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Release V0.3 #1

Merged
merged 19 commits into from
Oct 17, 2022
Merged

Release V0.3 #1

merged 19 commits into from
Oct 17, 2022

Commits on Oct 5, 2021

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Commits on Sep 20, 2022

  1. Graphs, Compats

    skleinbo committed Sep 20, 2022
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Commits on Oct 11, 2022

  1. Bump to v0.3

    Compatibility:
    * GrowthDynamics 0.6
    * Makie 0.17
    * Julia 1.6
    
    Note: Last version compat. w/ GrowthDynamics v0.6
    skleinbo committed Oct 11, 2022
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  2. Introduce TumorInspector

    - controls for radius filter
    - controls for plane view
    skleinbo committed Oct 11, 2022
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  3. Introduce slice plot

    A second plot is displayed underneath the 3d plot
    that shows a slice through a plane.
    If `plane` is not `nothing` in `tumorplot`,
    coordinates are projected into 2d.
    
    Controls are added to control orientation and
    offset of said plane, specifically:
     - text field for offset from origin (default: lattice midpoint)
     - +/- buttons to increment/decrement offset
     - buttons to orient in x,y,z direction and combinations thereof
    
    Imports are ordered alphabetically.
    LinearAlgebra is imported.
    skleinbo committed Oct 11, 2022
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  4. Restructure ColorMapping, simplyfy color_phylo

    ColorMapping now stores a vector of root genotypes and
    a dictionary mapping every genotype to a color.
    color_phylo rebuilds the latter on every call, making sure that
    root genotypes get assigned the same color again.
    
    Change the default depth in color_phylo from 1 to 2.
    
    Remove `transition` keyword. To be introduced later again.
    skleinbo committed Oct 11, 2022
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  5. color_phylo is the default for coloring

    Remove colormap as a coloring option.
    skleinbo committed Oct 11, 2022
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  6. Introduce color_lineage

    color_lineage colors the children of given root nodes.
    color_phylo is renamed to color_depth
    skleinbo committed Oct 11, 2022
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  7. Improve color_lineages!

    New kwarg `default` to specify a fallback color if a genotype
    is not covered, e.g. because the root of the phylogeny
    isn't in `roots`.
    
    In-place version.
    
    Further:
    - Default palette is based on Julia blue.
    - min_colors only returns transparent for genotype 0.
    skleinbo committed Oct 11, 2022
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  8. TumorInspector type and color settings

    Have TumorInspector(...) return a struct containing
    the figure, subplots, color/plane/radius settings for
    programmatic manipulation.
    
    Introduce color settings.
    - Currently: color lineages and color inner.
    - Control panel for either option.
    
    Radius filter can be switched between = and <=
    skleinbo committed Oct 11, 2022
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  9. Tidy imports from Graphs.jl

    skleinbo committed Oct 11, 2022
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  11. Import Graphs: SimpleDiGraph

    Note: When squashing combine with
    beb8f0d
    skleinbo committed Oct 11, 2022
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  12. Remove Okay/Cancel buttons

    Due to a bug where a call to close(window) results
    in a segfault, the use of either button would frequently result
    in the application crashing. Close the window with the title bar
    controls.
    skleinbo committed Oct 11, 2022
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  14. Multiple changes

    * calculate markersize from neighbor distance
    * FCC vertex
    * GeometryBasics v0.4
    * missing imports
    skleinbo committed Oct 11, 2022
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  16. Compat GeometryBasics v0.4

    skleinbo committed Oct 11, 2022
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  17. Compat (again)

    Fixes accidental reversion of earlier compat
    changes.
    skleinbo committed Oct 11, 2022
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