Teiphy

Latest version: v0.1.11

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0.1.5

With this release, `teiphy` now includes constant sites (i.e., variation units with only one substantive reading, after readings of trivial types have been merged with their parent readings) by default for all output formats (except STEMMA), and constant sites can be excluded from these outputs with the `--drop-constant` option. (But note that if you are using the output with likelihood-based phylogenetic software, you will probably want to use an ascertainment bias correction setting!)

0.1.4

Added code to check for a `listWit` element containing an explicit list of witnesses (and throw an exception if none is found), as well as code to print out warnings for all base sigla that occur in the collation, but not in the `listWit`.

0.1.3

This release incorporates the changes recommended in the _JOSS_ reviewers' generous feedback. These changes include the following features:
- support for date calibration blocks based on witness date ranges
- support for PHYLIP and FASTA outputs (for software such as RAxML)
- `StatesFormat=StatesPresent` is now the default setting for NEXUS output; if `StatesFormat=Frequency` is desired, the `--frequency` command-line option can be used to specify this.
- support for "long table" formatting for tabular output (NumPy, Pandas DataFrame, CSV, TSV, Excel)

This release is also the first release to be tracked by Zenodo.

0.1.2

The version of `teiphy` as submitted to the _Journal of Open Source Software_. Changes since the initial release include support for `origDate` elements containing chronological data under `witness` elements (current only used for conversion to STEMMA format); the addition of a `to_distance_matrix` method that returns a NumPy matrix of distances between witnesses; system tests to ensure that outputs for IQTREE, MrBayes, and STEMMA are validated by their respective programs; and further revisions to the paper and documentation.

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