Refgenconf

Fixed
- Removed use_2to3 for setuptools 58 compatibility.

Fixed

- `tqdm` package dependency issue; [134](https://github.com/refgenie/refgenconf/issues/134)

Added

- `list_seek_keys_values` method that lists values for all seek keys for the specified genome and asset
- `looper_refgenie_populate` looper plugin
- automatic `dir` seek_key support in `RefGenConf.seek` -- if the seek_key does not exist, `.` is returned by default

Fixed

- `RuntimeWarning` which has been raised when `strict_exists` was set to `None` in `RefGenConf.seek` method; [131](https://github.com/refgenie/refgenconf/issues/131)

Fixed

- issue with missing `assets` section in `RefGenConf.list` method. This situation occured after setting genome identity for nonexistent genome

Added

- `RefGenConf.populate` function to support `refgenie populate`
- `RefGenConf.populater` function to support `refgenie populater`
- `RefGenConf.seekr` function to support `refgenie seekr`
- `refgenconf.looper_refgenie_plugin` -- new looper plugin that populates refgenie paths with looper
- tag scanning for disallowed characters: `:`, `/`

Fixed

- issue with dangling symbolic links in `_refgenie_build` directory; [122](https://github.com/refgenie/refgenconf/issues/122)

Changed

- `RefGenConf.seek` to raise `refgenconf.MissingGenomeError`, rather than `yacman.UndefinedAliasError` if a nonexistent genome is specified

**After updating to this version your configuration file and genome assets will not be compatible with the software. Please refer to the [upgrade tutorial](config_upgrade_03_to_04.md) for instructions on how to migrate the config between versions.**

Changed

- instead of using human-readable names as genome identifiers refgenie uses sequence-derived digests in the config
- asset data moved to `data` directory
- asset files are now named after genome digests
- refgenieserver APIv3 is now used for remote assets retrieval
- `RefGenConf.genomes` becomes an `AliasedYacAttMap` object

Removed

- `as_string` and `order` option from `listr` method

Added

- `upgrade_config` function for genome configuration file migrating between versions
- `RefGenConf.compare` method for genome compatibility level determination
- `as_digests` option in `RefGenConf.listr` method
- genome config validation on `RefGenConf` object instantiation stage and on every write
- new progress bar in `RefGenConf.pull`
- `RefGenConf.get_ta`
- numerous `RefGenConf` object properties and methods related to genome aliases handling: `genome_aliases`, `genome_aliases_table`, `alias_dir`, `data_dir`, `get_genome_alias`, `get_genome_alias_digest`, `remove_genome_aliases`, `set_genome_alias`, `initialize_genome`. Refer to [API documentation](http://refgenie.databio.org/en/latest/autodoc_build/refgenconf/) for more specific information.
- `get_asset_table` method, which displays a concise assets table