- fixed bug where the plotting method ODESystem.plot_continuation would throw an error when PAR(14) was used as the time parameter for the x-axis
- fixed bug where the merging of branches caused the wrong diagnostic files to be pulled up for determining the solution stability / eigenvalue spectrum
- added a new utility function get_point_diagnostics in utility.py that extracts the correct diagnostics file from the Auto-07p output for a given solution
- changed get_solution_stability and get_solution_eigenvalues to use the new function in utility.py
- 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)
- debugged the QIF-SFA use example
- added zenodo doi to the readme and documentation
- removed bug with saving additional attributes on the ODESystem instance
- 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
- debugged circle CI config
- added readthedocs source files
- improved integration of pycobi and pandas
- 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
- first official version
- wrapper to Auto-07p
- automated fortran file generation via PyRates
- simplified handling of auto environment variables
- simplified parameter continuation
- visualization functions
- save and load results of parameter continuation/bifurcation analysis