Code refactor

[hrshdhgd]

• Use kghub_downloader as a standard package for downloading resources

  • All new kg download features should be a separate PR in the kghub-downloader repository.

• Run tox and correct all errors

  Currently tox yields the following errors:

• Command: tox -e lint

kg_microbe/transform_utils/uniprot/uniprot.py:1:1: D100 Missing docstring in public module
kg_microbe/transform_utils/uniprot/uniprot.py:9:1: F403 `from numpy import *` used; unable to detect undefined names
kg_microbe/transform_utils/uniprot/uniprot.py:21:7: D101 Missing docstring in public class
kg_microbe/transform_utils/uniprot/uniprot.py:22:9: D107 Missing docstring in `__init__`
kg_microbe/transform_utils/uniprot/uniprot.py:29:9: D401 First line of docstring should be in imperative mood: "Loads Uniprot data from api, then downloads after running once."
kg_microbe/transform_utils/uniprot/uniprot.py:61:9: D102 Missing docstring in public method
kg_microbe/transform_utils/uniprot/uniprot.py:78:9: D102 Missing docstring in public method
kg_microbe/transform_utils/uniprot/uniprot.py:106:9: D102 Missing docstring in public method
kg_microbe/transform_utils/uniprot/uniprot.py:111:9: D102 Missing docstring in public method
kg_microbe/transform_utils/uniprot/uniprot.py:120:121: E501 Line too long (357 > 120)
kg_microbe/utils/download_utils.py:1:1: D100 Missing docstring in public module
kg_microbe/utils/download_utils.py:34:5: D417 Missing argument descriptions in the docstring for `download_from_yaml`: `ignore_cache`, `mirror`, `output_dir`, `snippet_only`, `tags`
kg_microbe/utils/download_utils.py:42:5: D400 First line should end with a period
kg_microbe/utils/download_utils.py:42:5: D415 First line should end with a period, question mark, or exclamation point
kg_microbe/utils/download_utils.py:58:36: S506 Probable use of unsafe loader `FullLoader` with `yaml.load`. Allows instantiation of arbitrary objects. Consider `yaml.safe_load`.
kg_microbe/utils/download_utils.py:128:31: S310 Audit URL open for permitted schemes. Allowing use of `file:` or custom schemes is often unexpected.
kg_microbe/utils/download_utils.py:130:34: S310 Audit URL open for permitted schemes. Allowing use of `file:` or custom schemes is often unexpected.
kg_microbe/utils/download_utils.py:164:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:206:5: D205 1 blank line required between summary line and description
kg_microbe/utils/download_utils.py:206:5: D400 First line should end with a period
kg_microbe/utils/download_utils.py:206:5: D415 First line should end with a period, question mark, or exclamation point
kg_microbe/utils/download_utils.py:206:5: D414 Section has no content ("Returns")
kg_microbe/utils/download_utils.py:249:5: D417 Missing argument descriptions in the docstring for `elastic_search_query`: `index`, `preserve_order`, `query`, `request_timeout`, `scroll`
kg_microbe/utils/download_utils.py:288:5: D400 First line should end with a period
kg_microbe/utils/download_utils.py:288:5: D401 First line of docstring should be in imperative mood: "Parses a URL for any environment variables enclosed in {curly braces}"
kg_microbe/utils/download_utils.py:288:5: D415 First line should end with a period, question mark, or exclamation point
kg_microbe/utils/download_utils.py:301:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:314:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:368:121: E501 Line too long (141 > 120)
kg_microbe/utils/download_utils.py:376:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:388:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:448:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:454:5: F841 Local variable `first_response` is assigned to but never used
kg_microbe/utils/download_utils.py:456:21: E712 Comparison to `True` should be `cond is True` or `if cond:`
kg_microbe/utils/download_utils.py:460:13: F841 Local variable `next_response` is assigned to but never used
kg_microbe/utils/download_utils.py:467:5: D103 Missing docstring in public function
kg_microbe/utils/download_utils.py:477:24: B905 `zip()` without an explicit `strict=` parameter
Found 37 errors.

• tox -e docstr-coverage yields

kg-microbe/kg_microbe/transform_utils/uniprot/uniprot.py"
 - No module docstring
 - No docstring for `UniprotTransform`
 - No docstring for `UniprotTransform.__init__`
 - No docstring for `UniprotTransform.get_uniprot_values_from_file`
 - No docstring for `UniprotTransform.get_uniprot_values_organism`
 - No docstring for `UniprotTransform.parse_binding_site`
 - No docstring for `UniprotTransform.write_to_df`
 Needed: 9; Found: 2; Missing: 7; Coverage: 22.2%


kg_microbe/utils/download_utils.py"
 - No module docstring
 - No docstring for `mirror_to_bucket`
 - No docstring for `parse_ncbitaxon_json`
 - No docstring for `get_uniprot_values_organism`
 - No docstring for `write_to_empty_orgs`
 - No docstring for `check_for_file_existence_in_batch`
 - No docstring for `get_jobs`
 - No docstring for `parse_response`
 Needed: 12; Found: 4; Missing: 8; Coverage: 33.3%

Your code has docstrings in Google style but the rest of the project follows the reST style e.g.:

def download(*args, **kwargs) -> None:
    """
    Download from list of URLs (default: download.yaml) into data directory (default: data/raw).

    :param yaml_file: Specify the YAML file containing a list of datasets to download.
    :param output_dir: A string pointing to the directory to download data to.
    :param snippet_only: Download 5 kB of each uncompressed source, for testing and file checks.
    :param ignore_cache: If specified, will ignore existing files and download again.
    :return: None
    """

It would be nice to keep it uniform across the board.

[hrshdhgd]

I've corrected the GitHub workflow to run tox. Once the workflows pass, we can merge this PR

[hrshdhgd]

Closing in favor of #107