v0.8.8: Bug fixes for extracting the stability of solutions

• 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

v0.8.7: Support for complex-valued model templates

• 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.

v0.8.6: Improved creation of continuation summaries

• 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

v0.8.5: New method for creating ODESystem instances

• 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

v0.8.4: Improved variable name tracking

• 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

v0.8.3: Bugfix for Auto-07p constant counting

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

v0.8.2: Improved bifurcation diagram plotting

• 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

v0.8.1: Readthedocs requirements update

• 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

v0.8.0: New Variable/Parameter 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.

v0.7.3: Code re-organization

• 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