MannLabs · jalew188 · Dec 23, 2022 · Dec 22, 2022 · Dec 22, 2022 · Dec 23, 2022
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,11 +1,10 @@
 # How to contribute
 
-## How to get started
+## How to contribute to source code
 
-Before anything else, please install the git hooks that run automatic scripts during each commit and merge to strip the notebooks of superfluous metadata (and avoid merge conflicts). After cloning the repository, run the following command inside it:
-```
-nbdev_install_git_hooks
-```
+* Folk this GitHub repository to your personal repository.
+* Make changes/updates.
+* Make a PR back to the this repository.
 
 ## Did you find a bug?
 

diff --git a/HISTORY.md b/HISTORY.md
@@ -3,3 +3,11 @@
 ### 0.0.1
 
 * FEAT: Initial creation of AlphaBase.
+
+### 0.2.0
+
+First official release.
+
+### 0.2.1
+
+Using Sphinx and readthedocs for documentation.
diff --git a/README.md b/README.md
@@ -1,17 +1,11 @@
-AlphaBase
-================
-
-<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
-
-<a href="https://github.com/MannLabs/alphabase/workflows/Default%20installation%20and%20tests/badge.svg" alt="Pip Installation">
-<img src="https://github.com/MannLabs/alphabase/workflows/Default%20installation%20and%20tests/badge.svg" /></a>
-<a href="https://github.com/MannLabs/alphabase/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg" alt="GUI and PyPi releases">
-<img src="https://github.com/MannLabs/alphabase/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg"/></a>
-<a href="https://pypi.org/project/alphabase" alt="pypi">
-<img src="https://img.shields.io/pypi/v/alphabase" /></a>
-<a href="https://pypi.org/project/alphabase" alt="release">
-<img src="https://img.shields.io/pypi/dm/alphabase?color=blue&label=pip%20downloads"/></a>
-<img src="https://img.shields.io/pypi/pyversions/alphabase"/>
+# AlphaBase
+
+![Pip installation](https://github.com/MannLabs/alphabase/workflows/Default%20installation%20and%20tests/badge.svg)
+![PyPi releases](https://github.com/MannLabs/alphabase/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg)
+[![PyPI](https://img.shields.io/pypi/v/alphabase)](https://pypi.org/project/alphabase)
+[![pip downloads](https://img.shields.io/pypi/dm/alphabase?color=blue&label=pip%20downloads)](https://pypi.org/project/alphabase)
+![Python](https://img.shields.io/pypi/pyversions/alphabase)
+[![Documentation Status](https://readthedocs.org/projects/alphabase/badge/?version=latest)](https://alphabase.readthedocs.io/en/latest/?badge=latest)
 
 AlphaBase provides all basic python functionalities for AlphaPept
 ecosystem from the [Mann Labs at the Max Planck Institute of

diff --git a/alphabase/__init__.py b/alphabase/__init__.py
@@ -2,7 +2,7 @@
 
 
 __project__ = "alphabase"
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 __license__ = "Apache"
 __description__ = "An open-source Python package of the AlphaPept ecosystem"
 __author__ = "Mann Labs"

diff --git a/alphabase/constants/modification.py b/alphabase/constants/modification.py
@@ -11,6 +11,9 @@
 from alphabase.constants._const import CONST_FILE_FOLDER
 
 MOD_DF:pd.DataFrame = pd.DataFrame()
+"""
+Main entry of modification infomation (DataFrame fotmat).
+"""
 
 MOD_INFO_DICT:dict = {}
 #: Modification to formula str dict. {mod_name: formula str ('H(1)C(2)O(3)')}
@@ -353,36 +356,54 @@ def calc_modloss_mass(
     else:
         return _calc_modloss(mod_losses[::-1])[-3:0:-1]
 
+def add_a_new_modification(
+    mod_name:str, composition:str,
+    modloss_composition:str=''
+):
+    """
+    Add a new modification into :data:`MOD_DF`.
+
+    Parameters
+    ----------
+    mod_name : str
+        Mod name in alphabase format: mod@site, 
+        e.g. Mod@S
+    composition : str
+        chemical composition of this mod, 
+        e.g. "H(4)O(2)"
+    modloss_composition : str, optional
+        modloss compositions, e.g. "H(2)O(1)"), 
+        by default ''
+    """
+    MOD_DF.loc[mod_name,[
+        'mod_name','composition','modloss_composition',
+        'classification','unimod_id'
+    ]] = [
+        mod_name, composition, modloss_composition,
+        'User-added', 0
+    ]
+    MOD_DF.loc[mod_name,['mass','modloss']] = (
+        calc_mass_from_formula(composition),
+        calc_mass_from_formula(modloss_composition)
+    )
+    if MOD_DF.loc[mod_name, 'modloss'] > 0:
+        MOD_DF.loc[mod_name, 'modloss_importance'] = 1e6
+    MOD_DF.fillna(0, inplace=True)
+    update_all_by_MOD_DF()
+
 def add_new_modifications(new_mods:list):
-    """Add new modifications into MOD_DF
+    """Add multiple modifications into :data:`MOD_DF`,
+    it uses :meth:`add_a_new_modification()`.
 
     Parameters
     ----------
-    new_mods : list 
-        list of tuples. Tuple example:
-
+    new_mods : list of tuples
+        Tuple example:
+        (
         modname@site:str (e.g. Mod@S), 
-        chemical compositions:str (e.g. "H(4)O(2)"),
-        [optional] modloss compositions:str (e.g. "H(2)O(1)"),
+        composition:str (e.g. "H(4)O(2)"),
+        [optional] modloss composition:str (e.g. "H(2)O(1)"),
+        )
     """
     for items in new_mods:
-        if len(items) == 2:
-            mod, comp = items
-            modloss_comp = ''
-        else:
-            mod, comp, modloss_comp = items
-        MOD_DF.loc[mod,[
-            'mod_name','composition','modloss_composition',
-            'classification','unimod_id'
-        ]] = [
-            mod, comp, modloss_comp,
-            'User-added', 0
-        ]
-        MOD_DF.loc[mod,['mass','modloss']] = (
-            calc_mass_from_formula(comp),
-            calc_mass_from_formula(modloss_comp)
-        )
-        if MOD_DF.loc[mod, 'modloss'] > 0:
-            MOD_DF.loc[mod, 'modloss_importance'] = 1e6
-    MOD_DF.fillna(0, inplace=True)
-    update_all_by_MOD_DF()
+        add_a_new_modification(*items)
diff --git a/docs/conf.py b/docs/conf.py
@@ -23,7 +23,7 @@
 copyright = '2022, Mann Labs, MPIB'
 author = 'Mann Labs, MPIB'
 
-release = "0.2.1"
+release = "0.2.2"
 
 # -- General configuration ---------------------------------------------------
 

diff --git a/docs/notebooks.rst b/docs/notebooks.rst
@@ -1,5 +1,5 @@
 Tutorials and Notebooks
-====================
+========================
 
 Tutorials and notebooks about how to use AlphaBase.
 

diff --git a/nbs/README.md b/nbs/README.md
@@ -0,0 +1,3 @@
+# Jupyter notebooks for AlphaBase
+
+Check [docs/nbs](../docs/nbs) for more tutorial notebooks.
diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control
@@ -1,5 +1,5 @@
 Package: AlphaBase
-Version: 0.2.1
+Version: 0.2.2
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: AlphaBase

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-0.2.1-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-0.2.2-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.0.2.1</string>
+	<string>alphabase.0.2.2</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.2.1</string>
+	<string>0.2.2</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-0.2.1-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-0.2.2-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 0.2.1 --install-location /Applications/AlphaBase.app --scripts scripts AlphaBase.pkg
+pkgbuild --root dist/alphabase --identifier de.mpg.biochem.alphabase.app --version 0.2.2 --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 0.2.1</title>
+    <title>AlphaBase 0.2.2</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 "0.2.1"
+#define MyAppVersion "0.2.2"
 #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-0.2.1-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-0.2.2-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 = 0.2.1
+version = 0.2.2
 min_python = 3.7
 license = apache2
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Jupyter notebooks for AlphaBase

		Check [docs/nbs](../docs/nbs) for more tutorial notebooks.