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ENH: modifications in prep for the documentation (#85)

* MAINT: change app module to importing whole composable module

[CHANGED] this allows us to define different app types

* MAINT: changes in app module to existing

[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.

* MAINT: changes in app module to existing

[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.

* MAINT: changes in app module to existing

[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.

* MAINT: changes in app module to existing

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

[C... (continued)

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