[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

.github/workflows/pypi-publish.yml

@@ -48,4 +48,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -32,4 +32,4 @@ jobs:
     #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with tox
       run: |
-        tox
+        tox

.pre-commit-config.yaml

@@ -49,4 +49,4 @@ repos:
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.2.5
 #   hooks:
-#   - id: codespell
+#   - id: codespell

AUTHORS.md

@@ -1,4 +1,4 @@
 # Contributors
 
 * Jayaram Kancherla <[email protected]>
-* Max Hargreaves <[email protected]>
+* Max Hargreaves <[email protected]>

CHANGELOG.md

@@ -2,4 +2,4 @@
 
 ## Version 0.1 (development)
 
-- Initial release
+- Initial release

README.md

@@ -16,7 +16,7 @@ Package is published to [PyPI](https://pypi.org/project/pyBiocFileCache/)
 pip install pybiocfilecache
 ```
 
-#### Initialize a cache directory 
+#### Initialize a cache directory
 
 ```
 from pybiocfilecache import BiocFileCache

docs/requirements.txt

@@ -1,7 +1,7 @@
+furo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 recommonmark
 sphinx>=3.2.1
-furo

setup.py

@@ -1,11 +1,10 @@
-"""
-    Setup file for pyBiocFileCache.
-    Use setup.cfg to configure your project.
+"""Setup file for pyBiocFileCache. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.1.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.1.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
+
 from setuptools import setup
 
 if __name__ == "__main__":

src/pybiocfilecache/BiocFileCache.py

@@ -1,6 +1,4 @@
-"""
-Python Implementation of BiocFileCache
-"""
+"""Python Implementation of BiocFileCache."""
 
 import os
 from pathlib import Path
@@ -21,9 +19,7 @@
 
 
 class BiocFileCache:
-    """
-    Class to manage and cache files.
-    """
+    """Class to manage and cache files."""
 
     def __init__(self, cacheDirOrPath: Union[str, Path] = create_tmp_dir()):
         """Initialize BiocFileCache.
@@ -90,7 +86,13 @@ def add(
 
         # create new record in the database
         res = Resource(
-            **dict(rid=rid, rname=rname, rpath=rpath, rtype=rtype, fpath=str(fpath),)
+            **dict(
+                rid=rid,
+                rname=rname,
+                rpath=rpath,
+                rtype=rtype,
+                fpath=str(fpath),
+            )
         )
 
         # If this was higher up a parallel process could have added the key to
@@ -164,7 +166,7 @@ def _get(self, session: Session, rname: str) -> Optional[Resource]:
         return resource
 
     def get(self, rname: str) -> Optional[Resource]:
-        """get resource by name from cache.
+        """Get resource by name from cache.
 
         Args:
             rname (str): Name of the file to search.

src/pybiocfilecache/db/Base.py

@@ -13,7 +13,7 @@
 
 
 def create_schema(cache_dir: str) -> Tuple[Engine, sessionmaker]:
-    """Create the schema in the sqlite database
+    """Create the schema in the sqlite database.
 
     Args:
         cache_dir (str): Location where the cache directory

src/pybiocfilecache/db/schema.py

@@ -33,4 +33,3 @@ class Resource(Base):
 
     def __repr__(self):
         return "<Resource(id='%s', rname='%s')>" % (self.id, self.rname)
-

src/pybiocfilecache/utils.py

@@ -9,7 +9,7 @@
 
 
 def create_tmp_dir() -> str:
-    """create a temporary directory.
+    """Create a temporary directory.
 
     Returns:
         str: path to the directory
@@ -57,7 +57,7 @@ def copy_or_move(
 
 
 def setup_logging(loglevel):
-    """Setup basic logging
+    """Setup basic logging.
 
     Args:
       loglevel (int): minimum loglevel for emitting messages

tests/conftest.py

@@ -1,10 +1,9 @@
-"""
-    Dummy conftest.py for pybiocfilecache.
+"""Dummy conftest.py for pybiocfilecache.
 
-    If you don't know what this is for, just leave it empty.
-    Read more about conftest.py under:
-    - https://docs.pytest.org/en/stable/fixture.html
-    - https://docs.pytest.org/en/stable/writing_plugins.html
+If you don't know what this is for, just leave it empty.
+Read more about conftest.py under:
+- https://docs.pytest.org/en/stable/fixture.html
+- https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
 # import pytest

tests/data/test1.txt

@@ -1 +1 @@
-test1
+test1

tests/data/test2.txt

@@ -1 +1 @@
-test2
+test2