Switched to pyproject.toml based setup

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml # checks for correct yaml syntax for github actions ex.
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.2.2
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black

pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "src/simulatedmicroscopy/_version.py"
+
+[tool.black]
+line-length = 79
+target-version = ['py38', 'py39', 'py310', 'py311', 'py312']
+
+[tool.ruff]
+line-length = 79
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+
+ignore = [
+    "E501",
+    "E203",
+    "W503",
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py38"
+fix = true

setup.cfg

@@ -1,2 +1,61 @@
-[flake8]
-ignore=E501,E203,W503
+[metadata]
+name = simulatedmicroscopy
+
+description =  Python package to create synthetic (fluorescence) microscopy images of (nano)particles and convolution with a point spread function
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/rhoitink/simulatedmicroscopy
+author = Roy Hoitink
+author_email = L.D.Hoitink@uu.nl
+license = MIT
+license_files = LICENSE
+classifiers =
+    Development Status :: 4 - Beta
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Topic :: Scientific/Engineering :: Image Processing
+project_urls =
+    Bug Tracker = https://github.com/rhoitink/simulatedmicroscopy/issues
+    Documentation = https://github.com/rhoitink/simulatedmicroscopy#README.md
+    Source Code = https://github.com/rhoitink/simulatedmicroscopy
+    User Support = https://github.com/rhoitink/simulatedmicroscopy/issues
+
+[options]
+packages = find:
+install_requires =
+    numpy
+    matplotlib
+    h5py
+    scipy
+    scikit-image>=0.20.0
+
+python_requires = >=3.8
+include_package_data = True
+package_dir =
+    =src
+setup_requires = setuptools_scm
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+dev =
+    black
+    flake8
+    pytest
+    pytest-cov
+docs =
+    mkdocs
+    mkdocs-material
+    mkdocstrings[python]
+    mkdocs-gen-files
+    mkdocs-literate-nav

simulatedmicroscopy/__init__.py → src/simulatedmicroscopy/__init__.py

@@ -2,6 +2,10 @@
 from .image import Image, HuygensImage
 from .psf import HuygensPSF, GaussianPSF
 from .particle import Sphere, Shell, PointParticle, Spherocylinder, Cube
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
 
 __all__ = [
     "Coordinates",
@@ -14,6 +18,4 @@
     "Shell",
     "Spherocylinder",
     "Cube",
-]
-
-__version__ = "1.4.0"
+]

src/simulatedmicroscopy/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '1.4.1.dev7+g5e7fa38.d20240219'
+__version_tuple__ = version_tuple = (1, 4, 1, 'dev7', 'g5e7fa38.d20240219')