Create smoke tests

[connoryang1]

• [ ] BUG: dendropy.simulate.popgenism.FragmentedPopulations.generate_sequences (revisit)
• fails on https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/datamodel/charmatrixmodel.py#L998
• works on https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/model/coalescent.py#L761
• [x] dendropy.model.coalescent.discrete_time_to_coalescence
• fails with https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/model/coalescent.py#L74
• when pop_size = None (default), if n_genes <= 1 (integer), or pop_size < 1 (integer)
• [x] dendropy.model.coalescent.log_probability_of_coalescent_frames
• LaTeX doesn't render in documentation
• [x] citep
• [x] Mark gcd() as deprecated and remove internal use (calculate.mathfn)
• also factorial() in calculate.combinatorics
• [x] dendropy.calculate.treesum.summarize_node_ages_on_tree
• fails with https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/calculate/treesum.py#L264
• when checking seed_node
• [x] deprecate allow_negative_edges
• [x] BUG: dendropy.calculate.treesum.count_splits_on_trees (revisit)
• fails with https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/calculate/treesum.py#L317
• when both taxon_namespaces are empty (not equals None)
• so does dendropy.calculate.treesum.consensus_tree (calls count_splits_on_trees)
• [x] add is_mutable to docstring for Bipartition __init__
• [x] dendropy.interop.ete and dendropy.interop.biopython have required imports to test, worth adding to CI?
• [x] dendropy.model.discrete.simulate_discrete_chars and dendropy.model.discrete.simulate_discrete_char_dataset don't seem to work with a DiscreteCharacterEvolutionModel type argument as specified, because no stationary_sample attribute (works with NucleotideCharacterEvolutionModel)
• [x] dendropy.model.parismony.fitch_up_pass requires an argument preorder_node_list but calls it postorder_nodes in docstring https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/model/parsimony.py#L226
• [x] change preorder_nodes to preorder_node_iter and deprecate old kwarg
• [x] dendropy.model.reconcile.ContainingTree.clear https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/model/reconcile.py#L180
• domain_taxa doesn't seem to exist anywhere else in the code
• [x] dendropy.utility.bibtex.BibTexEntry initialization breaks on https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/bibtex.py#L115
• bug: __getattr__ too fancy
• plan to delete BibTexEntry and update basemodel.add_bibtex
• [x] dendropy.utility.container.NormalizedBitmaskDict https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/container.py#L266
• fails with default value fill_bitmask=None
• [x] add deprecation warning if neither arguments are provided
• [x] dendropy.utility.messaging.log_lines https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/messaging.py#L155
• fails with default value level=None
• [x] dendropy.utility.processing.enqueue_stream https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/processio.py#L77
• should this be readline()?
• [x] dendropy.calculate.treesum.TopologyCounter.hash_topology
• AssertionError: Bipartition is mutable: hash is unstable (revisit) https://gist.github.com/Nephrain/e809f613c511afdc3bf063e460ef77d3