Update Python support and add dev tooling configs

Expanded supported Python versions to 3.9–3.12 in CI and metadata, and updated minimum required Python version to 3.9 in environment and project files. Modernized installation instructions in README to use pip. Added development and testing dependencies, and included configuration for ruff, mypy, and pytest in pyproject.toml to improve code quality and testing workflows.

Author: edeno

.github/workflows/test_package_build.yml

@@ -75,7 +75,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: [ "3.10", "3.11" ]
+        python: [ "3.9", "3.10", "3.11", "3.12" ]
         package: [ "wheel", "sdist", "archive" ]
 
     steps:

README.md

@@ -20,7 +20,7 @@ Or
 
 ```bash
 git clone https://github.com/LorenFrankLab/track_linearization.git
-python setup.py install
+pip install .
 ```
 
 ### Usage
@@ -35,5 +35,5 @@ python setup.py install
 cd <package folder>
 conda env create -f environment.yml
 conda activate track_linearization
-python setup.py develop
+pip install -e .
 ```

environment.yml

@@ -3,7 +3,7 @@ channels:
 - defaults
 - conda-forge
 dependencies:
-- "python>=3.6"
+- "python>=3.9"
 - numpy
 - scipy
 - matplotlib

pyproject.toml

@@ -6,13 +6,20 @@ build-backend = "hatchling.build"
 name = "track_linearization"
 description = "A python package to map 2D trajectories to 1D."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { file = "LICENSE" }
 authors = [{ name = "Eric Denovellis", email = "[email protected]" }]
 classifiers = [
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
 ]
 dependencies = ["numpy", "scipy", "matplotlib", "pandas", "dask", "networkx>=3.2.1"]
 dynamic = ["version"]
@@ -22,8 +29,9 @@ dynamic = ["version"]
 "Bug Tracker" = "https://github.com/LorenFrankLab/track_linearization/issues"
 
 [project.optional-dependencies]
-test = ["black", "pytest", "pytest-cov", "jupyter", "nbconvert"]
+test = ["black", "pytest", "pytest-cov", "jupyter", "nbconvert", "ruff", "mypy"]
 opt = ["numba", "ipympl"]
+dev = ["black", "pytest", "pytest-cov", "jupyter", "nbconvert", "ruff", "mypy", "pre-commit"]
 
 [tool.hatch.version]
 source = "vcs"
@@ -36,3 +44,51 @@ exclude = [".git_archival.txt"]
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/track_linearization"]
+
+[tool.ruff]
+target-version = "py39"
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    "E",      # pycodestyle errors
+    "W",      # pycodestyle warnings
+    "F",      # pyflakes
+    "I",      # isort
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "UP",     # pyupgrade
+]
+ignore = [
+    "E501",   # line too long, handled by black
+]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]  # Ignore unused imports in __init__.py
+
+[tool.mypy]
+python_version = "3.9"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+disallow_untyped_decorators = true
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true
+
+[tool.pytest.ini_options]
+testpaths = ["src/track_linearization/tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--doctest-modules",
+    "--cov=track_linearization",
+    "--cov-report=html",
+    "--cov-report=term-missing",
+]