Merge branch 'main' into test-py312

.github/workflows/ci.yml

@@ -57,4 +57,4 @@ jobs:
  if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
  - name: Test with pytest
  run: |
- pytest -n 0 --durations 0 -v -m "not slow" -k ${{ matrix.pytest-file }}
+ pytest -n 0 --durations 0 -v -m "not slow" ${{ matrix.pytest-file }}

.gitignore

@@ -1,3 +1,163 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# For a library or package, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp
+
+
 .DS_Store
 **/.DS_Store
 docs/_build

.pre-commit-config.yaml

@@ -1,42 +1,88 @@
-exclude: '^docs/conf.py|.*key'
+ci:
+ autoupdate_commit_msg: "chore: update pre-commit hooks"
+ autofix_commit_msg: "style: pre-commit fixes"
+ autoupdate_schedule: "monthly"
 
-default_language_version:
- python: python3
+exclude: ".*key"
 
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.5.0
- hooks:
- - id: trailing-whitespace
- - id: check-added-large-files
- - id: check-ast
- - id: check-json
- - id: check-merge-conflict
- - id: check-xml
- - id: check-yaml
- - id: debug-statements
- - id: end-of-file-fixer
- - id: requirements-txt-fixer
- - id: mixed-line-ending
- args: ['--fix=no']
-
-- repo: https://github.com/PyCQA/isort
- rev: 5.12.0
- hooks:
- - id: isort
- args: ["--profile", "black"]
-
-- repo: https://github.com/psf/black-pre-commit-mirror
- rev: 23.11.0
- hooks:
- - id: black-jupyter
- language_version: python3
- args: [--line-length=100]
-
-- repo: https://github.com/pycqa/flake8
- rev: 6.1.0
- hooks:
- - id: flake8
- # black-compatible flake-8 config
- args: ['--max-line-length=100', # max recommended for sight disabilities
- '--extend-ignore=E203,F401'] # E203 is not PEP8 compliant
+ - repo: https://github.com/psf/black-pre-commit-mirror
+ rev: 24.3.0
+ hooks:
+ - id: black-jupyter
+ language_version: python3
+ args: [--line-length=100]
+
+ - repo: https://github.com/adamchainz/blacken-docs
+ rev: "1.16.0"
+ hooks:
+ - id: blacken-docs
+ additional_dependencies: [black==23.*]
+
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: "v4.5.0"
+ hooks:
+ - id: check-added-large-files
+ - id: check-case-conflict
+ - id: check-merge-conflict
+ - id: check-symlinks
+ - id: check-yaml
+ - id: debug-statements
+ - id: end-of-file-fixer
+ - id: mixed-line-ending
+ - id: name-tests-test
+ args: ["--pytest-test-first"]
+ - id: requirements-txt-fixer
+ - id: trailing-whitespace
+
+ - repo: https://github.com/pre-commit/pygrep-hooks
+ rev: "v1.10.0"
+ hooks:
+ - id: rst-backticks
+ - id: rst-directive-colons
+ - id: rst-inline-touching-normal
+
+ - repo: https://github.com/pre-commit/mirrors-prettier
+ rev: "v4.0.0-alpha.8"
+ hooks:
+ - id: prettier
+ types_or: [yaml, markdown, html, css, scss, javascript, json]
+ args: [--prose-wrap=preserve]
+
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: "v0.3.5"
+ hooks:
+ - id: ruff
+ args: ["--fix", "--show-fixes"]
+
+ # - repo: https://github.com/pre-commit/mirrors-mypy
+ # rev: "v1.6.1"
+ # hooks:
+ # - id: mypy
+ # files: src|tests
+ # args: []
+ # additional_dependencies:
+ # - pytest
+
+ - repo: https://github.com/codespell-project/codespell
+ rev: "v2.2.6"
+ hooks:
+ - id: codespell
+ types_or: [python, rst, markdown]
+
+ - repo: https://github.com/shellcheck-py/shellcheck-py
+ rev: "v0.10.0.1"
+ hooks:
+ - id: shellcheck
+
+ - repo: https://github.com/abravalheri/validate-pyproject
+ rev: v0.16
+ hooks:
+ - id: validate-pyproject
+
+ - repo: https://github.com/python-jsonschema/check-jsonschema
+ rev: 0.28.1
+ hooks:
+ - id: check-dependabot
+ - id: check-github-workflows
+ - id: check-readthedocs

.readthedocs.yaml

@@ -20,4 +20,4 @@ formats: all
 
 python:
  install:
- - requirements: docs/requirements.txt
+  - requirements: docs/requirements.txt

README.md

@@ -6,7 +6,7 @@
 <b>For developing and reproducing ML + HEP projects.</b>
 </p>
 
-______________________________________________________________________
+---
 
 <p align="center">
  <a href="#jetnet">JetNet</a> •
@@ -18,9 +18,7 @@ ______________________________________________________________________
  <a href="#references">References</a>
 </p>
 
-______________________________________________________________________
-
-
+---
 
 [![CI](https://github.com/jet-net/jetnet/actions/workflows/ci.yml/badge.svg)](https://github.com/jet-net/jetnet/actions)
 [![Documentation Status](https://readthedocs.org/projects/jetnet/badge/?version=latest)](https://jetnet.readthedocs.io/en/latest/)
@@ -32,15 +30,14 @@ ______________________________________________________________________
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10044601.svg)](https://doi.org/10.5281/zenodo.10044601)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05789/status.svg)](https://doi.org/10.21105/joss.05789)
 
-
-
-______________________________________________________________________
+---
 
 ## JetNet
 
 JetNet is an effort to increase accessibility and reproducibility in jet-based machine learning.
 
 Currently we provide:
+
 - Easy-to-access and standardised interfaces for the following datasets:
  - [JetNet](https://zenodo.org/record/6975118)
  - [TopTagging](https://zenodo.org/record/2603256)
@@ -55,10 +52,8 @@ Currently we provide:
  - Differentiable implementation of the energy mover's distance [[3](#references)]
 - And more general jet utilities.
 
-
 Additional functionality is under development, and please reach out if you're interested in contributing!
 
-
 ## Installation
 
 JetNet can be installed with pip:
@@ -81,17 +76,22 @@ Datasets can be downloaded and accessed quickly, for example:
 
 ```python
 from jetnet.datasets import JetNet, TopTagging
+
 # as numpy arrays:
-particle_data, jet_data = JetNet.getData(jet_type=["g", "q"], data_dir="./datasets/jetnet/", download=True)
+particle_data, jet_data = JetNet.getData(
+ jet_type=["g", "q"], data_dir="./datasets/jetnet/", download=True
+)
 # or as a PyTorch dataset:
-dataset = TopTagging(jet_type="all", data_dir="./datasets/toptagging/", split="train", download=True)
+dataset = TopTagging(
+ jet_type="all", data_dir="./datasets/toptagging/", split="train", download=True
+)
 ```
 
 Evaluation metrics can be used as such:
 
 ```python
 generated_jets = np.random.rand(50000, 30, 3)
-fpnd_score = jetnet.evaluation.fpnd(generated_jets, jet_type='g')
+fpnd_score = jetnet.evaluation.fpnd(generated_jets, jet_type="g")
 ```
 
 Loss functions can be initialized and used similarly to standard PyTorch in-built losses such as MSE:
@@ -189,11 +189,10 @@ Please further cite the following if you use these components of the library.
 
 Please cite the respective [qpth](https://locuslab.github.io/qpth/) or [cvxpy](https://github.com/cvxpy/cvxpy) libraries, depending on the method used (`qpth` by default), as well as the original EMD paper [[3]](#references).
 
-
 ## References
 
-[1] R. Kansal et al., *Particle Cloud Generation with Message Passing Generative Adversarial Networks*, [NeurIPS 2021](https://proceedings.neurips.cc/paper/2021/hash/c8512d142a2d849725f31a9a7a361ab9-Abstract.html) [[2106.11535](https://arxiv.org/abs/2106.11535)].
+[1] R. Kansal et al., _Particle Cloud Generation with Message Passing Generative Adversarial Networks_, [NeurIPS 2021](https://proceedings.neurips.cc/paper/2021/hash/c8512d142a2d849725f31a9a7a361ab9-Abstract.html) [[2106.11535](https://arxiv.org/abs/2106.11535)].
 
-[2] R. Kansal et al., *Evaluating Generative Models in High Energy Physics*, [Phys. Rev. D **107** (2023) 076017](https://doi.org/10.1103/PhysRevD.107.076017) [[2211.10295](https://arxiv.org/abs/2211.10295)].
+[2] R. Kansal et al., _Evaluating Generative Models in High Energy Physics_, [Phys. Rev. D **107** (2023) 076017](https://doi.org/10.1103/PhysRevD.107.076017) [[2211.10295](https://arxiv.org/abs/2211.10295)].
 
-[3] P. T. Komiske, E. M. Metodiev, and J. Thaler, _The Metric Space of Collider Events_, [Phys. Rev. Lett. __123__ (2019) 041801](https://doi.org/10.1103/PhysRevLett.123.041801) [[1902.02346](https://arxiv.org/abs/1902.02346)].
+[3] P. T. Komiske, E. M. Metodiev, and J. Thaler, _The Metric Space of Collider Events_, [Phys. Rev. Lett. **123** (2019) 041801](https://doi.org/10.1103/PhysRevLett.123.041801) [[1902.02346](https://arxiv.org/abs/1902.02346)].