Genomics-data-index

* [api]: Fixed creation of a default ete3 NodeStyle that caused errors if there was no X server.

* [api]: Restructured importing of ete3 graphics libraries so that they return an error message only on first use of the particular class (likely due to a missing installation of an X server). This is to allow other portions of GDI to function without installing an X server.

* [api]: Switch to using SeqRepo proxy from `biocommons.seqrepo` and removing dependency on `ga4gh.vrs`.
* [installation]: Remove fixed version of Perl when installing `mlst` as it now leads to package dependency issues.
* [developer]: Removing filtering of warnings.
* [developer]: Moved project metadata into `myproject.toml`.

* [analysis]: Updated conda environments for analysis to use gdi `0.8.0` (required me to release this version first).

* [ci]: Fixed GitHub integration tests.
* [installation]: Switch to the [vcfpy](https://vcfpy.readthedocs.io/) library for parsing VCFs.
* [installation]: GDI now works with Python >= 3.8, < 3.10.
* GDI will not currently work in Python 3.10 due in particular to this issue (https://github.com/etetoolkit/ete/issues/635), which does not exist below 3.10.
* [installation]: Removed restriction on version of snpeff.
* [analysis]: Added option `--no-snpeff-reference-check` to disable reference genome CDS and Protein checking when building snpeff database. To support building snpeff genome databases with problematic genomes (see https://github.com/pcingola/SnpEff/issues/388).
* [installation]: Removed requirement exact version of bcftools and htslib. Now only needs `bcftools>=1.13` and `htslib>=1.13`.
* [installation]: Removed restriction for version of sourmash. Now works with any sourmash version.

* [installation]: Downgraded scipy (`scipy<1.9`) in order to handle (https://github.com/biocore/scikit-bio/issues/1818) for installation of `scikit-bio`
* [installation]: Fix sourmash to be `sourmash<4.4` due to issues with `sourmash search` poducing empty CSV files in some cases.
* [installation]: Fixed `bcftools==1.13` and `htslib==1.13` so that appropriate command-line parameters (filling tags with `-t TYPE`) work. This restriction could later be removed.
* [analysis]: Fixed up order of conda channels for Snakemake pipeline dependencies (was causing installation issues).
* [analysis]: Fixed bug with ambiguous character (N) in indel and adjusted `iqtree` parameters to just use the maximum specified threads instead of measuring optimal threads.