diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 1c66a9d5..29665ca1 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.6.4 +current_version = 0.6.5 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/CITATION.cff b/CITATION.cff index 03a27d9d..244cc13e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -5,7 +5,7 @@ authors: given-names: Elena orcid: title: "AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics " -version: 6.3.0 +version: 0.6.5 doi: "10.1093/bioinformatics/btad461" date-released: 2023-12-11 repository-code: https://github.com/MannLabs/alphapeptstats diff --git a/HISTORY.md b/HISTORY.md index c4d4de78..ce8f97eb 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,5 +1,9 @@ # Changelog +# 0.6.5 +* FIX coloring of plot_sampledistribution issue #229 +* ADD nbformat requirement issue #230 + # 0.6.4 * FIX windows installer diff --git a/alphastats/DataSet_Plot.py b/alphastats/DataSet_Plot.py index e89a5c31..bda476e3 100644 --- a/alphastats/DataSet_Plot.py +++ b/alphastats/DataSet_Plot.py @@ -200,7 +200,7 @@ def plot_correlation_matrix(self, method: str = "pearson"): return plot def plot_sampledistribution( - self, method: str = "violin", color: bool = None, log_scale: bool = False + self, method: str = "violin", color: str = None, log_scale: bool = False ): """Plot Intensity Distribution for each sample. Either Violin or Boxplot @@ -221,10 +221,14 @@ def plot_sampledistribution( df = df.merge(self.metadata, how="inner", on=[self.sample]) if method == "violin": - fig = px.violin(df, x=self.sample, y="Intensity", color=color) + fig = px.violin(df, x=self.sample, y="Intensity", color=color, + template="simple_white+alphastats_colors" + ) elif method == "box": - fig = px.box(df, x=self.sample, y="Intensity", color=color) + fig = px.box(df, x=self.sample, y="Intensity", color=color, + template="simple_white+alphastats_colors" + ) else: raise ValueError( @@ -386,6 +390,7 @@ def plot_imputed_values(self): color="Imputation", opacity=0.8, hover_data=plot_df.columns, + template="simple_white+alphastats_colors" ) pass diff --git a/alphastats/__init__.py b/alphastats/__init__.py index 8e41fe2b..5b335499 100644 --- a/alphastats/__init__.py +++ b/alphastats/__init__.py @@ -1,5 +1,5 @@ __project__ = "alphastats" -__version__ = "0.6.4" +__version__ = "0.6.5" __license__ = "Apache" __description__ = "An open-source Python package for Mass Spectrometry Analysis" __author__ = "Mann Labs" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 9c03dddb..cdb15ba0 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: alphastats -Version: 0.6.4 +Version: 0.6.5 Architecture: all Maintainer: MannLabs Description: alphastats diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index c124b4d3..64a06223 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/alphastats-0.6.4-py3-none-any.whl" +pip install "../../dist/alphastats-0.6.5-py3-none-any.whl" # Creating the stand-alone pyinstaller folder pip install pyinstaller==5.8 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index c1bcae78..c7a3f31d 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,7 +9,7 @@ CFBundleIconFile alphapeptstats_logo.icns CFBundleIdentifier - alphastats.0.6.4 + alphastats.0.6.5 CFBundleShortVersionString 0.6.0 CFBundleInfoDictionaryVersion diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index fb4a5c39..9f5d5fe5 100755 --- 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/alphastats-0.6.4-py3-none-any.whl" +pip install "../../dist/alphastats-0.6.5-py3-none-any.whl" # Creating the stand-alone pyinstaller folder pip install pyinstaller==5.8 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 37dc27e8..c69038e9 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - AlphaPeptStats 0.6.4 + AlphaPeptStats 0.6.5 diff --git a/release/one_click_windows_gui/alphastats_innoinstaller.iss b/release/one_click_windows_gui/alphastats_innoinstaller.iss index 6436ee01..9ba0a677 100644 --- a/release/one_click_windows_gui/alphastats_innoinstaller.iss +++ b/release/one_click_windows_gui/alphastats_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "AlphaPeptStats" -#define MyAppVersion "0.6.4" +#define MyAppVersion "0.6.5" #define MyAppPublisher "MannLabs" #define MyAppURL "https://github.com/MannLabs/alphapeptstats" #define MyAppExeName "alphastats_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 a32b591e..67d671a4 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/alphastats-0.6.4-py3-none-any.whl" +pip install "../../dist/alphastats-0.6.5-py3-none-any.whl" # Creating the stand-alone pyinstaller folder pip install pyinstaller==5.8 diff --git a/requirements.txt b/requirements.txt index 927cc55b..de4ac1e2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -22,4 +22,4 @@ combat==0.3.3 xlsxwriter==3.1.0 pyteomics==4.6.0 openpyxl>=3.0.10 - +nbformat>=5.0 \ No newline at end of file diff --git a/setup.py b/setup.py index 3369f3c8..f4ac1a32 100644 --- a/setup.py +++ b/setup.py @@ -25,7 +25,7 @@ def create_pip_wheel(): requirements = get_requirements() setuptools.setup( name="alphastats", - version="0.6.4", + version="0.6.5", license="Apache", description="An open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics", long_description=get_long_description(), diff --git a/tests/test_DataSet.py b/tests/test_DataSet.py index 31aaa720..5e7df5d0 100644 --- a/tests/test_DataSet.py +++ b/tests/test_DataSet.py @@ -729,15 +729,6 @@ def test_batch_correction(self): first_value = self.obj.mat.values[0,0] self.assertAlmostEqual(0.0111, first_value, places=2) - def test_multicova_analysis(self): - self.obj.preprocess(imputation="knn", normalization="zscore", subset=True) - res, plot_list = self.obj.multicova_analysis( - covariates=["disease", "Alkaline phosphatase measurement"], - subset={"disease": ["healthy", "liver cirrhosis"]}, - ) - self.assertAlmostEqual(-0.3063, res['disease_fc'].iloc[1], places=2) - - def test_multicova_analysis_invalid_covariates(self): self.obj.preprocess(imputation="knn", normalization="zscore", subset=True) res, _ = self.obj.multicova_analysis(