Dms-variants

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Added
++++++++
- Added ``utils.tidy_to_corr``.

- Added ``binarymap`` module.

- Added ``globalepistasis`` module.

- Added ``ispline`` module.

Changed
++++++++
- Order of rows in data frames from ``CodonVariantTable.func_scores``.

- Updated ``codonvariant_sim_data.ipynb`` to be smaller and fit global epistasis models, and move plot formatting examples to a new dedicated notebook.

- Changed ``SigmoidPhenotypeSimulator`` so that the **enrichment** is a sigmoidal function of the latent phenotype, and the observed phenotype is the log (base 2) of the latent phenotype.
This change harmonizes the simulator with the definitions in the new ``globalepistasis`` module.
Also changed the input to the ``latentPhenotype`` and ``observedPhenotype`` methods.
Note that these are backwards-compatibility breaking changes.

Fixed
++++++
- Removed use of deprecated ``Bio.Alphabet``

--------

Added
++++++
- Capabilities to parse barcodes from Illumina data: FASTQ readers and ``IlluminaBarcodeParser``.

- ``CodonVariantTable.numCodonMutsByType`` method to get numerical values for codon mutations per variant.

- Can specify names of columns when initializing a ``CodonVariantTable``.

- ``CodonVariantTable.func_scores`` now takes ``libraries`` rather than ``combine_libs`` argument.

- Added ``CodonVariantTable.add_sample_counts_df`` method.

- Added ``CodonVariantTable.plotVariantSupportHistogram`` method.

- Added ``CodonVariantTable.avgCountsPerVariant`` and ``CodonVariantTable.plotAvgCountsPerVariant`` methods.

- Add custom ``plotnine`` theme in ``plotnine_themes`` and improved formatting of plots from ``CodonVariantTable``.

- Added ``sample_rename`` parameter to ``CodonVariantTable`` plotting methods.

- Added ``syn_as_wt`` to ``CodonVariantTable.classifyVariants``.

- Added ``random_seq`` and ``mutate_seq`` to ``simulate`` module.

Changed
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- Changed how ``variant_call_support`` set in ``simulate_CodonVariantTable``.

- Better xlimits on ``CodonVariantTable.plotCumulMutCoverage``.

Fixed
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- Docs /formatting in Jupyter notebooks.

- Fixed bugs that arose when ``pandas`` updated to 0.25 (related to ``groupby`` no longer dropping empty categories).

- Bugs in ``CodonVariantTable`` histogram plots when ``samples`` set.

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Initial release. Ported code from ``dms_tools2`` and made some improvements.