Setup pre-commit hoooks and change installation to use pyproject.toml

.coveragerc

@@ -0,0 +1,9 @@
+# .coveragerc
+
+[run]
+branch = True
+source = ic3_labels
+
+[report]
+
+omit = ic3_labels/__about__.py

.github/workflows/test_suite.yml

@@ -0,0 +1,45 @@
+name: Unit Tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [
+          "3.8",
+          "3.9",
+          "3.10",
+          "3.11",
+          "3.12",
+        ]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: pre-commit/action@v3.0.0
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[test]
+      - name: Test with pytest
+        run: |
+          coverage run -m pytest  -v -s
+      - name: Generate Coverage Report
+        run: |
+          coverage report -m
+        continue-on-error: false
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,67 @@
+# Adapted from simweights
+# SPDX-FileCopyrightText: © 2022 the SimWeights contributors
+#
+# SPDX-License-Identifier: BSD-2-Clause
+
+ci:
+  autoupdate_commit_msg: autoupdate pre-commit hooks
+  autoupdate_schedule: quarterly
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+  - repo: https://github.com/asottile/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        args: [-l 100]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5
+    hooks:
+      - id: ruff
+        args: [--fix, --show-fixes]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        args: [-L, livetime]
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-no-log-warn
+      - id: python-no-eval
+        exclude: ^tests/.*
+      - id: python-use-type-annotations
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.5
+    hooks:
+      - id: forbid-crlf
+      - id: forbid-tabs
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: [--pytest-test-first]
+      - id: trailing-whitespace
+        exclude: \.svg$

CONTRIBUTING.md

@@ -0,0 +1,24 @@
+# Contributing
+
+Welcome and thanks for considering to contribute to this repository!
+
+## Pre-commit Hooks
+
+When contributing to this project, please utilize the pre-commit hooks. If not installed yet, you will need to add the python package `pre-commit`:
+
+    pip install pre-commit
+
+Once the package is installed, simply install the pre-commit hooks defined in the repository by executing:
+
+    pre-commit install
+
+from within the repository directory.
+
+The pre-commit hooks will now automatically run when invoking `git commit`. Note, however, that this requires an active shell that has `pre-commit` installed.
+You can also manually run the pre-commit on single files or on all files via:
+
+    pre-commit run --all-files
+
+If you need to commit something even though there are errors (this should not have to be done!), then you can add the flag `--no-verify` to the `git commit` command. This will bypass the pre-commit hooks.
+
+Additional information is provided here: https://pre-commit.com/

README.md

@@ -1,2 +1,8 @@
+| Testing | Coverage |
+| :-----: | :------: |
+| [![Unit Tests](https://github.com/icecube/ic3_labels/actions/workflows/test_suite.yml/badge.svg)](https://github.com/icecube/ic3_labels/actions/workflows/test_suite.yml) | [![codecov](https://codecov.io/github/icecube/ic3_labels/graph/badge.svg?token=ZQ6K8V9F4U)](https://codecov.io/github/icecube/ic3_labels)
+
+
+
 # ic3-labels
 Helper functions and I3-Modules to create labels for IceCube data

ic3_labels/__about__.py

@@ -1,5 +1,17 @@
-__version__ = '1.1.0-dev'
+__version__ = "1.1.0-dev"
 __author__ = "Mirco Huennefeld"
 __author_email__ = "mirco.huennefeld@tu-dortmund.de"
-__description__ = "Creates MC labels for IceCube simulation data"
+__description__ = "MC weights and labels for IceCube simulation data"
 __url__ = "https://github.com/mhuen/ic3-labels"
+
+__version_major__ = 1
+__version_minor__ = 1
+__version_patch__ = 0
+__version_info__ = "-dev"
+
+__version__ = "{}.{}.{}{}".format(
+    __version_major__,
+    __version_minor__,
+    __version_patch__,
+    __version_info__,
+)

ic3_labels/__init__.py

@@ -1 +1,19 @@
-from ic3_labels.__about__ import __version__, __description__, __url__
+from .__about__ import (
+    __version_major__,
+    __version_minor__,
+    __version_patch__,
+    __version_info__,
+    __version__,
+    __description__,
+    __url__,
+)
+
+__all__ = [
+    "__version_major__",
+    "__version_minor__",
+    "__version_patch__",
+    "__version_info__",
+    "__version__",
+    "__description__",
+    "__url__",
+]

pyproject.toml

@@ -0,0 +1,77 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ic3_labels"
+description = "MC weights and labels for IceCube simulation data"
+readme = "README.md"
+dynamic = ["version"]
+authors = [
+    { name = "Mirco Huennefeld", email = "mirco.huennefeld@tu-dortmund.de" },
+]
+maintainers = [
+    { name = "Mirco Huennefeld", email = "mirco.huennefeld@tu-dortmund.de" },
+]
+requires-python = ">=3.7"
+
+dependencies = [
+    'numpy', 'click', 'pyyaml', 'scipy', 'MCEq', 'crflux',
+    'nuVeto',
+]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: BSD License",
+    "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 :: Physics",
+    "Topic :: Scientific/Engineering :: Statistics",
+]
+
+[project.optional-dependencies]
+dev = ["pre-commit","black","ruff"]
+test = ["pytest", "coverage", "codecov"]
+
+[project.urls]
+Homepage = "https://github.com/icecube/ic3_labels"
+Documentation = "https://github.com/icecube/ic3_labels"
+"Bug Tracker" = "https://github.com/icecube/ic3_labels/issues"
+Discussions = "https://github.com/icecube/ic3_labels/discussions"
+
+[tool.setuptools]
+packages = ["ic3_labels"]
+
+[tool.setuptools.dynamic]
+version = {attr = "ic3_labels.__version__"}
+
+[tool.black]
+line-length = 79
+target-version = ["py38"]
+
+[tool.ruff]
+# select = ["ALL"]
+fixable = ["I"]
+ignore = [
+    "D213",   # multi-line-summary-second-line incompatible with multi-line-summary-first-line
+    "D203",   # one-blank-line-before-class" incompatible with no-blank-line-before-class
+    "D401",   # non-imperative-mood
+    "D417",   # undocumented-param
+    "ANN101", # missing-type-self
+    "ANN401", # any-type
+    "FBT",    # flake8-boolean-trap
+    "INP",    # flake8-no-pep420
+    "T20",    # flake8-print
+    "TCH",    # flake8-type-checking
+    "S101",   # assert-used
+    "F401",   # imported but unused. NOTE: sooner or later, we should not ignore this
+    ]
+line-length = 79
+target-version = "py38"
+
+[tool.ruff.pydocstyle]
+convention = "numpy"

setup.py

@@ -1,26 +1,3 @@
-#!/usr/bin/env python
-import os
-from setuptools import setup, find_packages
+from setuptools import setup
 
-here = os.path.dirname(__file__)
-
-about = {}
-with open(os.path.join(here, 'ic3_labels', '__about__.py')) as fobj:
-    exec(fobj.read(), about)
-
-setup(
-    name='ic3_labels',
-    version=about['__version__'],
-    packages=find_packages(),
-    install_requires=[
-        'numpy', 'click', 'pyyaml', 'scipy', 'MCEq', 'crflux',
-        'nuVeto',
-    ],
-    include_package_data=True,
-    author=about['__author__'],
-    author_email=about['__author_email__'],
-    maintainer=about['__author__'],
-    maintainer_email=about['__author_email__'],
-    description=about['__description__'],
-    url=about['__url__']
-)
+setup()