Source Code for Module dep_check

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2010,2012,2014 Edward d'Auvergne                         # 
  4  # Copyright (C) 2009 Sebastien Morin                                          # 
  5  # Copyright (C) 2014 Troels E. Linnet                                         # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """Module for checking relax dependencies. 
 26   
 27  If essential dependencies are missing, then an error message is printed and the program terminated. 
 28  """ 
 29   
 30  # Python modules. 
 31  import platform 
 32  from os import F_OK, access, environ, sep 
 33  from re import sub 
 34  import sys 
 35   
 36   
 37 -def version_comparison(version1, version2): 
 38      """Compare software versions. 
 39   
 40      This will return: 
 41   
 42          - When version 1 is older, -1, 
 43          - When both versions are equal, 0, 
 44          - When version 1 is newer, 1. 
 45   
 46   
 47      @param version1:    The first version number. 
 48      @type version1:     str 
 49      @param version2:    The second version number. 
 50      @type version2:     str 
 51      @return:            The comparison result of the Python cmp() function applied to two lists of integers.  This will be one of [-1, 0, 1]. 
 52      @rtype:             int 
 53      """ 
 54   
 55      # Strip out trailing after release candidate. 
 56      version1 = sub(r'(rc\d)', '', version1) 
 57      version2 = sub(r'(rc\d)', '', version2) 
 58   
 59      # Strip out trailing zeros. 
 60      version1 = sub(r'(\.0+)*$', '', version1) 
 61      version2 = sub(r'(\.0+)*$', '', version2) 
 62   
 63      # Convert to a list of numbers. 
 64      version1 = [int(val) for val in version1.split('.')] 
 65      version2 = [int(val) for val in version2.split('.')] 
 66   
 67      # Return the comparison. 
 68      return (version1 > version2) - (version1 < version2) 
 69   
 70   
 71  # Essential packages. 
 72  ##################### 
 73   
 74  # numpy. 
 75  try: 
 76      import numpy 
 77      if version_comparison(numpy.version.version, '1.6') == -1: 
 78          sys.stderr.write("Version %s of the 'numpy' dependency is not supported, numpy >= 1.6 is required.\n" % numpy.version.version) 
 79          sys.exit(1) 
 80  except ImportError: 
 81      sys.stderr.write("The dependency 'numpy' has not been installed.\n") 
 82      sys.exit(1) 
 83   
 84  # Command line option parser. 
 85  try: 
 86      import optparse 
 87  except ImportError: 
 88      sys.stderr.write("The dependency 'Optik' has not been installed.\n") 
 89      sys.exit(1) 
 90   
 91  # Minfx python package check. 
 92  try: 
 93      import minfx 
 94      min_version = '1.0.11' 
 95      if not minfx.__version__ == 'trunk' and version_comparison(minfx.__version__, min_version) == -1: 
 96          sys.stderr.write("Version %s of the 'minfx' dependency is too old, minfx >= %s is required.\n" % (minfx.__version__, min_version)) 
 97          sys.exit(1) 
 98  except ImportError: 
 99      sys.stderr.write("The dependency 'minfx' has not been installed (see https://sourceforge.net/projects/minfx/).\n") 
100      sys.exit(1) 
101   
102  # Optional packages. 
103  #################### 
104  # Bmrblib python package check. 
105  try: 
106      import bmrblib 
107      bmrblib_module = True 
108  except ImportError: 
109      bmrblib_module = False 
110   
111  # wx module. 
112  try: 
113      import wx 
114      wx_module = True 
115  except ImportError: 
116      wx_module = False 
117      message = sys.exc_info()[1] 
118      wx_module_message = message.args[0] 
119   
120  # epydoc module. 
121  try: 
122      import epydoc 
123      epydoc_module = True 
124  except ImportError: 
125      epydoc_module = False 
126   
127  # Readline module (avoiding the damned ^[[?1034h escape code on Linux systems). 
128  try: 
129      import os 
130      if 'TERM' in os.environ and os.environ['TERM'] == 'xterm': 
131          os.environ['TERM'] = 'linux' 
132      import readline 
133      readline_module = True 
134  except ImportError: 
135      readline_module = False 
136   
137  # matplotlib module. 
138  try: 
139      import matplotlib 
140      matplotlib_module = True 
141      if not "DISPLAY" in environ: 
142          # Force matplotlib to not use any Xwindows backend. 
143          matplotlib.use('Agg') 
144  except ImportError: 
145      matplotlib_module = False 
146   
147  # runpy module. 
148  try: 
149      import runpy 
150      runpy_module = True 
151  except ImportError: 
152      runpy_module = False 
153   
154  # profile module (python development packages required). 
155  try: 
156      import profile 
157      profile_module = True 
158  except ImportError: 
159      profile_module = False 
160   
161  # profile C module (python development packages required). 
162  try: 
163      import cProfile 
164      cprofile_module = True 
165  except ImportError: 
166      cprofile_module = False 
167   
168  # BZ2 compression module. 
169  try: 
170      import bz2 
171      bz2_module = True 
172  except ImportError: 
173      message = sys.exc_info()[1] 
174      bz2_module = False 
175      bz2_module_message = message.args[0] 
176   
177  # Gzip compression module. 
178  try: 
179      import gzip 
180      gzip_module = True 
181  except ImportError: 
182      message = sys.exc_info()[1] 
183      gzip_module = False 
184      gzip_module_message = message.args[0] 
185   
186  # IO module. 
187  try: 
188      import io 
189      io_module = True 
190  except ImportError: 
191      message = sys.exc_info()[1] 
192      io_module = False 
193      io_module_message = message.args[0] 
194   
195  # Scipy import. 
196  try: 
197      import scipy 
198      scipy_module = True 
199  except: 
200      scipy_module = False 
201   
202  # VMD module imports. 
203  try: 
204      from Scientific.Visualization import VMD    # This requires Numeric to be installed (at least in Scientific 2.7.8). 
205      del VMD 
206      vmd_module = True 
207  except: 
208      vmd_module = False 
209   
210  # mpi4py. 
211  try: 
212      import mpi4py 
213      mpi4py_module = True 
214  except ImportError: 
215      message = sys.exc_info()[1] 
216      mpi4py_module = False 
217   
218      # The error message. 
219      mpi4py_message = """The dependency 'mpi4py' has not been installed. You should either: 
220   
221  1. Run without multiprocessor support i.e. remove the --multi mpi4py flag from the command line. 
222   
223  2. Install mpi4py. 
224   
225  3. Choose another multi processor method to give to the --multi command line flag.\n 
226      """ 
227   
228  # PyMOL. 
229  try: 
230      import pymol 
231      pymol_module = True 
232  except ImportError: 
233      message = sys.exc_info()[1] 
234      pymol_module = False 
235   
236  # XML. 
237  try: 
238      import xml 
239      xml_module = True 
240  except ImportError: 
241      message = sys.exc_info()[1] 
242      xml_module = False 
243  if xml_module: 
244      # The XML version mess! 
245      if hasattr(xml, '_MINIMUM_XMLPLUS_VERSION'): 
246          xml_version = "%s.%s.%s" % xml._MINIMUM_XMLPLUS_VERSION 
247          xml_type = 'internal' 
248      elif hasattr(xml, '__version__'): 
249          xml_version = xml.__version__ 
250          xml_type = 'PyXML' 
251      else: 
252          xml_version = '' 
253          xml_type = '' 
254   
255  # subprocess module. 
256  try: 
257      import subprocess 
258      subprocess_module = True 
259  except ImportError: 
260      message = sys.exc_info()[1] 
261      subprocess_module = False 
262      subprocess_module_message = message.args[0] 
263   
264  # NMRPipe showApod 
265  if subprocess_module: 
266      try: 
267          # Call function. 
268          Temp = subprocess.Popen('showApod', stdout=subprocess.PIPE) 
269   
270          # Communicate with program, and get output and error output. 
271          (output, errput) = Temp.communicate() 
272   
273          # Wait for finish and get return code. 
274          return_value = Temp.wait() 
275   
276          # Split the output into lines. 
277          line_split = output.splitlines() 
278   
279          # The first line, decoding Python 3 byte arrays. 
280          line = line_split[0] 
281          if hasattr(line, 'decode'): 
282              line = line.decode() 
283   
284          # Now make test. 
285          if line == 'showApod: Show Effect of Processing on Noise and Linewidth.': 
286              showApod_software = True 
287          else: 
288              showApod_software = False 
289   
290      # If software not available. 
291      except OSError: 
292          showApod_software = False 
293   
294  # If subprocess module not available, then do not allow showApod. 
295  else: 
296      showApod_software = False 
297   
298  # ctypes module. 
299  try: 
300      import ctypes 
301      ctypes_module = True 
302  except ImportError: 
303      message = sys.exc_info()[1] 
304      ctypes_module = False 
305      ctypes_module_message = message.args[0] 
306  try: 
307      from ctypes import Structure 
308      ctypes_structure_module = True 
309  except ImportError: 
310      message = sys.exc_info()[1] 
311      ctypes_structure_module = False 
312      ctypes_structure_module_message = message.args[0] 
313   
314   
315   
316   
317  # Compiled C modules. 
318  ##################### 
319   
320  # Relaxation curve fitting. 
321  try: 
322      from target_functions import relax_fit 
323      from target_functions.relax_fit import setup 
324      del setup 
325      C_module_exp_fn = True 
326  except ImportError: 
327      # The OS. 
328      system = platform.system() 
329   
330      # Does the compiled file exist. 
331      file = 'relax_fit.so' 
332      if system == 'Windows' or system == 'Microsoft': 
333          file = 'relax_fit.pyd' 
334      if not access('target_functions' + sep + file, F_OK): 
335          C_module_exp_fn_mesg = "ImportError: relaxation curve fitting is unavailable, the corresponding C modules have not been compiled." 
336   
337      # Show the full error. 
338      else: 
339          message = sys.exc_info()[1] 
340          C_module_exp_fn_mesg = "ImportError: " + repr(message) + "\nRelaxation curve fitting is unavailable, try compiling the C modules." 
341   
342      # Set the flag. 
343      C_module_exp_fn = False 
344