Corr extinction

config.py

@@ -5,30 +5,30 @@
 Usage: $ python config.py compile
 """
 
-import os
-import collections
-import ast
+#-- Make sure the script doesn't confuse the IvS io module with the standard
+#   Python io module.
 import sys
+sys.path = sys.path[1:]
+import os
 import glob as glob_module
 
 #-- You can add directories here, but be sure that the relative paths within
 #   those directories are correct!
-data_dirs = [os.getenv('ivsdata'),'/STER/pieterd/IVSDATA/', '/STER/kristofs/IVSdata','/STER/jorisv/IVSDATA/', 
-             '/STER/kenneth/Python_repository/','/home/ben/public_html/opacities','/STER/michelh/IVSDATA/']
-
+data_dirs = [os.getenv('ivsdata'),'/STER/jorisv/IVSDATA/',
+             '/STER/kenneth/Python_repository/','/STER/michelh/IVSDATA/',
+             os.path.join(os.path.expanduser('~'),'ComboCode','aux','ivsdata')]
+
 ivs_dirs = dict(coralie='/STER/coralie/',
                 hermes='/STER/mercator/hermes/')
-
-
 
 def get_datafile(relative_path,basename):
     """
     Reconstruct the location of a data file and check whether it exists.
-    
+
     If the file exists, it will return the absolute path of the filename.
-    
+
     If the file does not exist, it will raise an IOError.
-    
+
     @param relative_path: relative path starting from main data directory tree
     @type relative_path: str
     @param basename: filename
@@ -38,16 +38,16 @@ def get_datafile(relative_path,basename):
     """
     for data_dir in data_dirs:
         if data_dir is None: continue
-        
+
         filename = os.path.join(data_dir,relative_path,basename)
-        
+
         if os.path.isfile(filename):
             break
     else:
         str_data_dirs = ", ".join([idir for idir in data_dirs if idir is not None])
         relative_file = os.path.join(relative_path,basename)
         raise IOError, "File %s not found in any of the specified data directories %s"%(relative_file,str_data_dirs)
-    
+
     return filename
 
 
@@ -56,7 +56,7 @@ def get_datafile(relative_path,basename):
 def glob(relative_path,arg='*'):
     """
     Glob the files in a relative path.
-    
+
     @param relative_path: relative path starting from main data directory tree
     @type relative_path: str
     @param arg: argument to use in glob
@@ -70,17 +70,15 @@ def glob(relative_path,arg='*'):
         files += glob_module.glob(os.path.join(data_dir,relative_path,arg))
     files.sort()
     return files
-
 
 
 
-if __name__=="__main__":    
+
+if __name__=="__main__":
     import subprocess
     from ivs.aux import loggers
     import shutil
-    import time
     logger = loggers.get_basic_logger()
-
     to_install = ['spectra/pyrotin4',
                   'timeseries/deeming','timeseries/eebls','timeseries/multih',
                   'timeseries/pyclean','timeseries/pyKEP','timeseries/pyscargle',

readme.txt

@@ -10,12 +10,30 @@
     $ cd ivs
     $ git pull
 
+* Make sure that your python path points to the ivs folder, so that you can simply import
+using, for example:
+
+    >>> from ivs.statistics import linearregression
+
+  If your python repository is in, e.g., ~/python/ivs/ , you can put in your .bash_profile:
+
+    export PYTHONPATH=/home/YOURNAME/python:$PYTHONPATH
+
+  Warning: don't put ~/python/ivs in your Python path, but just ~/python.
+
+* For the next part of the installation, temporarily move the io folder elsewhere, e.g.
+
+    $ cd ivs
+    $ mv io io_backup
+
+* In the config.py file in the ivs folder, add the path where the IvS data catalogs (variable: data_dir) can be found. 
+
 * The IvS Python repository contains mostly python routines. Some of the time-critical
-functions, however, are written in fortran. To compile them you can run
+functions, however, are written in fortran. This assumes you have gfortran installed on your system. To compile them you can run
 
     $ python config.py compile
 
-If you want to specify your own fortran compiler you can do so with
+Alternatively, if you want to specify your own fortran compiler you can do so with
 
     $ python config.py compile f77
 
@@ -26,21 +44,12 @@ Note: sometimes the compilation process fails. If so, try to compile spectra/pyr
     $ cd ../
     $ python config.py compile
 
-* In the config file you may also change the paths where the data catalogs (variable: data_dir) can be found, if you are not using the default locations. 
-
-* Make sure that your python path points to the ivs folder, so that you can simply import
-using, for example:
-
-    >>> from ivs.statistics import linearregression
-
-  If your python repository is in, e.g., ~/python/ivs/ , you can put in your .bash_profile:
-
-    export PYTHONPATH=/home/YOURNAME/python:$PYTHONPATH
-
-Warning: don't put ~/python/ivs in your Python path, but just ~/python.
+* With the installation finished, move the io folder back:
 
+    $ cd ivs
+    $ mv io_backup io
 
-* To generate the documentation, simply run the script
+* To generate the documentation (which, as a user, you typically do not have to do), simply run the script
 
     $ python makedoc.py
 
@@ -66,3 +75,6 @@ Encountered errors and their solutions:
 numpy.distutils.fcompiler.CompilerNotFound: gnu95: f90 nor f77
 A: Install gfortran.
 
+2. Q: When I run "python config.py compile", I get the following error: 
+/bin/sh: f2py: command not found
+A: Install f2py. If you do have f2py installed, but under a different name for the executable (for instance, f2py-2.7), replace f2py with f2py-2.7 in config.py (search for cmd = ).