Merge pull request #237 from MannLabs/issue229_fix

Release 0.6.5
MannLabs · Aug 21, 2023 · 89843be · 89843be
2 parents a21d0f6 + 53a31f5
commit 89843be
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Showing 15 changed files with 24 additions and 24 deletions.
diff --git 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<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -9,7 +9,7 @@
 	<key>CFBundleIconFile</key>
 	<string>alphapeptstats_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphastats.0.6.4</string>
+	<string>alphastats.0.6.5</string>
 	<key>CFBundleShortVersionString</key>
 	<string>0.6.0</string>
 	<key>CFBundleInfoDictionaryVersion</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/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
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaPeptStats 0.6.4</title>
+    <title>AlphaPeptStats 0.6.5</title>
     <background mime-type="image/png" file="alphapeptstats_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/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
@@ -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
@@ -22,4 +22,4 @@ combat==0.3.3
 xlsxwriter==3.1.0
 pyteomics==4.6.0
 openpyxl>=3.0.10
-
+nbformat>=5.0
diff --git 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
@@ -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(