rmcar17 / piqtree2

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DEV: update multithreading branch (#2)

* DEV: don't brew update by default

[CHANGED] because of how homebrew works, this can
    screw up a users system!

* ENH: added piqtree_phylo(bootstrap_reps) argument

[NEW] defaults to None, which means no bootstrap

* ENH: added show_all argument to available_models()

[NEW] On by default, controls whether the full
    list of available models is shown in the
    representation of the returned table.

* ENH: name internal nodes of trees

[CHANGED] this is required to allow the cogent3 trees to be
    serialised as json.

* MAINT: address type hint issue

* DEV: macos only run brew update command during github action

* DEV: additional dependencies in pyproject.toml

[NEW] New feature is to enable download of docs data sets,
    which requires an additional dependency to be installed.

[NEW] Added a doc optional dependency group.

* ENH: add support for downloading sample data sets

[NEW] piqtree.dataset_names() and piqtree.download_dataset()
    functions to list and download sample data sets. The data sets are
    stored in this GitHub issue https://github.com/iqtree/piqtree2/issues/98.

    These functions used in the documentation.

* API: renamed substitution_model to submod_type

[CHANGED] argument names and attribute names

* API: renamed app from piqtree_jc_distances to piqtree_jc_dists

* DOC: fixed Model docstring

* API: added rateType.name property

[NEW] this is just the result of self.iqtree_str()

* API: new methods on model.Model

[NEW] class hashes as str(Model instance), to be used by model finder

[CHANGED]  Model.__repr__() now explicitly references the distinct types

* DEV: use cogent3.app.typing.

[CHANGED] This defn will be adjusted by the cogent3 devs as they migrate to new Alignment class.

* ENH: added new  piqtree_mfinder app for model_finder functionality

[NEW] added a _model_finder.get_model() function for constructing Model
    instances from a IQTREE2 model string.

[NEW] adde... (continued)

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