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Update ruff rules to ignore unused imports in __init__.py files #177

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merged 3 commits into from
Nov 3, 2023
Merged

Update ruff rules to ignore unused imports in __init__.py files #177

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17ff67c
config ruff to ignore init module imports
CunliangGeng Nov 3, 2023
aaf49fe
fix unexpected deletion of imports in mibig module init file
CunliangGeng Nov 3, 2023
48e795e
fix unit tests for BigscapeGCFLoader `_parse_gcf` method
CunliangGeng Nov 3, 2023
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2 changes: 2 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,8 @@ ignore = [

# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["A", "B", "C", "D", "E", "F", "I"]
ignore-init-module-imports = true


[tool.ruff.isort]
known-first-party = ["nplinker"]
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11 changes: 11 additions & 0 deletions src/nplinker/genomics/mibig/__init__.py
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@@ -1,4 +1,15 @@
import logging
from .mibig_downloader import download_and_extract_mibig_metadata
from .mibig_loader import MibigLoader
from .mibig_loader import parse_bgc_metadata_json
from .mibig_metadata import MibigMetadata


logging.getLogger(__name__).addHandler(logging.NullHandler())

__all__ = [
"download_and_extract_mibig_metadata",
"MibigLoader",
"MibigMetadata",
"parse_bgc_metadata_json",
]
14 changes: 5 additions & 9 deletions tests/genomics/test_bigscape_loader.py
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Expand Up @@ -34,12 +34,8 @@ def test_get_gcfs_without_mibig_only(self, loader):
assert isinstance(gcfs[0], GCF)

def test_parse_gcf(self, loader):
gcf_dict = BigscapeGCFLoader._parse_gcf(loader.cluster_file) # noqa
assert isinstance(gcf_dict, dict)
assert len(gcf_dict) == 114
gcf = gcf_dict["135"]
assert isinstance(gcf, GCF)
assert len(gcf.bgc_ids) == 4
assert gcf.bgc_ids == set(
("BGC0000145", "BGC0001041", "NC_009380.1.region004", "NZ_AZWK01000002.region002")
)
gcf_list = BigscapeGCFLoader._parse_gcf(loader.cluster_file) # noqa
assert isinstance(gcf_list, list)
assert len(gcf_list) == 114
for gcf in gcf_list:
assert isinstance(gcf, GCF)
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