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Issue54 #55

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merged 4 commits into from
Jun 24, 2018
Merged

Issue54 #55

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af0ab12
removed Panel and Panel4D since they have been deprecated in pandas.
Jun 22, 2018
9867376
Fixed syntax error.
Jun 22, 2018
1fc875a
Merge branch 'develop' into issue54
dilawar Jun 24, 2018
d487c0e
removed PanelD from tests as well.
Jun 24, 2018
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7 changes: 4 additions & 3 deletions pypet/parameter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,8 @@

import numpy as np
import scipy.sparse as spsp
from pandas import DataFrame, Series, Panel
from pandas import DataFrame, Series


import pypet.pypetconstants as pypetconstants
from pypet.naturalnaming import NNLeafNode
Expand Down Expand Up @@ -1954,7 +1955,7 @@ class Result(BaseResult):
__slots__ = ('_data_',)

SUPPORTED_DATA = set((np.ndarray, ObjectTable,
DataFrame, Series, Panel,
DataFrame, Series,
dict, tuple, list, np.matrix) +
pypetconstants.PARAMETER_SUPPORTED_DATA)

Expand Down Expand Up @@ -2484,4 +2485,4 @@ def _load(self, load_dict):
self.v_protocol = PickleParameter._get_protocol(dump)
for key in load_dict:
val = load_dict[key]
self._data[key] = pickle.loads(val)
self._data[key] = pickle.loads(val)
15 changes: 7 additions & 8 deletions pypet/storageservice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
import tables.parameters as ptpa

import numpy as np
from pandas import DataFrame, Series, Panel, HDFStore
from pandas import DataFrame, Series, HDFStore

import pypet.pypetconstants as pypetconstants
import pypet.pypetexceptions as pex
Expand Down Expand Up @@ -422,9 +422,6 @@ class HDF5StorageService(StorageService, HasLogger):
SERIES = pypetconstants.SERIES
''' Store data as pandas Series '''

PANEL = pypetconstants.PANEL
''' Store data as pandas Panel(4D) '''

SPLIT_TABLE = pypetconstants.SPLIT_TABLE
''' If a table was split due to too many columns'''

Expand All @@ -446,7 +443,6 @@ class HDF5StorageService(StorageService, HasLogger):
np.matrix: CARRAY,
DataFrame: FRAME,
Series: SERIES,
Panel: PANEL,
shared.SharedTable: SHARED_DATA,
shared.SharedArray: SHARED_DATA,
shared.SharedPandasFrame: SHARED_DATA,
Expand Down Expand Up @@ -3835,7 +3831,8 @@ def _prm_store_from_dict(self, fullname, store_dict, hdf5_group, store_flags, kw
flag=flag, **kwargs)
elif flag in (HDF5StorageService.SERIES,
HDF5StorageService.FRAME,
HDF5StorageService.PANEL):
# HDF5StorageService.PANEL
):
# self._logger.log(1, 'SUB-Storing %s PANDAS', key)
self._prm_write_pandas_data(key, data_to_store, hdf5_group, fullname,
flag, **kwargs)
Expand Down Expand Up @@ -4017,7 +4014,8 @@ def _shared_write_shared_data(self, key, hdf5_group, full_name, **kwargs):

elif flag in (HDF5StorageService.FRAME,
HDF5StorageService.SERIES,
HDF5StorageService.PANEL) :
# HDF5StorageService.PANEL
) :

self._prm_write_pandas_data(key, data,
hdf5_group,
Expand Down Expand Up @@ -4675,7 +4673,8 @@ def _prm_load_into_dict(self, full_name, load_dict, hdf5_group, instance,
to_load = self._prm_read_array(node, full_name)
elif load_type in (HDF5StorageService.FRAME,
HDF5StorageService.SERIES,
HDF5StorageService.PANEL):
# HDF5StorageService.PANEL
):
to_load = self._prm_read_pandas(node, full_name)
elif load_type.startswith(HDF5StorageService.SHARED_DATA):
to_load = self._prm_read_shared_data(node, instance)
Expand Down
4 changes: 1 addition & 3 deletions pypet/tests/testutils/data.py
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Expand Up @@ -264,8 +264,6 @@ def simple_calculations(traj, arg1, simple_kwarg):

myseries = myframe['TC1']

mypanel = pd.Panel({'Item1' : pd.DataFrame(np.ones((4, 3))),'Item2' : pd.DataFrame(np.ones((4, 2)))})

traj.f_add_result('myseries', myseries, comment='dd')
traj.f_store_item('myseries')
traj.f_add_result('mypanel', mypanel, comment='dd')
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@SmokinCaterpillar SmokinCaterpillar Jun 24, 2018 •
edited
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Can you remove this line, too? Otherwise the tests fail.

Expand Down Expand Up @@ -403,4 +401,4 @@ def compare_trajectories(self,traj1,traj2):

if not node.v_annotations.f_is_empty():
second_anns = traj2.f_get(node.v_full_name).v_annotations
self.assertTrue(str(node.v_annotations) == str(second_anns))
self.assertTrue(str(node.v_annotations) == str(second_anns))
6 changes: 1 addition & 5 deletions pypet/tests/unittests/parameter_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -818,11 +818,7 @@ def setUp(self):

myseries = myframe['TC1']

mypanel = pd.Panel({'Item1' : pd.DataFrame(np.random.randn(4, 3)),
'Item2' : pd.DataFrame(np.random.randn(4, 2))})

self.data['series'] = myseries
self.data['panel'] = mypanel

self.make_constructor()
self.make_results()
Expand Down Expand Up @@ -1053,4 +1049,4 @@ def make_results(self):

if __name__ == '__main__':
opt_args = parse_args()
run_suite(**opt_args)
run_suite(**opt_args)
7 changes: 0 additions & 7 deletions pypet/utils/comparisons.py
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Expand Up @@ -155,13 +155,6 @@ def nested_equal(a, b):
else:
return not np.any((a != b).data)

a_panel = isinstance(a, pd.Panel)
b_panel = isinstance(b, pd.Panel)
if a_panel != b_panel:
return False
if a_panel:
return nested_equal(a.to_frame(), b.to_frame())

a_series = isinstance(a, pd.Series)
b_series = isinstance(b, pd.Series)
if a_series != b_series:
Expand Down