Source Code for Module lib.warnings

  1  from __future__ import absolute_import 
  2  ############################################################################### 
  3  #                                                                             # 
  4  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
  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 containing all of the RelaxWarning objects.""" 
 25   
 26  # Python module imports. 
 27  import inspect 
 28  import warnings 
 29   
 30  # relax module imports. 
 31  from lib import ansi 
 32  from status import Status; status = Status() 
 33   
 34   
 35  # The warning formatting function. 
 36 -def format(message, category, filename, lineno, line=None): 
 37      """ Replacement for warnings.formatwarning to customise output format.""" 
 38   
 39      # Add the text 'RelaxWarning: ' to the start of the warning message. 
 40      message = "RelaxWarning: %s\n" % message 
 41   
 42      # Print stack-trace in pedantic mode. 
 43      if status.pedantic: 
 44          tb = "" 
 45          for frame in inspect.stack()[4:]: 
 46              file = frame[1] 
 47              lineNo = frame[2] 
 48              func = frame[3] 
 49              tb_frame = '  File "%s", line %i, in %s\n' % (file, lineNo, func) 
 50              try: 
 51                  context = frame[4][frame[5]] 
 52              except TypeError: 
 53                  pass 
 54              else: 
 55                  tb_frame = '%s    %s\n' % (tb_frame, context.strip()) 
 56              tb = tb_frame + tb 
 57          tb = "Traceback (most recent call last):\n%s" % tb 
 58          message = tb + message 
 59   
 60      # Text colouring 
 61      if ansi.enable_control_chars(stream=2): 
 62          # Strip the last newline, if it exists. 
 63          if message[-1] == '\n': 
 64              message = message[:-1] 
 65   
 66          # Reformat. 
 67          message = "%s%s%s\n" % (ansi.relax_warning, message, ansi.end) 
 68   
 69      # Return the warning message. 
 70      return message 
 71   
 72   
 73 -def setup(): 
 74      """Set up the warning system.""" 
 75   
 76      # Format warning messages. 
 77      warnings.formatwarning = format 
 78   
 79      # Set warning filters. 
 80      if status.pedantic: 
 81          warnings.filterwarnings('error', category=BaseWarning) 
 82      else: 
 83          warnings.filterwarnings('always', category=BaseWarning) 
 84   
 85   
 86   
 87  # Base class for all warnings. 
 88  ############################## 
 89   
 90 -class BaseWarning(Warning): 
 91 -    def __str__(self): 
 92          return str(self.text) 
 93   
 94   
 95  # Standard warnings. 
 96  #################### 
 97   
 98 -class RelaxWarning(BaseWarning): 
 99 -    def __init__(self, text): 
100          self.text = text 
101   
102   
103  # Sequence errors. 
104  ################## 
105   
106  # Cannot find the spin in the sequence. 
107 -class RelaxNoSpinWarning(BaseWarning): 
108 -    def __init__(self, spin_id): 
109          self.text = "Cannot find the spin %s within the sequence." % spin_id 
110   
111   
112  # PDB warnings. 
113  ############### 
114   
115  # Zero length interactomic vector. 
116 -class RelaxZeroVectorWarning(BaseWarning): 
117 -    def __init__(self, spin_id1, spin_id2): 
118          self.text = "The interatomic vector between the spins '%s' and '%s' is of zero length." % (spin_id1, spin_id2) 
119   
120   
121  # The atom is missing from the PDB file. 
122 -class RelaxNoAtomWarning(BaseWarning): 
123 -    def __init__(self, atom, res): 
124          self.text = "The atom %s could not be found for residue %i" % (atom, res) 
125   
126   
127  # The PDB file is missing. 
128 -class RelaxNoPDBFileWarning(BaseWarning): 
129 -    def __init__(self, file): 
130          self.text = "The PDB file %s cannot be found, no structures will be loaded." % file 
131   
132   
133  # Nuclear warnings. 
134  ################### 
135   
136  # Nucleus not set. 
137 -class RelaxNucleusWarning(BaseWarning): 
138 -    def __init__(self, spin_id=None): 
139          if spin_id != None: 
140              self.text = "The type of nucleus for the spin '%s' has not yet been set." % spin_id 
141          else: 
142              self.text = "The type of nucleus has not yet been set." 
143   
144  # Spin type not set. 
145 -class RelaxSpinTypeWarning(BaseWarning): 
146 -    def __init__(self, spin_id=None): 
147          if spin_id != None: 
148              self.text = "The nuclear isotope type for the spin '%s' has not yet been set.  Please use the spin.isotope user function to set the type." % spin_id 
149          else: 
150              self.text = "The nuclear isotope type has not yet been set.  Please use the spin.isotope user function to set the type." 
151   
152  # File warnings. 
153  ################ 
154   
155  # No data in file. 
156 -class RelaxFileEmptyWarning(BaseWarning): 
157 -    def __init__(self, file): 
158          self.text = "The file '%s' contains no data." % file 
159   
160   
161  # Misc. 
162  ####### 
163   
164  # Deselection warnings 
165 -class RelaxDeselectWarning(BaseWarning): 
166 -    def __init__(self, spin_id, reason): 
167          self.text = "The spin '%s' has been deselected because of %s." % (spin_id, reason) 
168