Relax 2.1.2 - Revision history

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-14T11:38:55Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Internal link to Modelfree4.

2015-12-15T16:14:37Z

Internal link to Modelfree4.

Bugman: Internal links to DASHA.

2015-12-15T15:08:14Z

Internal links to DASHA.

Bugman: Added the 'manual' parameter to {{infobox relax release}}.

2015-11-03T10:40:22Z

Added the 'manual' parameter to {{infobox relax release}}.

Bugman: Increased the sectioning depth.

2015-11-03T10:39:51Z

Increased the sectioning depth.

Bugman: Added an infobox.

2015-10-21T19:06:18Z

Added an infobox.

Bugman: /* See also */ Added a link to the API documentation.

2014-11-26T10:26:49Z

See also: Added a link to the API documentation.

Bugman: More user function HTML manual links.

2014-09-13T20:59:03Z

Bugman: Fixes for the user function links.

2014-09-13T20:57:26Z

Fixes for the user function links.

Bugman: Created a links section.

2014-09-13T20:07:42Z

Created a links section.

@@ Line 308: / Line 308: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_2.1.2 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2369 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2369|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/35 Gmane]
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00031.html Mail Archive]

@@ Line 130: / Line 130: @@
 *  The OMP model-free results file generation script now outputs for any relax version.
 *  Python 3 fix for the Mf.test_latex_table system test.  The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw string format r"""Text""" is now used.
-*  Python 3 support for Modelfree4 and [[DASHA]].  The subprocess.Popen class works with byte arrays rather than strings in Python 3+.  The Python objects are now interconverted when the Python 3 encode() and decode() methods are detected.
+*  Python 3 support for [[Modelfree4]] and [[DASHA]].  The subprocess.Popen class works with byte arrays rather than strings in Python 3+.  The Python objects are now interconverted when the Python 3 encode() and decode() methods are detected.
 *  Removed the pickle format information and arguments from the state user function definitions.
 *  Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.
@@ Line 286: / Line 286: @@
 *  Python 2.4 and earlier fixes for the Queuing module.  The TaskQueue class from http://code.activestate.com/recipes/475160/ which was added to Python 2.5+ has been added to the compat module.  This module is now used for all imports of the Queue class for all Python versions.
 *  Test suite bug fix - the GUI tests now cleanly terminate the interpreter thread.  This allows the test suite to terminate normally.  With different Python versions on different operating systems, this could sometimes cause the test suite to freeze at the end, the final printout to be missing, or other strange behaviour.
-*  Python 2.3- fixes - the Modelfree4 and [[DASHA]] system tests are now skipped if the subprocess module is missing.
+*  Python 2.3- fixes - the [[Modelfree4]] and [[DASHA]] system tests are now skipped if the subprocess module is missing.
 *  Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.  The unittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.
 *  Python 2.3 and earlier fix - the subprocess module is only imported when present.  This is for the stereochem_analysis auto-analysis, but the import kills all of the auto-analyses.

@@ Line 130: / Line 130: @@
 *  The OMP model-free results file generation script now outputs for any relax version.
 *  Python 3 fix for the Mf.test_latex_table system test.  The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw string format r"""Text""" is now used.
-*  Python 3 support for Modelfree4 and Dasha.  The subprocess.Popen class works with byte arrays rather than strings in Python 3+.  The Python objects are now interconverted when the Python 3 encode() and decode() methods are detected.
+*  Python 3 support for Modelfree4 and [[DASHA]].  The subprocess.Popen class works with byte arrays rather than strings in Python 3+.  The Python objects are now interconverted when the Python 3 encode() and decode() methods are detected.
 *  Removed the pickle format information and arguments from the state user function definitions.
 *  Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.
@@ Line 259: / Line 259: @@
 *  Fix for the Relax_data.test_delete system test for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].
 *  Fix for the Relax_data.test_read unit tests for the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function] changes.
-*  Fix to the Dasha system test needed for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].
+*  Fix to the [[DASHA]] system test needed for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].
 *  Fix for the N_state_model.test_monte_carlo_sims due to the changed sphere.pdb test suite file.
 *  Relaxation data is no longer loaded by relax_data.read if the values and errors are both None.
@@ Line 286: / Line 286: @@
 *  Python 2.4 and earlier fixes for the Queuing module.  The TaskQueue class from http://code.activestate.com/recipes/475160/ which was added to Python 2.5+ has been added to the compat module.  This module is now used for all imports of the Queue class for all Python versions.
 *  Test suite bug fix - the GUI tests now cleanly terminate the interpreter thread.  This allows the test suite to terminate normally.  With different Python versions on different operating systems, this could sometimes cause the test suite to freeze at the end, the final printout to be missing, or other strange behaviour.
-*  Python 2.3- fixes - the Modelfree4 and Dasha system tests are now skipped if the subprocess module is missing.
+*  Python 2.3- fixes - the Modelfree4 and [[DASHA]] system tests are now skipped if the subprocess module is missing.
 *  Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.  The unittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.
 *  Python 2.3 and earlier fix - the subprocess module is only imported when present.  This is for the stereochem_analysis auto-analysis, but the import kills all of the auto-analyses.

@@ Line 7: / Line 7: @@
 | type    = Python super-compatibility
 | date    = 17 October 2012
 }}

@@ Line 9: / Line 9: @@
 }}
-= Description =
+== Description ==
 <section begin=description/>
@@ Line 15: / Line 15: @@
 <section end=description/>
-= Download =
+== Download ==
 <section begin=download/>
@@ Line 21: / Line 21: @@
 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
@@ Line 29: / Line 29: @@
 <section end=metadata/>
-== Features ==
+=== Features ===
 <section begin=features/>
@@ Line 38: / Line 38: @@
 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
@@ Line 272: / Line 272: @@
 <section end=changes/>
-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
@@ Line 302: / Line 302: @@
 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
@@ Line 314: / Line 314: @@
 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/2.1/ The relax 2.1 API documentation]
 {{:relax release see also}}

← Older revision		Revision as of 19:06, 21 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 2.1.2
		+	\| prev = 2.1.1
		+	\| next = 2.2.0
		+	\| type = Python super-compatibility
		+	\| date = 17 October 2012
		+	}}

	= Description =		= Description =

← Older revision		Revision as of 10:26, 26 November 2014
Line 312:		Line 312:
	= See also =		= See also =

		+	* [http://www.nmr-relax.com/api/2.1/ The relax 2.1 API documentation]
	{{:relax release see also}}		{{:relax release see also}}

@@ Line 62: / Line 62: @@
 *  Removed an unused import of the Queue module from the multi-processor.
 *  Python 3 fix for the ScientificPython PDB reader unit tests.  The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now they are sorted prior to comparison.
-*  Redesigned the reset user function backend.  This now no only clears out the relax data store, but it also resets the GUI if present.  Some of the reset code comes from the tearDown() method of the GUI tests.  All windows but the main GUI window are closed and the relax controller gauges are set to zero and the log window text cleared.  These changes should allow GUI tests after an error or failure to pass, something which is currently problematic.
+*  Redesigned the [http://www.nmr-relax.com/manual/reset.html reset] user function backend.  This now no only clears out the relax data store, but it also resets the GUI if present.  Some of the reset code comes from the tearDown() method of the GUI tests.  All windows but the main GUI window are closed and the relax controller gauges are set to zero and the log window text cleared.  These changes should allow GUI tests after an error or failure to pass, something which is currently problematic.
 *  Disabled the initial relax intro printout from the GUI when running the test suite.  This prevents the intro text from appearing in the first failed test.
 *  Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2.  The object comparison method no longer converts dictionaries to strings for the comparison, as the string version is different in different Python versions.

@@ Line 87: / Line 87: @@
 *  Fix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.
 *  Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.
-*  Another fix for the [http://www.nmr-relax.com/manual/diffusion_tensor.init user function] - it was not completely converted.
+*  Another fix for the [http://www.nmr-relax.com/manual/diffusion_tensor_init.html diffusion_tensor.init user function] - it was not completely converted.
 *  Fix for the fixing of parameters in the model-free analyses.  The diffusion tensor set_fixed() method is now used.
 *  Fix for the XML output of the diffusion tensor - only the modifiable parameters are output.  This was the previous behaviour and is needed for the test suite to pass.
-*  Converted the [http://www.nmr-relax.com/manual/palmer.extract user function] to use the new diffusion tensor design.
+*  Converted the [http://www.nmr-relax.com/manual/palmer_extract.html palmer.extract user function] to use the new diffusion tensor design.
 *  The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed().
-*  The [http://www.nmr-relax.com/manual/fix user function] now uses the diffusion tensor set_fixed() method.
+*  The [http://www.nmr-relax.com/manual/fix.html fix user function] now uses the diffusion tensor set_fixed() method.
 *  Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the 'fixed' object.
 *  Fix for the model-free specific analysis duplicate_data() method for the new design.  The diffusion tensor __mod_attr__ object is now called _mod_attr.
@@ Line 128: / Line 128: @@
 *  Python 3 fix for the relax_io.open_write_file() function.  This now matches the behaviour of open_read_file() in that there are three different behaviours for opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for Python 3.0 to 3.2, and one for Python 3.3+).  All byte streams have been eliminated as open_write_file() is for creating text files.
 *  Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.
-*  For consistency between Python 2 and 3, the [http://www.nmr-relax.com/manual/grace.write user function] outputs to 15 decimal places.  This increased precision will only be of use in the relax test suite.
+*  For consistency between Python 2 and 3, the [http://www.nmr-relax.com/manual/grace_write.html grace.write user function] outputs to 15 decimal places.  This increased precision will only be of use in the relax test suite.
 *  Python 3 fix for the Pipes.test_pipe_bundle() system test.  The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.
 *  The C module compilation testing script now accepts the Python version as a first argument.
@@ Line 158: / Line 158: @@
 *  Python 3 fix for the user function docstring creation in the prompt UI mode.  Again this is the problem of a division now returning a float rather than an int.
 *  Python 3 bug fix for the N-state model target function setup.  The num_tensors variable needs to be an integer, but the Python 3 division will create a float type.
-*  Python 3 fix for the [http://www.nmr-relax.com/manual/results.read user function] matching that of state.load.
+*  Python 3 fix for the [http://www.nmr-relax.com/manual/results_read.html results.read user function] matching that of state.load.
 *  Python 3 bug fix for the relax_io.read_spin_data() function.  The built in max() function cannot handle the value of None, therefore the filter() function is used to remove all instances of None from the list.
-*  Python 3 bug fix for the [http://www.nmr-relax.com/manual/state.load user function].  The header line of pickled states (rather than the standard XML states) is of the b'' byte format.  This is now converted to a string, and the search expression is comparing it to the raw string r"<\?xml".
+*  Python 3 bug fix for the [http://www.nmr-relax.com/manual/state_load.html state.load user function].  The header line of pickled states (rather than the standard XML states) is of the b'' byte format.  This is now converted to a string, and the search expression is comparing it to the raw string r"<\?xml".
 *  Better support for both Python 2 and 3 in the relax data store.  The 2to3 script was used on all of the files in the data package.
 *  Python 3 preparation - the relax data store (the data package) now supports both Python 2 and 3.
@@ Line 242: / Line 242: @@
 *  Removed all of the xrange() calls from the system tests as these are not necessary.  This is in preparation for Python 3.
 *  Some changes in preparation for Python 3.
-*  Removed the 'force flag' text from the RelaxWarning messages output by the [http://www.nmr-relax.com/manual/bruker.read user function].  The force flag arguments of the generic_fns.mol_res_spin.name_spin() and generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to None to suppress the text.
+*  Removed the 'force flag' text from the RelaxWarning messages output by the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read user function].  The force flag arguments of the generic_fns.mol_res_spin.name_spin() and generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to None to suppress the text.
 *  Fixes for the checks in the Mf.test_mf_auto_analysis() GUI test for the recent test suite data changes.
 *  The CSA setting in the model-free auto GUI analysis now defaults to the '@N*' spin ID.  Previously no spin ID was being used so that the protons where also having their CSA values set to that of the nitrogens.  Now the execution checking code skips the proton CSA check.
@@ Line 248: / Line 248: @@
 *  Fix for the comment on the 'Export' button in the BMRB export window.
 *  Lots of editing of the model-free GUI section of the user manual.
-*  Fix for the Relax_data.test_delete system test for the changes to the [http://www.nmr-relax.com/manual/relax_data.read user function].
+*  Fix for the Relax_data.test_delete system test for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].
-*  Fix for the Relax_data.test_read unit tests for the [http://www.nmr-relax.com/manual/relax_data.read user function] changes.
+*  Fix for the Relax_data.test_read unit tests for the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function] changes.
-*  Fix to the Dasha system test needed for the changes to the [http://www.nmr-relax.com/manual/relax_data.read user function].
+*  Fix to the Dasha system test needed for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].
 *  Fix for the N_state_model.test_monte_carlo_sims due to the changed sphere.pdb test suite file.
 *  Relaxation data is no longer loaded by relax_data.read if the values and errors are both None.
@@ Line 289: / Line 289: @@
 *  Fix for [https://gna.org/bugs/?20210 bug #20210] - relax now runs again without having wxPython installed.
 *  Bug fix for the BMRB system test initialisation for when the bmrblib module is missing.  The base __init__() method needs to be initialised first.
-*  Fix for [https://gna.org/bugs/?20201 bug #20201].  The [http://www.nmr-relax.com/manual/bruker.read user function] can now handle the situation where multiple spins per residue are already loaded prior to the user function call.  The isotope value from the DC file is now translated to the element name and this is used as part of the spin ID string.
+*  Fix for [https://gna.org/bugs/?20201 bug #20201].  The [http://www.nmr-relax.com/manual/bruker_read.html bruker.read user function] can now handle the situation where multiple spins per residue are already loaded prior to the user function call.  The isotope value from the DC file is now translated to the element name and this is used as part of the spin ID string.
 *  Fix for [https://gna.org/bugs/?20197 bug #20197 - the PyMOL and Molmol macro failure].  The macro creation now only operates on spins called 'N' and assumes these are the backbone nitrogens.  The sidechain tryptophan indole NH data will need to be detected and added later.
 *  Fix for [https://gna.org/bugs/?20198 bug #20198 - the relaxation data back-calculation error].  The problem was that the call to the model-free overfit_deselect() method was deselecting any spins lacking relaxation data.  This should not happen, as no spins need to have relaxation data for this calculation.