Merge pull request #174 from NPLinker/add_init_to_module

Add or update `__init__.py`

src/nplinker/annotations.py

@@ -15,8 +15,8 @@
 import csv
 import os
 from deprecated import deprecated
-from nplinker.metabolomics.spectrum import GNPS_KEY
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import GNPS_KEY
+from nplinker.metabolomics import Spectrum
 from .logconfig import LogConfig
 
 

src/nplinker/metabolomics/__init__.py

@@ -1,5 +1,10 @@
 import logging
+from .molecular_family import MolecularFamily
+from .singleton_family import SingletonFamily
+from .spectrum import GNPS_KEY
+from .spectrum import Spectrum
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
+__all__ = ['MolecularFamily', 'SingletonFamily', 'GNPS_KEY', 'Spectrum']

src/nplinker/metabolomics/abc.py

@@ -1,8 +1,8 @@
 from abc import ABC
 from abc import abstractmethod
 from collections.abc import Sequence
-from nplinker.metabolomics.molecular_family import MolecularFamily
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import MolecularFamily
+from nplinker.metabolomics import Spectrum
 
 
 class SpectrumLoaderBase(ABC):

src/nplinker/metabolomics/gnps/__init__.py

@@ -0,0 +1,21 @@
+import logging
+from .gnps_annotation_loader import GNPSAnnotationLoader
+from .gnps_downloader import GNPSDownloader
+from .gnps_extractor import GNPSExtractor
+from .gnps_file_mapping_loader import GNPSFileMappingLoader
+from .gnps_format import gnps_format_from_archive
+from .gnps_format import gnps_format_from_file_mapping
+from .gnps_format import gnps_format_from_task_id
+from .gnps_format import GNPSFormat
+from .gnps_molecular_family_loader import GNPSMolecularFamilyLoader
+from .gnps_spectrum_loader import GNPSSpectrumLoader
+
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+
+__all__ = [
+    "GNPSAnnotationLoader", "GNPSDownloader", "GNPSExtractor",
+    "GNPSFileMappingLoader", "GNPSFormat", "GNPSMolecularFamilyLoader",
+    "GNPSSpectrumLoader", "gnps_format_from_archive",
+    "gnps_format_from_file_mapping", "gnps_format_from_task_id"
+]

src/nplinker/metabolomics/gnps/gnps_downloader.py

@@ -1,9 +1,9 @@
 from os import PathLike
 from pathlib import Path
 from typing_extensions import Self
-from nplinker.metabolomics.gnps.gnps_format import gnps_format_from_task_id
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
 from nplinker.utils import download_url
+from .gnps_format import gnps_format_from_task_id
+from .gnps_format import GNPSFormat
 
 
 class GNPSDownloader:

src/nplinker/metabolomics/gnps/gnps_extractor.py

@@ -3,8 +3,8 @@
 from pathlib import Path
 import zipfile
 from nplinker import utils
-from nplinker.metabolomics.gnps.gnps_format import gnps_format_from_archive
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from .gnps_format import gnps_format_from_archive
+from .gnps_format import GNPSFormat
 
 
 class GNPSExtractor:

src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py

@@ -1,8 +1,8 @@
 import csv
 from os import PathLike
+from nplinker.metabolomics import MolecularFamily
+from nplinker.metabolomics import SingletonFamily
 from nplinker.metabolomics.abc import MolecularFamilyLoaderBase
-from nplinker.metabolomics.molecular_family import MolecularFamily
-from nplinker.metabolomics.singleton_family import SingletonFamily
 from nplinker.utils import is_file_format
 
 

src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py

@@ -1,8 +1,8 @@
 from os import PathLike
 from pyteomics import mgf
 from nplinker.logconfig import LogConfig
+from nplinker.metabolomics import Spectrum
 from nplinker.metabolomics.abc import SpectrumLoaderBase
-from nplinker.metabolomics.spectrum import Spectrum
 
 
 logger = LogConfig.getLogger(__name__)

src/nplinker/metabolomics/load_gnps.py

@@ -4,9 +4,9 @@
 from typing import Any
 from deprecated import deprecated
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.gnps.gnps_format import gnps_format_from_file_mapping
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import Spectrum
+from nplinker.metabolomics.gnps import gnps_format_from_file_mapping
+from nplinker.metabolomics.gnps import GNPSFormat
 from nplinker.strain_collection import StrainCollection
 from nplinker.strains import Strain
 

src/nplinker/metabolomics/molecular_family.py

@@ -1,9 +1,12 @@
-from typing_extensions import Self
-from nplinker.metabolomics.spectrum import Spectrum
+from __future__ import annotations
+from typing import TYPE_CHECKING
 from nplinker.strain_collection import StrainCollection
 from nplinker.strains import Strain
 
 
+if TYPE_CHECKING:
+    from .spectrum import Spectrum
+
 class MolecularFamily():
 
     def __init__(self, family_id: str):

src/nplinker/nplinker.py

@@ -9,8 +9,8 @@
 from .loader import DatasetLoader
 from .loader import NPLINKER_APP_DATA_DIR
 from .logconfig import LogConfig
-from .metabolomics.molecular_family import MolecularFamily
-from .metabolomics.spectrum import Spectrum
+from .metabolomics import MolecularFamily
+from .metabolomics import Spectrum
 from .pickler import save_pickled_data
 from .scoring.link_collection import LinkCollection
 from .scoring.metcalf_scoring import MetcalfScoring

src/nplinker/pairedomics/downloader.py

@@ -6,8 +6,8 @@
 from nplinker.genomics.mibig import download_and_extract_mibig_metadata
 from nplinker.globals import PFAM_PATH
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.gnps.gnps_downloader import GNPSDownloader
-from nplinker.metabolomics.gnps.gnps_extractor import GNPSExtractor
+from nplinker.metabolomics.gnps import GNPSDownloader
+from nplinker.metabolomics.gnps import GNPSExtractor
 from nplinker.utils import download_url
 from . import podp_download_and_extract_antismash_data
 from .runbigscape import podp_run_bigscape

src/nplinker/pairedomics/strain_mappings_generator.py

@@ -3,8 +3,7 @@
 from os import PathLike
 from pathlib import Path
 from jsonschema import validate
-from nplinker.metabolomics.gnps.gnps_file_mapping_loader import \
-    GNPSFileMappingLoader
+from nplinker.metabolomics.gnps import GNPSFileMappingLoader
 from nplinker.schemas import GENOME_BGC_MAPPINGS_SCHEMA
 from nplinker.schemas import validate_podp_json
 from nplinker.strain_collection import StrainCollection

src/nplinker/pickler.py

@@ -17,8 +17,8 @@
 from .genomics import BGC
 from .genomics import GCF
 from .logconfig import LogConfig
-from .metabolomics.molecular_family import MolecularFamily
-from .metabolomics.spectrum import Spectrum
+from .metabolomics import MolecularFamily
+from .metabolomics import Spectrum
 
 
 logger = LogConfig.getLogger(__name__)

src/nplinker/scoring/linking/data_links.py

@@ -4,9 +4,9 @@
 import pandas as pd
 from nplinker.genomics.gcf import GCF
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.molecular_family import MolecularFamily
-from nplinker.metabolomics.singleton_family import SingletonFamily
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import MolecularFamily
+from nplinker.metabolomics import SingletonFamily
+from nplinker.metabolomics import Spectrum
 from .utils import calc_correlation_matrix
 from .utils import isinstance_all
 

src/nplinker/scoring/linking/link_finder.py

@@ -5,8 +5,8 @@
 from scipy.stats import hypergeom
 from nplinker.genomics.gcf import GCF
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.molecular_family import MolecularFamily
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import MolecularFamily
+from nplinker.metabolomics import Spectrum
 from . import LINK_TYPES
 from .utils import isinstance_all
 

src/nplinker/scoring/metcalf_scoring.py

@@ -5,21 +5,21 @@
 import pandas as pd
 from nplinker.genomics import GCF
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.molecular_family import MolecularFamily
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import MolecularFamily
+from nplinker.metabolomics import Spectrum
 from nplinker.pickler import load_pickled_data
 from nplinker.pickler import save_pickled_data
-from .linking import LINK_TYPES
 from .linking import DataLinks
-from .linking import LinkFinder
 from .linking import isinstance_all
+from .linking import LINK_TYPES
+from .linking import LinkFinder
 from .methods import ScoringMethod
 from .object_link import ObjectLink
 
 
 if TYPE_CHECKING:
-    from ..nplinker import NPLinker
     from . import LinkCollection
+    from ..nplinker import NPLinker
 
 logger = LogConfig.getLogger(__name__)
 

src/nplinker/scoring/np_class_scoring.py

@@ -4,7 +4,7 @@
 from nplinker.genomics import BGC
 from nplinker.genomics import GCF
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import Spectrum
 from nplinker.scoring.metcalf_scoring import MetcalfScoring
 from nplinker.scoring.methods import ScoringMethod
 from nplinker.scoring.object_link import ObjectLink

src/nplinker/scoring/rosetta/spec_lib.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 from sortedcontainers import SortedList
-from nplinker.metabolomics.gnps.gnps_spectrum_loader import GNPSSpectrumLoader
+from nplinker.metabolomics.gnps import GNPSSpectrumLoader
 from ...logconfig import LogConfig
 from .rosetta_functions import fast_cosine
 

src/nplinker/scoring/rosetta_scoring.py

@@ -2,7 +2,7 @@
 from nplinker.genomics.bgc import BGC
 from nplinker.genomics.gcf import GCF
 from nplinker.logconfig import LogConfig
-from nplinker.metabolomics.molecular_family import MolecularFamily
+from nplinker.metabolomics import MolecularFamily
 from nplinker.scoring.methods import ScoringMethod
 from nplinker.scoring.object_link import ObjectLink
 from nplinker.scoring.rosetta.rosetta import Rosetta

tests/conftest.py

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

tests/metabolomics/conftest.py

@@ -2,7 +2,7 @@
 import shutil
 import httpx
 import pytest
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSFormat
 from nplinker.utils import extract_archive
 from .. import GNPS_DATA_DIR
 

tests/metabolomics/test_gnps_annotation_loader.py

@@ -1,7 +1,6 @@
 import pytest
-from nplinker.metabolomics.gnps.gnps_annotation_loader import \
-    GNPSAnnotationLoader
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSAnnotationLoader
+from nplinker.metabolomics.gnps import GNPSFormat
 
 
 @pytest.mark.parametrize("workflow, expected",

tests/metabolomics/test_gnps_downloader.py

@@ -1,7 +1,7 @@
 import zipfile
 import pytest
-from nplinker.metabolomics.gnps.gnps_downloader import GNPSDownloader
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSDownloader
+from nplinker.metabolomics.gnps import GNPSFormat
 
 
 @pytest.fixture(scope="module", autouse=True)

tests/metabolomics/test_gnps_extractor.py

@@ -1,8 +1,8 @@
 import filecmp
 from pathlib import Path
 import pytest
-from nplinker.metabolomics.gnps.gnps_extractor import GNPSExtractor
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSExtractor
+from nplinker.metabolomics.gnps import GNPSFormat
 
 
 def test_unknown_workflow(gnps_zip_files, tmpdir):

tests/metabolomics/test_gnps_file_mapping_loader.py

@@ -1,7 +1,6 @@
 import pytest
-from nplinker.metabolomics.gnps.gnps_file_mapping_loader import \
-    GNPSFileMappingLoader
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSFileMappingLoader
+from nplinker.metabolomics.gnps import GNPSFormat
 
 
 @pytest.mark.parametrize("workflow, num_spectra, filename",

tests/metabolomics/test_gnps_format.py

@@ -1,8 +1,8 @@
 import pytest
-from nplinker.metabolomics.gnps.gnps_format import gnps_format_from_archive
-from nplinker.metabolomics.gnps.gnps_format import gnps_format_from_file_mapping
-from nplinker.metabolomics.gnps.gnps_format import gnps_format_from_task_id
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import gnps_format_from_archive
+from nplinker.metabolomics.gnps import gnps_format_from_file_mapping
+from nplinker.metabolomics.gnps import gnps_format_from_task_id
+from nplinker.metabolomics.gnps import GNPSFormat
 
 
 @pytest.mark.parametrize(

tests/metabolomics/test_gnps_molecular_family_loader.py

@@ -1,7 +1,6 @@
 import pytest
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
-from nplinker.metabolomics.gnps.gnps_molecular_family_loader import \
-    GNPSMolecularFamilyLoader
+from nplinker.metabolomics.gnps import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSMolecularFamilyLoader
 
 
 @pytest.mark.parametrize("workflow, num_families, num_spectra",

tests/metabolomics/test_gnps_spectrum_loader.py

@@ -1,6 +1,6 @@
 import pytest
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
-from nplinker.metabolomics.gnps.gnps_spectrum_loader import GNPSSpectrumLoader
+from nplinker.metabolomics.gnps import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSSpectrumLoader
 
 
 @pytest.mark.parametrize("workflow, num_spectra",

tests/metabolomics/test_load_gnps.py

@@ -1,6 +1,6 @@
 from itertools import chain
 import pytest
-from nplinker.metabolomics.gnps.gnps_format import GNPSFormat
+from nplinker.metabolomics.gnps import GNPSFormat
 from nplinker.metabolomics.load_gnps import _load_clusterinfo_old
 from nplinker.metabolomics.load_gnps import _messy_strain_naming_lookup
 from nplinker.metabolomics.load_gnps import _parse_mzxml_header

tests/metabolomics/test_spectrum.py

@@ -1,5 +1,5 @@
 import pytest
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import Spectrum
 
 
 @pytest.fixture

tests/scoring/conftest.py

@@ -1,7 +1,7 @@
 from pytest import fixture
 from nplinker.genomics import GCF
-from nplinker.metabolomics.molecular_family import MolecularFamily
-from nplinker.metabolomics.spectrum import Spectrum
+from nplinker.metabolomics import MolecularFamily
+from nplinker.metabolomics import Spectrum
 from nplinker.nplinker import NPLinker
 from nplinker.scoring import MetcalfScoring
 from nplinker.scoring.linking import DataLinks

tests/scoring/test_data_links.py

@@ -1,7 +1,7 @@
 import pandas as pd
 from pandas.testing import assert_frame_equal
 import pytest
-from nplinker.metabolomics.singleton_family import SingletonFamily
+from nplinker.metabolomics import SingletonFamily
 
 
 def test_init(datalinks):

tests/test_loader.py

@@ -3,8 +3,8 @@
 import pytest
 from nplinker.globals import STRAIN_MAPPINGS_FILENAME
 from nplinker.loader import DatasetLoader
-from nplinker.metabolomics.gnps.gnps_extractor import GNPSExtractor
-from nplinker.metabolomics.gnps.gnps_spectrum_loader import GNPSSpectrumLoader
+from nplinker.metabolomics.gnps import GNPSExtractor
+from nplinker.metabolomics.gnps import GNPSSpectrumLoader
 from nplinker.strain_collection import StrainCollection
 from . import DATA_DIR