0.6.8

Removes a bad tag in cmake

0.6.7

Make CGAL optional, Pure python installs with PyPi and conda-forge

0.6.4

Bug fix with CGAL5.0

0.6.3

mainly bug fix, attempting to simplify conda-feedstock install

0.6.2

Mainly bug fix

0.6.1

Modified spherical monolayer creation

0.6.0

What's new in 0.6.0

Topology

Some bug fixes for 3D rearangements

Collisions

Puts an exact kernel in c_collisions.cpp

We switched to CodeCoV for coverage reports (purely from hype/style motivations)

SolverIVP disapeared

In the absence of a clear way to deal with rearangement, we had to let this go for now, it may come back later...

Behaviors

• We add two basics function in actions for sheet tissue : increase and decrease. In the near future, we will removed deprecated function that increase and decrease will replace (such as growth, shrink, contract and relax).

History and HistoryHdf5

• new HistoryHdf5 class that records each time point in a hdf file instead of in memory.

• new browse_history function that creates a widget to slide through the different time points with an ipyvolume 3D view

Draw

• the color entries in edge and face specs can now be functions that take a sheet object as sole argument:

specs = {
    "edge":{
        'color':'lightslategrey',
        'visible':True
    },
    "face":{
        'color': lambda sheet : sheet.face_df["apoptosis"],
        'colormap':'Reds',
        'visible':True
    }
}

This way, the color is updated at each function call, without having to define a new function.

Utils

• new get_next function returns the indexes of the next half-edge for every edge (e.g the edge whose srce is the trgt of the current edge)

0.5.0

Major rewrite of the rearangements

We now allow for rosettes to form, and split type1 transition in two steps: merging of edges bellow the critical length and spliting more than rank 3 vertices (or more than rank 4 in 3D). The splitting frequency is governed by two settings p_4 and p5p.This follows Finegan et al 2019. See doc/notebooks/Rosettes.ipynb for a demo.

A look a the diffs in sheet_topology and bulk_topology should convince the reader that this should result in a major increase in stability.

Automated reconnection is now treated as an event (treated by an EventManager instance), see tyssue.behavior.base_events.reconnect.

In EulerSolver, this avoids raising TopologyChangeError at least in explicit Euler. Topology changes in IVPSolver are not supported for now.

Viscous solver

• added a bounds attribute to EulerSolver. This simply clips the displacement to avoid runaway conditions.

Core and topology

• A new update_rank method allows to compute the rank of a vertex (as the number of flat edges connected to it). This required to move the connectivity module to utils to avoid circular imports.

• We explicitly allow two sided faces to be created by collapse_edge or remove_face, they are directly eliminated.

0.4.0

Fixed readthedocs pipe and some bugs

0.4.rc1

Update requirements.txt