Reorganize sources (#305)

src/pyobo/cli/database_utils.py

@@ -27,7 +27,8 @@
     get_xrefs_df,
 )
 from ..getters import IterHelperHelperDict, iter_helper, iter_helper_helper
-from ..sources import ncbigene, pubchem
+from ..sources import pubchem
+from ..sources.ncbi import ncbigene
 from ..utils.path import ensure_path
 from ..xrefdb.sources import iter_xref_plugins
 

src/pyobo/sources/__init__.py

@@ -15,38 +15,30 @@
 from .cvx import CVXGetter
 from .depmap import DepMapGetter
 from .dictybase_gene import DictybaseGetter
-from .drugbank import DrugBankGetter
-from .drugbank_salt import DrugBankSaltGetter
+from .drugbank import DrugBankGetter, DrugBankSaltGetter
 from .drugcentral import DrugCentralGetter
 from .expasy import ExpasyGetter
 from .famplex import FamPlexGetter
 from .flybase import FlyBaseGetter
 from .gard import GARDGetter
 from .geonames import GeonamesFeatureGetter, GeonamesGetter
 from .gtdb import GTDBGetter
-from .gwascentral_phenotype import GWASCentralPhenotypeGetter
-from .gwascentral_study import GWASCentralStudyGetter
-from .hgnc import HGNCGetter
-from .hgncgenefamily import HGNCGroupGetter
-from .icd10 import ICD10Getter
-from .icd11 import ICD11Getter
+from .gwascentral import GWASCentralPhenotypeGetter, GWASCentralStudyGetter
+from .hgnc import HGNCGetter, HGNCGroupGetter
+from .icd import ICD10Getter, ICD11Getter
 from .interpro import InterProGetter
 from .itis import ITISGetter
 from .kegg import KEGGGeneGetter, KEGGGenomeGetter, KEGGPathwayGetter
 from .mesh import MeSHGetter
 from .mgi import MGIGetter
-from .mirbase import MiRBaseGetter
-from .mirbase_family import MiRBaseFamilyGetter
-from .mirbase_mature import MiRBaseMatureGetter
+from .mirbase import MiRBaseFamilyGetter, MiRBaseGetter, MiRBaseMatureGetter
 from .msigdb import MSigDBGetter
-from .ncbi_gc import NCBIGCGetter
-from .ncbigene import NCBIGeneGetter
+from .ncbi import NCBIGCGetter, NCBIGeneGetter
 from .nlm import NLMCatalogGetter, NLMPublisherGetter
 from .npass import NPASSGetter
 from .omim_ps import OMIMPSGetter
 from .pathbank import PathBankGetter
-from .pfam import PfamGetter
-from .pfam_clan import PfamClanGetter
+from .pfam import PfamClanGetter, PfamGetter
 from .pid import PIDGetter
 from .pombase import PomBaseGetter
 from .pubchem import PubChemCompoundGetter

src/pyobo/sources/chembl/__init__.py

@@ -0,0 +1,7 @@
+"""Resources from ChEMBL."""
+
+from .chembl_compound import ChEMBLCompoundGetter
+
+__all__ = [
+    "ChEMBLCompoundGetter",
+]

src/pyobo/sources/chembl.py → src/pyobo/sources/chembl/chembl_compound.py

@@ -1,7 +1,4 @@
-"""Converter for ChEMBL.
-
-Run with ``python -m pyobo.sources.chembl -vv``.
-"""
+"""Converter for ChEMBL Compounds."""
 
 import logging
 from collections.abc import Iterable

src/pyobo/sources/drugbank/__init__.py

@@ -0,0 +1,9 @@
+"""Resources from DrugBank."""
+
+from .drugbank import DrugBankGetter
+from .drugbank_salt import DrugBankSaltGetter
+
+__all__ = [
+    "DrugBankGetter",
+    "DrugBankSaltGetter",
+]

src/pyobo/sources/drugbank.py → src/pyobo/sources/drugbank/drugbank.py

@@ -14,11 +14,11 @@
 import pystow
 from tqdm.auto import tqdm
 
-from ..getters import NoBuildError
-from ..struct import Obo, Reference, Term
-from ..struct.typedef import has_inchi, has_salt, has_smiles
-from ..utils.cache import cached_pickle
-from ..utils.path import prefix_directory_join
+from ...getters import NoBuildError
+from ...struct import Obo, Reference, Term
+from ...struct.typedef import has_inchi, has_salt, has_smiles
+from ...utils.cache import cached_pickle
+from ...utils.path import prefix_directory_join
 
 __all__ = [
     "DrugBankGetter",

src/pyobo/sources/drugbank_salt.py → src/pyobo/sources/drugbank/drugbank_salt.py

@@ -16,7 +16,7 @@
 from collections.abc import Iterable
 
 from .drugbank import iterate_drug_info
-from ..struct import Obo, Reference, Term
+from ...struct import Obo, Reference, Term
 
 __all__ = [
     "DrugBankSaltGetter",

src/pyobo/sources/gwascentral/__init__.py

@@ -0,0 +1,9 @@
+"""Resources from GWAS Central."""
+
+from .gwascentral_phenotype import GWASCentralPhenotypeGetter
+from .gwascentral_study import GWASCentralStudyGetter
+
+__all__ = [
+    "GWASCentralPhenotypeGetter",
+    "GWASCentralStudyGetter",
+]

src/pyobo/sources/gwascentral_phenotype.py → src/pyobo/sources/gwascentral/gwascentral_phenotype.py

@@ -5,10 +5,11 @@
 
 from tqdm.auto import tqdm, trange
 
-from pyobo.sources.gwascentral_study import VERSION
 from pyobo.struct import Obo, Reference, Term
 from pyobo.utils.path import ensure_path
 
+from .gwascentral_study import VERSION
+
 __all__ = [
     "GWASCentralPhenotypeGetter",
 ]

src/pyobo/sources/hgnc/__init__.py

@@ -0,0 +1,9 @@
+"""Resources from HGNC."""
+
+from .hgnc import HGNCGetter
+from .hgncgenefamily import HGNCGroupGetter
+
+__all__ = [
+    "HGNCGetter",
+    "HGNCGroupGetter",
+]

src/pyobo/sources/hgncgenefamily.py → src/pyobo/sources/hgnc/hgncgenefamily.py

@@ -5,9 +5,9 @@
 
 import pandas as pd
 
-from ..struct import Obo, Reference, SynonymTypeDef, Term, has_citation
-from ..struct.typedef import enables, exact_match, from_species
-from ..utils.path import ensure_path
+from ...struct import Obo, Reference, SynonymTypeDef, Term, has_citation
+from ...struct.typedef import enables, exact_match, from_species
+from ...utils.path import ensure_path
 
 __all__ = [
     "HGNCGroupGetter",

src/pyobo/sources/icd/__init__.py

@@ -0,0 +1,9 @@
+"""Resources from ICD."""
+
+from .icd10 import ICD10Getter
+from .icd11 import ICD11Getter
+
+__all__ = [
+    "ICD10Getter",
+    "ICD11Getter",
+]

src/pyobo/sources/icd10.py → src/pyobo/sources/icd/icd10.py

@@ -9,14 +9,14 @@
 
 from tqdm.auto import tqdm
 
-from ..sources.icd_utils import (
+from .icd_utils import (
     ICD10_TOP_LEVEL_URL,
     get_child_identifiers,
     get_icd,
     visiter,
 )
-from ..struct import Obo, Reference, Synonym, Term, has_category
-from ..utils.path import prefix_directory_join
+from ...struct import Obo, Reference, Synonym, Term, has_category
+from ...utils.path import prefix_directory_join
 
 __all__ = [
     "ICD10Getter",

src/pyobo/sources/icd11.py → src/pyobo/sources/icd/icd11.py

@@ -18,8 +18,8 @@
     get_icd_11_mms,
     visiter,
 )
-from ..struct import Obo, Reference, Synonym, Term, TypeDef, default_reference
-from ..utils.path import prefix_directory_join
+from ...struct import Obo, Reference, Synonym, Term, TypeDef, default_reference
+from ...utils.path import prefix_directory_join
 
 __all__ = [
     "ICD11Getter",

src/pyobo/sources/icd_utils.py → src/pyobo/sources/icd/icd_utils.py

@@ -19,8 +19,8 @@
 from pystow.config_api import ConfigError
 from tqdm.auto import tqdm
 
-from ..getters import NoBuildError
-from ..struct import Term
+from ...getters import NoBuildError
+from ...struct import Term
 
 TOKEN_URL = "https://icdaccessmanagement.who.int/connect/token"  # noqa:S105
 

src/pyobo/sources/mirbase/__init__.py

@@ -0,0 +1,11 @@
+"""Resources from miRBase."""
+
+from .mirbase import MiRBaseGetter
+from .mirbase_family import MiRBaseFamilyGetter
+from .mirbase_mature import MiRBaseMatureGetter
+
+__all__ = [
+    "MiRBaseFamilyGetter",
+    "MiRBaseGetter",
+    "MiRBaseMatureGetter",
+]

src/pyobo/sources/mirbase.py → src/pyobo/sources/mirbase/mirbase.py

@@ -6,12 +6,13 @@
 
 from tqdm.auto import tqdm
 
-from pyobo.sources.mirbase_constants import BASE_URL, _assert_frozen_version
 from pyobo.struct import Obo, Reference, Synonym, Term, from_species
 from pyobo.struct.typedef import has_mature
 from pyobo.utils.cache import cached_mapping
 from pyobo.utils.path import ensure_df, ensure_path, prefix_directory_join
 
+from .mirbase_constants import BASE_URL, _assert_frozen_version
+
 __all__ = [
     "MiRBaseGetter",
 ]

src/pyobo/sources/mirbase_family.py → src/pyobo/sources/mirbase/mirbase_family.py

@@ -5,12 +5,13 @@
 import pandas as pd
 from tqdm.auto import tqdm
 
-from pyobo.sources.mirbase_constants import (
+from pyobo.struct import Obo, Reference, Term, has_member
+
+from .mirbase_constants import (
     get_premature_df,
     get_premature_family_df,
     get_premature_to_prefamily_df,
 )
-from pyobo.struct import Obo, Reference, Term, has_member
 
 __all__ = [
     "MiRBaseFamilyGetter",

src/pyobo/sources/mirbase_mature.py → src/pyobo/sources/mirbase/mirbase_mature.py

@@ -5,9 +5,10 @@
 import pandas as pd
 from tqdm.auto import tqdm
 
-from pyobo.sources.mirbase_constants import get_mature_df
 from pyobo.struct import Obo, Reference, Synonym, Term
 
+from .mirbase_constants import get_mature_df
+
 __all__ = [
     "MiRBaseMatureGetter",
 ]

src/pyobo/sources/ncbi/__init__.py

@@ -0,0 +1,9 @@
+"""Resources from NCBI."""
+
+from .ncbi_gc import NCBIGCGetter
+from .ncbigene import NCBIGeneGetter
+
+__all__ = [
+    "NCBIGCGetter",
+    "NCBIGeneGetter",
+]

src/pyobo/sources/ncbigene.py → src/pyobo/sources/ncbi/ncbigene.py

@@ -7,8 +7,8 @@
 import pandas as pd
 from tqdm.auto import tqdm
 
-from ..struct import Obo, Reference, Term, from_species
-from ..utils.path import ensure_df
+from ...struct import Obo, Reference, Term, from_species
+from ...utils.path import ensure_df
 
 __all__ = [
     "NCBIGeneGetter",

src/pyobo/sources/pfam/__init__.py

@@ -0,0 +1,9 @@
+"""Resources from PFAM."""
+
+from .pfam import PfamGetter
+from .pfam_clan import PfamClanGetter
+
+__all__ = [
+    "PfamClanGetter",
+    "PfamGetter",
+]

src/pyobo/sources/pfam.py → src/pyobo/sources/pfam/pfam.py

@@ -4,8 +4,8 @@
 
 import pandas as pd
 
-from ..struct import Obo, Reference, Term
-from ..utils.path import ensure_df
+from ...struct import Obo, Reference, Term
+from ...utils.path import ensure_df
 
 __all__ = [
     "PfamGetter",

src/pyobo/sources/pfam_clan.py → src/pyobo/sources/pfam/pfam_clan.py

@@ -5,7 +5,7 @@
 from tqdm.auto import tqdm
 
 from .pfam import get_pfam_clan_df
-from ..struct import Obo, Reference, Term
+from ...struct import Obo, Reference, Term
 
 __all__ = [
     "PfamClanGetter",