From 17ff67cc7e452fcd284bac9785dfc0c12889703c Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Fri, 3 Nov 2023 11:36:29 +0100 Subject: [PATCH 1/3] config ruff to ignore init module imports This will prevent unused imports in `__init__.py` being removed when using ruff fix. --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 1f42f41a..1ace3108 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"] From aaf49fe9b0038131715cca197d9b886e190e360f Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Fri, 3 Nov 2023 11:44:55 +0100 Subject: [PATCH 2/3] fix unexpected deletion of imports in mibig module init file --- src/nplinker/genomics/mibig/__init__.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/nplinker/genomics/mibig/__init__.py b/src/nplinker/genomics/mibig/__init__.py index bf44b00a..d2e1f0d8 100644 --- a/src/nplinker/genomics/mibig/__init__.py +++ b/src/nplinker/genomics/mibig/__init__.py @@ -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", +] From 48e795eeeba764dded5fbdc7d2466d2c67793749 Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Fri, 3 Nov 2023 12:03:44 +0100 Subject: [PATCH 3/3] fix unit tests for BigscapeGCFLoader `_parse_gcf` method --- tests/genomics/test_bigscape_loader.py | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/tests/genomics/test_bigscape_loader.py b/tests/genomics/test_bigscape_loader.py index 4512bdc2..c5a22307 100644 --- a/tests/genomics/test_bigscape_loader.py +++ b/tests/genomics/test_bigscape_loader.py @@ -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)