build(deps): update dendropy requirement from >=4.5.2 to >=5.0.8

[dependabot]

Updates the requirements on dendropy to permit the latest version.

Changelog

Sourced from dendropy's changelog.

Release 4.5.2

• Support for user-specified random seed in RaXML wrapper (thanks @​NoahAmsel)
• MUCH faster label lookup (thanks Sam Nicholls / @​SamStudio8 !)
• Faster birth-death tree generation (thanks @​NicolaDM !)
• Storage of supplemental NEXUS blocks
• Fix type: "PhylogeneticIndependentConstrasts" => "PhylogeneticIndependentContrasts"

Release 4.4.0

• Calculation of birth-death likelihoods.
• Bipartitions inherit rooting state of trees.
• Patristic paths between tips can be tracked in PatristicDistanceMatrix.
• Character column metadata annotations now actually possible.
• Standard character matrix defaults to 0-9 alphabet instead of just 01.
• Reorganization of package directory: from "$HOME/dendropy" and "$HOME/dendropy/test" to more modern "$HOME/src/dendropy" and "$HOME/tests" respectively.

Release 4.3.0

• [SumTrees]: Important bugfix in tracking splits on consensus tree from rooted trees: previously it was possible for a split on the consensus tree to be ignored, resulting in a null (0) edge length and no (0.0) support.
• Added sumlabels.py application.
• Birth-death tree (dendropy.model.birth_death_tree) now allows for preservation of extinct tips.
• Improved performance of character subset export

Release 4.2.0

• 0 branch lengths assigned to randomly resolved polytomies.
• Explicitly set rooting for NJ and UPGMA trees.
• Faster pruning (kyungtaekLIM)
• Fix nesting bug in raised KeyError in basemodel.AnnotationSet.deepcopy (Steve Bond)
• Catch edge case during deepcopy when Edge object has no _annotations (Steve Bond)
• Optimizations and fixes for various population genetic calculations (Andrew Guy)
• newickreader: Parse jplace style edge numbering. (Ben J Woodcroft)
• Calculate probability of gene tree(s) in species trees under the Multispecies Coalescent model.
• New approaches to calculate distances between unlabeled trees of different sizes: dendropy.profiledistance and dendropy.calculate.treecompare.TreeShapeKernel.
• When parsing Newick/NEXUS, allow for internal node labels to be associated with either nodes or edges.

Release 4.1.0

New or Updated Features ^^^^^^^^^^^^^^^^^^^^^^^

-   [SumTrees]: tip-dating/non-contemporaneous tip age assignment using the "``--tip-ages``" argument (http://dendropy.org/programs/sumtrees.html#setting-the-node-ages-of-the-summary-trees).
-   [SumTrees]: "``--min-clade-freq``" applies to all summary targets (i.e., not just consensus trees, but user-specified as well as, e.g. MCCT trees).
-   Fast, flexible, and powerful tree and subtree cloning, extracting only nodes/taxa of interest (http://dendropy.org/primer/treemanips.html#extracting-trees-and-subtrees-from-an-existing-tree).

... (truncated)

Commits

• 0ea048f bump version v5.0.7 -> v5.0.8
• bed0e75 Patch unconverted RST in README
• f8c7312 bump version v5.0.6 -> v5.0.7
• ef56911 Merge pull request #221 from jeetsukumaran/actions-runner
• 717237c Note setuptools pin is a guess
• e1d80ee Put upper bound on setuptools
• 40089e2 Install/upgrade setuptools, don't pin
• d20d598 Further downgrade setuptools
• 1a1b0ed Clean up requirements.txt handling in CI
• 3c00f90 Pin attrs for compat
• Additional commits viewable in compare view

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