Updates

README.rst

@@ -15,15 +15,15 @@ Download the latest stable code from `PyPI <https://pypi.org/project/bio2bel>`_
 
 .. code-block:: sh
 
-   $ python3 -m pip install bio2bel
+   $ python -m pip install bio2bel
 
 or get the latest from GitHub with:
 
 .. code-block:: sh
 
    $ git clone https://github.com/bio2bel/bio2bel.git
    $ cd bio2bel
-   $ python3 -m pip install -e .
+   $ python -m pip install -e .
 
 or check the `installation instructions <http://bio2bel.readthedocs.io/en/latest/#installation>`_.
 

setup.cfg

@@ -4,7 +4,7 @@
 [metadata]
 name = bio2bel
 version = 0.3.9-dev
-description = A package for converting biological data sources to BEL
+description = A framework for converting biological data sources to BEL
 long_description = file: README.rst
 
 # URLs associated with the project
@@ -34,6 +34,8 @@ classifiers =
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
     Programming Language :: Python
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3 :: Only
     Topic :: Scientific/Engineering :: Bio-Informatics
@@ -54,7 +56,7 @@ install_requires =
     pandas
     tqdm
     easy_config
-    pybel<0.16.0
+    pybel>=0.15.0<0.16.0
     bel_resources>=0.0.3
     pyobo>=0.2.2
 

src/bio2bel/cli.py

@@ -33,7 +33,8 @@
 commands = {}
 for name, manager_cls in MANAGERS.items():
     commands[name] = manager_cls.get_cli()
-    commands[name].help = f'*Manage {name}'
+    # can not use single asterick, causes documentation build failure
+    commands[name].help = f'# Manage {name}'
 
 main = click.Group(commands=commands)
 main.help = f'Bio2BEL Command Line Utilities on {sys.executable}\nBio2BEL v{get_version()}'

src/bio2bel/io/automate.py

@@ -10,7 +10,7 @@
 from contextlib import redirect_stdout
 from typing import Any, Mapping, Optional, Tuple
 
-from pybel import BELGraph, from_nodelink_gz, to_nodelink_gz, to_tsv
+from pybel import BELGraph, from_nodelink_gz, to_nodelink_gz, to_triples_file
 from ..manager.bel_manager import BELManagerMixin
 from ..utils import get_data_dir
 
@@ -42,7 +42,7 @@ def ensure_tsv(name: str, *, manager_kwargs: Optional[Mapping[str, Any]] = None)
     if os.path.exists(path):
         return path
     graph = ensure_graph(name, manager_kwargs=manager_kwargs)
-    to_tsv(graph, path)
+    to_triples_file(graph, path)
     return path
 
 

src/bio2bel/utils.py

@@ -13,6 +13,7 @@
 from urllib.request import urlretrieve
 
 import requests
+from botocore.client import BaseClient
 from pkg_resources import UnknownExtra, VersionConflict, iter_entry_points
 
 from .constants import BIO2BEL_DIR, config
@@ -29,8 +30,6 @@
 
 logger = logging.getLogger(__name__)
 
-S3Client = 'botocore.client.BaseClient'
-
 
 def get_data_dir(module_name: str) -> str:
     """Ensure the appropriate Bio2BEL data directory exists for the given module, then returns the file path.
@@ -63,7 +62,7 @@ def ensure_path(
     use_requests: bool = False,
     force: bool = False,
     bucket: Optional[str] = None,
-    s3_client: Optional[S3Client] = None,
+    s3_client: Optional[BaseClient] = None,
 ) -> str:
     """Download a file if it doesn't exist.
 
@@ -109,7 +108,7 @@ def _get_s3_key(prefix: str, path: str) -> str:
     return os.path.join(prefix, path.name)
 
 
-def _has_file(s3_client: S3Client, *, bucket: str, key: str) -> bool:
+def _has_file(s3_client: BaseClient, *, bucket: str, key: str) -> bool:
     from botocore.errorfactory import ClientError
 
     try:
@@ -120,7 +119,7 @@ def _has_file(s3_client: S3Client, *, bucket: str, key: str) -> bool:
         return True
 
 
-def _ensure_s3_client(s3_client: Optional[S3Client]) -> S3Client:
+def _ensure_s3_client(s3_client: Optional[BaseClient]) -> BaseClient:
     if s3_client is None:
         import boto3
         s3_client = boto3.client('s3')