Reece Hart

Use pytest fixtures rather than instantiating new conections

1

``` snafu$ for w in 'connect(' VariantMapper AssemblyMapper Normalizer Validator; do printf "%d $w\n" $(fgrep $w tests/*.py|wc -l); done 18 connect( 16 VariantMapper 15 AssemblyMapper 11 Normalizer 10 Validator ```...

The hgvs test code was based on unittest and nose. Now that we've switched to pytest, there are many places where we can clean up the home-brewed looping over test...

Some tests create a parser for each test. That's extremely expensive. Instead, use a fixture with session scope. Example: test_hgvs_alignmentmapper.py creates 6 parsers where one would suffice.

Clean-up testing

2

The hgvs package has many tests, including many tests for essentially the same code paths. For this issue * Make per-gene tests optional. Instead, test by functionality. * Fail fast....

The models are sprinkled through the top level. Instead, move them to hgvs/models and have a single import for them.

Enable additional / alternative config via environment variables

3

config.py reads the default config file from _data/defaults.ini. We should provide a mechanism to also read a custom config file (e.g., specified by env var `HGVS_CONFIG_FILE`) that overrides values in...

Provide utility to generate transcript variants from HGVS-ish expressions with gene names

7

Unfortunately, some authors generate bogus HGVS expressions that use gene names rather than reference sequences. This issue should provide functionality to generate plausible expressions. For example for TNFSF1A has 4...

Implement hgvs babelfish: hgvs ↔ {vcf, vmc, spdi, beacon, brcaexchange}

3

There are several alternative variant formats. This issue intends to implement a module to facilitate conversions between those and the hgvs data model. Planned formats: * vcf * [vmc](https://github.com/ga4gh/vmc) *...

Add tests for RefAlt representations

3

While testing representations for identity variants for #424, I wrote a script (`misc/refalt-repr-examples.py`) to summarize representations for mock variants. Although we have some existing representation tests, these examples should be...

implement linters / static analyzers

2

See https://jeffknupp.com/blog/2016/12/09/how-python-linters-will-save-your-large-python-project/