diff --git a/.bumpversion.cfg b/.bumpversion.cfg index fb26d411..e03d3dfb 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.4.1 +current_version = 1.0.0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/alphabase/__init__.py b/alphabase/__init__.py index 5c1bddf3..e9bcb152 100644 --- a/alphabase/__init__.py +++ b/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", diff --git a/docs/conf.py b/docs/conf.py index ad2ba025..dcd6c65f 100644 --- a/docs/conf.py +++ b/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 --------------------------------------------------- diff --git a/nbdev_nbs/peptide/mass_calc.ipynb b/nbdev_nbs/peptide/mass_calc.ipynb index aecb05ec..4800f32d 100644 --- a/nbdev_nbs/peptide/mass_calc.ipynb +++ b/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)" ] diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index ec271c21..3c685dee 100644 --- a/release/one_click_linux_gui/control +++ b/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 Description: AlphaBase diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 56409dc1..c588de99 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/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 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 6855ce17..4f7c4a70 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 - alphabase.0.4.1 + alphabase.1.0.0 CFBundleShortVersionString - 0.4.1 + 1.0.0 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 6b473886..ee9aa620 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/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 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 890b5c5a..4b67bad6 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - AlphaBase 0.4.1 + AlphaBase 1.0.0 diff --git a/release/one_click_windows_gui/alphabase_innoinstaller.iss b/release/one_click_windows_gui/alphabase_innoinstaller.iss index bd2ed118..0210ff48 100644 --- 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 "0.4.1" +#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" diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 69643505..bc0a2881 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/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 diff --git a/settings.ini b/settings.ini index bcf733bb..1a37b243 100644 --- a/settings.ini +++ b/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