Source Code for Module dep_check

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2014 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, 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 float(numpy.version.version[:3]) < 1.6: 
 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  except ImportError: 
137      matplotlib_module = False 
138   
139  # runpy module. 
140  try: 
141      import runpy 
142      runpy_module = True 
143  except ImportError: 
144      runpy_module = False 
145   
146  # profile module (python development packages required). 
147  try: 
148      import profile 
149      profile_module = True 
150  except ImportError: 
151      profile_module = False 
152   
153  # profile C module (python development packages required). 
154  try: 
155      import cProfile 
156      cprofile_module = True 
157  except ImportError: 
158      cprofile_module = False 
159   
160  # BZ2 compression module. 
161  try: 
162      import bz2 
163      bz2_module = True 
164  except ImportError: 
165      message = sys.exc_info()[1] 
166      bz2_module = False 
167      bz2_module_message = message.args[0] 
168   
169  # Gzip compression module. 
170  try: 
171      import gzip 
172      gzip_module = True 
173  except ImportError: 
174      message = sys.exc_info()[1] 
175      gzip_module = False 
176      gzip_module_message = message.args[0] 
177   
178  # IO module. 
179  try: 
180      import io 
181      io_module = True 
182  except ImportError: 
183      message = sys.exc_info()[1] 
184      io_module = False 
185      io_module_message = message.args[0] 
186   
187  # Scipy import. 
188  try: 
189      import scipy 
190      scipy_module = True 
191  except: 
192      scipy_module = False 
193   
194  # VMD module imports. 
195  try: 
196      from Scientific.Visualization import VMD    # This requires Numeric to be installed (at least in Scientific 2.7.8). 
197      del VMD 
198      vmd_module = True 
199  except: 
200      vmd_module = False 
201   
202  # mpi4py. 
203  try: 
204      import mpi4py 
205      mpi4py_module = True 
206  except ImportError: 
207      message = sys.exc_info()[1] 
208      mpi4py_module = False 
209   
210      # The error message. 
211      mpi4py_message = """The dependency 'mpi4py' has not been installed. You should either: 
212   
213  1. Run without multiprocessor support i.e. remove the --multi mpi4py flag from the command line. 
214   
215  2. Install mpi4py. 
216   
217  3. Choose another multi processor method to give to the --multi command line flag.\n 
218      """ 
219    
220  # PyMOL. 
221  try: 
222      import pymol 
223      pymol_module = True 
224  except ImportError: 
225      message = sys.exc_info()[1] 
226      pymol_module = False 
227   
228  # XML. 
229  try: 
230      import xml 
231      xml_module = True 
232  except ImportError: 
233      message = sys.exc_info()[1] 
234      xml_module = False 
235  if xml_module: 
236      # The XML version mess! 
237      if hasattr(xml, '_MINIMUM_XMLPLUS_VERSION'): 
238          xml_version = "%s.%s.%s" % xml._MINIMUM_XMLPLUS_VERSION 
239          xml_type = 'internal' 
240      elif hasattr(xml, '__version__'): 
241          xml_version = xml.__version__ 
242          xml_type = 'PyXML' 
243      else: 
244          xml_version = '' 
245          xml_type = '' 
246   
247  # subprocess module. 
248  try: 
249      import subprocess 
250      subprocess_module = True 
251  except ImportError: 
252      message = sys.exc_info()[1] 
253      subprocess_module = False 
254      subprocess_module_message = message.args[0] 
255   
256  # NMRPipe showApod 
257  if subprocess_module: 
258      try: 
259          # Call function. 
260          Temp = subprocess.Popen('showApod', stdout=subprocess.PIPE) 
261   
262          # Communicate with program, and get output and error output. 
263          (output, errput) = Temp.communicate() 
264   
265          # Wait for finish and get return code. 
266          return_value = Temp.wait() 
267   
268          # Split the output into lines. 
269          line_split = output.splitlines() 
270   
271          # The first line, decoding Python 3 byte arrays. 
272          line = line_split[0] 
273          if hasattr(line, 'decode'): 
274              line = line.decode() 
275   
276          # Now make test. 
277          if line == 'showApod: Show Effect of Processing on Noise and Linewidth.': 
278              showApod_software = True 
279          else: 
280              showApod_software = False 
281   
282      # If software not available. 
283      except OSError: 
284          showApod_software = False 
285   
286  # If subprocess module not available, then do not allow showApod. 
287  else: 
288      showApod_software = False 
289   
290  # ctypes module. 
291  try: 
292      import ctypes 
293      ctypes_module = True 
294  except ImportError: 
295      message = sys.exc_info()[1] 
296      ctypes_module = False 
297      ctypes_module_message = message.args[0] 
298  try: 
299      from ctypes import Structure 
300      ctypes_structure_module = True 
301  except ImportError: 
302      message = sys.exc_info()[1] 
303      ctypes_structure_module = False 
304      ctypes_structure_module_message = message.args[0] 
305   
306   
307   
308   
309  # Compiled C modules. 
310  ##################### 
311   
312  # Relaxation curve fitting. 
313  try: 
314      from target_functions import relax_fit 
315      from target_functions.relax_fit import setup 
316      del setup 
317      C_module_exp_fn = True 
318  except ImportError: 
319      # The OS. 
320      system = platform.system() 
321   
322      # Does the compiled file exist. 
323      file = 'relax_fit.so' 
324      if system == 'Windows' or system == 'Microsoft': 
325          file = 'relax_fit.pyd' 
326      if not access('target_functions' + sep + file, F_OK): 
327          C_module_exp_fn_mesg = "ImportError: relaxation curve fitting is unavailable, the corresponding C modules have not been compiled." 
328   
329      # Show the full error. 
330      else: 
331          message = sys.exc_info()[1] 
332          C_module_exp_fn_mesg = "ImportError: " + repr(message) + "\nRelaxation curve fitting is unavailable, try compiling the C modules." 
333   
334      # Set the flag. 
335      C_module_exp_fn = False 
336