Changeset 298

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Timestamp:
11/06/08 16:42:57 (2 months ago)
Author:
pierre
Message:

Sorry for this commit on all the import headers. I hope I'm not breaking anything. Tests are passed at least. Numpy is now a non optionnal package, otherwise, all the exotic package that may be used in your functions should be put in the main init file, and therefore here we will centralized the warning messages

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  • trunk/src/__init__.py

    r295 r298  
    88# dependency here, in order to centralizz the warning 
    99# messages and the check 
    10 dependencies = {'numpy' : {'website' : 'http://numpy.scipy.org/' , 'is_present' : False, 'check':False}, 
    11                 'pylab' : {'website' : 'http://matplotlib.sourceforge.net/', 'is_present' : False, 'check':False}, 
     10dependencies = {'pylab' : {'website' : 'http://matplotlib.sourceforge.net/', 'is_present' : False, 'check':False}, 
    1211                'tables': {'website' : 'http://www.pytables.org/moin' , 'is_present' : False, 'check':False}, 
    1312                'psyco' : {'website' : 'http://psyco.sourceforge.net/', 'is_present' : False, 'check':False}, 
    …… 
    1514                'PIL'   : {'website' : 'http://www.pythonware.com/products/pil/', 'is_present':False, 'check':False}, 
    1615                'scipy' : {'website' : 'http://numpy.scipy.org/' , 'is_present' : False, 'check':False}, 
     16                'NeuroTools.facets.hdf5' : {'website' : None, 'is_present' : False, 'check':False}, 
     17                'srblib' : {'website' : 'http://www.sdsc.edu/srb/index.php/Python', 'is_present' : False, 'check':False}, 
    1718                ## Add here your extensions ### 
    1819               } 
    19  
    20  
    21  
    22  
    2320 
    2421 

  • trunk/src/analysis.py

    r295 r298  
    77""" 
    88 
    9 import os 
    10 from NeuroTools.__init__ import check_dependency 
    11  
    12 if check_dependency('numpy'): 
    13     import numpy 
    14  
     9import os, numpy 
     10from NeuroTools import check_dependency 
    1511 
    1612 

  • trunk/src/datastore/__init__.py

    r213 r298  
    2424 
    2525import warnings 
    26 try: 
    27     from django_orm import DjangoORMDataStore 
    28 except ImportError: 
    29     warnings.warn("DjangoORMDataStore not available, as we can't import django") 
     26from NeuroTools import check_dependency 
     27 
     28from django_orm import DjangoORMDataStore 
    3029from shelve_ds import ShelveDataStore 
    3130 

  • trunk/src/datastore/keygenerators.py

    r213 r298  
    22Key generators for data store objects 
    33""" 
    4 import hashlib # requires Python 2.5 
    5 import pickle 
     4import hashlib, pickle 
    65 
    76def hash_pickle(component): 

  • trunk/src/datastore/shelve_ds.py

    r213 r298  
    55from datastore.interface import AbstractDataStore 
    66from datastore.keygenerators import join_with_underscores 
    7 import os.path 
    8 import shelve 
     7import os.path, shelve 
     8 
    99 
    1010class ShelveDataStore(AbstractDataStore): 

  • trunk/src/facets/fkbtools.py

    r187 r298  
    44""" 
    55 
    6 try: 
     6from NeuroTools import check_dependency 
     7 
     8if check_dependency('PIL'): 
     9    import PIL 
     10 
     11if check_dependency('tables'): 
     12    import tables 
     13 
     14use_hdf5 = check_dependency('NeuroTools.facets.hdf5') 
     15if use_hdf5: 
    716    import NeuroTools.facets.hdf5.FileExtension as file_extension 
    817    import NeuroTools.facets.hdf5.Movie as movie 
    9     use_hdf5 = True 
    10 except ImportError: 
    11     print "Failed to load HDF5 tools" 
    12     use_hdf5 = False 
    13 import srblib 
    14  
    15 import os, sys 
    16 import zipfile 
    17 import PIL 
    18 import numpy 
    19 import tempfile 
    20 import shutil 
    21 import subprocess 
    22 import srblib 
    23 import tables 
    24 import logging 
    25 import time 
     18 
     19if check_dependency('srblib'): 
     20    import srblib 
     21 
     22import os, sys, zipfile, tempfile, shutil, subprocess, logging, time, numpy 
     23 
    2624 
    2725def getFromURL(url): 

  • trunk/src/facets/mixedutils.py

    r284 r298  
    55""" 
    66 
    7  
     7from NeuroTools import check_dependency 
    88 
    99def save_image(arr, filename): 
    …… 
    2525""" 
    2626 
    27 try: 
    28     from NeuroTools.facets import FileExtension as file_extension 
    29 except ImportError: 
    30     print "Warning: unable to import FileExtension" 
    31 try: 
    32     from NeuroTools.facets.fkbtools import png_to_hdf5, hdf5_to_png 
    33 except ImportError: 
    34     print "Warning: unable to import fkbtools" 
    35 import os 
    36 import sys 
     27if check_dependency('NeuroTools.facets.hdf5'): 
     28    from NeuroTools.facets.hdf5 import FileExtension as file_extension 
     29 
     30from NeuroTools.facets.fkbtools import png_to_hdf5, hdf5_to_png 
     31import os, sys 
     32 
    3733 
    3834def show(url): 

  • trunk/src/io.py

    r295 r298  
    1 from NeuroTools.__init__ import check_dependency 
    2  
    3 import os, logging, cPickle 
     1from NeuroTools import check_dependency 
     2 
     3import os, logging, cPickle, numpy 
    44DEFAULT_BUFFER_SIZE = 10000 
    5  
    6 if check_dependency('numpy'): 
    7     import numpy 
    8  
    95 
    106 

  • trunk/src/parameters.py

    r295 r298  
    77""" 
    88 
    9 import urllib, copy, warnings  # to be replaced with srblib 
     9import urllib, copy, warnings, numpy, numpy.random  # to be replaced with srblib 
    1010from urlparse import urlparse 
    11 from NeuroTools.__init__ import check_dependency 
     11from NeuroTools import check_dependency 
    1212from NeuroTools.random import ParameterDist, GammaDist, UniformDist, NormalDist 
    13  
    14 if check_dependency('numpy'): 
    15     import numpy 
    16     import numpy.random 
    1713 
    1814 

  • trunk/src/plotting.py

    r295 r298  
    77 
    88 
    9 import sys 
    10 from NeuroTools.__init__ import check_dependency 
     9import sys, numpy 
     10from NeuroTools import check_dependency 
    1111 
    1212 
    …… 
    1717    from matplotlib.lines import Line2D 
    1818    from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas 
    19  
    20  
    21 if check_dependency('numpy'): 
    22     import numpy 
    2319 
    2420# Check availability of PIL 

  • trunk/src/random.py

    r295 r298  
    11# Classes for specifiying a parameter by a statistical distribution 
    22 
    3 from NeuroTools.__init__ import check_dependency 
     3from NeuroTools import check_dependency 
    44 
    5 if check_dependency('numpy'): 
    6     import numpy 
    7     import numpy.random 
     5import numpy, numpy.random 
    86 
    97have_scipy = check_dependency('scipy') 

  • trunk/src/sandbox.py

    r127 r298  
    77 
    88""" 
    9 import copy,os,numpy 
     9import copy, os, numpy 
    1010from NeuroTools.parameters import ParameterSet 
    1111 

  • trunk/src/signals.py

    r295 r298  
    66 
    77import os, re 
    8 from NeuroTools.__init__ import check_dependency, check_numpy_version 
     8from NeuroTools import check_dependency, check_numpy_version 
    99from NeuroTools import analysis 
    1010from NeuroTools.io import * 
    …… 
    1515    psyco.full() 
    1616 
    17 if check_dependency('numpy'): 
    18     import numpy 
    19     newnum = check_numpy_version() 
     17import numpy 
     18newnum = check_numpy_version() 
    2019 
    2120ENABLE_PLOTS = check_dependency('pylab') 
    …… 
    2322    import pylab 
    2423else: 
    25     MATPLOTLIB_ERROR = "No pylab pacakge have been detected" 
     24    MATPLOTLIB_ERROR = "No pylab package have been detected" 
    2625 
    2726class SpikeTrain(object): 

  • trunk/src/stgen.py

    r295 r298  
    44# TODO make it generate spiketrains? 
    55 
    6 from NeuroTools.__init__ import check_dependency 
     6from NeuroTools import check_dependency 
    77 
    88have_gsl = check_dependency('pygsl') 
    …… 
    1010    import pygsl 
    1111 
    12 if check_dependency('numpy'): 
    13     from numpy import array, log 
    14     import numpy 
     12from numpy import array, log 
     13import numpy 
    1514 
    1615 

  • trunk/src/visual_logging.py

    r196 r298  
    55 
    66""" 
    7 import zipfile 
    8 import pylab 
     7import zipfile, atexit, os 
     8from NeuroTools import check_dependency 
    99from datetime import datetime 
    10 import atexit 
    11 import os 
    1210from logging import CRITICAL, DEBUG, ERROR, FATAL, INFO, WARN, WARNING, NOTSET 
    1311from time import sleep 
     12 
     13if check_dependency('pylab'): 
     14    import pylab 
    1415 
    1516_filename = 'visual_log.zip' 

  • trunk/test/test_signals.py

    r295 r298  
    55from NeuroTools import signals, io 
    66import numpy, unittest, os 
    7 from NeuroTools.__init__ import check_numpy_version 
     7from NeuroTools.__init__ import check_numpy_version, check_dependency 
    88newnum = check_numpy_version() 
    99 
    10 try : 
     10ENABLE_PLOTS = check_dependency('pylab') 
     11if ENABLE_PLOTS: 
    1112    import pylab 
    12     ENABLE_PLOTS     = True 
    13 except ImportError: 
    14     ENABLE_PLOTS     = False 
    15     MATPLOTLIB_ERROR = """ 
    16     Matplotlib not detected so plots are disabled.  
    17     To turn on plots, please install the Matplotlib package 
    18     """ 
    19     print MATPLOTLIB_ERROR 
     13 
    2014 
    2115def arrays_are_equal(a, b):