Towards PEP8 compatibility

Names of modules have been changed following PEP8
recommandations. Thus, for example, Core/peakFunctions.py becomes
core/peak_functions.py. Module ICython has been renamed to
cython. Also, Script env.sh has been modified to allow optional
download of the data base.

.travis.yml

@@ -31,9 +31,8 @@ install:
   - source activate IC
   - pip install hypothesis-numpy
   - pip install flaky
-  - source env.sh
+  - source env.sh 1
 
 script:
     - python setup.py develop
     - pytest
-

env.sh

@@ -1,3 +1,8 @@
+#!/bin/bash
+#echo -n "Enter 0 to use an existing copy of DB or 1 to download a new copy --> "
+#echo "your choice is $download"
 export ICDIR=`pwd`
+export ICTDIR=$ICDIR/invisible_cities/
 export PYTHONPATH=$ICDIR:$PYTHONPATH
-python $ICDIR/invisible_cities/Database/download.py
+
+python $ICDIR/invisible_cities/database/download.py

invisible_cities/Cities/diomira_ms.py → invisible_cities/cities/diomira.py

@@ -1,19 +1,21 @@
 from __future__ import print_function
+
 import sys
 from glob import glob
 from time import time
 
 import numpy as np
 import tables as tb
 
-import invisible_cities.Core.tblFunctions as tbl
-from invisible_cities.Core.Configure import configure, print_configuration
-from invisible_cities.Core.Nh5 import FEE
-import invisible_cities.Core.mplFunctions as mpl
-import invisible_cities.Core.wfmFunctions as wfm
-from invisible_cities.Core.RandomSampling import NoiseSampler as SiPMsNoiseSampler
-from invisible_cities.Database import loadDB
-import invisible_cities.Sierpe.FEE as FE
+import invisible_cities.core.tbl_functions as tbl
+from invisible_cities.core.configure import configure, print_configuration
+from invisible_cities.core.nh5 import FEE
+import invisible_cities.core.mpl_functions as mpl
+import invisible_cities.core.wfm_functions as wfm
+from invisible_cities.core.random_sampling\
+     import NoiseSampler as SiPMsNoiseSampler
+from invisible_cities.database import loadDB
+import invisible_cities.sierpe.fee as FE
 
 
 class Diomira:

invisible_cities/Cities/diomira_ms_run.py → invisible_cities/cities/diomira_run.py

@@ -5,16 +5,16 @@
 import os
 from time import time
 
-from Core.Configure import configure
-from Cities.diomira_ms import Diomira
+from invisible_cities.core.configure import configure
+from invisible_cities.cities.diomira import Diomira
 
-ffile = os.environ['ICDIR'] + '/tests/electrons_40keV_z250_RWF.h5'
+ffile = os.environ['ICTDIR'] + '/tests/electrons_40keV_z250_RWF.h5'
 try:
     os.system("rm -f {}".format(ffile))
 except(IOError):
     pass
 
-ffile = os.environ['ICDIR'] + '/Config/diomira_ms.conf'
+ffile = os.environ['ICTDIR'] + '/config/diomira.conf'
 CFP = configure(['DIOMIRA','-c',ffile])
 fpp = Diomira()
 files_in = glob(CFP['FILE_IN'])

invisible_cities/Cities/diomira_test.py → invisible_cities/cities/diomira_test.py

@@ -1,28 +1,28 @@
 from __future__ import print_function
 from __future__ import absolute_import
 
+import os
 from glob import glob
 import tables as tb
 import numpy as np
 
-from invisible_cities.Core.Configure import configure
-import invisible_cities.Core.tblFunctions as tbl
-import invisible_cities.Core.system_of_units as units
-from invisible_cities.Sierpe import FEE
-import invisible_cities.ICython.Sierpe.BLR as blr
-from invisible_cities.Database import loadDB
-from invisible_cities.Cities.diomira_ms import Diomira
-import os
+from invisible_cities.core.configure import configure
+import invisible_cities.core.tbl_functions as tbl
+import invisible_cities.core.system_of_units as units
+from invisible_cities.sierpe import fee as FEE
+import invisible_cities.cython.sierpe.BLR as blr
+from invisible_cities.database import loadDB
+from invisible_cities.cities.diomira import Diomira
 
 def test_diomira_run():
     """ Tests that DIOMIRA runs on default config parameters """
-    ffile = os.environ['ICDIR'] + '/invisible_cities/tests/electrons_40keV_z250_RWF.h5'
+    ffile = os.environ['ICTDIR'] + '/tests/electrons_40keV_z250_RWF.h5'
     try:
         os.system("rm -f {}".format(ffile))
     except(IOError):
         pass
 
-    ffile = os.environ['ICDIR'] + '/invisible_cities/Config/diomira_ms.conf'
+    ffile = os.environ['ICTDIR'] + '/config/diomira.conf'
     CFP = configure(['DIOMIRA','-c',ffile])
     fpp = Diomira()
     files_in = glob(CFP['FILE_IN'])
@@ -41,7 +41,7 @@ def test_diomira_run():
 
 def test_diomira_fee_table():
     """ tests that FEE table reads back correctly with expected values"""
-    path = os.environ['ICDIR'] + '/invisible_cities/tests/'
+    path = os.environ['ICTDIR'] + '/tests/'
 
     ffile ='electrons_40keV_z250_RWF.h5'
     e40rwf= tb.open_file(path+ffile,'r+')
@@ -76,7 +76,7 @@ def test_diomira_cwf_blr():
        the BLR within 1 %.
     """
     eps = 1.
-    path = os.environ['ICDIR'] + '/invisible_cities/tests/'
+    path = os.environ['ICTDIR'] + '/tests/'
     ffile ='electrons_40keV_z250_RWF.h5'
     e40rwf= tb.open_file(path+ffile,'r+')
     pmtrwf = e40rwf.root.RD.pmtrwf

invisible_cities/Cities/IRENE.py → invisible_cities/cities/irene.py

@@ -8,19 +8,20 @@
 import tables as tb
 import matplotlib.pyplot as plt
 
-from Core.Nh5 import RunInfo, EventInfo
-from Core.Nh5 import S12, S2Si
-import Core.mplFunctions as mpl
-import Core.wfmFunctions as wfm
-import Core.peakFunctions as pf
-import Core.tblFunctions as tbl
-from Core.Configure import configure, define_event_loop, print_configuration
-
-import ICython.Sierpe.BLR as blr
-import ICython.Core.peakFunctions as cpf
-from ICython.Core.system_of_units import SystemOfUnits
-
-from Database import loadDB
+from invisible_cities.core.nh5 import RunInfo, EventInfo
+from invisible_cities.core.Nh5 import S12, S2Si
+import invisible_cities.core.mpl_functions as mpl
+import invisible_cities.core.wfm_functions as wfm
+import invisible_cities.core.peak_functions as pf
+import invisible_cities.core.tbl_functions as tbl
+from invisible_cities.core.configure\
+ import configure, define_event_loop, print_configuration
+
+import invisible_cities.cython.sierpe.BLR as blr
+import invisible_cities.cython.core.peak_functions as cpf
+from invisible_cities.cython.core.system_of_units import SystemOfUnits
+
+from invisible_cities.database import loadDB
 
 units = SystemOfUnits()
 

invisible_cities/Core/Configure.py → invisible_cities/core/configure.py

@@ -5,7 +5,7 @@
 import sys
 import os
 
-from invisible_cities.Core.LogConfig import logger
+from invisible_cities.core.log_config import logger
 
 
 def print_configuration(options):

invisible_cities/Core/coreFunctions_perf.py → invisible_cities/core/core_functions_performance.py

@@ -5,8 +5,8 @@
 
 from time import time
 import numpy as np
-import wfmFunctions as wfm
-import ICython.Core.peakFunctions as cpf
+import invisible_cities.core.wfm_functions as wfm
+import invisible_cities.cython.core.peak_functions as cpf
 
 
 t = np.arange(1.,100., 0.1, dtype=np.double)

invisible_cities/Core/mplFunctions.py → invisible_cities/core/mpl_functions.py

@@ -10,10 +10,10 @@
 # from mpl_toolkits.mplot3d import Axes3D
 # from IPython.display import HTML
 
-import invisible_cities.Core.coreFunctions as cf
-import invisible_cities.Core.system_of_units as units
-import invisible_cities.Core.wfmFunctions as wfm
-import invisible_cities.Core.tblFunctions as tbl
+import invisible_cities.core.core_functions as cf
+import invisible_cities.core.system_of_units as units
+import invisible_cities.core.wfm_functions as wfm
+import invisible_cities.core.tbl_functions as tbl
 
 
 # matplotlib.style.use("ggplot")
@@ -39,24 +39,6 @@ def histo(x, nbins, title="hsimple", xlabel="", ylabel="Frequency"):
     plt.ylabel(ylabel)
 
 
-def HSimple1(x, nbins, title="hsimple", xlabel="", ylabel="Frequency",
-             save=False, filename="hsimple.png", filepath="./"):
-    """an interface for plt.hist with some decorations and default options"""
-
-    plt.hist(x, nbins, histtype="bar", alpha=0.75)
-    plt.title(title)
-    plt.xlabel(xlabel)
-    plt.ylabel(ylabel)
-
-    if save:
-        pathfile = filepath+filename
-        print("saving histogram %s in %s" % (filename, pathfile))
-        plt.savefig(pathfile, bbox_inches="tight")
-        plt.close()
-    else:
-        plt.figure()
-
-
 def plts(signal, signal_start=0, signal_end=1e+4, offset=5):
     """Plot a signal in a give interval, control offset by hand."""
     ax1 = plt.subplot(1, 1, 1)
@@ -75,14 +57,14 @@ def plot_signal(signal_t, signal, title="signal",
     ax1 = plt.subplot(1, 1, 1)
     ax1.set_xlim([signal_start, signal_end])
     ax1.set_ylim([0, ymax])
-    SetPlotLabels(xlabel="t ({})".format(t_units),
+    set_plot_labels(xlabel="t ({})".format(t_units),
                   ylabel="signal ({})".format(units))
     plt.title(title)
     plt.plot(signal_t, signal)
     plt.show()
 
 
-def SetPlotLabels(xlabel="", ylabel="", grid=True):
+def set_plot_labels(xlabel="", ylabel="", grid=True):
     """Short cut to set labels in plots."""
     plt.xlabel(xlabel)
     plt.ylabel(ylabel)

invisible_cities/Core/peakFunctions.py → invisible_cities/core/peak_functions.py

@@ -6,14 +6,14 @@
 import math
 import numpy as np
 import pandas as pd
-import Core.system_of_units as units
-import ICython.Sierpe.BLR as blr
-import ICython.Core.peakFunctions as pf
-from Database import loadDB
-import matplotlib.pyplot as plt
 from time import time
 import tables as tb
+import matplotlib.pyplot as plt
 
+import invisible_cities.core.system_of_units as units
+import invisible_cities.cython.sierpe.BLR as blr
+import invisible_cities.cython.core.peak_functions as pf
+from invisible_cities.database import loadDB
 
 
 def pmt_sum(CWF, adc_to_pes):

invisible_cities/Core/pmapsFunctions.py → invisible_cities/core/pmaps_functions.py

@@ -8,9 +8,9 @@
 import numpy as np
 import pandas as pd
 import tables as tb
-import Core.system_of_units as units
-import ICython.Core.pmapsFunctions as cpm
 import matplotlib.pyplot as plt
+import invisible_cities.core.system_of_units as units
+import invisible_cities.cython.core.pmaps_functions as cpm
 
 
 def read_PMAPS(path, pmap_file):

invisible_cities/Core/RandomSampling.py → invisible_cities/core/random_sampling.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import invisible_cities.Database.loadDB as DB
+import invisible_cities.database.loadDB as DB
 
 
 class NoiseSampler:

invisible_cities/Core/tblFunctions.py → invisible_cities/core/tbl_functions.py

@@ -16,9 +16,9 @@
 import tables as tb
 import pandas as pd
 
-import invisible_cities.Core.wfmFunctions as wfm
-import invisible_cities.Database.loadDB as DB
-import invisible_cities.Sierpe.FEE as FE
+import invisible_cities.core.wfm_functions as wfm
+import invisible_cities.database.loadDB as DB
+import invisible_cities.sierpe.fee as FE
 
 
 def filters(name):

invisible_cities/Core/wfmFunctions.py → invisible_cities/core/wfm_functions.py

@@ -264,8 +264,6 @@ def rebin_waveform(t, e, stride = 40):
     return T, E
 
 
-
-
 def rebin_df(df, stride=40):
     """Applies rebin_wf to a dataframe.
 

invisible_cities/Core/wfmFunctions_test.py → invisible_cities/core/wfm_functions_test.py

@@ -4,8 +4,8 @@
 from hypothesis.strategies import lists, integers, floats
 from hypothesis.extra.numpy import arrays
 
-from . import wfmFunctions as wfm
-import invisible_cities.ICython.Core.peakFunctions as cpf
+from . import wfm_functions as wfm
+import invisible_cities.cython.core.peak_functions as cpf
 import numpy as np
 
 

invisible_cities/Database/download.py → invisible_cities/database/download.py

@@ -7,7 +7,7 @@
 
 
 def loadDB():
-    dbfile = os.environ['ICDIR'] + '/invisible_cities/Database/localdb.sqlite3'
+    dbfile = os.environ['ICTDIR'] + '/database/localdb.sqlite3'
     try:
         os.remove(dbfile)
     except:

invisible_cities/Database/loadDB.py → invisible_cities/database/loadDB.py

@@ -9,8 +9,8 @@
     from future_builtins import map
 
 
-DATABASE_LOCATION = '/invisible_cities/Database/localdb.sqlite3'
-    
+DATABASE_LOCATION = '/invisible_cities/database/localdb.sqlite3'
+
 def tmap(*args):
     return tuple(map(*args))
 

invisible_cities/Sierpe/FEE.py → invisible_cities/sierpe/fee.py

@@ -8,8 +8,8 @@
 
 import numpy as np
 from scipy import signal
-import invisible_cities.Core.system_of_units as units
-import invisible_cities.Database.loadDB as DB
+import invisible_cities.core.system_of_units as units
+import invisible_cities.database.loadDB as DB
 
 # globals describing FEE
 PMT_GAIN = 1.7e6
@@ -399,4 +399,3 @@ def daq_decimator(f_sample1, f_sample2, signal_in):
 
     scale = int(f_sample1 / f_sample2)
     return signal.decimate(signal_in, scale, ftype='fir', zero_phase=False)
-

invisible_cities/Sierpe/FEE_test.py → invisible_cities/sierpe/fee_test.py

@@ -7,8 +7,8 @@
 from hypothesis.strategies import lists, floats
 from flaky import flaky
 
-import invisible_cities.Sierpe.FEE as FE
-import invisible_cities.Core.system_of_units as units
+import invisible_cities.sierpe.fee as FE
+import invisible_cities.core.system_of_units as units
 import numpy as np
 
 def signal_i_th():
@@ -95,5 +95,3 @@ def test_FEE():
     energy_mea2=np.sum(signal_r2[1000:11000])
     energy_in2=np.sum(signal_i*FE.i_to_adc())
     diff = np.abs(100.*((energy_in2-energy_mea2)/energy_in2))
-
-

invisible_cities/tests/test_db.py

@@ -1,6 +1,6 @@
 import tables
-from invisible_cities.Database import download
-import invisible_cities.Database.loadDB as DB
+from invisible_cities.database import download
+import invisible_cities.database.loadDB as DB
 import os
 
 

setup.py

@@ -14,6 +14,6 @@
       author_email = 'nextic@TODO.org',
       license      = 'TODO',
       packages     = ['invisible_cities'],
-      ext_modules  = cythonize('invisible_cities/ICython**/*.pyx'),
+      ext_modules  = cythonize('invisible_cities/cython**/*.pyx'),
       include_dirs = [numpy_include],
 )