v0.3.3

• Rewrite effectors specs with default values

• do not raise error if HI transition impossible

• adds sheet_from_cell_centers and various point generators

• adss "normals" method to extrude

0.3.3rc1

version 0.3.3rc1 (#127)



* remove boost version constrain in environment.yml

* sets ref_effector as optional in model_factory

* fixes #120

* fixes uncaught bug in find_IHs

* refactored solver 

* new topo_changed attribute

* Bug fixes with solver decorators, history refactoring

* reindroduced segment assignement after IH

0.3.2

Fixes a bug in generation.ellipsoid_sheet

0.3.1

New features

• Neighborhood code for cells (eptm.get_neighbors and eptm.get_neighborhood)

• added a ClosedSheetGeometry class

Bug fixes

• fixed bug introducing nan values in cell history

• debugged IH transition and HI transitions decorators

• fixed default list of datasets in io.hdf5.load_datasets

• pass specification as optional in Monolayer

• fix bug in get_outer_sheet

• fixed bugs in lumen volume

• fiexes bug in get_opposite_faces

0.3.0

What's new in 0.3

Solvers

The solvers.quasistatic.QSSolver class provides a refactored solver that includes automatic Type 1, Type 3 and collision detection solving after each function evaluation. Use it with:

solver = QSSolver(with_t1=True, with_t3=True, with_t3=True)
solver.find_energy_min(sheet, **minimize_kwargs)

The function signature is a bit different from the previous sheet_vertex_solver.Solver as key-word arguments are directly passed to scipy minimize function. You thus need to replace:

solver_kw = {'minimize': {'method': 'L-BFGS-B',
                          'options': {'ftol': 1e-8,
                                      'gtol': 1e-8}}}
solver.find_energy_min(sheet, **solver_kw)

by:

solver_kw = {'method': 'L-BFGS-B',
             'options': {'ftol': 1e-8,
                         'gtol': 1e-8}}}
solver.find_energy_min(sheet, **solver_kw)

to use the new solver.
Note that sheet_vertex_solver.Solver is still available.

Behavior

Event management refactoring

We refactored event management with a keyword arguments only design to make passing complex parameter dictionnaries easier.

Actions and events where added for monolayer objects.

There is now an option in the manager append methods kwargs to add unique event or not.

Licence

We switched to GPL to be able to use CGAL without worrying. If this is
a problem to you, we can offer accomodations.

Vizualisation

The use of the top level draw.sheet_view function is encouraged. It is now possible to specify visibility at the single face level with a "visible" column in the face DataFrame.

Core

• Added a History class to handle time series of sheet movements

Geometry

• Lumen volume calculation on a new geometry class (#110)
• Create a new segment vertex category : lateral in Monolayer
• adds finally statement to scale_unscale utils
• Change 'sagittal' key word by 'lateral' key word

Dynamics

New quasitatic solver class.

New effectors

• Add LumenVolumeElasticity effector
• added SurfaceTension effector

Bug fixes

• reset catched ValueError to Exception waiting for pandas to publish 0.24
• Better opposite management and validation for Sheet, closes #72
• Correction of color face (#85)
• fixes reset_specs warning formatting bug
• Correction of segment category for new faces create in IH transition

Misc

The codebase now uses black to format all the code base.

Pruning

• removed old isotropic model
• removes multisheet (#105)

0.3.rc5

don't raise for git_revision exception in setup.py'

v0.2.3

• Bug fix with 2D area grad
• Early support (not yet tested) for periodic boundary conditions

0.2.2 release

intermediary release to enjoy latest functionalities in conda

0.2.1

Sets integer instead of bool as defaults for masks

0.2 release

This is a major release.

Notable changes from 0.1

Model factory and effectors

We changed completely the way models are defined. For the quasi-static models currently supported, the models are defined through a model_factory function that collects a list of effector objects, defining the individual interaction. This way, it is easy to change the model components "on site".

New EvenManager mechanism in tyssue.behavior

Letting go of the ugly time_table mechanism, it should be easier to define adaptable event sequences

Generation as a separate module

Note that from tyssue.core.generation import ... should be replaced by from tyssue.generation import ...

get_opposite moved from core.object to sheet

It is also now a method of Sheet

Note You need to change from tyssue.core import get_opposite to tyssue.core.sheet import get_opposite

Ellipsoid geometry, derived from cylindrical, and ellipsoid generation functions

Most of the Reveresible Network Recombination from Okuda et al has been implemented

3D models are well supported (for division and I-H / H-I transitions. Some work as yet to be done on quasistatic models