Changelogs » Anypytools

PyUp Safety actively tracks 362,670 Python packages for vulnerabilities and notifies you when to upgrade.



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


  - Fixed pytest deprecation warnings.


  - 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.


  - Update documentation to use markdown.
  - Add error message when no files are found with
  `search_subdir` arguments (fixes [69](


  - Fix deprecation warnings in pytest plugin.


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


  - 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.
  app =  AnyPyProcess()
  results = app.start_marco(macro_list)
  df = results.to_dataframe(
  - Documentation on how to use the `to_dataframe()` method has been added to the tutorials.


Add methods for exporing simuation output as a pandas dataframe.
  app =  AnyPyProcess()
  results = app.start_marco(macro_list)
  df = results.to_dataframe(index_var="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]`.


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


Fixed a bug when using explicit logfile arguments to `start_macro` did not work with the
  `search_subdirs` argument.


Fixed a small issue with using AnyPyTools with pytest 6.0.0rc1


Adressed a deprecation warning from pytest plugin due to API change in pytest 5.4


Fixed regression with Python 3.8 where model output could not be serialzed. This
  happend because empty folders (represented by "...") would become the python elipsis object.


  - 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


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


  - Progressbars are now draw using [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.


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


  - 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`.


  - Add a work-around for a bug in AnyBody \< 7.2.2 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.


  - Pytest plugin: Option to set the `faltal_warnings` variable as a list
  to select the warnings which should trigger an error.
  - Pytest plugin: Deprecated the `warnings_to_include` variable. Instead use the `fatal_warnings`
  variable to select specific warnings.


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


  - Removed an `--runslow` argument in pytest plugin api. This setting caused problem when the user defined it them self.


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


  - Add an option to the pytest plugin to set the `debug_mode` for the console application.
  - 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 collection module.


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


  - 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).


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


  - Source code now formatted with [black]( formatter.
  - 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.
  - Support for legacy Python (2) was dropped. This also removes the dependency on the `future` package.
  - Fixed a regression when accessing the output of the `start_macro` command
  (`AnyPyProcessOutputList`) for aggregated results across multiple macros.


  - Minor problem with building documentation with sphinx 1.8.


  - Make sure anypytools works in IPython/Jupyter even when ipywidgets is not installed.
  - Fix problem with dump'ing 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.
  - Added a simple functionality to save hdf5 files from the pytest plugin.


  - Fix regression in for {class}`AnyPyTools.macro_comands.SetValue_random` which caused a
  crash when generating macros.


  - 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`
  - Better error message when `anybodycon.exe` can not be found.


  - Pytest plugin adds support for specifying `warnings_to_include`,
  `fatal_warnings` in the header of AnyScript test files.
  - The output from pytest plugin is restructured to be more readable.


  - Added option to the set the priority of the macro operations.
  The option is an argument to {class}`AnyPyProcess()`.
  from anypytools import IDLE_PRIORITY_CLASS
  app = AnyPyProcess(priority = IDLE_PRIORITY_CLASS)
  Default is `BELOW_NORMAL_PRIORITY_CLASS`, and possible values are
  - Added argument `fatal_warnings` to {class}`AnyPyProcess()` which
  treat warnings as errors when running macros.
  app = AnyPyProces(warnings_to_include=['OBJ.MCH.KIN9'], fatal_warnings=True)
  The argument will only triggers for specific warnings given
  by `warnings_to_include` argument.
  - Macro operation now run with slightly lower priority (BELOW_NORMAL_PRIORITY_CLASS) to prevent
  Windows to become unusable when running many processes.
  - Fixed a bug preventing really large variables to be read by AnyPyTools. The AnyBody Modeling System
  could split really large data matrixes across several lines in the log files which meant they
  were not picked up. The function {func}`` has been
  rewritten to fix this.
  - The AnyScript Pygments plugin is no longer part of AnyPyTools. It now has its own library


  - Fix crash when `--define` option was not provided.


  - Add option to the pytest plugin, to set the define statements with an argument to pytest.


  - Wrong error report when AnyBody exists abnormally during batch processing.


  - Always append 'exit' command to all macros. Seems to solve problem with AMS not shutting down correctly.
  - Only enable pytest plugin on Windows platform


  - Bug where no AMS license was not detected as a failed macro.


  - Crash when the starting pytest plug-in when no AnyBody licenses are available
  - Pytest plugin support for the `ANYBODY_PATH_AMMR` path statement which will be
  used in the AMS 7.1


  - The pytest plugin can now get the BM configurations directly from the
  AMMR if they are availble. The will be for AMMR 2. This will eliminate
  the problem of keeping AnyPyTools in sync with the AMMR.


  - Update pytest plugin to support AMMR 2.0 Parameters. AMMR 1 parameters
  are still supported using `--ammr-version` argument to pytest.


  - Support new BodyModel statements, which starts and end with a underscore.
  > - Improved exception handling when trying to access data which
  >   is not avaible in the output.
  - Detect if AnyBodyCon exited from a license problem and report
  that in the log files.
  - Refactor `_execute_anybodycon()` into a public function.
  > - Remove the deprecated `disp` argument to the `AnyPyProcess` class.


  - Updates and fixes to the documentation website.
  - Added flake8 testing on Travis CI
  - Fix crash using pytest on systems where git is not installed.


**Merged pull requests:**
  - Fix PEP8 issues and remaining pytest issues
  - Update Documentaion and tutorials
  - Add SaveData MacroCommand for saving hdf5 files
  - Fix Crash on Python 2.7 when using h5py_wrapper
  - Setup Travis-CI for building documentation for publishing on
  - Refactor the library for the new library documention.
  - Added `AnyPyProcessOutputList.tolist()` converting results to native Python
  \[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


\[Full Changelog\](<>)


The before times... See GitHub for a full
  \[Full Changelog\](<>)


\[Full Changelog\](<>)