Relax 2.2.4 - Revision history

Bugman: /* Changes */ Switch to the {{minfx homepage}} and {{bmrblib homepage}} templates to remove dead Gna! links.

2020-10-16T21:06:03Z

Changes: Switch to the {{minfx homepage}} and {{bmrblib homepage}} templates to remove dead Gna! links.

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

2020-10-14T11:32:49Z

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

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

2015-11-03T10:36:10Z

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

Bugman: Increased the sectioning depth.

2015-10-21T19:34:08Z

Increased the sectioning depth.

Bugman: Added an infobox.

2015-10-21T19:33:22Z

Added an infobox.

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

2014-11-26T10:29:00Z

See also: Added a link to the API documentation.

Bugman: User function HTML manual links.

2014-09-11T16:25:34Z

User function HTML manual links.

Bugman: Formatting of all symbols/parameters.

2014-09-11T16:24:13Z

Formatting of all symbols/parameters.

Bugman: Tracker links with full descriptions.

2014-09-11T16:22:43Z

Tracker links with full descriptions.

Bugman: Created a links section.

2014-09-11T15:03:03Z

Created a links section.

@@ Line 40: / Line 40: @@
 <section begin=changes/>
-*  Updated the release checklist document to include the correct instructions for minfx and bmrblib.  These are the packages bundled with relax (http://gna.org/projects/minfx/ and http://gna.org/projects/bmrblib/)
+*  Updated the release checklist document to include the correct instructions for minfx and bmrblib.  These are the packages bundled with relax ({{minfx homepage}} and {{bmrblib homepage}})
 *  Improvements for Python 2 and 3 compatibility.  Much of the Python 2 verses 3 compatibility, as well as different Python 2 version compatibility and different Python 3 version compatibility, code has been shifted into the compat module.  The different parts of relax now import from the compat module for modules/packages with different import semantics for different Python versions.  In addition the different handling of the bz2 and gzip module for reading and writing files has been shifted from 'relax_io' into 'compat'.
 *  Updated the 2to3 checklist document to include multiple threads for faster operation.

@@ Line 81: / Line 81: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_2.2.4 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2384 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2384|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/41 Gmane]
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00037.html Mail Archive]

@@ Line 8: / Line 8: @@
 | type     = Major bugfix
 | date     = 10 December 2013
 }}

@@ Line 10: / Line 10: @@
 }}
-= Description =
+== Description ==
 <section begin=description/>
@@ Line 16: / Line 16: @@
 <section end=description/>
-= Download =
+== Download ==
 <section begin=download/>
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 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
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 <section end=metadata/>
-== Features ==
+=== Features ===
 <section begin=features/>
@@ Line 36: / Line 36: @@
 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
@@ Line 59: / Line 59: @@
 <section end=changes/>
-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
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 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
@@ Line 87: / Line 87: @@
 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/2.2/ The relax 2.2 API documentation]
 {{:relax release see also}}

← Older revision		Revision as of 19:33, 21 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 2.2.4
		+	\| prev = 2.2.3
		+	\| next = 2.2.5
		+	\| keywords = Python 3, RMSD, test suite, user functions
		+	\| type = Major bugfix
		+	\| date = 10 December 2013
		+	}}

	= Description =		= Description =

← Older revision		Revision as of 10:29, 26 November 2014
Line 84:		Line 84:
	= See also =		= See also =

		+	* [http://www.nmr-relax.com/api/2.2/ The relax 2.2 API documentation]
	{{:relax release see also}}		{{:relax release see also}}

@@ Line 39: / Line 39: @@
 *  Created the Mf.test_bug_20613_auto_mf_diff_tensor_pdb system test to catch [https://gna.org/bugs/?20613 bug #20613].  This was reported by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt>.  This test is a direct copy of the Mf.test_bug_20563_missing_ri_error system test.  The only change is that the local tm global model results file (in the local_tm/aic/ directory) has been modified.  This results were read into relax, the file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb loaded into the data pipe, and the results saved again.  This triggers the bug as the problem is the presence of structural data with the local tm global model being selected in the auto-analysis.
 *  Shifted all of the model-free specific analysis class documentation variables to the top.  This is simply for better organisation of the code.
-*  Created the model-free write_doc class variable talking about the field strength independent Rex value.  This has been added to the value.display and value.write user functions to explain that Rex values are very small and that the user needs to scale them up.
+*  Created the model-free write_doc class variable talking about the field strength independent Rex value.  This has been added to the [http://www.nmr-relax.com/manual/value_display.html value.display] and [http://www.nmr-relax.com/manual/value_write.html value.write] user functions to explain that Rex values are very small and that the user needs to scale them up.
 *  Shifted all of the documentation variables to the top of the specific API_base class.  This is for better organisation.
 *  Added the write_doc class variable to the specific analysis API class as a empty string.  This is to fix the unit tests.
-*  Created the front end for the new structure.create_rotor_pdb user function.  This will be used to create a PDB representation of a rotor motional model.
+*  Created the front end for the new [http://www.nmr-relax.com/manual/structure_create_rotor_pdb.html structure.create_rotor_pdb user function].  This will be used to create a PDB representation of a rotor motional model.
-*  Added file, directory and overwrite force arguments to the structure.create_rotor_pdb user function.
+*  Added file, directory and overwrite force arguments to the [http://www.nmr-relax.com/manual/structure_create_rotor_pdb.html structure.create_rotor_pdb user function].
-*  Started to implement the backend of the structure.create_rotor_pdb user function.
+*  Started to implement the backend of the [http://www.nmr-relax.com/manual/structure_create_rotor_pdb.html structure.create_rotor_pdb user function].
 *  The internal structural object MolContainer.add_atom() method now returns the index of the new atom.
 *  Created the internal structural object MolContainer.last_residue() method.
-*  Fully implemented the structure.create_rotor_pdb user function.  For this, the generic_fns.structure.geometric.create_rotor_propellers() function was created.
+*  Fully implemented the [http://www.nmr-relax.com/manual/structure_create_rotor_pdb.html structure.create_rotor_pdb user function].  For this, the generic_fns.structure.geometric.create_rotor_propellers() function was created.
 <section end=changes/>
@@ Line 61: / Line 61: @@
 *  Python 3 updates and fixes using the 2to3 program.
 *  Bug fix for the external Scientific Python Geometry package.  This is a strange Python 3 issue only triggered when the epydoc Python package is installed.
-*  Fix for [https://gna.org/bugs/?20613 bug #20613, the failure of the diffusion tensor PDB creation].  This was reported by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt>.  The problem was that the diffusion tensor PDB representation structure.create_diff_tensor_pdb user function was being called even when the local tm global model was selected.  This naturally failed as there is no global diffusion tensor.  Now this user function is avoided for the local tm global model.
+*  Fix for [https://gna.org/bugs/?20613 bug #20613, the failure of the diffusion tensor PDB creation].  This was reported by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt>.  The problem was that the diffusion tensor PDB representation [http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html structure.create_diff_tensor_pdb user function] was being called even when the local tm global model was selected.  This naturally failed as there is no global diffusion tensor.  Now this user function is avoided for the local tm global model.
-*  Fix for the value.write user function for very small parameter values (Rex for example).  This was reported by Martin Ballaschk <ballaschk att fmp-berlin dott de> in the thread http://thread.gmane.org/gmane.science.nmr.relax.user/1397/focus=1402 and by by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt> in the unrelated bug report at https://gna.org/bugs/?20613.  The formatting string "20.15f" has been changed to "20.15g" to allow Python to decide if the normal decimal or exponential form of the number should be printed.
+*  Fix for the [http://www.nmr-relax.com/manual/value_write.html value.write user function] for very small parameter values (Rex for example).  This was reported by Martin Ballaschk <ballaschk att fmp-berlin dott de> in the thread http://thread.gmane.org/gmane.science.nmr.relax.user/1397/focus=1402 and by by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt> in the unrelated bug report at https://gna.org/bugs/?20613.  The formatting string "20.15f" has been changed to "20.15g" to allow Python to decide if the normal decimal or exponential form of the number should be printed.
 *  Fix for a strange and extremely rare typo bug in the model-free specific analysis code.  This was identified by Manish Chaubey <manish dott chaubey att tuebingen dott mpg dott de> in the message at http://thread.gmane.org/gmane.science.nmr.relax.user/1422.  This only occurs if a relaxation data error of zero is encountered and is a bug in the RelaxError message explaining the problem with the data.
 <section end=bugfixes/>

@@ Line 33: / Line 33: @@
 *  Improvements for Python 2 and 3 compatibility.  Much of the Python 2 verses 3 compatibility, as well as different Python 2 version compatibility and different Python 3 version compatibility, code has been shifted into the compat module.  The different parts of relax now import from the compat module for modules/packages with different import semantics for different Python versions.  In addition the different handling of the bz2 and gzip module for reading and writing files has been shifted from 'relax_io' into 'compat'.
 *  Updated the 2to3 checklist document to include multiple threads for faster operation.
-*  Eliminated the os.devnull import flag dep_check.devnull_import.  This is not needed as the compat relax module defines os.devnull for Python <= 2.3.  The devnull module is no longer part of the relax information printout.
+*  Eliminated the os.devnull import flag dep_check.devnull_import.  This is not needed as the compat relax module defines os.devnull for Python &le; 2.3.  The devnull module is no longer part of the relax information printout.
-*  Added a more informative error message if the platform module is missing.  This is for Python <= 2.2.  The file from http://hg.python.org/cpython/file/2.3/Lib/platform.py can simply be copied into the lib/pythonX.X/ directory to fix this.
+*  Added a more informative error message if the platform module is missing.  This is for Python &le; 2.2.  The file from http://hg.python.org/cpython/file/2.3/Lib/platform.py can simply be copied into the lib/pythonX.X/ directory to fix this.
 *  Slight change to the message printed if the platform module is missing.
 *  Modified the script for running the relax test-suite on multiple Python versions.  The pre-2.2 Python versions are now commented out as well as the abortive Python 3.0.