Changelog

This is link to the CHANGELOG available at GitHub repository.

implemented support for complex variable types. Pass the keyword argument “float_precision=complex” to the ODESystem.from_yaml or .from_template commands in order to generate complex-valued model files.

updated how summaries of solution branches are generated to save computation time (results are now merged first, such that a summary is created only once)
fixed a minor bug with the extraction of solutions via their keys
improved how the continuation direction for automated bidirectional continuations is handled

added a method ODESystem.from_template that allows to instantiate ODESystem from a pyrates.CircuitTemplate
method ODESystem.from_yaml now creates a pyrates.CircuitTemplate from a YAML file first, and then passes it to ODESystem.from_template
updated CircleCI config: Dropped support for Python 3.6, added support for Python 3.10

updated readthedocs configuration
updates to ODESystem.extract and the plotting functions that use it: Users can now flexibly switch between using the parameter/variable indices when specifying the variables to plot, or whether they want to use the pyrates-style naming scheme
added option to ODESystem.run to store only the minimum and maximum of each selected state variable for periodic solutions (set keyword argument reduce_limit_cycle=True)
debugged scenario where initial condition was run, but not explicitly labeled, which caused issues with extracting starting points from the solution branch
debugged issue with selecting specific variables and parameters that should be saved in the continuation summary
added private method ODESystem._map_var that ensures stable mapping between user-provided variable names and intrinsic variable names

Bug fix for the new parameter naming system: ODESystem now accounts for the blocked Auto-07p parameter vector entries

updated plotting method ODESystem.plot_continuation: It can now automatically plot a legend for all bifurcation points in a bifurcation diagram
Keyword argument added to ODESystem.plot_continuation: “bifurcation_legend” can be set to True or False to turn bifurcation type legends on/off
Bifurcation markers are now plotted via the matplotlib.pyplot.plot function rather than the matplotlib.pyplot.scatter function

updates of the readthedocs requirements
minor bugfix in “pycobi.py”, where the new variable/parameter naming changes from 0.8.0 were interfering with the old naming system

added mapping functionalities that allow to use the pyrates-based names for variables and parameters in the model rather than the auto naming style
implemented the changes with the ODESystem.run and ODESystem.extract methods
dataframes return by ODESystem.run now contain the pyrates-like variable names in the column header
ODESystem.__init__ now takes a couple of new arguments: The “eq_file” is a positional argument that ties an ODESystem instance to a single fortran equation file. “params” and “state_vars” allow to provide the parameter and state variable names that can be used instead of the indexing style of auto.
the parameter and state-variable names that can be provided to the ODESystem.__init__ method can be directly obtained from the CircuitTemplate.get_run_func that is also used by the ODESystem.from_yaml method.

added a bugfix that allows to merge solution branches that included multiple branches that might arise from a automated switching at a branch point
fixed a bug with the readthedocs website not displaying math correctly
updated version dependency on numpy (enforced by issues between the newest version of numpy and Auto-07p)

improved docstrings of all public methods of ODESystem
moved most static methods of ODESystem to a separate utility package
added API section to readthedocs documentation
moved period doubling continuation and automated 2D bifurcation analysis to extra package automated_continuation

added use example for the QIF-SFA model to the documentation
improved support for pandas.DataFrames as the main results storage data type
added the pyrates model template as an attribute to the ODESystem
added the option of clearing all generated fortran/auto files via the ODESystem.close_session() method

summaries of parameter continuations are now stored and returned as pandas.DataFrame instances
added ODESystem.__getitem__ method that allows to directly access parameter continuation summaries via their keys
added ODESystem.close_session method that changes the working directory of the system to the directory prior to initialization of ODESystem
added possibility to call pytest scripts with auto-07p directory as additional command line argument (–auto_dir)
updated gitignore
added new tests

added new badges to the readme
added official support for Python 3.9
added CircleCI config
removed bug from the ODESystem.from_yaml method, where the run function was generated for a discrete time-step solver by default

debugged PyPI integation

changed package name from PyAuto to PyCoBi