Infrastructure

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
     args: ['--fix=no']
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: '6.1.0'  # pick a git hash / tag to point to
+    rev: '7.0.0'  # pick a git hash / tag to point to
     hooks:
     -   id: flake8
         additional_dependencies:
@@ -35,7 +35,7 @@ repos:
           - flake8-copyright
 
 -   repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.2.0
     hooks:
     - id: black
 
@@ -45,20 +45,20 @@ repos:
       - id: rst-backticks
 
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     args: ["--profile", "black"]
 
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.15.1
   hooks:
   -   id: pyupgrade
       args: [--py38-plus]
 
 - repo: https://github.com/commitizen-tools/commitizen
-  rev: 3.10.0
+  rev: v3.18.4
   hooks:
     - id: commitizen
       stages: [commit-msg]

docs/conf.py

@@ -1,7 +1,8 @@
-# -*- coding: utf-8 -*-
-
-import sys, os
+"""Configuration for Sphinx documentation."""
+import os
+import sys
 import time
+
 try:
     from importlib.metadata import version as _version
 except ImportError:
@@ -10,7 +11,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath("../"))
 
 # -- General configuration -----------------------------------------------------
 
@@ -40,20 +41,20 @@
 autosummary_generate = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['templates']
+templates_path = ["templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'pspec_likelihood'
-copyright = u'%s, HERA-Team' % (time.localtime()[0])
+project = "pspec_likelihood"
+copyright = "%s, HERA-Team" % (time.localtime()[0])
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -68,11 +69,10 @@
 ]
 
 
-
 # The short X.Y version.
-version = _version('pspec_likelihood')
+version = _version("pspec_likelihood")
 # The full version, including alpha/beta/rc tags.
-release = _version('pspec_likelihood')
+release = _version("pspec_likelihood")
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation
@@ -87,7 +87,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 # default_role = None
@@ -104,7 +104,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -114,7 +114,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'furo'
+html_theme = "furo"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -143,7 +143,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -187,27 +187,30 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pspec_likelihood_doc'
+htmlhelp_basename = "pspec_likelihood_doc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-# 'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-# 'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-# 'preamble': '',
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'pspec_likelihood.tex', u'pspec_likelihood Documentation',
-   u'HERA-Team', 'manual'),
+    (
+        "index",
+        "pspec_likelihood.tex",
+        "pspec_likelihood Documentation",
+        "HERA-Team",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -236,8 +239,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'pspec_likelihood', u'pspec_likelihood Documentation',
-     [u'HERA-Team'], 1)
+    ("index", "pspec_likelihood", "pspec_likelihood Documentation", ["HERA-Team"], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -250,9 +252,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'pspec_likelihood', u'pspec_likelihood Documentation',
-   u'Steven Murray', 'pspec_likelihood', 'Likelihoods from UVPSpec objects.',
-   'Miscellaneous'),
+    (
+        "index",
+        "pspec_likelihood",
+        "pspec_likelihood Documentation",
+        "Steven Murray",
+        "pspec_likelihood",
+        "Likelihoods from UVPSpec objects.",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
@@ -266,9 +274,11 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {"http://docs.python.org/": None}
 
-mathjax_path = "http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+mathjax_path = (
+    "http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+)
 
 #
 # #===============================================================================

pyproject.toml

@@ -1,7 +1,65 @@
 [build-system]
-requires = ["setuptools>=45", "wheel"]
+requires = ["setuptools>=60", "wheel", "setuptools_scm>=8.0", "numpy"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "pspec-likelihood"
+description = "A flexible likelihood for 21cm power spectrum estimates"
+readme = "README.rst"
+authors = [
+    {name="Steven Murray", email="[email protected]"},
+    {name="Adelie Gorce", email="[email protected]"}
+]
+license = {text="MIT"}
+requires-python = ">=3.9"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Topic :: Scientific/Engineering :: Physics",
+    "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",
+    "Programming Language :: Python :: Implementation :: CPython",
+]
+dependencies = [
+    "hera_pspec",
+    "hera_sim",
+    "pyuvdata",
+    "attrs",
+    "astropy",
+    "numpy",
+    "scipy",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+docs = [
+    "sphinx>=1.7.5",
+    "numpydoc",
+    "nbsphinx",
+    "furo",
+    "ipython"
+]
+tests = [
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+    "pre-commit"
+]
+dev = [
+    "setuptools_scm",
+    "ruff",
+    "pspec-likelihood[docs,tests]"
+]
 
 [tool.pytest.ini_options]
 minversion = "6.0"
@@ -21,3 +79,55 @@ version_variable = [
 ]
 upload_to_repository = false
 branch = "main"
+
+
+[tool.ruff]
+line-length = 88
+target-version = "py39"
+
+[tool.ruff.lint]
+extend-select = [
+  "UP",   # pyupgrade
+  "E",    # pycodestyle
+  "W",    # pycodestyle warning
+  "C90",  # mccabe complexity
+  "I",    # isort
+  "N",    # pep8-naming
+  "D",    # docstyle
+  # "ANN"   # type annotations
+  "B",    # bugbear
+  "A",    # builtins
+  "C4",   # comprehensions
+  "DTZ",  # datetime
+  "FA",   # future annotations
+  "PIE",  # flake8-pie
+  "T",    # print statements
+  "PT",   # pytest-style
+  "Q",    # quotes
+  "SIM",  # simplify
+  "PTH",  # use Pathlib
+  "ERA",  # kill commented code
+  "NPY",  # numpy-specific rules
+  "PERF", # performance
+  # "FURB", # refurb
+  "RUF",  # ruff-specific rules
+]
+ignore = [
+    "A003",     # class attribute shadows python builtin
+    "B008",     # function call in argument defaults
+]
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = [
+    "D103",  # ignore missing docstring in tests
+    "T",     # print statements
+]
+"docs/conf.py" = [
+    "A",  # conf.py can shadow builtins
+    "ERA",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'
+
+[tool.ruff.lint.mccabe]
+max-complexity = 15