Update pystow (#40)

* Update pystow

* Update mock

.flake8

@@ -23,6 +23,7 @@ ignore =
     E501
     # ignore binary operator line breaks
     W504
+    W503
 
 # flake8-import-order
 application-import-names =

setup.cfg

@@ -59,6 +59,7 @@ install_requires =
     pybel>=0.15.0<0.16.0
     bel_resources>=0.0.3
     pyobo>=0.2.2
+    pystow
 
 # Random options
 zip_safe = false

src/bio2bel/cli.py

@@ -10,7 +10,7 @@
 import click
 from tqdm import tqdm
 
-from .constants import config
+from pybel import config
 from .manager import AbstractManager, get_bio2bel_manager_classes
 from .manager.bel_manager import BELManagerMixin
 from .manager.namespace_manager import BELNamespaceManagerMixin
@@ -30,13 +30,17 @@
     help='Database connection string.',
 )
 
-commands = {}
-for name, manager_cls in MANAGERS.items():
-    commands[name] = manager_cls.get_cli()
-    # can not use single asterick, causes documentation build failure
-    commands[name].help = f'# Manage {name}'
 
-main = click.Group(commands=commands)
+def _get_commands():
+    rv = {}
+    for name, manager_cls in MANAGERS.items():
+        rv[name] = manager_cls.get_cli()
+        # can not use single asterick, causes documentation build failure
+        rv[name].help = f'# Manage {name}'
+    return rv
+
+
+main = click.Group(commands=_get_commands())
 main.help = f'Bio2BEL Command Line Utilities on {sys.executable}\nBio2BEL v{get_version()}'
 
 

src/bio2bel/compath/__init__.py

@@ -6,5 +6,8 @@
 unifying framework for integrating them.
 """
 
-from .manager import CompathManager, get_compath_manager_classes, get_compath_modules  # noqa: F401
+from .manager import (  # noqa: F401
+    CompathManager, get_compath_manager_classes, get_compath_managers,
+    get_compath_modules, iter_compath_managers,
+)
 from .mixins import CompathPathwayMixin, CompathProteinMixin  # noqa: F401

src/bio2bel/compath/manager.py

@@ -9,6 +9,7 @@
 import types
 import typing
 from collections import Counter
+from functools import lru_cache
 from typing import Iterable, List, Mapping, Optional, Set, Tuple, Type
 
 import click
@@ -32,6 +33,8 @@
 __all__ = [
     'CompathManager',
     'get_compath_manager_classes',
+    'iter_compath_managers',
+    'get_compath_managers',
 ]
 
 logger = logging.getLogger(__name__)
@@ -133,7 +136,7 @@ def get_proteins_by_hgnc_ids(self, hgnc_ids: Iterable[str]) -> List[CompathProte
     def _help_get_proteins(self, protein_column, queries: Iterable[str]) -> List[CompathProteinMixin]:
         return self._query_protein().filter(protein_column.in_(queries)).all()
 
-    def search_genes(self, query: str, *, limit: Optional[int] = None) -> Optional[CompathPathwayMixin]:
+    def search_genes(self, query: str, *, limit: Optional[int] = None) -> List[CompathProteinMixin]:
         """Filter genes by HGNC gene symbol.
 
         :param query: part of an HGNC identifier or gene symbol
@@ -156,7 +159,7 @@ def search_pathways(self, query: str, *, limit: Optional[int] = None) -> List[Co
         :param limit: limit number of results
         """
         _query = self._query_pathway().filter(or_(
-            self.pathway_model.name.contains(query),
+            self.pathway_model.name.ilike(f'%{query}%'),
             self.pathway_model.identifier.contains(query),
         ))
 
@@ -395,8 +398,11 @@ def enrich_pathways(self, graph: BELGraph) -> None:
         pathway_identifiers = {
             node.identifier
             for node in graph
-            if isinstance(node,
-                          pybel.dsl.BiologicalProcess) and node.namespace.lower() == self.module_name and node.identifier
+            if (
+                isinstance(node, pybel.dsl.BiologicalProcess)
+                and node.namespace.lower() == self.module_name
+                and node.identifier
+            )
         }
         for pathway_identifier in pathway_identifiers:
             pathway = self.get_pathway_by_id(pathway_identifier)
@@ -418,6 +424,18 @@ def get_compath_modules() -> Mapping[str, types.ModuleType]:
     return dict(_get_modules('compath'))
 
 
+@lru_cache()
 def get_compath_manager_classes() -> Mapping[str, Type[CompathManager]]:
     """Get all ComPath manager classes."""
     return dict(_get_managers('compath'))
+
+
+def iter_compath_managers(*args, **kwargs) -> Iterable[Tuple[str, CompathManager]]:
+    """Iterate over ComPath managers."""
+    for name, cls in _get_managers('compath'):
+        yield name, cls(*args, **kwargs)
+
+
+def get_compath_managers(*args, **kwargs) -> Mapping[str, CompathManager]:
+    """Get instantiated ComPath classes."""
+    return dict(iter_compath_managers(*args, **kwargs))

src/bio2bel/constants.py

@@ -5,7 +5,7 @@
 import os
 
 import click
-from easy_config import EasyConfig
+import pystow
 
 _USER_CONFIG_DIRECTORY = os.path.abspath(os.path.join(os.path.expanduser('~'), '.config'))
 DEFAULT_CONFIG_PATHS = [
@@ -25,37 +25,7 @@
     os.path.join(_USER_CONFIG_DIRECTORY, 'pybel', 'pybel.ini'),
 ]
 
-
-class Config(EasyConfig):
-    """Configuration for Bio2BEL."""
-
-    NAME = 'bio2bel'
-    FILES = DEFAULT_CONFIG_PATHS
-
-    #: The directory in which Bio2BEL data is stored
-    directory: str = os.path.join(os.path.expanduser('~'), '.bio2bel')
-
-    #: The default name of the Bio2BEL database with SQLite
-    default_cache_name: str = 'bio2bel.db'
-
-    #: The SQLAlchemy connection string to the database
-    connection: str = None
-
-    def __post_init__(self):
-        os.makedirs(self.directory, exist_ok=True)
-        if self.connection is None:
-            self.connection = f'sqlite:///{os.path.join(self.directory, self.default_cache_name)}'
-
-
-config = Config.load(_lookup_config_envvar='config')
-BIO2BEL_DIR = config.directory
-DEFAULT_CACHE_CONNECTION = config.connection
-
-
-def get_global_connection() -> str:
-    """Return the global connection string."""
-    return config.connection
-
+BIO2BEL_HOME = pystow.get('bio2bel')
 
 directory_option = click.option(
     '-d', '--directory',

src/bio2bel/models.py

@@ -27,9 +27,9 @@
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import Session, sessionmaker
 
-from .constants import get_global_connection
+from .utils import get_connection
 
-log = logging.getLogger(__name__)
+logger = logging.getLogger(__name__)
 
 Base = declarative_base()
 
@@ -146,8 +146,7 @@ def _store_helper(model: Action, session: Optional[Session] = None) -> None:
 def _make_session(connection: Optional[str] = None) -> Session:
     """Make a session."""
     if connection is None:
-        connection = get_global_connection()
-
+        connection = get_connection()
     engine = create_engine(connection)
 
     create_all(engine)

src/bio2bel/testing.py

@@ -86,7 +86,7 @@ def mock_connection() -> str:
             """Get the connection enclosed by this class."""
             return self.connection
 
-        self.mock_global_connection = mock.patch('bio2bel.models.get_global_connection', mock_connection)
+        self.mock_global_connection = mock.patch('bio2bel.models.get_connection', mock_connection)
         self.mock_module_connection = mock.patch('bio2bel.utils.get_connection', mock_connection)
 
 

src/bio2bel/utils.py

@@ -16,7 +16,8 @@
 from botocore.client import BaseClient
 from pkg_resources import UnknownExtra, VersionConflict, iter_entry_points
 
-from .constants import BIO2BEL_DIR, config
+import pybel.config
+from .constants import BIO2BEL_HOME
 
 __all__ = [
     'get_data_dir',
@@ -38,7 +39,7 @@ def get_data_dir(module_name: str) -> str:
     :return: The module's data directory
     """
     module_name = module_name.lower()
-    data_dir = os.path.join(BIO2BEL_DIR, module_name)
+    data_dir = os.path.join(BIO2BEL_HOME, module_name)
     os.makedirs(data_dir, exist_ok=True)
     return data_dir
 
@@ -126,7 +127,7 @@ def _ensure_s3_client(s3_client: Optional[BaseClient]) -> BaseClient:
     return s3_client
 
 
-def get_connection(*, connection: Optional[str] = None) -> str:
+def get_connection(connection: Optional[str] = None) -> str:
     """Return the SQLAlchemy connection string if it is set.
 
     Order of operations:
@@ -141,11 +142,10 @@ def get_connection(*, connection: Optional[str] = None) -> str:
     6. Check the bio2bel config file for default
     7. Fall back to standard default cache connection
 
-    :param module_name: The name of the module to get the configuration for
     :param connection: get the SQLAlchemy connection string
     :return: The SQLAlchemy connection string based on the configuration
     """
-    return connection or config.connection
+    return connection or pybel.config.connection
 
 
 def get_bio2bel_modules() -> Mapping[str, types.ModuleType]:

src/bio2bel/web/application.py

@@ -11,8 +11,8 @@
 from flask_admin import Admin
 from pkg_resources import VersionConflict, iter_entry_points
 
-from bio2bel.constants import DEFAULT_CACHE_CONNECTION
 from bio2bel.manager.connection_manager import build_engine_session
+from pybel import config
 
 log = logging.getLogger(__name__)
 
@@ -59,7 +59,7 @@ def create_application(connection: Optional[str] = None) -> Flask:
     flask_bootstrap.Bootstrap(app)
     Admin(app)
 
-    connection = connection or DEFAULT_CACHE_CONNECTION
+    connection = connection or config.connection
     engine, session = build_engine_session(connection)
 
     for name, add_admin in add_admins.items():