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ENH: modifications in prep for the documentation #85

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Merged
merged 29 commits into from
Nov 7, 2024
Merged

ENH: modifications in prep for the documentation #85

merged 29 commits into from
Nov 7, 2024

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GavinHuttley
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[CHANGED] this allows us to define different app types
[CHANGED] import whole composable module as this allows us to
    define different app types

[CHANGED] make the piqtree_phylo a class to demo benefits
    in terms of the display of user help.

[NEW] added substitution_mode.get_model() function which returns
    the enum given a string or enum. Modified Model to use this.
    This makes it easier for users to define the substitution
    models. A user should only ever have to import cogent3 to
    get everythjing they need from piqtree2.
[CHANGED] import whole composable module as this allows us to
    define different app types

[CHANGED] make the piqtree_phylo a class to demo benefits
    in terms of the display of user help.

[NEW] added substitution_mode.get_model() function which returns
    the enum given a string or enum. Modified Model to use this.
    This makes it easier for users to define the substitution
    models. A user should only ever have to import cogent3 to
    get everythjing they need from piqtree2.
[CHANGED] import whole composable module as this allows us to
    define different app types

[CHANGED] make the piqtree_phylo a class to demo benefits
    in terms of the display of user help.

[NEW] added substitution_mode.get_model() function which returns
    the enum given a string or enum. Modified Model to use this.
    This makes it easier for users to define the substitution
    models. A user should only ever have to import cogent3 to
    get everythjing they need from piqtree2.
[CHANGED] import whole composable module as this allows us to
    define different app types

[CHANGED] make the piqtree_phylo a class to demo benefits
    in terms of the display of user help.

[NEW] added substitution_mode.get_model() function which returns
    the enum given a string or enum. Modified Model to use this.
    This makes it easier for users to define the substitution
    models. A user should only ever have to import cogent3 to
    get everythjing they need from piqtree2.
[NEW] this provides access to the available_... functions

[CHANGED] Added titles to all the tables that get returned
@GavinHuttley GavinHuttley requested a review from rmcar17 October 17, 2024 04:56
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@rmcar17 rmcar17 left a comment

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Looks mostly good, I think we just need to think about how to support things like rate heterogeneity etc. properly with the apps

@rmcar17 rmcar17 merged commit a1e572a into iqtree:main Nov 7, 2024
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2 participants