Author: bugman Date: Tue Dec 2 13:35:41 2014 New Revision: 26895 URL: http://svn.gna.org/viewcvs/relax?rev=26895&view=rev Log: Merged revisions 26874-26876,26885 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk ........ r26874 | bugman | 2014-11-30 11:10:41 +0100 (Sun, 30 Nov 2014) | 5 lines Updated the manual_c_module.py C module compilation development script for the recent changes. The exponential_inv.c and exponential_sat.c files need to be compiled as well. ........ r26875 | bugman | 2014-11-30 11:11:45 +0100 (Sun, 30 Nov 2014) | 5 lines Python 3 fix for the relax_fit_exp_3param_inv_neg.py system test script. The xrange() function does not exist in Python 3, so was replaced by range(). ........ r26876 | bugman | 2014-11-30 18:38:12 +0100 (Sun, 30 Nov 2014) | 5 lines Updated the memory_leak_test_relax_fit.py development script for the C module changes. This is only the docstring description which changed. ........ r26885 | bugman | 2014-12-01 20:18:24 +0100 (Mon, 01 Dec 2014) | 6 lines Epydoc docstring fixes for the lib.io module - keyword arguments were not correctly identified. These were identified by Troels in the post at http://thread.gmane.org/gmane.science.nmr.relax.scm/24565/focus=7384 ........ Modified: branches/frame_order_cleanup/ (props changed) branches/frame_order_cleanup/devel_scripts/manual_c_module.py branches/frame_order_cleanup/devel_scripts/memory_leak_test_relax_fit.py branches/frame_order_cleanup/lib/io.py branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py Propchange: branches/frame_order_cleanup/ ------------------------------------------------------------------------------ --- svnmerge-integrated (original) +++ svnmerge-integrated Tue Dec 2 13:35:41 2014 @@ -1 +1 @@ -/trunk:1-26871 +/trunk:1-26891 Modified: branches/frame_order_cleanup/devel_scripts/manual_c_module.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/manual_c_module.py?rev=26895&r1=26894&r2=26895&view=diff ============================================================================== --- branches/frame_order_cleanup/devel_scripts/manual_c_module.py (original) +++ branches/frame_order_cleanup/devel_scripts/manual_c_module.py Tue Dec 2 13:35:41 2014 @@ -25,8 +25,10 @@ # Python 3.2 installed in the home directory. cmd.append("gcc -o target_functions/c_chi2.os -c -I%s -fPIC target_functions/c_chi2.c" % include) cmd.append("gcc -o target_functions/exponential.os -c -I%s -fPIC target_functions/exponential.c" % include) +cmd.append("gcc -o target_functions/exponential_inv.os -c -I%s -fPIC target_functions/exponential_inv.c" % include) +cmd.append("gcc -o target_functions/exponential_sat.os -c -I%s -fPIC target_functions/exponential_sat.c" % include) cmd.append("gcc -o target_functions/relax_fit.os -c -I%s -fPIC target_functions/relax_fit.c" % include) -cmd.append("gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os target_functions/exponential.os target_functions/relax_fit.os") +cmd.append("gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os target_functions/exponential.os target_functions/exponential_inv.os target_functions/exponential_sat.os target_functions/relax_fit.os") # Execute the commands. Modified: branches/frame_order_cleanup/devel_scripts/memory_leak_test_relax_fit.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/memory_leak_test_relax_fit.py?rev=26895&r1=26894&r2=26895&view=diff ============================================================================== --- branches/frame_order_cleanup/devel_scripts/memory_leak_test_relax_fit.py (original) +++ branches/frame_order_cleanup/devel_scripts/memory_leak_test_relax_fit.py Tue Dec 2 13:35:41 2014 @@ -2,14 +2,16 @@ Run with a debugging compiled version of Python, eg: -/data/python/pydebug/bin/python relax relax_fit.py +/data/python/pydebug/bin/python relax devel_scripts/memory_leak_test_relax_fit.py and build the C module with: gcc -o target_functions/c_chi2.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/c_chi2.c gcc -o target_functions/exponential.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/exponential.c +gcc -o target_functions/exponential_inv.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/exponential_inv.c +gcc -o target_functions/exponential_sat.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/exponential_sat.c gcc -o target_functions/relax_fit.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/relax_fit.c -gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os target_functions/exponential.os target_functions/relax_fit.os +gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os target_functions/exponential.os target_functions/exponential_inv.os target_functions/exponential_sat.os target_functions/relax_fit.os """ Modified: branches/frame_order_cleanup/lib/io.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/io.py?rev=26895&r1=26894&r2=26895&view=diff ============================================================================== --- branches/frame_order_cleanup/lib/io.py (original) +++ branches/frame_order_cleanup/lib/io.py Tue Dec 2 13:35:41 2014 @@ -119,13 +119,13 @@ def extract_data(file=None, dir=None, file_data=None, sep=None): """Return all data in the file as a list of lines where each line is a list of line elements. - @param file: The file to extract the data from. + @keyword file: The file to extract the data from. @type file: str or file object - @param dir: The path where the file is located. If None and the file argument is a string, then the current directory is assumed. + @keyword dir: The path where the file is located. If None and the file argument is a string, then the current directory is assumed. @type dir: str or None - @param file_data: If the file data has already been extracted from the file, it can be passed into this function using this argument. If data is supplied here, then the file_name and dir args are ignored. + @keyword file_data: If the file data has already been extracted from the file, it can be passed into this function using this argument. If data is supplied here, then the file_name and dir args are ignored. @type file_data: list of str - @param sep: The character separating the columns in the file data. If None, then whitespace is assumed. + @keyword sep: The character separating the columns in the file data. If None, then whitespace is assumed. @type sep: str @return: The file data. @rtype: list of lists of str @@ -178,9 +178,9 @@ def get_file_path(file_name=None, dir=None): """Generate and expand the full file path. - @param file_name: The name of the file to extract the data from. + @keyword file_name: The name of the file to extract the data from. @type file_name: str - @param dir: The path where the file is located. If None, then the current directory is assumed. + @keyword dir: The path where the file is located. If None, then the current directory is assumed. @type dir: str @return: The full file path. @rtype: str @@ -204,7 +204,7 @@ def io_streams_restore(verbosity=1): """Restore all IO streams to the Python defaults. - @param verbosity: The verbosity level. + @keyword verbosity: The verbosity level. @type verbosity: int """ @@ -223,11 +223,11 @@ def io_streams_log(file_name=None, dir=None, verbosity=1): """Turn on logging, sending both STDOUT and STDERR streams to a file. - @param file_name: The name of the file. + @keyword file_name: The name of the file. @type file_name: str - @param dir: The path where the file is located. If None, then the current directory is assumed. + @keyword dir: The path where the file is located. If None, then the current directory is assumed. @type dir: str - @param verbosity: The verbosity level. + @keyword verbosity: The verbosity level. @type verbosity: int """ @@ -258,13 +258,13 @@ def io_streams_tee(file_name=None, dir=None, compress_type=0, verbosity=1): """Turn on teeing to split both STDOUT and STDERR streams and sending second part to a file. - @param file_name: The name of the file. + @keyword file_name: The name of the file. @type file_name: str - @param dir: The path where the file is located. If None, then the current directory is assumed. + @keyword dir: The path where the file is located. If None, then the current directory is assumed. @type dir: str - @param compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression. + @keyword compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression. @type compress_type: int - @param verbosity: The verbosity level. + @keyword verbosity: The verbosity level. @type verbosity: int """ @@ -295,9 +295,9 @@ def mkdir_nofail(dir=None, verbosity=1): """Create the given directory, or exit without raising an error if the directory exists. - @param dir: The directory to create. + @keyword dir: The directory to create. @type dir: str - @param verbosity: The verbosity level. + @keyword verbosity: The verbosity level. @type verbosity: int """ @@ -319,11 +319,11 @@ def open_read_file(file_name=None, dir=None, verbosity=1): """Open the file 'file' and return all the data. - @param file_name: The name of the file to extract the data from. + @keyword file_name: The name of the file to extract the data from. @type file_name: str - @param dir: The path where the file is located. If None, then the current directory is assumed. + @keyword dir: The path where the file is located. If None, then the current directory is assumed. @type dir: str - @param verbosity: The verbosity level. + @keyword verbosity: The verbosity level. @type verbosity: int @return: The open file object. @rtype: file object @@ -374,17 +374,17 @@ def open_write_file(file_name=None, dir=None, force=False, compress_type=0, verbosity=1, return_path=False): """Function for opening a file for writing and creating directories if necessary. - @param file_name: The name of the file to extract the data from. + @keyword file_name: The name of the file to extract the data from. @type file_name: str - @param dir: The path where the file is located. If None, then the current directory is assumed. + @keyword dir: The path where the file is located. If None, then the current directory is assumed. @type dir: str - @param force: Boolean argument which if True causes the file to be overwritten if it already exists. + @keyword force: Boolean argument which if True causes the file to be overwritten if it already exists. @type force: bool - @param compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression. If no compression is given but the file name ends in '.gz' or '.bz2', then the compression will be automatically set. + @keyword compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression. If no compression is given but the file name ends in '.gz' or '.bz2', then the compression will be automatically set. @type compress_type: int - @param verbosity: The verbosity level. + @keyword verbosity: The verbosity level. @type verbosity: int - @param return_path: If True, the function will return a tuple of the file object and the full file path. + @keyword return_path: If True, the function will return a tuple of the file object and the full file path. @type return_path: bool @return: The open, writable file object and, if the return_path is True, then the full file path is returned as well. @rtype: writable file object (if return_path, then a tuple of the writable file and the full file path) Modified: branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py?rev=26895&r1=26894&r2=26895&view=diff ============================================================================== --- branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py (original) +++ branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py Tue Dec 2 13:35:41 2014 @@ -55,7 +55,7 @@ # Load the data twice to test data deletion. for iter in range(2): # Loop over the spectra. - for i in xrange(len(names)): + for i in range(len(names)): # Load the peak intensities. spectrum.read_intensities(file=names[i]+'.list', dir=data_path, spectrum_id=names[i], int_method=ds.int_type)