Source Code for Module dep_check

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2015 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
 18  # You should have received a copy of the GNU General Public License           # 
 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module for checking relax dependencies. 
 25   
 26  If essential dependencies are missing, then an error message is printed and the program terminated. 
 27  """ 
 28   
 29  # Python modules. 
 30  import platform 
 31  from os import F_OK, access, environ, sep 
 32  from re import sub 
 33  import sys 
 34   
 35   
 36 -def version_comparison(version1, version2): 
 37      """Compare software versions. 
 38   
 39      This will return: 
 40   
 41          - When version 1 is older, -1, 
 42          - When both versions are equal, 0, 
 43          - When version 1 is newer, 1. 
 44   
 45   
 46      @param version1:    The first version number. 
 47      @type version1:     str 
 48      @param version2:    The second version number. 
 49      @type version2:     str 
 50      @return:            The comparison result of the Python cmp() function applied to two lists of integers.  This will be one of [-1, 0, 1]. 
 51      @rtype:             int 
 52      """ 
 53   
 54      # Strip out trailing zeros. 
 55      version1 = sub(r'(\.0+)*$', '', version1) 
 56      version2 = sub(r'(\.0+)*$', '', version2) 
 57   
 58      # Convert to a list of numbers. 
 59      version1 = [int(val) for val in version1.split('.')] 
 60      version2 = [int(val) for val in version2.split('.')] 
 61   
 62      # Return the comparison. 
 63      return (version1 > version2) - (version1 < version2) 
 64   
 65   
 66  # Essential packages. 
 67  ##################### 
 68   
 69  # numpy. 
 70  try: 
 71      import numpy 
 72      if version_comparison(numpy.version.version, '1.6') == -1: 
 73          sys.stderr.write("Version %s of the 'numpy' dependency is not supported, numpy >= 1.6 is required.\n" % numpy.version.version) 
 74          sys.exit() 
 75  except ImportError: 
 76      sys.stderr.write("The dependency 'numpy' has not been installed.\n") 
 77      sys.exit() 
 78   
 79  # Command line option parser. 
 80  try: 
 81      import optparse 
 82  except ImportError: 
 83      sys.stderr.write("The dependency 'Optik' has not been installed.\n") 
 84      sys.exit() 
 85   
 86  # Minfx python package check. 
 87  try: 
 88      import minfx 
 89      min_version = '1.0.11' 
 90      if not minfx.__version__ == 'trunk' and version_comparison(minfx.__version__, min_version) == -1: 
 91          sys.stderr.write("Version %s of the 'minfx' dependency is too old, minfx >= %s is required.\n" % (minfx.__version__, min_version)) 
 92          sys.exit() 
 93  except ImportError: 
 94      sys.stderr.write("The dependency 'minfx' has not been installed (see https://sourceforge.net/projects/minfx/).\n") 
 95      sys.exit() 
 96   
 97  # Optional packages. 
 98  #################### 
 99  # Bmrblib python package check. 
100  try: 
101      import bmrblib 
102      bmrblib_module = True 
103  except ImportError: 
104      bmrblib_module = False 
105   
106  # wx module. 
107  try: 
108      import wx 
109      wx_module = True 
110  except ImportError: 
111      wx_module = False 
112      message = sys.exc_info()[1] 
113      wx_module_message = message.args[0] 
114   
115  # epydoc module. 
116  try: 
117      import epydoc 
118      epydoc_module = True 
119  except ImportError: 
120      epydoc_module = False 
121   
122  # Readline module (avoiding the damned ^[[?1034h escape code on Linux systems). 
123  try: 
124      import os 
125      if 'TERM' in os.environ and os.environ['TERM'] == 'xterm': 
126          os.environ['TERM'] = 'linux' 
127      import readline 
128      readline_module = True 
129  except ImportError: 
130      readline_module = False 
131   
132  # matplotlib module. 
133  try: 
134      import matplotlib 
135      matplotlib_module = True 
136      if not "DISPLAY" in environ: 
137          # Force matplotlib to not use any Xwindows backend. 
138          matplotlib.use('Agg') 
139  except ImportError: 
140      matplotlib_module = False 
141   
142  # runpy module. 
143  try: 
144      import runpy 
145      runpy_module = True 
146  except ImportError: 
147      runpy_module = False 
148   
149  # profile module (python development packages required). 
150  try: 
151      import profile 
152      profile_module = True 
153  except ImportError: 
154      profile_module = False 
155   
156  # profile C module (python development packages required). 
157  try: 
158      import cProfile 
159      cprofile_module = True 
160  except ImportError: 
161      cprofile_module = False 
162   
163  # BZ2 compression module. 
164  try: 
165      import bz2 
166      bz2_module = True 
167  except ImportError: 
168      message = sys.exc_info()[1] 
169      bz2_module = False 
170      bz2_module_message = message.args[0] 
171   
172  # Gzip compression module. 
173  try: 
174      import gzip 
175      gzip_module = True 
176  except ImportError: 
177      message = sys.exc_info()[1] 
178      gzip_module = False 
179      gzip_module_message = message.args[0] 
180   
181  # IO module. 
182  try: 
183      import io 
184      io_module = True 
185  except ImportError: 
186      message = sys.exc_info()[1] 
187      io_module = False 
188      io_module_message = message.args[0] 
189   
190  # Scipy import. 
191  try: 
192      import scipy 
193      scipy_module = True 
194  except: 
195      scipy_module = False 
196   
197  # VMD module imports. 
198  try: 
199      from Scientific.Visualization import VMD    # This requires Numeric to be installed (at least in Scientific 2.7.8). 
200      del VMD 
201      vmd_module = True 
202  except: 
203      vmd_module = False 
204   
205  # mpi4py. 
206  try: 
207      import mpi4py 
208      mpi4py_module = True 
209  except ImportError: 
210      message = sys.exc_info()[1] 
211      mpi4py_module = False 
212   
213      # The error message. 
214      mpi4py_message = """The dependency 'mpi4py' has not been installed. You should either: 
215   
216  1. Run without multiprocessor support i.e. remove the --multi mpi4py flag from the command line. 
217   
218  2. Install mpi4py. 
219   
220  3. Choose another multi processor method to give to the --multi command line flag.\n 
221      """ 
222    
223  # PyMOL. 
224  try: 
225      import pymol 
226      pymol_module = True 
227  except ImportError: 
228      message = sys.exc_info()[1] 
229      pymol_module = False 
230   
231  # XML. 
232  try: 
233      import xml 
234      xml_module = True 
235  except ImportError: 
236      message = sys.exc_info()[1] 
237      xml_module = False 
238  if xml_module: 
239      # The XML version mess! 
240      if hasattr(xml, '_MINIMUM_XMLPLUS_VERSION'): 
241          xml_version = "%s.%s.%s" % xml._MINIMUM_XMLPLUS_VERSION 
242          xml_type = 'internal' 
243      elif hasattr(xml, '__version__'): 
244          xml_version = xml.__version__ 
245          xml_type = 'PyXML' 
246      else: 
247          xml_version = '' 
248          xml_type = '' 
249   
250  # subprocess module. 
251  try: 
252      import subprocess 
253      subprocess_module = True 
254  except ImportError: 
255      message = sys.exc_info()[1] 
256      subprocess_module = False 
257      subprocess_module_message = message.args[0] 
258   
259  # NMRPipe showApod 
260  if subprocess_module: 
261      try: 
262          # Call function. 
263          Temp = subprocess.Popen('showApod', stdout=subprocess.PIPE) 
264   
265          # Communicate with program, and get output and error output. 
266          (output, errput) = Temp.communicate() 
267   
268          # Wait for finish and get return code. 
269          return_value = Temp.wait() 
270   
271          # Split the output into lines. 
272          line_split = output.splitlines() 
273   
274          # The first line, decoding Python 3 byte arrays. 
275          line = line_split[0] 
276          if hasattr(line, 'decode'): 
277              line = line.decode() 
278   
279          # Now make test. 
280          if line == 'showApod: Show Effect of Processing on Noise and Linewidth.': 
281              showApod_software = True 
282          else: 
283              showApod_software = False 
284   
285      # If software not available. 
286      except OSError: 
287          showApod_software = False 
288   
289  # If subprocess module not available, then do not allow showApod. 
290  else: 
291      showApod_software = False 
292   
293  # ctypes module. 
294  try: 
295      import ctypes 
296      ctypes_module = True 
297  except ImportError: 
298      message = sys.exc_info()[1] 
299      ctypes_module = False 
300      ctypes_module_message = message.args[0] 
301  try: 
302      from ctypes import Structure 
303      ctypes_structure_module = True 
304  except ImportError: 
305      message = sys.exc_info()[1] 
306      ctypes_structure_module = False 
307      ctypes_structure_module_message = message.args[0] 
308   
309   
310   
311   
312  # Compiled C modules. 
313  ##################### 
314   
315  # Relaxation curve fitting. 
316  try: 
317      from target_functions import relax_fit 
318      from target_functions.relax_fit import setup 
319      del setup 
320      C_module_exp_fn = True 
321  except ImportError: 
322      # The OS. 
323      system = platform.system() 
324   
325      # Does the compiled file exist. 
326      file = 'relax_fit.so' 
327      if system == 'Windows' or system == 'Microsoft': 
328          file = 'relax_fit.pyd' 
329      if not access('target_functions' + sep + file, F_OK): 
330          C_module_exp_fn_mesg = "ImportError: relaxation curve fitting is unavailable, the corresponding C modules have not been compiled." 
331   
332      # Show the full error. 
333      else: 
334          message = sys.exc_info()[1] 
335          C_module_exp_fn_mesg = "ImportError: " + repr(message) + "\nRelaxation curve fitting is unavailable, try compiling the C modules." 
336   
337      # Set the flag. 
338      C_module_exp_fn = False 
339