AnyPyTools - AnyPyTools v.1.17.0

Changed: * Temporary macro files *.anymcr are now always deleted after a run.

Scientific Software - Peer-reviewed - Python
Published by melund 11 months ago

AnyPyTools - AnyPyTools v.1.17.0

Fixed: * Fixed issue with parsing nan values from AnyBody in multi dimensional arrays. * Fixed an issue preventing the pytest plugin from ignoring missing RunDurationCPUThread objects.

Scientific Software - Peer-reviewed - Python
Published by melund 12 months ago

AnyPyTools - AnyPyTools v.1.16.1

Fixed:

• Fixed issue with parsing 'nan' values from AnyBody in multi dimensional arrays.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v.1.16.0

Fixed: Resolved an issue where exporting 2D output to pandas dataframes failed. Now, 2D outputs (3D when a function of time) are flattened into 1D arrays for compatibility. For example, rotation matrices are split into 9 separate columns, similar to how 3D vectors are split into 3 columns.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v1.15.4

Fixed:

Even more minor fixes to AMS 8.2 compatibility

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v1.15.3

Fix: * More fixes the pytest plugin and how it handles upcoming AnyBody 8.2

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v1.15.2

Fixed:

Updated the pytest plugin to handles the way AnyBody 8.2 reports missing RunTest operations.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v1.15.1

Fixed: * Fixed an issue parsing output when AnyBody prints "-nan" in the output values. This is now just treated as NaN.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v1.15.0

v1.15.0

Added: * Improved formatting of output when running AnyPyTools in Jupyter notebooks. * Add type anotation to the output of the start_macro function.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v1.14.0

Added: * Replace tqdm with rich progress for enhanced task progress visualization * Write temp macro files together with the log files.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v.1.13.1

Fixed: * Fixed and syntax issue when removing logfiles when simulation fails.

Scientific Software - Peer-reviewed - Python
Published by melund about 1 year ago

AnyPyTools - AnyPyTools v.1.13.1

Fixed: * Permission problems removing log files no longer causes a error message, but is silently ignored. Hence, it doesn't cause a simulation to appear as failed to external tools.

Scientific Software - Peer-reviewed - Python
Published by melund over 1 year ago

AnyPyTools - AnyPyTools v.1.13.0

Added: * Added a "LoadData" macro command can generate the macro for loading h5 files. * Allow the "AnyBodyCon" executable on path to have any valid windows executable extension (exe, bat, cmd etc.). This will allow users to use custom shim of the AnyBodyCon executables to point else where.

Scientific Software - Peer-reviewed - Python
Published by melund over 1 year ago

AnyPyTools - AnyPyTools v.1.12.2

Fixed:

• Fixed type annotation which broke compability with older versions of Python.

Scientific Software - Peer-reviewed - Python
Published by melund almost 2 years ago

AnyPyTools - AnyPyTools v.1.12.1

Fixed: * Fixed a crash when stopping simulations with ctrl-c. It should now shutdown more gracefully. * Fixed a bug making it was hard to stop simulations which were not running in parrallel. Now simulations are always started on separate threads, which makes it possible to stop them with ctrl-c.

Added: * Added a some python annotations to the code base, which should provide better type hints in IDEs.

Scientific Software - Peer-reviewed - Python
Published by melund almost 2 years ago

AnyPyTools - AnyPyTools v.1.12.0

Added:

• Introduced a new way of controlling AnyBodyCon processes, which forces the process to automatically terminate when the Python process ends. This prevents the need to manually close the AnyBodyCon processes if the parent process was force killed.

Scientific Software - Peer-reviewed - Python
Published by melund almost 2 years ago

AnyPyTools - AnyPyTools version 1.11.6

• Fixed an issue with AnyPyTools not finding the correct AnyBody version in the Windows Registry for AnyBody newer than 8.0.1

Scientific Software - Peer-reviewed - Python
Published by melund about 2 years ago

AnyPyTools - AnyPyTools version 1.11.5

Fixed:

• Speed up importing by avoiding importing scipy until it is needed.

Scientific Software - Peer-reviewed - Python
Published by melund about 2 years ago

AnyPyTools - AnyPyTools version 1.11.4

Fixed:

• Fix regression in windows registry lookup which caused AnyPyTools to crash.

Scientific Software - Peer-reviewed - Python
Published by melund over 2 years ago

AnyPyTools - AnyPyTools version 1.11.3

Added:

• Correctly detect installations of AnyBody version 8 on the machines.

Fixed:

• Allow the pytest plugin to work even if the machine doesn't have AnyBody installed.

Scientific Software - Peer-reviewed - Python
Published by melund over 2 years ago

AnyPyTools - AnyPyTools version 1.11.2

Fixed:

• Fix fix a backwards compatibiility problem when using the AnyPyTools Pytest plugin and old versions of AMMR (<2.3).

Scientific Software - Peer-reviewed - Python
Published by melund over 2 years ago

AnyPyTools - AnyPyTools version 1.11.1

Fixed:

• Fix crash with version handling when AnyBody could not be found.

Scientific Software - Peer-reviewed - Python
Published by melund over 2 years ago

AnyPyTools - AnyPyTools version 1.11

Changed:

• If AnyBody is on the PATH variable, then AnyPyTools will no use that version, before looking for AnyBody in the registration database.
  

Scientific Software - Peer-reviewed - Python
Published by melund over 2 years ago

AnyPyTools - AnyPyTools version 1.10.1

Fixed:

• Fix an issue with the pytest plugin when running tests with --load-only option and the "RunDurationCPU" output.
• Fix a deprecation warning from Pandas when exporting to dataframes.

Scientific Software - Peer-reviewed - Python
Published by melund over 2 years ago

AnyPyTools - AnyPyTools version 1.10.0

Added:

• When running with "AnyBody" > 7.5 the pytest plugin will now save the timing information for how quickly the model loaded and how quickly the test ran. The output is added to the xml output from pytest.

Fixed:

• Fix regression when specifying "#defines" from the pytest plugin.

Scientific Software - Peer-reviewed - Python
Published by melund almost 3 years ago

AnyPyTools - AnyPyTools version 1.9.1

Fixed: - Fixed an regression with newer Numpy versions. Numpy used to allow combining output data from AnyBody even when some arrays had different sizes.

Scientific Software - Peer-reviewed - Python
Published by melund almost 3 years ago

AnyPyTools - AnyPyTools version 1.9.0

Fixed: - Fixed issue which would cauase macros to execute twice when running the GUI version of AnyBody.

Added: - Added a interactive_mode argument to the {class}AnyPyProcess <anypytools.AnPyProcess> class. Setting this argument will automaticially lauch the GUI version of AnyBody with the macro commands. Futher it will not automatically exit AnyBody once the macro commands has finished. This must be done manually by the user.

Scientific Software - Peer-reviewed - Python
Published by melund over 3 years ago

AnyPyTools - AnyPyTools version 1.8.2

Fixed: - Fix a bug in the results.to_dataframe() function when also specifying interpolation. Now interpolation actually works again. Thanks to Enrico De Pieri and Marc Bandi for spotting and fixing this.

Scientific Software - Peer-reviewed - Python
Published by melund over 3 years ago

AnyPyTools - AnyPyTools version 1.8.1

Added: - pytest plugin: Added an option to avoid deselecting tests which doesn't save hdf5 files when using the --anytest-output option.

pytest --anytest-output=some-folder --no-anytest-deselect

Scientific Software - Peer-reviewed - Python
Published by melund over 3 years ago

AnyPyTools - AnyPyTools version 1.8.0

Fixed: - Fixed deprecation warning from the pytest plugin

Added: - When writing AnyScript test files it is now possible to access the pytest test-file object in the header section of the AnyScript file. The file object is available in the name space as the self variable.

Removed: - Removed the option of implicitly writing defines in the headers of any test files.

Scientific Software - Peer-reviewed - Python
Published by melund almost 4 years ago

AnyPyTools - AnyPyTools version 1.7.8

Fixed:

• Fix a bug with pytest plugin when saving output data from files.

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.7

Fixed:

• Fix minor problem in repr for AnyPyProcessOutput.
• Fix a problem where the pytest plugin would crash if AnyBody could not be found

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.6

Fixed: - Fix small issues in tutorials. - Fix issues when reading NaNs produced by AnyBody

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.5

Fixed:

• Return code on linux is now correctly intercepted and reported.

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.4

Fixed: - Fixed pytest deprecation warnings. - Remove a stray debug print

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.3

Fixed:

• Fixed a bug on linux when anybody was using it own internal Python hooks. Redirecting the output on the linux would cause python initialization to fail.

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.2

Changed: - Add error message when no files are found with search_subdir arguments (fixes #69). - Update documentation to use markdown.

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.1

Fixed:

• Fix deprecation warnings in pytest plugin.

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools version 1.7.0

Added:

• AnyPyTools can now be used on linux if the AnyBody Modeling System is installed using wine

Scientific Software - Peer-reviewed - Python
Published by melund over 4 years ago

AnyPyTools - AnyPyTools v.1.6.0

Changed: * The to_dataframe() methods have been updated. They now return a dataframe without an index by default.

They also now support interpolation of the data.

```python app = AnyPyProcess() results = app.startmarco(macrolist)

df = results.to_dataframe(
  interp_var="Main.MyStudy.Output.Abscissa.t",
  interp_val=linspace(0,1,50)
)

```

Added:

• Documentation on how to use the to_dataframe() method has been added to the tutorials.

Scientific Software - Peer-reviewed - Python
Published by melund almost 5 years ago

AnyPyTools - AnyPyTools version 1.5.0

Add methods for exporing simuation output as a pandas dataframe.

```python app = AnyPyProcess() results = app.startmarco(macrolist)

df = results.todataframe(indexvar="Main.MyStudy.Output.Abscissa.t") ```

The data has too be consistent across all macros. That means that the index_var must be present in all simulations. Also note that since pandas dataframes are 2D any 3D data will be flattened. For example 3D vectors which will be saved into three columns in the dataframe. E.g. r[0], r[1], r[2].

Scientific Software - Peer-reviewed - Python
Published by melund almost 5 years ago

AnyPyTools - AnyPyTools version 1.4.7

• Ensure that 'nan' values returned from AnyBody are treated as "float('nan')" when returned to Python.

Scientific Software - Peer-reviewed - Python
Published by melund about 5 years ago

AnyPyTools - AnyPyTools version 1.4.6

Scientific Software - Peer-reviewed - Python
Published by melund almost 6 years ago

AnyPyTools - AnyPyTools version 1.4.5

Fixed a small issue with using AnyPyTools with pytest 6.0.0rc1

Scientific Software - Peer-reviewed - Python
Published by melund almost 6 years ago

AnyPyTools - AnyPyTools version 1.4.4

• Addressed a deprecation warning from pytest plugin due to API change in pytest 5.4
• Fix a syntax warning triggered in Python 3.8

Scientific Software - Peer-reviewed - Python
Published by melund almost 6 years ago

AnyPyTools - AnyPyTools version 1.4.3

Fixed regression with Python 3.8 where model output could not be serialzed.

Scientific Software - Peer-reviewed - Python
Published by melund almost 6 years ago

AnyPyTools - AnyPyTools version 1.4.2

Fixed:

• A potential bug when using the pytest plugin and expected errors in AnyScript test files.
• Fixed a bug with the pytest plugin not working with pytest 5.4

Scientific Software - Peer-reviewed - Python
Published by melund about 6 years ago

AnyPyTools - AnyPyTools version 1.4.1

• Fixed a bug where log files would be removed even if the processing failed.

Scientific Software - Peer-reviewed - Python
Published by melund over 6 years ago

AnyPyTools - AnyPyTools version 1.4

• Progressbars are now draw using tqdm <https://github.com/tqdm/tqdm>__. This enables error messages while the progress bar is rendering, and solves a problem with detecting when the code is running in Jupyter notebook and not.
• Running the pytest plugin with the --anytest-save argument now deselects all tests which doesn't save data to HDF 5 files.
• New option for running the GUI version of AMS with AnyPyTools instead of the console.
• Task meta info (i.e. task_logfile, task_macro etc.) are now hidden by default in the when printing the object witht the default __repr__()
• The return_task_info argument to AnyPyProcess class is now deprecated and task information is always include in the output.

Scientific Software - Peer-reviewed - Python
Published by melund over 6 years ago

AnyPyTools - AnyPyTools version 1.3.0

Changed: - Changed the interface for the pytest plugin when saving hdf5 files from anybody tests.

Scientific Software - Peer-reviewed - Python
Published by melund over 6 years ago

AnyPyTools - AnyPyTools version 1.2.2

• Fixed problem with Ctrl-C events not working. scipy.stats used some fortran routines which hijacked the key event and caused a crash instead.

• Fixed an issue with process time not being reported correctly.

• Fixed an issue with macros which were a mixture of normal strings and macro-command helper classes from anypytools.macro_commands.

Scientific Software - Peer-reviewed - Python
Published by melund over 6 years ago

AnyPyTools - AnyPyTools version 1.2.1

Fixed:

• Add a work-around for a bug in AnyBody <= 7.2.1 which cause the AnyBody console
  to start in interactive mode when launched from AnyPyTools. This could cause the console application to hang if something fails in AnyBody.

Scientific Software - Peer-reviewed - Python
Published by melund almost 7 years ago

AnyPyTools - AnyPyTools version 1.2.0

Added:

• Pytest plugin: Option to set the fatal_warnings variable as a list to select the warnings which should trigger an error.

Removed:

• Deprecated the warnings_to_include variable. Instead, use the fatal_warningsvariable to select specific warnings.

Scientific Software - Peer-reviewed - Python
Published by melund almost 7 years ago

AnyPyTools - AnyPyTools version 1.1.5

Fixed:

• Fix a bug with pytest plugin which caused expected errors to still show up in the error list.

Scientific Software - Peer-reviewed - Python
Published by melund almost 7 years ago

AnyPyTools - AnyPyTools version 1.1.4

Fixed: * Removed an --runslow argument in pytest plugin api, which caused a problem when users needed to set the same argument manually.

Scientific Software - Peer-reviewed - Python
Published by melund almost 7 years ago

AnyPyTools - AnyPyTools version 1.1.3

Added:

• Add an option to add pytest markers to in the AnyScript test files. This is done by setting pytest_markers=["slow"] in the header. It is the same as decorating Python tests with @pytest.mark.slow.

Scientific Software - Peer-reviewed - Python
Published by melund about 7 years ago

AnyPyTools - AnyPyTools version 1.1.2

Added:

• Add an option to the pytest plugin to set the debug_mode for the console application.

Fixed:

• Pytest plugin can now handle new error messages from the upcoming AnyBody Modeling System 7.2.

• Deprecation warnings from using abstract base classes in the Python collections module.

Scientific Software - Peer-reviewed - Python
Published by melund over 7 years ago

AnyPyTools - AnyPyTools version 1.1.1

Fixed:

Fix bug in pytest plugin when pytest-xdist is installed.

Scientific Software - Peer-reviewed - Python
Published by melund over 7 years ago

AnyPyTools - AnyPyTools version 1.1.0

Added:

• Added an logfile argument to the app.start_macro() function. This allow for setting an explicit name for a log file. If start_macro() runs muliple instances the logfile will have the task number appended.
• Added debug_mode option to the AnyPyProcess class. This will the debug mode of the console application (e.g. the /deb # flag).

Scientific Software - Peer-reviewed - Python
Published by melund over 7 years ago

AnyPyTools - AnyPyTools version 1.0.1

Fixed:

• Fixed a problem with pytest plugin when the pytest-xdist plugin is missing.

Scientific Software - Peer-reviewed - Python
Published by melund over 7 years ago

AnyPyTools - AnyPyTools version 1.0.0

Changed:

• Source code now formatted with black formatter.

Added:

• Added a feature to the pytest plugin to save HDF5 files when running AnyScript tests. The purpose of this feature is to easily generated data for comparing the simulation of two different models or the same model with a different version of AMS.

Removed:

• Support for legacy Python (2) was dropped. This also removes the dependency on the future package.

Fixed:

• Fixed a regression when accessing the output of the start_macro command (AnyPyProcessOutputList) for aggregated results across multiple macros.

Scientific Software - Peer-reviewed - Python
Published by melund over 7 years ago

AnyPyTools - AnyPyTools version 0.14.1

Fixed:

• Make sure anypytools works in IPython/Jupyter even when ipywidgets is not installed.
  
• Fix problem with exporting (dump) variables which are references in the AnyBody Output structure. Now the variables will have the same name in the output as given in the dump command.
• Fix problem with log-files beeing removed if AnyBody crashed or exited unexpectedly.
  
• Fixed issue with building documentation with sphinx 1.8.
  

Added:

• Added a simple functionality to save hdf5 files from the pytest plugin.

Scientific Software - Peer-reviewed - Python
Published by melund over 7 years ago

AnyPyTools - AnyPyTools version 0.13

Fixed:

• Fix regression in for :class:AnyPyTools.macro_comands.SetValue_random which caused a crash when generating macros.

Scientific Software - Peer-reviewed - Python
Published by melund almost 8 years ago

AnyPyTools - AnyPyTools version 0.12

Fixed:

• Missing newlines in error output from pytest plugin.
• Fix a problem where the ignore_errors argument to :class:AnyPyProcess() could not filter warnings when they were considered as errors with the fatal_warnings arguments.

Changed:

• Better error message when anybodycon.exe can not be found.

Scientific Software - Peer-reviewed - Python
Published by melund about 8 years ago

AnyPyTools -

Scientific Software - Peer-reviewed - Python
Published by melund over 8 years ago