rename strains.py to strain.py

Change filename `strains.py` to `strain.py` to make file names consistent.

src/nplinker/genomics/antismash/antismash_loader.py

@@ -5,7 +5,7 @@
 from Bio import SeqRecord
 from nplinker.genomics import BGC
 from nplinker.logconfig import LogConfig
-from nplinker.strains import Strain
+from nplinker.strain import Strain
 from nplinker.utils import list_dirs
 from nplinker.utils import list_files
 from ..abc import BGCLoaderBase

src/nplinker/genomics/bgc.py

@@ -6,7 +6,7 @@
 
 
 if TYPE_CHECKING:
-    from ..strains import Strain
+    from ..strain import Strain
     from .gcf import GCF
 
 logger = LogConfig.getLogger(__name__)

src/nplinker/genomics/gcf.py

@@ -5,7 +5,7 @@
 
 
 if TYPE_CHECKING:
-    from nplinker.strains import Strain
+    from nplinker.strain import Strain
     from .bgc import BGC
 
 logger = LogConfig.getLogger(__name__)

src/nplinker/genomics/mibig/mibig_loader.py

@@ -1,6 +1,6 @@
 import os.path
 from nplinker.logconfig import LogConfig
-from nplinker.strains import Strain
+from nplinker.strain import Strain
 from nplinker.utils import list_files
 from ..abc import BGCLoaderBase
 from ..bgc import BGC

src/nplinker/loader.py

@@ -24,9 +24,9 @@
 from nplinker.pairedomics.downloader import PODPDownloader
 from nplinker.pairedomics.runbigscape import run_bigscape
 from nplinker.pairedomics.strain_mappings_generator import podp_generate_strain_mappings
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
 from nplinker.strain_loader import load_user_strains
-from nplinker.strains import Strain
 
 
 try:

src/nplinker/metabolomics/load_gnps.py

@@ -7,8 +7,8 @@
 from nplinker.metabolomics import Spectrum
 from nplinker.metabolomics.gnps import GNPSFormat
 from nplinker.metabolomics.gnps import gnps_format_from_file_mapping
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 
 
 logger = LogConfig.getLogger(__name__)

src/nplinker/metabolomics/molecular_family.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 from typing import TYPE_CHECKING
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 
 
 if TYPE_CHECKING:

src/nplinker/metabolomics/spectrum.py

@@ -1,5 +1,5 @@
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 from nplinker.utils import sqrt_normalise
 
 

src/nplinker/nplinker.py

@@ -20,7 +20,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
-    from .strains import Strain
+    from .strain import Strain
 
 logger = LogConfig.getLogger(__name__)
 

src/nplinker/pairedomics/strain_mappings_generator.py

@@ -6,8 +6,8 @@
 from nplinker.metabolomics.gnps import GNPSFileMappingLoader
 from nplinker.schemas import GENOME_BGC_MAPPINGS_SCHEMA
 from nplinker.schemas import validate_podp_json
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 from .podp_antismash_downloader import GenomeStatus
 from .podp_antismash_downloader import get_best_available_genome_id
 

src/nplinker/scoring/linking/data_links.py

@@ -13,8 +13,8 @@
 
 
 if TYPE_CHECKING:
+    from nplinker.strain import Strain
     from nplinker.strain_collection import StrainCollection
-    from nplinker.strains import Strain
 
 logger = LogConfig.getLogger(__name__)
 

src/nplinker/strain_collection.py

@@ -5,7 +5,7 @@
 from jsonschema import validate
 from nplinker.schemas import STRAIN_MAPPINGS_SCHEMA
 from .logconfig import LogConfig
-from .strains import Strain
+from .strain import Strain
 
 
 logger = LogConfig.getLogger(__name__)

src/nplinker/strain_loader.py

@@ -3,7 +3,7 @@
 from jsonschema import validate
 from nplinker.logconfig import LogConfig
 from nplinker.schemas import USER_STRAINS_SCHEMA
-from .strains import Strain
+from .strain import Strain
 
 
 logger = LogConfig.getLogger(__name__)

tests/conftest.py

@@ -2,8 +2,8 @@
 from nplinker.globals import STRAIN_MAPPINGS_FILENAME
 from nplinker.metabolomics import Spectrum
 from nplinker.metabolomics.metabolomics import load_spectra
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 from . import DATA_DIR
 from . import GNPS_DATA_DIR
 

tests/genomics/test_bgc.py

@@ -1,6 +1,6 @@
 from nplinker.genomics import BGC
 from nplinker.genomics import GCF
-from nplinker.strains import Strain
+from nplinker.strain import Strain
 
 
 def test_default():

tests/genomics/test_gcf.py

@@ -1,8 +1,8 @@
 import pytest
 from nplinker.genomics import BGC
 from nplinker.genomics import GCF
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 
 
 @pytest.fixture()

tests/genomics/test_genomics.py

@@ -10,8 +10,8 @@
 from nplinker.genomics import map_bgc_to_gcf
 from nplinker.genomics import map_strain_to_bgc
 from nplinker.globals import GENOME_BGC_MAPPINGS_FILENAME
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 from .. import DATA_DIR
 
 

tests/pairedomics/test_strain_mappings_generator.py

@@ -7,8 +7,8 @@
 from nplinker.pairedomics import get_mappings_strain_id_bgc_id
 from nplinker.pairedomics import get_mappings_strain_id_spectrum_id
 from nplinker.pairedomics import podp_generate_strain_mappings
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 
 
 def test_podp_generate_strain_mappings(monkeypatch, tmp_path):

tests/scoring/conftest.py

@@ -6,8 +6,8 @@
 from nplinker.scoring import MetcalfScoring
 from nplinker.scoring.linking import DataLinks
 from nplinker.scoring.linking import LinkFinder
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 from .. import DATA_DIR
 
 

tests/test_strain.py

@@ -1,4 +1,4 @@
-from nplinker.strains import Strain
+from nplinker.strain import Strain
 
 
 def test_default():

tests/test_strain_collection.py

@@ -1,7 +1,7 @@
 import json
 import pytest
+from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
-from nplinker.strains import Strain
 
 
 @pytest.fixture

tests/test_strain_loader.py

@@ -1,7 +1,7 @@
 import json
 import pytest
+from nplinker.strain import Strain
 from nplinker.strain_loader import load_user_strains
-from nplinker.strains import Strain
 
 
 @pytest.fixture