Package updates

.github/workflows/ci_cron_weekly.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python to build docs with sphinx
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.13'
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/ci_tests.yml

@@ -24,13 +24,19 @@ jobs:
         include:
           - name: Code style checks
             os: ubuntu-latest
-            python: '3.11'
+            python: '3.13'
             toxenv: codestyle
 
-          - name: Python 3.11 with all optional dependencies and coverage checking
+          - name: Python 3.13 with required dependencies and coverage checking
             os: ubuntu-latest
-            python: '3.11'
-            toxenv: py311-test-alldeps-cov
+            python: '3.13'
+            toxenv: py313-test-cov
+
+          - name: Python 3.13 with nightly wheels for key dependencies
+            continue-on-error: true
+            os: ubuntu-latest
+            python: '3.13'
+            toxenv: py313-test-devdeps
 
     steps:
     - name: Checkout code

.readthedocs.yml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.13"
 
 sphinx:
   builder: html

docs/conf.py

@@ -25,65 +25,73 @@
 # Thus, any C-extensions that are needed to build the documentation will *not*
 # be accessible, and the documentation will not build correctly.
 
-import os
 import sys
 import datetime
-from importlib import import_module
+from importlib import metadata
+import pathlib
+import tomllib
+from packaging.version import parse
+
 
 try:
     from sphinx_astropy.conf.v1 import *  # noqa
 except ImportError:
-    print('ERROR: the documentation requires the sphinx-astropy package to be installed')
+    print(
+        "ERROR: the documentation requires the sphinx-astropy package to be installed"
+    )
     sys.exit(1)
 
-# Get configuration information from setup.cfg
-from configparser import ConfigParser
-conf = ConfigParser()
 
-conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')])
-setup_cfg = dict(conf.items('metadata'))
+project_file = pathlib.Path(__file__).resolve().parents[1] / "pyproject.toml"
+if not project_file.is_file():
+    raise FileNotFoundError(f"{project_file} does not exist!")
+with open(project_file, "rb") as f:
+    project_metadata = tomllib.load(f)
+
+project_version = parse(metadata.version(project_metadata["project"]["name"]))
 
 # -- General configuration ----------------------------------------------------
 
 # By default, highlight as Python 3.
-highlight_language = 'python3'
+highlight_language = "python3"
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.2'
+# needs_sphinx = '1.2'
 
 # To perform a Sphinx version check that needs to be more specific than
 # major.minor, call `check_sphinx_version("X.Y.Z")` here.
 # check_sphinx_version("1.2.1")
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns.append('_templates')
+exclude_patterns = [
+    "_build",
+    "_templates",
+    "include/*.rst",
+    "help/*.rst",
+    "scripts/*.rst",
+]
 
 # This is added to the end of RST files - a good place to put substitutions to
 # be used globally.
-rst_epilog += """
-"""
+# rst_epilog += """
+# """
 
 # -- Project information ------------------------------------------------------
 
 # This does not *have* to match the package name, but typically does
-project = setup_cfg['name']
-author = setup_cfg['author']
-copyright = '{0}, {1}'.format(
-    datetime.datetime.now().year, setup_cfg['author'])
+project = project_metadata["project"]["name"]
+author = project_metadata["project"]["authors"][0]["name"]
+copyright = "{0}, {1}".format(datetime.datetime.now().year, author)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-import_module(setup_cfg['name'])
-package = sys.modules[setup_cfg['name']]
-
 # The short X.Y version.
-version = package.__version__.split('-', 1)[0]
+version = project_version.public
 # The full version, including alpha/beta/rc tags.
-release = package.__version__
-
+release = str(project_version.local)
 
 # -- Options for HTML output --------------------------------------------------
 
@@ -97,43 +105,43 @@
 
 # Add any paths that contain custom themes here, relative to this directory.
 # To use a different custom theme, add the directory containing the theme.
-#html_theme_path = []
+# html_theme_path = []
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes. To override the custom theme, set this to the
 # name of a builtin theme or the name of a custom theme in html_theme_path.
-#html_theme = None
+# html_theme = None
 
 
 html_theme_options = {
-    'logotext1': 'pytelpoint',  # white,  semi-bold
-    'logotext2': '',  # orange, light
-    'logotext3': ':docs'   # white,  light
-    }
+    "logotext1": "pytelpoint",  # white,  semi-bold
+    "logotext2": "",  # orange, light
+    "logotext3": ":docs",  # white,  light
+}
 
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = 'static/Logo.png'
+# html_logo = 'static/Logo.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = 'static/mmt.ico'
+html_favicon = "static/mmt.ico"
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = ''
+# html_last_updated_fmt = ''
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = '{0} v{1}'.format(project, release)
+html_title = "{0} v{1}".format(project, release)
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = project + 'doc'
+htmlhelp_basename = project + "doc"
 
 # Prefixes that are ignored for sorting the Python module index
 modindex_common_prefix = ["pytelpoint."]
@@ -143,38 +151,25 @@
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [('index', project + '.tex', project + u' Documentation',
-                    author, 'manual')]
+latex_documents = [
+    ("index", project + ".tex", project + " Documentation", author, "manual")
+]
 
 
 # -- Options for manual page output -------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [('index', project.lower(), project + u' Documentation',
-              [author], 1)]
-
-
-# -- Options for the edit_on_github extension ---------------------------------
-
-if setup_cfg.get('edit_on_github').lower() == 'true':
-
-    extensions += ['sphinx_astropy.ext.edit_on_github']
-
-    edit_on_github_project = setup_cfg['github_project']
-    edit_on_github_branch = "main"
-
-    edit_on_github_source_root = ""
-    edit_on_github_doc_root = "docs"
+man_pages = [("index", project.lower(), project + " Documentation", [author], 1)]
 
 # -- Resolving issue number to links in changelog -----------------------------
-github_issues_url = 'https://github.com/{0}/issues/'.format(setup_cfg['github_project'])
+github_issues_url = "https://github.com/mmtobservatory/{0}/issues/".format(project)
 
 
 # -- Options for linkcheck output -------------------------------------------
 linkcheck_retry = 5
 linkcheck_ignore = [
-    r'https://github\.com/mmtobservatory/pytelpoint/(?:issues|pull)/\d+',
+    r"https://github\.com/mmtobservatory/pytelpoint/(?:issues|pull)/\d+",
 ]
 linkcheck_timeout = 180
 linkcheck_anchors = False

pyproject.toml

@@ -1,7 +1,118 @@
-[build-system]
+[project]
+name = "pytelpoint"
+dynamic = ["version"]
+authors = [
+    { name = "T. E. Pickering", email = "te.pickering@gmail.com"}
+]
+license = {file = "licenses/LICENSE.rst"}
+readme = "README.rst"
+description = "Python utilities for analyzing telescope pointing and tracking via probabilistic methods."
+requires-python = ">=3.13"
+dependencies = [
+    "astropy",
+    "scipy",
+    "matplotlib",
+    "arviz",
+    "corner",
+    "pymc",
+    "pandas",
+]
+
+[project.optional-dependencies]
+test = [
+    "tox",
+    "coverage",
+    "pytest-astropy",
+    "black",
+    "flake8",
+    "coverage",
+    "pytest-benchmark",
+]
+docs = [
+    "sphinx-astropy",
+]
+extra = [
+    "ipympl",
+    "ipykernel",
+]
+
+[project.scripts]
+fix_mmtwfs_csvs = "pytelpoint.scripts.fix_csvs:main"
+fix_mmirs_exposure_time = "pytelpoint.scripts.fix_mmirs_exposure_time:main"
+rename_mmirs_files = "pytelpoint.scripts.rename_mmirs_files:main"
+reanalyze = "pytelpoint.scripts.reanalyze:main"
+
+[project.urls]
+Repository = "https://github.com/mmtobservatory/pytelpoint.git"
+Documentation = "https://pytelpoint.readthedocs.io/"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"pytelpoint.test_data" = ["**"]
+
+[tool.setuptools.packages]
+find = {}
 
-requires = ["setuptools",
-            "setuptools_scm",
-            "wheel"]
+[tool.setuptools_scm]
+version_file = "pytelpoint/version.py"
+
+[build-system]
+requires = [
+    "setuptools",
+    "setuptools_scm",
+]
 
 build-backend = 'setuptools.build_meta'
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+testpaths = [
+    "pytelpoint/tests",
+    "docs",
+]
+astropy_header = false
+doctest_plus = "enabled"
+text_file_format = "rst"
+addopts = [
+    "--color=yes",
+    "--doctest-rst",
+]
+xfail_strict = false
+filterwarnings = [
+    "error",
+    "ignore:numpy\\.ufunc size changed:RuntimeWarning",
+    "ignore:numpy\\.ndarray size changed:RuntimeWarning",
+    # numpy 2 deprecation warnings from astropy.units
+    "ignore:.*__array__ implementation doesn't accept a copy keyword:DeprecationWarning",
+]
+
+[tool.coverage]
+
+    [tool.coverage.run]
+        omit = [
+            "pytelpoint/conftest.py",
+            "pytelpoint/tests/*",
+            "pytelpoint/version*",
+            "*/pytelpoint/conftest.py",
+            "*/pytelpoint/tests/*",
+            "*/pytelpoint/version*",
+        ]
+
+    [tool.coverage.report]
+        exclude_lines = [
+            # Have to re-enable the standard pragma
+            "pragma: no cover",
+            # Don't complain about packages we have installed
+            "except ImportError",
+            # Don't complain if tests don't hit defensive assertion code:
+            "raise AssertionError",
+            "raise NotImplementedError",
+            # Don't complain about script hooks
+            "'def main(.*):'",
+            # Ignore branches that don't pertain to this version of Python
+            "pragma: py{ignore_python_version}",
+            # Don't complain about IPython completion helper
+            "def _ipython_key_completions_",
+        ]

pytelpoint/__init__.py

@@ -1,9 +1,3 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
-# Packages may add whatever they like to this file, but
-# should keep this content at the top.
-# ----------------------------------------------------------------------------
-from ._astropy_init import *   # noqa
-# ----------------------------------------------------------------------------
-
 __all__ = []