------------------------
 

diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control
@@ -1,7 +1,7 @@
 Package: AlphaBase
-Version: 0.2.3
+Version: 0.3.0
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: AlphaBase
-  AlphaBase is an open-source Python package in the AlphaPept ecosystem.
+  AlphaBase is an open-source Python package in the AlphaX ecosystem.
   AlphaBase was developed by the Mann Labs at the Max Planck Institute of Biochemistry and University of Copenhagen and is freely available with an Apache License. Additional third-party licenses are applicable for external Python packages (see https://github.com/MannLabs/AlphaBase for more details.).
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/alphabase-0.2.3-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-0.3.0-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

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>alphabase.0.2.3</string>
+	<string>alphabase.0.3.0</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.2.3</string>
+	<string>0.3.0</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/alphabase-0.2.3-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-0.3.0-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/alphabase --identifier de.mpg.biochem.alphabase.app --version 0.2.3 --install-location /Applications/AlphaBase.app --scripts scripts AlphaBase.pkg
+pkgbuild --root dist/alphabase --identifier de.mpg.biochem.alphabase.app --version 0.3.0 --install-location /Applications/AlphaBase.app --scripts scripts AlphaBase.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path AlphaBase.pkg dist/alphabase_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>AlphaBase 0.2.3</title>
+    <title>AlphaBase 0.3.0</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/alphabase_innoinstaller.iss b/release/one_click_windows_gui/alphabase_innoinstaller.iss
@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaBase"
-#define MyAppVersion "0.2.3"
+#define MyAppVersion "0.3.0"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphabase"
 #define MyAppExeName "alphabase_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/alphabase-0.2.3-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-0.3.0-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

diff --git a/settings.ini b/settings.ini
@@ -4,7 +4,7 @@
 ### Python library ###
 repo = alphabase
 lib_name = alphabase
-version = 0.2.3
+version = 0.3.0
 min_python = 3.7
 license = apache2
 
@@ -31,8 +31,8 @@ audience = Developers
 author = Wen-Feng Zeng, Sander Willems, Maximilian Strauss
 author_email = wzeng@biochem.mpg.de, jalew188@gmail.com
 copyright = MannLabs
-description = Base functionalities for AlphaPept Ecosystems
-keywords = proteomics, mass spec, alphapept, infrastucture
+description = Base functionalities for AlphaX Ecosystems
+keywords = proteomics, mass spec, alphaX, infrastucture
 language = English
 status = 2
 user = MannLabs