bump sqlalchemy to >2.0 (#7)

- Migrate sqlalchemy to 2.0 but not yet supported for the development version (2.1)
- Sync tests and pre-commit configuration with the rest of the biocpy packages
- Minor edits to tests

Author: jkanche

.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

@@ -13,13 +13,18 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
 
+    name: Python ${{ matrix.python-version }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -32,4 +37,4 @@ jobs:
     #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with tox
       run: |
-        tox
+        tox

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+- repo: https://github.com/PyCQA/docformatter
+  rev: v1.7.5
+  hooks:
+    - id: docformatter
+      additional_dependencies: [tomli]
+      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+      # --config, ./pyproject.toml
+
+- repo: https://github.com/psf/black
+  rev: 24.4.0
+  hooks:
+  - id: black
+    language_version: python3
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.3.7
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - 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

pyproject.toml

@@ -6,3 +6,18 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 # See configuration details in https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+exclude = ["tests"]
+extend-ignore = ["F821"]
+
+[tool.ruff.pydocstyle]
+convention = "google"
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
+[tool.black]
+force-exclude = "__init__.py"

setup.cfg

@@ -47,7 +47,7 @@ package_dir =
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    sqlalchemy>=1.4,<2.0
+    sqlalchemy>=2,<2.1
 
 [options.packages.find]
 where = src

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

tests/test_cache.py

@@ -1,5 +1,4 @@
 import os
-import shutil
 
 from pybiocfilecache.BiocFileCache import BiocFileCache
 
@@ -12,7 +11,7 @@
 
 def test_create_cache():
     bfc = BiocFileCache(CACHE_DIR)
-    assert os.path.exists(CACHE_DIR == True)
+    assert os.path.exists(CACHE_DIR)
 
     bfc.purge()
 
@@ -22,16 +21,16 @@ def test_add_get_operations():
 
     bfc.add("test1", os.getcwd() + "/tests/data/test1.txt")
     rec1 = bfc.get("test1")
-    assert rec1 != None
+    assert rec1 is not None
 
     bfc.add("test2", os.getcwd() + "/tests/data/test2.txt")
     rec2 = bfc.get("test2")
-    assert rec2 != None
+    assert rec2 is not None
 
-    frec1 = open(rec1.rpath, "r").read()
+    frec1 = open(rec1.rpath, "r").read().strip()
     assert frec1 == "test1"
 
-    frec2 = open(rec2.rpath, "r").read()
+    frec2 = open(rec2.rpath, "r").read().strip()
     assert frec2 == "test2"
 
     bfc.purge()
@@ -42,14 +41,14 @@ def test_remove_operations():
 
     bfc.add("test1", os.getcwd() + "/tests/data/test1.txt")
     rec1 = bfc.get("test1")
-    assert rec1 != None
+    assert rec1 is not None
 
     bfc.add("test2", os.getcwd() + "/tests/data/test2.txt")
     rec2 = bfc.get("test2")
-    assert rec2 != None
+    assert rec2 is not None
 
     bfc.remove("test1")
     rec1 = bfc.get("test1")
-    assert rec1 == None
+    assert rec1 is None
 
     bfc.purge()