changelog.md

What's new in 0.8.0

Core

• Set an "id" column by default
• Add force inference algorithm in sheet class, based on method describe in Brodland et al. 2014.
• New get_simple_index to "quickly" get a non-oriented, full edge representation of the epithelium
• New euler_characteristic function to asses wether polyhedrons are closed

Geometry

• Add two new geometry classes.

History

• Fix drop index name in retrieve method.
• Make HistoryHdf5 record every columns by default

Behaviors

• Removes the sheet_events.relax deprecated function

Dynamics

• More coherent use of is_active

Topology

• close_cell now raises an error if the cell has more than one hole
• changed the algorythm for 3D cell division to have a more robust way to attribute faces to the daughter cells (see return_verts argument in get_division_edges)
• do not check for condition_4 on division

Generation

• Adds a Lloyd relaxation step for spherical sheet generation (needs to be generalized)

What's new in 0.7.0

Coordinate system and vertex ordering

• Added "rx", "ry", "rz" columns, reprensenting the source vertex positions relative to face center
• The face_projected_pos method has been rewritten with a much faster implementation.
• There is now a "phi" angle representing the angle in the face plane.
• There is a new order optional parameter to reset_index and sanitize that re-indexes edge_df such that the vertices for each face are contiguous and ordered clockwize in the face plane.
• The face_polygons method benefits from this rewrite, so does the 2D sheet_view.

Quasi-static solver

• Added periodic boundary conditions support

Generation

• adds spherical sheet and monolayers from CGAL

Install

• CGAL-less version installable with pip

Geometry & Dynamics

• New geometry classes
• BorderElasticity, RadialTension, and BarrierElasticity effectors
• Effectors now take nested dictionnaries as specs, instead of dictionnary of sets:

    specs = {
        "face": {
            "is_alive": 1,
            "perimeter": 1.0,
            "perimeter_elasticity": 0.1,
            "prefered_perimeter": 3.81,
        }
    }

Instead of the previous:

    specs = {
        "face": {
            "is_alive",
            "perimeter",
            "perimeter_elasticity",
            "prefered_perimeter",
        }
    }

This allows to give default values to the paramters directly in the effector class definition, and to have a specs attribute for the model directly.

A warning is raised if the effector definition uses the old style.

• Cell division on periodic boundary conditions

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)

What's new in 0.5

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.

What's new in 0.4

Time dependant solvers

• Added two time-dependant solvers solvers.viscous.EulerSolver and solvers.viscous.IVPSolver -- see the demo

• Added a connectivity matrices module

• removed layer type 1 transition (maybe a bit harshly)

• rewrote effectors specification with default values

• added a merge_border function to put single edges at a 2D sheet border, and a trim_borders option to the sheet.remove() and sheet.sanitize() methods

Pipes

• collision detection should now be an optional dependency
• doc/notebooks is now synched with the tyssue-demo repo
• new make nbtest uses nbval to run the notebooks under pytest (provinding some kind of integration tests)

What's new in 0.3.1

• Collision detection also works for the outer layers of bulk tissues, i.e. collisions of the apical or basal surfaces are avoided for a monolayer.

• Added get_neighbors and get_neighborhood method to Epithelium to allow local patch queries in bulk epithelia (was initially only possible for 2D sheets).

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)
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)