Upgrade Pandas and make a hack-y fix for pandas issue. Closes #67

onecodex · Oct 24, 2017 · 73c4171 · 73c4171
1 parent 1134d6b
commit 73c4171
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Showing 5 changed files with 6 additions and 9 deletions.
diff --git a/onecodex/viz/__init__.py b/onecodex/viz/__init__.py
@@ -3,9 +3,4 @@
 from onecodex.viz._distance import plot_distance
 from onecodex.viz._metadata import plot_metadata
 
-# If users want to put special characters in their plot labels
-import sys
-reload(sys)
-sys.setdefaultencoding('utf-8')
-
 __all__ = ['plot_heatmap', 'plot_pca', 'plot_distance', 'plot_metadata']
diff --git a/onecodex/viz/_metadata.py b/onecodex/viz/_metadata.py
@@ -61,7 +61,8 @@ def plot_metadata(analyses, metadata='created_at', statistic=None, tax_id=None,
     elif pd.api.types.is_bool_dtype(md[metadata]) or \
             pd.api.types.is_categorical_dtype(md[metadata]) or \
             pd.api.types.is_object_dtype(md[metadata]):
-        md.fillna(value='N/A', inplace=True)
+        na = {field: 'N/A' for field in md.columns}
+        md.fillna(value=na, inplace=True)
         sns.boxplot(x=metadata, y='_data', data=md, palette='pastel', **kwargs)
     else:
         raise OneCodexException('Unplottable column type for metadata {}'.format(metadata))

diff --git a/onecodex/viz/_pca.py b/onecodex/viz/_pca.py
@@ -34,7 +34,8 @@ def plot_pca(analyses, threshold=None,
     pca_vals = pd.DataFrame(pca_vals, index=df.index)
     pca_vals.rename(columns=lambda x: "PCA{}".format(x + 1), inplace=True)
     metadata.index = df.index
-    plot_data = pd.concat([pca_vals, metadata.fillna('N/A')], axis=1)
+    na = {field: 'N/A' for field in metadata.columns}
+    plot_data = pd.concat([pca_vals, metadata.fillna(na)], axis=1)
 
     # Scatter plot of PCA
     sns.set(style=kwargs.pop('style', 'darkgrid'))

diff --git a/requirements.txt b/requirements.txt
@@ -8,7 +8,7 @@ requests_toolbelt>=0.7.0
 
 # extensions
 numpy>=1.11.0
-pandas==0.19.2
+pandas>=0.20.0,<0.21.0
 matplotlib>=1.5.1
 networkx>=1.11
 seaborn==0.8

diff --git a/setup.py b/setup.py
@@ -31,7 +31,7 @@
     include_package_data=True,
     zip_safe=False,
     extras_require={
-        'all': ['numpy>=1.11.0', 'pandas>=0.18.1', 'matplotlib>1.5.1',
+        'all': ['numpy>=1.11.0', 'pandas>=0.20.0,<0.21.0', 'matplotlib>1.5.1',
                 'seaborn>=0.8', 'scikit-learn>=0.19.0', 'scikit-bio==0.4.2',
                 'networkx>=1.11'],
         'testing': ['flake8', 'testfixtures', 'responses', 'coverage', 'pytest==3.0.5',