build: upgraded all dependencies and tools

.github/workflows/codeql-analysis.yml

@@ -9,16 +9,16 @@
 # the `language` matrix defined below to confirm you have the correct set of
 # supported CodeQL languages.
 #
-name: "CodeQL"
+name: CodeQL
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ main ]
+    branches: [main]
   schedule:
-    - cron: '22 18 * * 5'
+  - cron: 22 18 * * 5
 
 jobs:
   analyze:
@@ -32,7 +32,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        language: [ 'python' ]
+        language: [python]
         # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
         # Learn more about CodeQL language support at https://git.io/codeql-language-support
 

.github/workflows/coverage.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.13]
 
     steps:
     - uses: actions/checkout@v2
@@ -23,17 +23,14 @@ jobs:
     - name: Generate coverage report
       run: |
         coverage erase
-        pytest --cov=codemetrics --cov-branch --cov-report=xml --cov-config=setup.cfg
+        pytest --cov=codemetrics --cov-branch --cov-report=xml --cov-config=pyproject.toml
         coverage xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: true
-# Codacy does not seem to support coverage.xml out of the box
-#   - name: Codacy Coverage Reporter
-#     uses: codacy/codacy-coverage-reporter-action@master
-#     with:
-#       project-token: ${{secrets.CODACY_PROJECT_TOKEN}}
+        files: ./coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
 
 
 

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.13'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/python-app.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -29,6 +29,7 @@ wheels/
 
 # Local files that should stay so
 local/
+.vscode/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

.pre-commit-config.yaml

@@ -1,40 +1,39 @@
 default_stages:
-- commit
+- pre-commit
 repos:
 - hooks:
   - id: commitizen
     stages:
     - commit-msg
   repo: https://github.com/commitizen-tools/commitizen
-  rev: v2.24.0
+  rev: master
 - hooks:
   - id: check-added-large-files
   - id: check-merge-conflict
+  - id: check-toml
   - id: debug-statements
   - id: detect-private-key
-  - id: requirements-txt-fixer
   repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v6.0.0
 - hooks:
   - args:
     - --autofix
     - --indent
     - '2'
     id: pretty-format-yaml
   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.3.0
-- hooks:
-  - id: black
-    language_version: python3.8
-  repo: https://github.com/python/black
-  rev: 22.3.0
-- hooks:
-  - additional_dependencies:
-    - flake8-comprehensions>=3.1.0
-    id: flake8
-    language: python_venv
-  repo: https://gitlab.com/pycqa/flake8
-  rev: 3.9.2
+  rev: v2.15.0
+- repo: https://github.com/abravalheri/validate-pyproject
+  rev: v0.24.1
+  hooks:
+  - id: validate-pyproject
+    files: pyproject\.toml$
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.13.0
+  hooks:
+  - id: ruff-check
+    args: [--fix]
+  - id: ruff-format
 - hooks:
   - args:
     - --install-types
@@ -43,11 +42,7 @@ repos:
     files: codemetrics/
     id: mypy
   repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.942
-- hooks:
-  - id: isort
-  repo: https://github.com/pre-commit/mirrors-isort
-  rev: v5.10.1
+  rev: v1.18.1
 - hooks:
   - always_run: false
     entry: python -m unittest

CONTRIBUTING.rst

@@ -66,7 +66,7 @@ Ready to contribute? Here's how to set up `codemetrics` for local development.
 
     $ mkvirtualenv codemetrics
     $ cd codemetrics/
-    $ python setup.py develop
+    $ python -m pip install -e .[develop]
 
 4. Create a branch for local development::
 
@@ -78,11 +78,9 @@ Ready to contribute? Here's how to set up `codemetrics` for local development.
    tests, including testing other Python versions with tox::
 
     $ flake8 codemetrics tests
-    $ python setup.py test or py.test
+    $ python -m unittest discover tests
     $ tox
 
-   To get flake8 and tox, just pip install them into your virtualenv.
-
 6. Commit your changes and push your branch to GitHub::
 
     $ git add .
@@ -122,7 +120,7 @@ Then run::
     $ tox -p  # there should be no errors.
     $ vim HISTORY.rst
     $ bump2version patch  # possible: major / minor / patch.
-    $ vim setup.cfg  # bump2version does not update all references.
+    $ vim pyproject.toml  # bump2version does not update all references.
     $ git push
     $ git tag vx.y.z
     $ git push --tags

MANIFEST.in

@@ -1,8 +1,8 @@
-include AUTHORS.md
-include CONTRIBUTING.md
-include HISTORY.md
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
 include LICENSE.txt
-include README.md
+include README.rst
 
 recursive-include tests *
 recursive-exclude * __pycache__

Makefile

@@ -54,13 +54,13 @@ lint: ## check style with flake8
 	flake8 codemetrics tests
 
 test: ## run tests quickly with the default Python
-	python setup.py test
+	python -m unittest discover tests
 
 test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source codemetrics setup.py test
+	coverage run --source codemetrics -m pytest tests
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
@@ -80,9 +80,8 @@ release: dist ## package and upload a release
 	twine upload dist/*
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m build
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	python setup.py install
+	python -m pip install .

codemetrics/core.py

@@ -11,6 +11,7 @@
 import sklearn.feature_extraction.text
 
 from . import internals, scm
+from typing import Optional
 
 __all__ = [
     "get_mass_changes",
@@ -23,7 +24,9 @@
 
 
 def get_mass_changes(
-    log: pd.DataFrame, min_path: int = None, max_changes_per_path: float = None
+    log: pd.DataFrame,
+    min_path: Optional[int] = None,
+    max_changes_per_path: Optional[float] = None,
 ) -> pd.DataFrame:
     """Extract mass changesets from the SCM log data frame.
 
@@ -61,7 +64,7 @@ def get_mass_changes(
 
 def get_ages(
     data: pd.DataFrame,
-    by: typing.Sequence[str] = None,
+    by: Optional[typing.Sequence[str]] = None,
 ) -> pd.DataFrame:
     """Generate age of each file based on last change.
 

codemetrics/git.py

@@ -14,6 +14,7 @@
 
 from . import internals, scm
 from .internals import log
+from typing import Optional
 
 default_client = "git"
 
@@ -60,7 +61,10 @@ class _GitLogCollector(scm.ScmLogCollector):
     ]
 
     def __init__(
-        self, git_client: str = default_client, cwd: pl.Path = None, _pdb: bool = False
+        self,
+        git_client: str = default_client,
+        cwd: Optional[pl.Path] = None,
+        _pdb: bool = False,
     ):
         """Initialize.
 
@@ -190,9 +194,9 @@ def process_log_entries(
     def get_log(
         self,
         path: str = ".",
-        after: dt.datetime = None,
-        before: dt.datetime = None,
-        progress_bar: tqdm.tqdm = None,
+        after: Optional[dt.datetime] = None,
+        before: Optional[dt.datetime] = None,
+        progress_bar: Optional[tqdm.tqdm] = None,
     ) -> pd.DataFrame:
         """Retrieve log from git.
 
@@ -230,7 +234,7 @@ def get_log(
 class _GitFileDownloader(scm.ScmDownloader):
     """Download files from Subversion."""
 
-    def __init__(self, git_client: str = None, cwd: pl.Path = None):
+    def __init__(self, git_client: Optional[str] = None, cwd: Optional[pl.Path] = None):
         """Initialize downloader.
 
         Args:
@@ -251,7 +255,6 @@ def _download(
 
 
 class GitProject(scm.Project):
-
     """Project for git SCM."""
 
     def __init__(self, cwd: pl.Path = pl.Path("."), client: str = "git"):
@@ -285,11 +288,11 @@ def download(self, data: pd.DataFrame) -> scm.DownloadResult:
     def get_log(
         self,
         path: str = ".",
-        after: dt.datetime = None,
-        before: dt.datetime = None,
-        progress_bar: tqdm.tqdm = None,
+        after: Optional[dt.datetime] = None,
+        before: Optional[dt.datetime] = None,
+        progress_bar: Optional[tqdm.tqdm] = None,
         # FIXME: Needed for Subversion though may be a better way.
-        relative_url: str = None,
+        relative_url: Optional[str] = None,
         _pdb: bool = False,
     ) -> pd.DataFrame:
         """Entry point to retrieve git log.
@@ -318,7 +321,7 @@ def get_log(
 
 
 def download(
-    data: pd.DataFrame, client: str = None, cwd: pl.Path = None
+    data: pd.DataFrame, client: Optional[str] = None, cwd: Optional[pl.Path] = None
 ) -> scm.DownloadResult:
     """Downloads files from Subversion.
 

codemetrics/internals.py

@@ -10,6 +10,7 @@
 import typing
 
 import pandas as pd
+from typing import Optional
 
 log = logging.getLogger("codemetrics")
 log.addHandler(logging.NullHandler())
@@ -27,7 +28,7 @@ def get_now():
     return dt.datetime.now(dt.timezone.utc)
 
 
-def get_year_ago(from_date: dt.datetime = None):
+def get_year_ago(from_date: Optional[dt.datetime] = None):
     """Get current time stamp minus 1 year.
 
     Decrements by one the year of the date returned by `get_now()`.

codemetrics/pbar.py

@@ -8,6 +8,7 @@
 import tqdm
 
 import codemetrics as cm
+from typing import Optional
 
 
 class ProgressBarAdapter:
@@ -17,7 +18,10 @@ class ProgressBarAdapter:
     """
 
     def __init__(
-        self, progress_bar: tqdm.tqdm, after: dt.datetime, ascending: bool = None
+        self,
+        progress_bar: tqdm.tqdm,
+        after: dt.datetime,
+        ascending: Optional[bool] = None,
     ):
         """Creates adapter to update the progress bar based on days retrieved.