v1.0.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.1
+current_version = 1.0.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

alphabase/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphabase"
-__version__ = "0.4.1"
+__version__ = "1.0.0"
 __license__ = "Apache"
 __description__ = "An infrastructure Python package of the AlphaX ecosystem"
 __author__ = "Mann Labs"
@@ -13,13 +13,13 @@
     "software",
     "AlphaX ecosystem",
 ]
-__python_version__ = ">=3.8,<3.10"
+__python_version__ = ">=3.8"
 __classifiers__ = [
-    "Development Status :: 1 - Planning",
+    # "Development Status :: 1 - Planning",
     # "Development Status :: 2 - Pre-Alpha",
     # "Development Status :: 3 - Alpha",
     # "Development Status :: 4 - Beta",
-    # "Development Status :: 5 - Production/Stable",
+    "Development Status :: 5 - Production/Stable",
     # "Development Status :: 6 - Mature",
     # "Development Status :: 7 - Inactive"
     "Intended Audience :: Science/Research",

docs/conf.py

@@ -23,7 +23,7 @@
 copyright = '2022, Mann Labs, MPIB'
 author = 'Mann Labs, MPIB'
 
-release = "0.4.1"
+release = "1.0.0"
 
 # -- General configuration ---------------------------------------------------
 

nbdev_nbs/peptide/mass_calc.ipynb

@@ -61,6 +61,23 @@
     "### Testing"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "seq, mods, mod_sites = 'AGHCEWQMK', ['Carbamidomethyl@C', 'Oxidation@M'], [4, 4]\n",
+    "b,y,pepmass = calc_b_y_and_peptide_mass(seq, mods, mod_sites)\n",
+    "assert np.allclose(b, [  71.03711379,  128.05857751,  265.11748936,  441.14305266,\n",
+    "         570.18564575,  756.2649587 ,  884.32353621, 1015.3640213 ]\n",
+    ")\n",
+    "assert np.allclose(y, [1090.43243521, 1033.41097149,  896.35205963,  720.32649633,\n",
+    "         591.28390324,  405.20459029,  277.14601279,  146.1055277 ]\n",
+    ")\n",
+    "assert np.allclose(pepmass, 1161.46954899713)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -72,8 +89,8 @@
     "assert np.allclose(b, [  71.03711379,  128.05857751,  265.11748936,  425.14813804,\n",
     "         554.19073113,  740.27004408,  868.32862159, 1015.3640213 ]\n",
     ")\n",
-    "assert np.allclose(y, [  [1090.43243521, 1033.41097149,  896.35205963,  736.32141095,\n",
-    "         607.27881786,  421.19950491,  293.14092741,  146.1055277 ] ]\n",
+    "assert np.allclose(y, [1090.43243521, 1033.41097149,  896.35205963,  736.32141095,\n",
+    "         607.27881786,  421.19950491,  293.14092741,  146.1055277 ]\n",
     ")\n",
     "assert np.allclose(pepmass, 1161.46954899713)"
    ]
@@ -88,8 +105,24 @@
     "assert np.allclose(b_frags[0], [  71.03711379,  128.05857751,  265.11748936,  425.14813804,\n",
     "         554.19073113,  740.27004408,  868.32862159, 1015.3640213 ]\n",
     ")\n",
-    "assert np.allclose(y_frags[0], [  [1090.43243521, 1033.41097149,  896.35205963,  736.32141095,\n",
-    "         607.27881786,  421.19950491,  293.14092741,  146.1055277 ] ]\n",
+    "assert np.allclose(y_frags[0], [  1090.43243521, 1033.41097149,  896.35205963,  736.32141095,\n",
+    "         607.27881786,  421.19950491,  293.14092741,  146.1055277 ]\n",
+    ")\n",
+    "assert np.allclose(pepmasses[0], 1161.46954899713)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b_frags,y_frags,pepmasses=calc_b_y_and_peptide_masses_for_same_len_seqs([seq]*2, [mods,[]], [[4,4],[]])\n",
+    "assert np.allclose(b_frags[0], [  71.03711379,  128.05857751,  265.11748936,  441.14305266,\n",
+    "         570.18564575,  756.2649587 ,  884.32353621, 1015.3640213 ]\n",
+    ")\n",
+    "assert np.allclose(y_frags[0], [1090.43243521, 1033.41097149,  896.35205963,  720.32649633,\n",
+    "         591.28390324,  405.20459029,  277.14601279,  146.1055277 ]\n",
     ")\n",
     "assert np.allclose(pepmasses[0], 1161.46954899713)"
    ]

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: AlphaBase
-Version: 0.4.1
+Version: 1.0.0
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: AlphaBase

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-0.4.1-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-1.0.0-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphabase.0.4.1</string>
+	<string>alphabase.1.0.0</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.4.1</string>
+	<string>1.0.0</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/alphabase-0.4.1-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-1.0.0-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 0.4.1 --install-location /Applications/AlphaBase.app --scripts scripts AlphaBase.pkg
+pkgbuild --root dist/alphabase --identifier de.mpg.biochem.alphabase.app --version 1.0.0 --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

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 0.4.1</title>
+    <title>AlphaBase 1.0.0</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" />

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 "0.4.1"
+#define MyAppVersion "1.0.0"
 #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"

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-0.4.1-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-1.0.0-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

settings.ini

@@ -4,7 +4,7 @@
 ### Python library ###
 repo = alphabase
 lib_name = alphabase
-version = 0.4.1
+version = 1.0.0
 min_python = 3.7
 license = apache2