Fix issue with py.test, doctest, and pandas output #4
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standage
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Sep 11, 2024
This update includes several changes and new features. - A new `refr` module to retrieve reference genome sequences for a specified panel of microhaplotype loci (closes #4) - A switch to a subcommand design for the command-line interface - Additional tests, including tests that depend on `hg38.fasta` not included in the source code distribution. - Extensive refactoring of the core code and tests in support of the previous points
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The pandas output in some doctests was being truncated no matter how wide the terminal is. In any case, we don't want the doctests to be influenced by terminal width. See pytest-dev/pytest#4030 for all the fun details.
This update forces pandas to assume that the terminal is very wide so that it will not truncate or wrap while printing dataframes to the terminal. This only applies to the testing environment. Printing dataframes from an interactive session will still invoke the default pandas behavior, which is probably for the best. The
microhapdbcommand skirts the issue by calling theto_string()method when printing a dataframe.