repo setup using scientific-python/cookies

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Andrew Walter.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the vector package developers nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+# ARI_SXN_SimBeamline
+
+[![Actions Status][actions-badge]][actions-link]
+[![Documentation Status][rtd-badge]][rtd-link]
+
+[![PyPI version][pypi-version]][pypi-link]
+[![Conda-Forge][conda-badge]][conda-link]
+[![PyPI platforms][pypi-platforms]][pypi-link]
+
+[![GitHub Discussion][github-discussions-badge]][github-discussions-link]
+
+<!-- SPHINX-START -->
+
+<!-- prettier-ignore-start -->
+[actions-badge]:            https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git/workflows/CI/badge.svg
+[actions-link]:             https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git/actions
+[conda-badge]:              https://img.shields.io/conda/vn/conda-forge/ARI_SXN_SimBeamline
+[conda-link]:               https://github.com/conda-forge/ARI_SXN_SimBeamline-feedstock
+[github-discussions-badge]: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github
+[github-discussions-link]:  https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git/discussions
+[pypi-link]:                https://pypi.org/project/ARI_SXN_SimBeamline/
+[pypi-platforms]:           https://img.shields.io/pypi/pyversions/ARI_SXN_SimBeamline
+[pypi-version]:             https://img.shields.io/pypi/v/ARI_SXN_SimBeamline
+[rtd-badge]:                https://readthedocs.org/projects/ARI_SXN_SimBeamline/badge/?version=latest
+[rtd-link]:                 https://ARI_SXN_SimBeamline.readthedocs.io/en/latest/?badge=latest
+
+<!-- prettier-ignore-end -->

docs/conf.py

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+from __future__ import annotations
+
+import importlib.metadata
+
+project = "ARI_SXN_SimBeamline"
+copyright = "2024, Andrew Walter"
+author = "Andrew Walter"
+version = release = importlib.metadata.version("ari_sxn_simbeamline")
+
+extensions = [
+    "myst_parser",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
+    "sphinx_copybutton",
+]
+
+source_suffix = [".rst", ".md"]
+exclude_patterns = [
+    "_build",
+    "**.ipynb_checkpoints",
+    "Thumbs.db",
+    ".DS_Store",
+    ".env",
+    ".venv",
+]
+
+html_theme = "furo"
+
+myst_enable_extensions = [
+    "colon_fence",
+]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+}
+
+nitpick_ignore = [
+    ("py:class", "_io.StringIO"),
+    ("py:class", "_io.BytesIO"),
+]
+
+always_document_param_types = True

docs/index.md

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+# ARI_SXN_SimBeamline
+
+```{toctree}
+:maxdepth: 2
+:hidden:
+
+```
+
+```{include} ../README.md
+:start-after: <!-- SPHINX-START -->
+```
+
+## Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`

noxfile.py

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+from __future__ import annotations
+
+import argparse
+import shutil
+from pathlib import Path
+
+import nox
+
+DIR = Path(__file__).parent.resolve()
+
+nox.needs_version = ">=2024.3.2"
+nox.options.sessions = ["lint", "pylint", "tests"]
+nox.options.default_venv_backend = "uv|virtualenv"
+
+
+@nox.session
+def lint(session: nox.Session) -> None:
+    """
+    Run the linter.
+    """
+    session.install("pre-commit")
+    session.run(
+        "pre-commit", "run", "--all-files", "--show-diff-on-failure", *session.posargs
+    )
+
+
+@nox.session
+def pylint(session: nox.Session) -> None:
+    """
+    Run PyLint.
+    """
+    # This needs to be installed into the package environment, and is slower
+    # than a pre-commit check
+    session.install(".", "pylint")
+    session.run("pylint", "ari_sxn_simbeamline", *session.posargs)
+
+
+@nox.session
+def tests(session: nox.Session) -> None:
+    """
+    Run the unit and regular tests.
+    """
+    session.install(".[test]")
+    session.run("pytest", *session.posargs)
+
+
+@nox.session(reuse_venv=True)
+def docs(session: nox.Session) -> None:
+    """
+    Build the docs. Pass "--serve" to serve. Pass "-b linkcheck" to check links.
+    """
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--serve", action="store_true", help="Serve after building")
+    parser.add_argument(
+        "-b", dest="builder", default="html", help="Build target (default: html)"
+    )
+    args, posargs = parser.parse_known_args(session.posargs)
+
+    if args.builder != "html" and args.serve:
+        session.error("Must not specify non-HTML builder with --serve")
+
+    extra_installs = ["sphinx-autobuild"] if args.serve else []
+
+    session.install("-e.[docs]", *extra_installs)
+    session.chdir("docs")
+
+    if args.builder == "linkcheck":
+        session.run(
+            "sphinx-build", "-b", "linkcheck", ".", "_build/linkcheck", *posargs
+        )
+        return
+
+    shared_args = (
+        "-n",  # nitpicky mode
+        "-T",  # full tracebacks
+        f"-b={args.builder}",
+        ".",
+        f"_build/{args.builder}",
+        *posargs,
+    )
+
+    if args.serve:
+        session.run("sphinx-autobuild", *shared_args)
+    else:
+        session.run("sphinx-build", "--keep-going", *shared_args)
+
+
+@nox.session
+def build_api_docs(session: nox.Session) -> None:
+    """
+    Build (regenerate) API docs.
+    """
+
+    session.install("sphinx")
+    session.chdir("docs")
+    session.run(
+        "sphinx-apidoc",
+        "-o",
+        "api/",
+        "--module-first",
+        "--no-toc",
+        "--force",
+        "../src/ari_sxn_simbeamline",
+    )
+
+
+@nox.session
+def build(session: nox.Session) -> None:
+    """
+    Build an SDist and wheel.
+    """
+
+    build_path = DIR.joinpath("build")
+    if build_path.exists():
+        shutil.rmtree(build_path)
+
+    session.install("build")
+    session.run("python", "-m", "build")

pyproject.toml

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+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+
+[project]
+name = "ARI_SXN_SimBeamline"
+authors = [
+  { name = "Andrew Walter", email = "[email protected]" },
+]
+description = "Code required for a simulated beamline version of ARI and SXN beamlines"
+readme = "README.md"
+license.file = "LICENSE"
+requires-python = ">=3.8"
+classifiers = [
+  "Development Status :: 1 - Planning",
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Developers",
+  "License :: OSI Approved :: BSD License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "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",
+  "Typing :: Typed",
+]
+dynamic = ["version"]
+dependencies = []
+
+[project.optional-dependencies]
+test = [
+  "pytest >=6",
+  "pytest-cov >=3",
+]
+dev = [
+  "pytest >=6",
+  "pytest-cov >=3",
+]
+docs = [
+  "sphinx>=7.0",
+  "myst_parser>=0.13",
+  "sphinx_copybutton",
+  "sphinx_autodoc_typehints",
+  "furo>=2023.08.17",
+]
+
+[project.urls]
+Homepage = "https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git"
+"Bug Tracker" = "https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git/issues"
+Discussions = "https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git/discussions"
+Changelog = "https://github.com/NSLS-II-ARI/ARI_SXN_SimBeamline.git/releases"
+
+
+[tool.hatch]
+version.source = "vcs"
+build.hooks.vcs.version-file = "src/ari_sxn_simbeamline/_version.py"
+
+[tool.hatch.envs.default]
+features = ["test"]
+scripts.test = "pytest {args}"
+
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+filterwarnings = [
+  "error",
+]
+log_cli_level = "INFO"
+testpaths = [
+  "tests",
+]
+
+
+[tool.coverage]
+run.source = ["ari_sxn_simbeamline"]
+report.exclude_also = [
+  '\.\.\.',
+  'if typing.TYPE_CHECKING:',
+]
+
+[tool.mypy]
+files = ["src", "tests"]
+python_version = "3.8"
+warn_unused_configs = true
+strict = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+warn_unreachable = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+
+[[tool.mypy.overrides]]
+module = "ari_sxn_simbeamline.*"
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+
+
+[tool.ruff]
+src = ["src"]
+
+[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
+]
+ignore = [
+  "PLR09",    # Too many <...>
+  "PLR2004",  # Magic value used in comparison
+  "ISC001",   # Conflicts with formatter
+]
+isort.required-imports = ["from __future__ import annotations"]
+# Uncomment if using a _compat.typing backport
+# typing-modules = ["ari_sxn_simbeamline._compat.typing"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["T20"]
+"noxfile.py" = ["T20"]
+
+
+[tool.pylint]
+py-version = "3.8"
+ignore-paths = [".*/_version.py"]
+reports.output-format = "colorized"
+similarities.ignore-imports = "yes"
+messages_control.disable = [
+  "design",
+  "fixme",
+  "line-too-long",
+  "missing-module-docstring",
+  "missing-function-docstring",
+  "wrong-import-position",
+]