v3.0.0

🎆 Major Changes

• Removed geometry and physics modules
• Removed use of Geometry and Physics objects
• Moved plot functions from topotools to a new visualization module
• Removed materials and metrics modules in favor of creating detailed examples
• Removed the term Generic from all class names to improve readability #api

🚀 New features

• Added a solvers module containing classes that define a generic api for using arbitrary numerical solvers
• Added an integrators module containing classes that define the api for transient solvers
• Added a wrapper to leverage the scipy.integrate.ivp_solve function for transient problems
• Added Demo network generator which includes geometry models already assigned and ready for instant use
• Added official support for mixtures, including pore-scale models for first-approximation calculations of pure and mixture properties
• Added topotools.find_interface_throats to find throats between two sets of pores
• Added SteadyStateSolution class for storing the results of steady state algorithms
• Added TransientSolution class for storing results of transient algorithms at each time step, including ability to interpolate between times
• Added mechanism to declare any property to be variable (i.e. a function of the solved quantity)
• Added a params attribute to all objects for storing scalar values and constants
• Added support to the dictionary objects for pn['param.foo'] which looks up values from pn.params['foo'] in a way that works seamlessly with existing pore-scale models
• Added x as a property to Transport classes for easy access to the solved quantity
• Added ability to compute the physical properties of arbitrary pure gases and liquids using correlations from the chemicals package
• Added a framework for computing properties of mixtures as a function of composition using correlations from the chemicals package
• Added generate_voxel_image to visualization module
• Added a set of pore-scale topology models under models.network
• Added plot_network_jupyter function to visualization module which creates an interactive visualization using Plotly
• Created a contrib folder/module for putting experimental and beta features, and well as contributions before they are adopted into the main code base
• Added TransientMultiPhysics class to the contrib folder
• Added new plot_network function based on vispy to contrib folder
• Revised the settings attribute on objects to work more like python's dataclasses with settings as attributes, while also enforcing their type

🍰 Enhancements

• Adopted rich package for formatting logger messages
• Added ScipyCG to the solvers module (uses scipy.sparse.linalg.cg)
• Added intersecting_cones/pyramids size factor models, as well as hybrid cones_and_cylinders which adopt intersecting cones/pyramids as needed
• Re-implemented the percolation algorithms for better consistency between them
• Added call method to ModelWrapper so they can run themselves directly with zero effort by user
• Enhanced BV formulations to allow variable number of electrons
• Created openpnm.models.collections containing dict files of preset models for all sub-classes to simplify instantiation
• Allowed setting of default solver in the workspace.settings
• Enhance _validate_data_health to account for throats without an assigned conductance model
• Augmented getitem on dictionaries to return a numeric value if used as a key, so pn[1.0] returns 1.0. This allows passing in scalar values to pore-scale models with no need to assign that scalar to all locations first
• Add tqdm progress bar for Newton iterations in ReactiveTransport
• Added asmask argument to neighbor lookup functions
• Added ability to delete nested/hierarchical keys simultaneously (i.e. del obj['pore.nested'])
• Added a pore-scale model function for generating values according to a given a histogram
• Added a check for stall in ReactiveTransport
• Relaxed convergence checks in ReactiveTransport to facilitate iterative solves
• Project, models, and settings are now pretty-printed when evaluated at REPL (IPython console)
• Updated math functions in misc to accept an array of props instead of individual args
• added get_conduit_data method to Base class
• Enhanced versioning so that dev builds get their own "build number" as X.Y.Z.devN

🔧 Maintenance

• Got code coverage to 90%
• Removed several minor dependencies including flatdict which is no longer maintained
• The dependencies in requirements.txt are now synced with those in setup.py
• Stopped getting logger from root level to prevent interfering with other packages' outputs
• Fixed exporting transient data to paraview to work with new TransientSolution class
• Settings are applied after calling super().init and they are no longer passed up the init chain
• Moved iterative props machinery to Algorithm
• Fixed string splitting at dots to work better with multi-dot name
• Improved handling of missing keys on Phase objects for cleaner tracebacks when autointerpolation is enables
• Major refactor of topotools module into library of functions requiring no openpnm specific classes
• Modules/submodules in setup.py are now automatically filled using setuptools package
• Replaced for-loop with numpy unbuffered operations in surface area models
• Reorganized openpnm.models.misc/phase/physics modules to keep namespace clean
• Removed relaxation_source from ReactiveTransportSettings as we no longer apply relaxation to source term
• Leveraged __all__ functionality throughout code to control imports of functions
• Added a runtime check to see if x0 contains infs/nans
• Refactored Transport to put boundary condition functions in a mixin
• Added unit tests for Salome, COMSOL, and STL I/O classes
• Changed regenerate_models to work when models lack regen_mode argument
• Removed cache_b, changed cache_A to cache since b is very small
• Removed numba deprecation warning
• Updated list of rules to be ignored by flake8 style check
• Removed freeze_models option from ModelsMixin
• Deleted many unused functions from utils.misc
• Added style check workflow to actions
• Refactor Transport and subclassed algorithms' run method
• Switched to scipy's convergence checker
• Refactor of set_label
• Removed "internal" label from Bravais and CubicDual
• Broke up Base class into several mixins for more control of inheritance #maint

⚠️ API changes

• Complete removal of Geometry and Physics objects, in favor of Network and Phase handling all related data and models directly
• Renamed models.topology to models.network
• Removed PETSc solver wrapper (needs to be revisited)
• Removed MixedInvasionPercolation(Coop) and OrdinaryPercolation algorithms until they can be better supported
• Replaced target keyword with network or phase throughout all pore-scale models, except ones that are truly general
• Conduit properties and now stored as Nt-by-3 arrays instead of dicts
• Changed how source terms are tracked from obj.settings['sources'] to obj[pore.sources'] to be consistent with how boundary conditions are tracked (i.e. alg['pore.bc.rate'])
• Changed the behavior of the mode argument when adding boundary conditions
• Converted the Project class to a minimal pseudo-list, with no extraneous methods inherited from list cluttering the namespace
• Initialization of Base2 objects no longer accepts settings
• Exposed iterative_props, removed set_variable_props
• Removed ModelsMixin from Algorithm since algorithms don't typically need models
• Removed prefix and name from settings
• Refined the Butler-Volmer model formulations to match Newman's book
• Created Drainage class in algorithms with more limited scope to replace OrdinaryPercolation and Porosimetry
• Removed nlin_max_iter from ReactiveTransportSettings in favor of newton_maxiter
• Move Multiphase to contrib folder to indicate it is experimental
• Transport algorithms' run method now returns one or more Solution objects inside dictionary named according to the quantity they contain
• Made network a mandatory argument on phase and algorithm objects
• Renamed tomask and toindices to to_mask and to_indices since the underscore is the common convention in other packages like pandas
• Moved get_domain_area and get_domain_length from attributes on transport algorithms to topotools, for more general use
• Made phase a mandatory argument in algorithms instead of allowing it to be set in settings after the fact
• Removed old multiphysics algorithms (PNP) in preparation for new approach
• Removed effective property calculation methods from Transport since these can be computed by users themselves
• Complete rewrite/redesign of linear solvers and transient algorithms
• Added a Solution object for returning data from algorithms
• Added a Solver class to handle matrix math which is passed as an argument to run methods
• Removed StickAndBall geometry class (use SpheresAndCylinders instead)
• Removed classic_ordinary_diffusion and classic_hagen_poiseuille conductance models
• Refactored conductance models to work with size factors rather than shape factors
• Removed redundant sympy source models and made generic one much easier to use
• Removed num_points argument from Delaunay/Voronoi classes in favor points=int
• Removed spacing and shape attribute from Cubic and moved to topotools as functions
• Removed setup method from algorithms in favor of adding to settings attribute directly
• Deprecated models.geometry.pore_area/throat_area in favour of pore/throat_cross_sectional_area

🐛 Bugfixes

• Calling regenerate_models on a mixture now first regenerates each component
• Fixed a critical bug in duplicate_throats
• Fixed color_by argument in plot_coordinates/connections to accept partial list of values if pores/throats specified
• Fixed ReactiveTransport's run method to accept instantiated solver, not the class itself
• Fixed a bug in XDMF output where dimensions were reversed
• Fixed bug in lens and pendular_ring models
• Fixed bug in Transport to properly check for connected network including connections with boundary conditions
• Fixed regex bug in setup.cfg that broke the 4th digit counter

📗 Documentation

• Reorganized examples folder and documentation website
• Refactored and automated generation of the documentation
• Completely rewrote examples to form comprehensive tutorials and reference docs
• Fixed module docstrings to satisfy sphinx
• Updated list of options in docstrings to use tables
• Applied docrep and matplotlib's substituion throughout the package to make docstrings more consistent
• Removed tables of classes, methods and attributes from docstrings, and moved to sphinx docs instead
• Fixed hydraulic conductance equation in docstring