Author: bugman
Date: Tue Dec 2 21:54:35 2014
New Revision: 26904
URL: http://svn.gna.org/viewcvs/relax?rev=26904&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/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/devel_scripts/manual_c_module.py
branches/space_mapping_refactor/devel_scripts/memory_leak_test_relax_fit.py
branches/space_mapping_refactor/lib/io.py
branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
Propchange: branches/space_mapping_refactor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Dec 2 21:54:35 2014
@@ -1 +1 @@
-/trunk:1-26871
+/trunk:1-26871,26874-26885
Modified: branches/space_mapping_refactor/devel_scripts/manual_c_module.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/devel_scripts/manual_c_module.py?rev=26904&r1=26903&r2=26904&view=diff
==============================================================================
--- branches/space_mapping_refactor/devel_scripts/manual_c_module.py
(original)
+++ branches/space_mapping_refactor/devel_scripts/manual_c_module.py Tue
Dec 2 21:54:35 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/space_mapping_refactor/devel_scripts/memory_leak_test_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/devel_scripts/memory_leak_test_relax_fit.py?rev=26904&r1=26903&r2=26904&view=diff
==============================================================================
---
branches/space_mapping_refactor/devel_scripts/memory_leak_test_relax_fit.py
(original)
+++
branches/space_mapping_refactor/devel_scripts/memory_leak_test_relax_fit.py
Tue Dec 2 21:54:35 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/space_mapping_refactor/lib/io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/io.py?rev=26904&r1=26903&r2=26904&view=diff
==============================================================================
--- branches/space_mapping_refactor/lib/io.py (original)
+++ branches/space_mapping_refactor/lib/io.py Tue Dec 2 21:54:35 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/space_mapping_refactor/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py?rev=26904&r1=26903&r2=26904&view=diff
==============================================================================
---
branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
(original)
+++
branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
Tue Dec 2 21:54:35 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)
r26904 - in /branches/space_mapping_refactor: ./ devel_scripts/ lib/ test_suite/system_tests/scripts/