Scheduled monthly dependency update for February

requirement/include/lint.txt

@@ -1 +1 @@
-flake8==3.6.0
+flake8==3.7.4

requirement/include/test-management.txt

@@ -1,3 +1,3 @@
 codecov==2.0.15
 coverage>=4.4
-tox==3.6.1
+tox==3.7.0

requirement/main.txt

@@ -1,14 +1,14 @@
-alembic==1.0.5
-SQLAlchemy==1.2.15
+alembic==1.0.7
+SQLAlchemy==1.2.17
 PyYAML>=4.2b1
-psycopg2-binary==2.7.6.1
+psycopg2-binary==2.7.7
 python-dateutil==2.7.5
 scipy==1.2.0
 scikit-learn==0.20.2
 tables==3.3.0 # pyup: ignore
 matplotlib<2.2 # pyup: ignore
-pandas==0.23.4
-boto3==1.9.71
+pandas==0.24.0
+boto3==1.9.86
 click==7.0
 inflection==0.3.1
 numpy>=1.12
@@ -17,7 +17,7 @@ retrying==1.3.3
 Dickens==1.0.1
 signalled-timeout==1.0.0
 s3fs==0.2.0
-wrapt==1.10.11
+wrapt==1.11.1
 argcmdr==0.6.0
 sqlparse==0.2.4
 pebble==4.3.9

requirement/test.txt

@@ -4,7 +4,7 @@ csvkit==1.0.3
 factory_boy==2.11.1
 testing.postgresql==1.3.0
 pytest<4.0.0 # pyup: ignore
-pytest-cov==2.6.0
+pytest-cov==2.6.1
 moto==1.3.7
-fakeredis==0.16.0
+fakeredis==1.0
 hypothesis==4.4.1

src/triage/component/catwalk/storage.py

@@ -538,7 +538,6 @@ def save(self):
             mode="w",
             complevel=4,
             complib="zlib",
-            format="table",
         )
         hdf.put(self.matrix_uuid, self.matrix.apply(pd.to_numeric), data_columns=True)
         hdf.close()

src/triage/component/metta/metta_io.py

@@ -227,7 +227,7 @@ def _store_matrix(metadata, df_data, title, directory, format="hd5"):
                     df_data[col] = df_data[col].astype(float)
 
             hdf = pd.HDFStore(
-                matrix_fname, mode="w", complevel=5, complib="zlib", format="table"
+                matrix_fname, mode="w", complevel=5, complib="zlib",
             )
             hdf.put(title, df_data, data_columns=True)
             hdf.close()

src/triage/util/db.py

@@ -24,6 +24,10 @@ def __init__(self, url, *, creator=sqlalchemy.create_engine, **kwargs):
     def __reduce__(self):
         return (self.__reconstruct__, (self.url, self.creator, self.kwargs))
 
+    def __reduce_ex__(self, protocol):
+        # wrapt requires reduce_ex to be implemented
+        return self.__reduce__()
+
     @classmethod
     def __reconstruct__(cls, url, creator, kwargs):
         return cls(url, creator=creator, **kwargs)