refactor: migrate setup configuration to pyproject.toml

Moved all package metadata and dependencies from setup.cfg and setup.py to pyproject.toml for a more modern and standardized project setup. Updated pre-commit hooks and made minor corrections in the code to align with the new configurations.

Author: jonas-eschle

.pre-commit-config.yaml

@@ -20,13 +20,12 @@ repos:
       - id: debug-statements
       - id: end-of-file-fixer
   - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.49"
+    rev: "0.50"
     hooks:
       - id: check-manifest
-        args: [ --update, --no-build-isolation ]
-        additional_dependencies: [ setuptools-scm, setuptools-scm-git-archive ]
+        args: [ --update ]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.12.0
     hooks:
       - id: mypy
         files: src
@@ -46,13 +45,13 @@ repos:
       - id: rst-directive-colons
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         args: [ --py38-plus ]
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.5.0
+    rev: v2.7.0
     hooks:
       - id: setup-cfg-fmt
         args: [ --max-py-version=3.12, --include-version-classifiers ]
@@ -64,7 +63,7 @@ repos:
 
       - id: nbqa-pyupgrade
         additional_dependencies: [ pyupgrade ]
-        args: [ --py38-plus ]
+        args: [ --py39-plus ]
 
 
   - repo: https://github.com/roy-ht/pre-commit-jupyter
@@ -85,7 +84,7 @@ repos:
       - id: rm-unneeded-f-str
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.3
+    rev: 0.29.4
     hooks:
       - id: check-github-workflows
       - id: check-github-actions
@@ -102,7 +101,7 @@ repos:
     hooks:
       - id: ruff
         types_or: [ python, pyi, jupyter ]
-        args: [ --fix, --unsafe-fixes, --show-fixes , --line-length=120]
+        args: [ --fix, --unsafe-fixes, --show-fixes , --line-length=120 ]
       # Run the formatter.
       - id: ruff-format
         types_or: [ python, pyi, jupyter ]

pyproject.toml

@@ -1,13 +1,97 @@
 [build-system]
-requires = [
-    "setuptools>=42",
-    "setuptools_scm[toml]>=3.4"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "hepstats"
+description = "statistics tools and utilities"
+authors = [{ name = "Matthieu Marinangeli", email = "[email protected]" }]
+maintainers = [{ name = "Scikit-HEP", email = "[email protected]" }]
+license = { text = "BSD 3-Clause License" }
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: C++",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development",
+    "Topic :: Utilities",
+]
+urls = { Homepage = "https://github.com/scikit-hep/hepstats" }
+requires-python = ">=3.9"
+dependencies = [
+    "asdf",
+    "numpy",
+    "pandas",
+    "scipy",
+    "tqdm",
+    "uhi",
+]
+dynamic = ["version"]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.optional-dependencies]
+dev = [
+    "hepstats[docs]",
+    "hepstats[test]",
+    "pre-commit",
+]
+docs = [
+    "matplotlib",
+    "pydata-sphinx-theme",
+    "sphinx>=3.1.2",
+    "sphinx-autodoc-typehints",
+    "sphinx-copybutton",
+    "sphinxcontrib-bibtex>=2.0.0",
 ]
+doc = ["hepstats[docs]"]  # alias
+test = [
+    "pytest",
+    "pytest-cov",
+    "pytest-runner",
+    "zfit>=0.20.0",
+]
+zfit = ["zfit>=0.20.0"]
+
+
+
+[tool.pytest.ini_options]
+junit_family = "xunit2"
+testpaths = ["tests"]
+
+[tool.check-manifest]
+ignore = ["src/hepstats/_version.py"]
+
+[tool.build_sphinx]
+project = "hepstats"
+source-dir = "docs"
+build-dir = "docs/_build"
+all-files = "1"
+warning-is-error = "0"
 
-build-backend = "setuptools.build_meta"
 
-[tool.setuptools_scm]
-write_to = "src/hepstats/version.py"
+[tool.hatch]
+version.source = "vcs"
+build.hooks.vcs.version-file = "src/hepstats/_version.py"
 
 [tool.ruff]
 #src = ["src"]
@@ -20,41 +104,42 @@ exclude = [
 ]
 [tool.ruff.lint]
 extend-select = [
-    "B",        # flake8-bugbear
-    "I",        # isort
-    "ARG",      # flake8-unused-arguments
-    "C4",       # flake8-comprehensions
-    "EM",       # flake8-errmsg
-    "ICN",      # flake8-import-conventions
-    "G",        # flake8-logging-format
-    "PGH",      # pygrep-hooks
-    "PIE",      # flake8-pie
-    "PL",       # pylint
-    "PT",       # flake8-pytest-style
-    "PTH",      # flake8-use-pathlib
-    "RET",      # flake8-return
-    "RUF",      # Ruff-specific
-    "SIM",      # flake8-simplify
-    "T20",      # flake8-print
-    "UP",       # pyupgrade
-    "YTT",      # flake8-2020
-    "EXE",      # flake8-executable
-    "NPY",      # NumPy specific rules
-    "PD",       # pandas-vet
+    "B", # flake8-bugbear
+    "I", # isort
+    "ARG", # flake8-unused-arguments
+    "C4", # flake8-comprehensions
+    "EM", # flake8-errmsg
+    "ICN", # flake8-import-conventions
+    "G", # flake8-logging-format
+    "PGH", # pygrep-hooks
+    "PIE", # flake8-pie
+    "PL", # pylint
+    "PT", # flake8-pytest-style
+    "PTH", # flake8-use-pathlib
+    "RET", # flake8-return
+    "RUF", # Ruff-specific
+    "SIM", # flake8-simplify
+    "T20", # flake8-print
+    "UP", # pyupgrade
+    "YTT", # flake8-2020
+    "EXE", # flake8-executable
+    "NPY", # NumPy specific rules
+    "PD", # pandas-vet
 ]
 ignore = [
-    "UP007",    # type annotation upgrade, breaks pydantic for Python 3.9 (remove once above)
-    "PLR09",    # Too many <...>
-    "PLR2004",  # Magic value used in comparison
-    "ISC001",   # Conflicts with formatter
-    "RET505",   # This is sometimes wanted, protets against accidental intendation
-    "PD901",    # "avoid using `df[...].values`" -> no, this is a very good name if there is only one df
-    "PD011",    # "replace `df[...].values` with `df[...].to_numpy()`" -> not yet, it's not deprecated.
+    "UP007", # type annotation upgrade, breaks pydantic for Python 3.9 (remove once above)
+    "PLR09", # Too many <...>
+    "PLR2004", # Magic value used in comparison
+    "ISC001", # Conflicts with formatter
+    "RET505", # This is sometimes wanted, protets against accidental intendation
+    "PD901", # "avoid using `df[...].values`" -> no, this is a very good name if there is only one df
+    "PD011", # "replace `df[...].values` with `df[...].to_numpy()`" -> not yet, it's not deprecated.
     # Prefer to have a single way to access the data if we don't care about whether it's a numpy array or not.
-    "PLW0603",  # updating global variables with a function is bad, but we use it for
-    "PLW2901",  # "for loop overwritten by assignment" -> we use this to update the loop variable
-    "PD013",    # "melt over stack": df function, but triggers on tensors
-    "NPY002",   # "Use rnd generator in numpy" -> we use np.random for some legacy stuff but do use the new one where we can
+    "PLW0603", # updating global variables with a function is bad, but we use it for
+    "PLW2901", # "for loop overwritten by assignment" -> we use this to update the loop variable
+    "PD013", # "melt over stack": df function, but triggers on tensors
+    "NPY002", # "Use rnd generator in numpy" -> we use np.random for some legacy stuff but do use the new one where we can
+    "T201", # "print used" -> we use print for displaying information in verbose mode
 
 ]
 isort.required-imports = ["from __future__ import annotations"]

setup.cfg

@@ -160,7 +160,7 @@ def _convert_to_binned(self, loss, asimov_bins):
         """Converts the loss to binned if necessary."""
 
         for unbinned_loss, binned_loss in self.UNBINNED_TO_BINNED_LOSS.items():
-            if type(loss) == unbinned_loss:
+            if type(loss) is unbinned_loss:
                 datasets = []
                 models = []
                 for d, m, nbins in zip(loss.data, loss.model, asimov_bins):
@@ -171,7 +171,7 @@ def _convert_to_binned(self, loss, asimov_bins):
                     models.append(model_binned)
                 loss = binned_loss(model=models, data=datasets, constraints=loss.constraints)
                 break
-            if type(loss) == binned_loss:
+            if type(loss) is binned_loss:
                 break
         else:
             loss = False