"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "docs/CHANGES" between
relax-4.1.3.src.tar.bz2 and relax-5.0.0.src.tar.bz2

About: relax allows the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported.

CHANGES  (relax-4.1.3.src.tar.bz2):CHANGES  (relax-5.0.0.src.tar.bz2)
############################################################################### ###############################################################################
# # # #
# Copyright (C) 2006-2016,2019 Edward d'Auvergne # # Copyright (C) 2006-2016,2019-2020 Edward d'Auvergne #
# # # #
# This file is part of the program relax (http://www.nmr-relax.com). # # This file is part of the program relax (http://www.nmr-relax.com). #
# # # #
# This program is free software: you can redistribute it and/or modify # # This program is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by # # it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or # # the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. # # (at your option) any later version. #
# # # #
# This program is distributed in the hope that it will be useful, # # This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. # # GNU General Public License for more details. #
# # # #
# You should have received a copy of the GNU General Public License # # You should have received a copy of the GNU General Public License #
# along with this program. If not, see <http://www.gnu.org/licenses/>. # # along with this program. If not, see <http://www.gnu.org/licenses/>. #
# # # #
############################################################################### ###############################################################################
Version 5.0.0
(25 August 2020, from master)
https://sourceforge.net/p/nmr-relax/code/ci/5.0.0/tree/
Features:
* Support for wxPython-Phoenix.
* Bmrblib: This Python package is now once again optional and relax can
run without it.
* MS Windows builds are now 64-bit by default.
* Major improvements to relax text output.
Changes:
* TestSuite: Skipped tests are no longer run when individual tests are s
upplied on the command line. The RelaxTestLoader.loadTestsFromNames() method ha
s been implemented to gracefully handle the skipping of tests when only a single
test is run.
* Travis CI config: Fixes for PyPI numpy no longer being compatible with
Python 2.7. Older versions of numpy now need to be manually specified for the
Python 2.7 job.
* Travis CI config: Attempt at making the MS Windows build job run again
. The Travis CI infrastructure has changed yet again and the Windows job fails
in the setup stage. These changes are just a guess to try to make this work aga
in.
* Travis CI config: 2nd attempt at making the MS Windows build job run a
gain. Chocolatey was automatically installing the new Python 3.8.0 but the path
s pointed to the 3.7 version. Now the 3.7.4 Python version is explicitly specif
ied.
* SCons: Change for the MS Windows build architecture from the default o
f 32-bit to 64-bit. Previously the default was 32-bit compilation on all Window
s systems, via the WIN_TARGET_OVERRIDE flag, as official Python never used to re
lease 64-bit builds for Windows systems. As this is no longer the case, the 32-
bit override is now only set for the old Python 2 versions.
* Travis CI config: Creation of a job for testing relax on an arm64 CPU.
The system Python and its packages are used to avoid timeouts on arm64. Insta
lling the Python packages via pip prior to running causes a Travis CI time out,
as most of the 50 minutes allowed are used up by the compilation of SciPy. Desp
ite the successful installation of the wxPython site-package on the system Pytho
n3, the GUI tests are not activated as there is a problem with xvfb on the arm64
Travis CI jobs.
* N_state_model.test_populations system test: Loosened two of the checks
to allow arm64 to pass.
* wxPython: Added the dep_check.old_wx flag for differentiating between
Classic and Phoenix.
* wxPython-Phoenix: Fix for the wx.BoxSizer.AddSpacer() function calls.
The old wxPython conversion of the size argument to (size, size) breaks the lay
out, so that the tuple arguments are essential. However tuple arguments are not
allowed in wxPython-Phoenix. Therefore the dep_check.old_wx flag is used to di
fferentiate the behaviour of the different wxPythons.
* wxPython-Phoenix: Fix for the old wx.Sizer.DeleteWindows() method. Th
is method no longer exists, so instead the Clear() method with the deleteWindows
argument (or delete_windows in Phoenix) is used instead.
* wxPython-Phoenix: Fix for the missing wx.SystemSettings_GetMetric() fu
nction. This has been switched to wx.SystemSettings.GetMetric() which is presen
t in the original wxPython and Phoenix.
* wxPython-Phoenix: Fixes for the relax gui About dialog. The wx.Frame.
Center() function call only works if the window is shown (i.e. it is broken in t
he test suite), and the wx.DC.EndDrawing() function has been dropped in Phoenix.
* wxPython-Phoenix: Fixes for the GUI sequence and file input elements.
The wx.Frame.Center() function call only works if the window is shown (i.e. it
is broken in the test suite).
* wxPython-Phoenix: Support for the splash screen. The wx.SplashScreen
and associated variables have shifted into wx.adv.
* wxPython-Phoenix: Support for the relax icon. The wx.IconBundle.AddIc
onFromFile() function have been replaced by wx.IconBundle.AddIcon() in the curre
nt phoenix.
* wxPython-Phoenix: Fix for the spin viewer window. The wx.Window.GetCl
ientSizeTuple() function does not exist in Phoenix. However this can simply be
replaced by wx.Window.GetClientSize() in the current code.
* Deletion hack: The wx.Bitmap.HasAlpha() function is missing in current
phoenix.
* relax GUI: Fix for the window icons.
* wxPython-Phoenix: Switch away from the depreciated wx.Menu.AppendItem(
) function. Classic still requires the calls to this function, but phoenix now
uses wx.Menu.Append() instead.
* wxPython: Renamed the dep_check.old_wx flag to dep_check.wx_classic.
* wxPython-Phoenix: Prominent feedback warning the user about using unst
able Phoenix versions. This includes both a RelaxWarning on start up and placin
g the warning text in red in the center of the blank relax GUI main window. Cur
rently all Phoenix versions are labelled as unstable, however this can be change
d in the future directly in the dep_check module.
* wxPython-Phoenix: Switch away from the depreciated wx.ToolBar.AddLabel
Tool() function. This is still used for "Classic". For Phoenix, the wx.ToolBar
.AddTool() function is used instead.
* wxPython-Phoenix: Switch away from the depreciated wx.Window.SetToolTi
pString() function. Instead wx.Window.SetToolTip(wx.ToolTip(text)) is used for
both "Classic" and Phoenix.
* wxPython-Phoenix: Switch from wx.NamedColour() to wx.Colour() in the r
elax controller. "Classic" still uses the old function.
* wxPython-Phoenix: Switch from the depreciated wx.Text.GetSizeTuple() t
o wx.Text.GetSize(). This seems to work on "Classic" as well.
* wxPython-Phoenix: Switch from the depreciated wx.TreeCtrl.GetItemPyDat
a() function. "Classic" is still using this function, but Phoenix is now using
wx.TreeCtrl.GetItemData().
* wxPython-Phoenix: Switch from the depreciated wx.TreeCtrl.SetDimension
s() function. Instead SetSize() is now being used for Phoenix.
* wxPython-Phoenix: Switch from the depreciated wx.TreeCtrl.SetPyData()
function. "Classic" is still using this function, but Phoenix is now using wx.T
reeCtrl.SetItemData().
* wxPython-Phoenix: Switch from the depreciated wx.StockCursor() wrapper
function. The overloaded wx.Cursor class can be used instead in Phoenix.
* wxPython-Phoenix: Switch from the depreciated wx.EmptyBitmap() wrapper
function. Instead Phoenix versions can simply use the overloaded wx.Bitmap cla
ss with the same arguments.
* wxPython-Phoenix: Switch from wrapper to overloaded functions for the
wx.ListCtrl elements.
* Python 3.8 support: The platform.linux_distibution() function no longe
r exists. This is now replaced by the distro site-package. The lib.compat pack
age deals with this difference.
* Model-free analysis: Obscure syntax error bug fix for an issue highlig
hted by Python 3.8. The error in the set_xh_vect() function. This is only enco
untered when reading an ancient relax 1.2 model-free results file.
* Travis CI config: Changes as suggested by the experimental Travis CI B
uild Config Explorer. The config text was pasted into https://config.travis-ci.
com/explore and changed as suggested.
* Travis CI config: Shifted the OpenMPI required packages into an apt 'a
ddons' section.
* Travis CI config: Shifted the API doc 'build' specific parts into the
jobs matrix. This allows an environmental variable to be removed and a simplifi
cation of the 'script' section.
* Travis CI config: Shifted the FSF copyright validation specific parts
into the jobs matrix. This allows an environmental variable to be removed and a
simplification of the 'script' section.
* Travis CI config: Removal of the now unused TEST environmental variabl
e.
* Travis CI config: Simplification of the single processor and OpenMPI e
xecution. The MPIRUN and RELAX_ARGS arguments have been introduced. These are
normally unset but, for the OpenMPI jobs, they are set to "mpirun -np 2" and "--
multi=mpi4py" respectively. This allows the duplicated entries for the informat
ion printout and test suite execution to be collapsed into one.
* Travis CI config: Removal of the 'pip upgraded package' job. This job
does not seem to be necessary for testing relax.
* Travis CI config: Conversion of the Ubuntu Xenial job to Ubuntu Bionic
.
* Travis CI config: Removal of the 'language' key in the jobs matrix whe
n the value is 'python'. This is a duplication as the language is set to Python
outside of the matrix.
* Multi-processor: Shifted the processor type checking into the initial
command line parsing. This allows a non-zero error code to be returned to the s
hell.
* Travis CI config: Shifted the echoing of environmental vars into a new
'before_script' section. This allows the echoing to occur for all jobs.
* Scons: Improvements to the string formatting and the printout for the
C module compilation. This includes showing the target architecture for MS Wind
ows compilation.
* Scons: Document the environmental variables used.
* Information printout: Improved output for Python3 compiled C modules.
The bytesteam is now decoded.
* Scons: The MS Windows binary target architecture is now determined by
the Python binary arch.
* Test suite: Implementation of a command line option for disabling IO c
apture. This was previously handled by using the debug command line option whic
h simply prevented IO capture. This type of output is very hard to parse by eye
, as the tests are not well separated and the debugging output is very verbose.
Now the --no-capt or --no-capture option has been implement to disable the IO c
apture. The debug command line option no longer disables IO capture, rather it
allows for finer control of the test suite in that verbose debugging output is n
ow only shown for tests that do not pass. When IO capture is disabled, extra fo
rmatted output is used to provide clear separators, titles, descriptions and end
ings for each test.
* Test suite: Argument reordering and better docstring documentation in
the relax test suite runners.
* Test suite: All adjustable widths are now set using the value of statu
s.text_width. This include the separators for the tests and the test suite summ
ary lines at the end.
* Fix for Python 2.5 support.
* Command line processing: Switch from the depreciated optparse Python m
odule to argparse. The argument parsing code and help text has also been improv
ed.
* Travis CI config: Added the relax --test and --version modes.
* Travis CI config: Alphabetical ordering of the environmental variable
printouts.
* Help: Improvements to the help printout, including new descriptions fo
r the argument groups.
* Status object: Improved logic for determining the ideal text width for
relax.
* Travis CI config: Added testing of the relax --help mode.
* Test suite: Added text wrapping set to the relax text width for the te
st description. This is the description shown when running without IO capture.
* Information printout: Improved formatting for MS Windows. The repr()
function results in '\\' for path separators rather than '\', causing the format
ting to be out.
* Information printout: Remove an accidentally committed debugging print
out.
* Test suite: Addition of a new command line option for listing all of t
he test names. The new '--list-tests' option will cause the names of the tests
to be printed out and not run any tests.
* Travis CI config: Try to force a Py2 compatible version of kiwisolver,
as needed by matplotlib.
* Travis CI config: The virtual machines with Python2 now seem to requir
e SCons be manually installed.
* Test suite: Fixes for the Palmer.test_palmer_omp system test. The mod
elfree4 binary type 'linux-x86_64-gcc' seems to now produce slightly different r
esults with newer system libraries. The checks in this test have been updated t
o reflect this.
Bugfixes:
* GUI: Bug fix for the deletion of analysis tabs on Python 3. The value
of None cannot be compared to an integer. This bug appears to only be triggere
d by another bug - a GUI tearDown() or deletion failure on MS Windows with wxPyt
hon-Phoenix and Python 3.
* Bug fix: Restoration of the simple user function menus.
Version 4.1.3 Version 4.1.3
(14 June 2019, from master) (14 June 2019, from master)
https://sourceforge.net/p/nmr-relax/code/ci/4.1.3/tree/ https://sourceforge.net/p/nmr-relax/code/ci/4.1.3/tree/
Features: Features:
N/A N/A
Changes: Changes:
* FSF Copyright Validation configuration: Blacklisted the PDF user manua l. This allows the checking of relax tags to pass. * FSF Copyright Validation configuration: Blacklisted the PDF user manua l. This allows the checking of relax tags to pass.
* Release checklist document: Describe the relax fork of latex2html. * Release checklist document: Describe the relax fork of latex2html.
 End of changes. 2 change blocks. 
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