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ran black on NetPyNE #616

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14 changes: 9 additions & 5 deletions netpyne/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,19 +4,23 @@
NetPyNE consists of a number of sub-packages and modules.
"""

__version__ = '1.0.0.2'
__version__ = "1.0.0.2"
import os, sys
display = os.getenv('DISPLAY')
nogui = (sys.argv.count('-nogui')>0)

display = os.getenv("DISPLAY")
nogui = sys.argv.count("-nogui") > 0

__gui__ = True

if nogui: # completely disables graphics (avoids importing matplotlib)
__gui__ = False

elif not display or len(display) == 0: # if no display env available (e.g. clusters) uses 'Agg' backend to plot
elif (
not display or len(display) == 0
): # if no display env available (e.g. clusters) uses 'Agg' backend to plot
import matplotlib
matplotlib.use('Agg')

matplotlib.use("Agg")

from netpyne import analysis
from netpyne import batch
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62 changes: 54 additions & 8 deletions netpyne/analysis/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,10 @@
from __future__ import absolute_import

from future import standard_library

standard_library.install_aliases()
import warnings

warnings.filterwarnings("ignore")

# -------------------------------------------------------------------------------------------------------------------
Expand All @@ -21,22 +23,50 @@
# -------------------------------------------------------------------------------------------------------------------
# Import utils methods
# -------------------------------------------------------------------------------------------------------------------
from .utils import exception, _showFigure, _saveFigData, getCellsInclude, getCellsIncludeTags, _roundFigures, \
_smooth1d, syncMeasure, invertDictMapping, checkAvailablePlots
from .utils import (
exception,
_showFigure,
_saveFigData,
getCellsInclude,
getCellsIncludeTags,
_roundFigures,
_smooth1d,
syncMeasure,
invertDictMapping,
checkAvailablePlots,
)


# -------------------------------------------------------------------------------------------------------------------
# Import connectivity-related functions
# -------------------------------------------------------------------------------------------------------------------
from .network import plotConn, _plotConnCalculateFromSim, _plotConnCalculateFromFile, plot2Dnet, plotShape, calculateDisynaptic, \
plot2Dfiring
from .network import (
plotConn,
_plotConnCalculateFromSim,
_plotConnCalculateFromFile,
plot2Dnet,
plotShape,
calculateDisynaptic,
plot2Dfiring,
)


# -------------------------------------------------------------------------------------------------------------------
# Import spike-related functions
# -------------------------------------------------------------------------------------------------------------------
from .spikes import calculateRate, plotRates, plotSyncs, plotRaster, plotSpikeHist, plotSpikeStats, \
plotRatePSD, plotRateSpectrogram, popAvgRates, plotfI, calculatefI
from .spikes import (
calculateRate,
plotRates,
plotSyncs,
plotRaster,
plotSpikeHist,
plotSpikeStats,
plotRatePSD,
plotRateSpectrogram,
popAvgRates,
plotfI,
calculatefI,
)


# -------------------------------------------------------------------------------------------------------------------
Expand Down Expand Up @@ -68,9 +98,25 @@
# -------------------------------------------------------------------------------------------------------------------

try:
from .interactive import iplotDipole, iplotDipoleSpectrogram, iplotDipolePSD, iplotRaster, iplotSpikeHist, iplotRatePSD, iplotTraces, iplotLFP, iplotConn, iplotRxDConcentration, iplot2Dnet, iplotSpikeStats, iplotGranger
from .interactive import (
iplotDipole,
iplotDipoleSpectrogram,
iplotDipolePSD,
iplotRaster,
iplotSpikeHist,
iplotRatePSD,
iplotTraces,
iplotLFP,
iplotConn,
iplotRxDConcentration,
iplot2Dnet,
iplotSpikeStats,
iplotGranger,
)
except:
print('Warning: could not import interactive plotting functions; make sure the "bokeh" package is installed.')
print(
'Warning: could not import interactive plotting functions; make sure the "bokeh" package is installed.'
)


# -------------------------------------------------------------------------------------------------------------------
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