chore: update cruft

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/usnistgov/cookiecutter-nist-python.git",
-  "commit": "fcf6a1b310af2e6b051bae186dbdd5be5d9bf229",
+  "commit": "ce1bec36acf76cc95cb3f865f059b8804fea4b7a",
   "checkout": "develop",
   "context": {
     "cookiecutter": {
@@ -19,7 +19,7 @@
       "__answers": "",
       "_copy_without_render": [],
       "_template": "https://github.com/usnistgov/cookiecutter-nist-python.git",
-      "_commit": "fcf6a1b310af2e6b051bae186dbdd5be5d9bf229"
+      "_commit": "ce1bec36acf76cc95cb3f865f059b8804fea4b7a"
     }
   },
   "directory": null

.pre-commit-config.yaml

@@ -99,7 +99,7 @@ repos:
   # * uv
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.5.29
+    rev: 0.5.30
     hooks:
       - id: uv-lock
         args: [--locked]

README.md

@@ -108,7 +108,7 @@ $ conda/condax install -c conda-forge pyproject2conda
 
 [rich]: https://github.com/Textualize/rich
 [shellingham]: https://github.com/sarugaku/shellingham
-[typer]: https://github.com/tiangolo/typer
+[typer]: https://github.com/fastapi/typer
 
 If using pip, to install with [rich] and [shellingham] support, either install
 them your self, or use:

docs/conf.py

@@ -45,29 +45,19 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "sphinx.ext.autosectionlabel",
-    # "IPython.sphinxext.ipython_directive",
-    # "IPython.sphinxext.ipython_console_highlighting",
-    # "nbsphinx",
-    # - easier external links
-    # "sphinx.ext.extlinks",
-    # - view source code on created page
-    # "sphinx.ext.viewcode",
-    # - view source code on github
     "sphinx.ext.linkcode",
-    # - add copy button
     "sphinx_copybutton",
-    # - redirect stuff?
-    # "sphinxext.rediraffe",
-    # - pretty things up?
-    # "sphinx_design"
-    # - myst stuff
-    # "myst_nb",
     "myst_parser",
     "sphinx_click",
 ]
 
-nitpicky = True
 autosectionlabel_prefix_document = True
+nitpicky = True
+suppress_warnings = ["autosectionlabel.*"]
+nitpick_ignore = [
+    ("py:class", "Command"),
+    ("py:class", "typer.core.TyperGroup"),
+]
 
 # -- myst stuff ---------------------------------------------------------
 myst_enable_extensions = [
@@ -265,7 +255,7 @@ def _get_version() -> str:
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -418,12 +408,12 @@ def _get_ipython_savefig_dir() -> str:
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
-    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
-    "numpy": ("https://numpy.org/doc/stable", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
-    "numba": ("https://numba.readthedocs.io/en/stable/", None),
-    "matplotlib": ("https://matplotlib.org/stable/", None),
-    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+    # "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    # "numpy": ("https://numpy.org/doc/stable", None),
+    # "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    # "numba": ("https://numba.readthedocs.io/en/stable/", None),
+    # "matplotlib": ("https://matplotlib.org/stable/", None),
+    # "xarray": ("https://docs.xarray.dev/en/stable/", None),
 }
 
 linkcheck_ignore = ["https://doi.org/"]

docs/index.md

@@ -7,9 +7,7 @@
 ```{toctree}
 :maxdepth: 1
 
-<!-- example -->
 installation
-<!-- examples/index -->
 reference/index
 license
 contributing

requirements/lock/py312-uvxrun-tools.txt

@@ -235,34 +235,38 @@ crashtest==0.3.1 \
     --hash=sha256:300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680 \
     --hash=sha256:42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd
     # via clikit, conda-lock
-cryptography==44.0.0 ; sys_platform == 'linux' \
-    --hash=sha256:1923cb251c04be85eec9fda837661c67c1049063305d6be5721643c22dd4e2b7 \
-    --hash=sha256:37d76e6863da3774cd9db5b409a9ecfd2c71c981c38788d3fcfaf177f447b731 \
-    --hash=sha256:3c672a53c0fb4725a29c303be906d3c1fa99c32f58abe008a82705f9ee96f40b \
-    --hash=sha256:404fdc66ee5f83a1388be54300ae978b2efd538018de18556dde92575e05defc \
-    --hash=sha256:4ac4c9f37eba52cb6fbeaf5b59c152ea976726b865bd4cf87883a7e7006cc543 \
-    --hash=sha256:62901fb618f74d7d81bf408c8719e9ec14d863086efe4185afd07c352aee1d2c \
-    --hash=sha256:660cb7312a08bc38be15b696462fa7cc7cd85c3ed9c576e81f4dc4d8b2b31591 \
-    --hash=sha256:708ee5f1bafe76d041b53a4f95eb28cdeb8d18da17e597d46d7833ee59b97ede \
-    --hash=sha256:761817a3377ef15ac23cd7834715081791d4ec77f9297ee694ca1ee9c2c7e5eb \
-    --hash=sha256:831c3c4d0774e488fdc83a1923b49b9957d33287de923d58ebd3cec47a0ae43f \
-    --hash=sha256:84111ad4ff3f6253820e6d3e58be2cc2a00adb29335d4cacb5ab4d4d34f2a123 \
-    --hash=sha256:8b3e6eae66cf54701ee7d9c83c30ac0a1e3fa17be486033000f2a73a12ab507c \
-    --hash=sha256:9e6fc8a08e116fb7c7dd1f040074c9d7b51d74a8ea40d4df2fc7aa08b76b9e6c \
-    --hash=sha256:a01956ddfa0a6790d594f5b34fc1bfa6098aca434696a03cfdbe469b8ed79285 \
-    --hash=sha256:abc998e0c0eee3c8a1904221d3f67dcfa76422b23620173e28c11d3e626c21bd \
-    --hash=sha256:b15492a11f9e1b62ba9d73c210e2416724633167de94607ec6069ef724fad092 \
-    --hash=sha256:be4ce505894d15d5c5037167ffb7f0ae90b7be6f2a98f9a5c3442395501c32fa \
-    --hash=sha256:c5eb858beed7835e5ad1faba59e865109f3e52b3783b9ac21e7e47dc5554e289 \
-    --hash=sha256:cd4e834f340b4293430701e772ec543b0fbe6c2dea510a5286fe0acabe153a02 \
-    --hash=sha256:d2436114e46b36d00f8b72ff57e598978b37399d2786fd39793c36c6d5cb1c64 \
-    --hash=sha256:eb33480f1bad5b78233b0ad3e1b0be21e8ef1da745d8d2aecbb20671658b9053 \
-    --hash=sha256:eca27345e1214d1b9f9490d200f9db5a874479be914199194e746c893788d417 \
-    --hash=sha256:ed3534eb1090483c96178fcb0f8893719d96d5274dfde98aa6add34614e97c8e \
-    --hash=sha256:f3f6fdfa89ee2d9d496e2c087cebef9d4fcbb0ad63c40e821b39f74bf48d9c5e \
-    --hash=sha256:f53c2c87e0fb4b0c00fa9571082a057e37690a8f12233306161c8f4b819960b7 \
-    --hash=sha256:f5e7cb1e5e56ca0933b4873c0220a78b773b24d40d186b6738080b73d3d0a756 \
-    --hash=sha256:f677e1268c4e23420c3acade68fac427fffcb8d19d7df95ed7ad17cdef8404f4
+cryptography==44.0.1 ; sys_platform == 'linux' \
+    --hash=sha256:00918d859aa4e57db8299607086f793fa7813ae2ff5a4637e318a25ef82730f7 \
+    --hash=sha256:1e8d181e90a777b63f3f0caa836844a1182f1f265687fac2115fcf245f5fbec3 \
+    --hash=sha256:1f9a92144fa0c877117e9748c74501bea842f93d21ee00b0cf922846d9d0b183 \
+    --hash=sha256:21377472ca4ada2906bc313168c9dc7b1d7ca417b63c1c3011d0c74b7de9ae69 \
+    --hash=sha256:24979e9f2040c953a94bf3c6782e67795a4c260734e5264dceea65c8f4bae64a \
+    --hash=sha256:2a46a89ad3e6176223b632056f321bc7de36b9f9b93b2cc1cccf935a3849dc62 \
+    --hash=sha256:322eb03ecc62784536bc173f1483e76747aafeb69c8728df48537eb431cd1911 \
+    --hash=sha256:436df4f203482f41aad60ed1813811ac4ab102765ecae7a2bbb1dbb66dcff5a7 \
+    --hash=sha256:4f422e8c6a28cf8b7f883eb790695d6d45b0c385a2583073f3cec434cc705e1a \
+    --hash=sha256:53f23339864b617a3dfc2b0ac8d5c432625c80014c25caac9082314e9de56f41 \
+    --hash=sha256:5fed5cd6102bb4eb843e3315d2bf25fede494509bddadb81e03a859c1bc17b83 \
+    --hash=sha256:610a83540765a8d8ce0f351ce42e26e53e1f774a6efb71eb1b41eb01d01c3d12 \
+    --hash=sha256:6c8acf6f3d1f47acb2248ec3ea261171a671f3d9428e34ad0357148d492c7864 \
+    --hash=sha256:6f76fdd6fd048576a04c5210d53aa04ca34d2ed63336d4abd306d0cbe298fddf \
+    --hash=sha256:72198e2b5925155497a5a3e8c216c7fb3e64c16ccee11f0e7da272fa93b35c4c \
+    --hash=sha256:887143b9ff6bad2b7570da75a7fe8bbf5f65276365ac259a5d2d5147a73775f2 \
+    --hash=sha256:888fcc3fce0c888785a4876ca55f9f43787f4c5c1cc1e2e0da71ad481ff82c5b \
+    --hash=sha256:8e6a85a93d0642bd774460a86513c5d9d80b5c002ca9693e63f6e540f1815ed0 \
+    --hash=sha256:94f99f2b943b354a5b6307d7e8d19f5c423a794462bde2bf310c770ba052b1c4 \
+    --hash=sha256:9b336599e2cb77b1008cb2ac264b290803ec5e8e89d618a5e978ff5eb6f715d9 \
+    --hash=sha256:a2d8a7045e1ab9b9f803f0d9531ead85f90c5f2859e653b61497228b18452008 \
+    --hash=sha256:b8272f257cf1cbd3f2e120f14c68bff2b6bdfcc157fafdee84a1b795efd72862 \
+    --hash=sha256:bf688f615c29bfe9dfc44312ca470989279f0e94bb9f631f85e3459af8efc009 \
+    --hash=sha256:d9c5b9f698a83c8bd71e0f4d3f9f839ef244798e5ffe96febfa9714717db7af7 \
+    --hash=sha256:dd7c7e2d71d908dc0f8d2027e1604102140d84b155e658c20e8ad1304317691f \
+    --hash=sha256:df978682c1504fc93b3209de21aeabf2375cb1571d4e61907b3e7a2540e83026 \
+    --hash=sha256:e403f7f766ded778ecdb790da786b418a9f2394f36e8cc8b796cc056ab05f44f \
+    --hash=sha256:eb3889330f2a4a148abead555399ec9a32b13b7c8ba969b72d8e500eb7ef84cd \
+    --hash=sha256:f4daefc971c2d1f82f03097dc6f216744a6cd2ac0f04c68fb935ea2ba2a0d420 \
+    --hash=sha256:f51f5705ab27898afda1aaa430f34ad90dc117421057782022edf0600bec5f14 \
+    --hash=sha256:fd0ee90072861e276b0ff08bd627abec29e32a53b2be44e41dbcdf87cbee2b00
     # via secretstorage
 decorator==5.1.1 \
     --hash=sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330 \
@@ -1066,9 +1070,9 @@ urllib3==1.26.20 \
     --hash=sha256:0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e \
     --hash=sha256:40c2dc0c681e47eb8f90e7e27bf6ff7df2e677421fd46756da1161c39ca70d32
     # via conda-lock, requests, twine
-virtualenv==20.29.1 \
-    --hash=sha256:4e4cb403c0b0da39e13b46b1b2476e505cb0046b25f242bee80f62bf990b2779 \
-    --hash=sha256:b8b8970138d32fb606192cb97f6cd4bb644fa486be9308fb9b63f81091b5dc35
+virtualenv==20.29.2 \
+    --hash=sha256:fdaabebf6d03b5ba83ae0a02cfe96f48a716f4fae556461d180825866f75b728 \
+    --hash=sha256:febddfc3d1ea571bdb1dc0f98d7b45d24def7428214d4fb73cc486c9568cce6a
     # via conda-lock, pre-commit
 wcwidth==0.2.13 \
     --hash=sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859 \

ruff.toml

@@ -35,37 +35,23 @@ ignore = [
     "D105",    # - Missing magic method docstring
     "D107",    # - Missing docstring in __init__
     "D203",    # - 1 blank line required before class docstring
+    "D205",    # - blank line after summary
     "D212",    # - Multi-line docstring summary should start at the first line
+    "D400",    # - First line should end with a period
+    "D401",    # - First line of docstring should be in imperative mood: "{first_line}"
+    "DOC201",  # - Missing return from documentation
+    "DOC501",  # - Missing raises from documentation
     "E501",    # - line too long - let formatter fix this
     "E731",    # - do not assign a lambda expression, use a def
     "FBT",     # - bools are ok
+    "S404",    # - Want to use subprocess sometimes
+    "S603",    # - subprocess-without-shell-equals-true
+    "S607",    # - start-process-with-partial-path
     "PLC0415", # - import should be at top level (leads to issues with imports in func?)
     "TID252",  # - Allow relative imports
 ]
-# Use extend-ignore for project specific ignores (avoid changing ignore directly)
-extend-ignore = [
-    # "ANN",     # - Annotations (just use mypy/pyright)
-    # "D102",    # - Missing docstring in public method
-    # "D103",    # - Missing docstring in public function
-    # "D202",    # - blank line after docstring
-    "D205", # - blank line after summary
-    "D400", # - First line should end with a period
-    "D401", # - First line of docstring should be in imperative mood: "{first_line}"
-    # "D415",    # - First line should end with a period, question mark, or exclamation point
-    # "D417",    # - Missing argument description in the docstring for {definition}: {name} (bad with docfiller)
-    "DOC201", # - Missing return from documentation
-    "DOC501", # - Missing raises from documentation
-    # "DOC202",  # - Missing return from documentation
-    # "E402",    # - module level import not at top of file
-    # "ERA",     # - eradicate (want to keep some stuff)
-    # "ISC",     # - flake8-implicit-str-concat
-    "NPY", # - not using numpy?
-    # "SLF001",  # - flake8-self (private access sometimes OK)
-    "PD", # - not using pandas?
-    # "PLR2004", # - numbers in comparison sometimes ok
-    # "PLR0913", # - complexity sometimes ok
-    # "PLR0917", # - complexity sometimes ok
-]
+# Use extend-ignore for project specific ignores. Prefer lint.extend-per-file-ignores."src/**/*.py" below
+# extend-ignore = [ ]
 isort.known-first-party = [
     "pyproject2conda",
 ]
@@ -75,36 +61,22 @@ pylint.max-positional-args = 15
 pylint.max-public-methods = 30
 
 [lint.per-file-ignores]
-"**/*.ipynb" = [
-    "B018",
-    "D100",
-    "INP001",
-]
 "docs/conf.py" = [
-    "ERA",
-    "INP001",
+    "ERA",    # - Some helpful commented out code in conf.py
+    "INP001", # - Namespace package fine for docs
 ]
 "noxfile.py" = [
-    "RUF009",
+    "RUF009", # - Allow `add_option` for DataClassParser
 ]
 "tests/*.py" = [
-    "D",
-    "S101",
-]
-"tools/*.py" = [
-    "A",
-    "D102",
-    "DOC402",
-    "S",
-    "SLF001",
+    "D",    # - Don't need to document tests
+    "S101", # - Assert is fine with tests
 ]
 
 # Project specific ignores (avoid changing per-file-ignores directly)
 # extend-per-file-ignores."path/to/file.py" = [ ... ]
 [lint.extend-per-file-ignores]
 "**/cli.py" = [
-    # "ARG001",
-    # "D102",
     "FA100",
     "PLR0913",
     "PLR0917",
@@ -117,5 +89,5 @@ pylint.max-public-methods = 30
     "PT011",
 ]
 "tools/cog_utils.py" = [
-    "D",
+    "D103",
 ]

src/pyproject2conda/cli.py

@@ -528,7 +528,7 @@ def wrapped(*args: Any, **kwargs: Any) -> R:
 @add_verbose_logger(logger)
 def create_list(
     filename: PYPROJECT_CLI = DEFAULT_TOML_PATH,
-    # verbose: VERBOSE_CLI = None,  # noqa: ERA001
+    verbose: VERBOSE_CLI = None,  # noqa: ARG001
 ) -> None:
     """List available extras."""
     logger.info("filename: %s", filename)
@@ -563,7 +563,7 @@ def yaml(
     header: HEADER_CLI = None,
     custom_command: CUSTOM_COMMAND_CLI = None,
     overwrite: OVERWRITE_CLI = Overwrite.force,
-    # verbose: VERBOSE_CLI = None,  # noqa: ERA001
+    verbose: VERBOSE_CLI = None,  # noqa: ARG001
     deps: DEPS_CLI = None,
     reqs: REQS_CLI = None,
     allow_empty: Annotated[bool, ALLOW_EMPTY_OPTION] = False,
@@ -625,7 +625,7 @@ def requirements(
     header: HEADER_CLI = None,
     custom_command: CUSTOM_COMMAND_CLI = None,
     overwrite: OVERWRITE_CLI = Overwrite.force,
-    # verbose: VERBOSE_CLI = None,  # noqa: ERA001
+    verbose: VERBOSE_CLI = None,  # noqa: ARG001
     reqs: REQS_CLI = None,
     allow_empty: Annotated[bool, ALLOW_EMPTY_OPTION] = False,
     remove_whitespace: Annotated[bool, REMOVE_WHITESPACE_OPTION] = False,
@@ -759,7 +759,7 @@ def conda_requirements(
     # paths,
     deps: DEPS_CLI = None,
     reqs: REQS_CLI = None,
-    # verbose: VERBOSE_CLI = None,  # noqa: ERA001
+    verbose: VERBOSE_CLI = None,  # noqa: ARG001
 ) -> None:
     """
     Create requirement files for conda and pip.
@@ -830,7 +830,7 @@ def to_json(
     skip_package: SKIP_PACKAGE_CLI = False,
     deps: DEPS_CLI = None,
     reqs: REQS_CLI = None,
-    # verbose: VERBOSE_CLI = None,  # noqa: ERA001
+    verbose: VERBOSE_CLI = None,  # noqa: ARG001
     overwrite: OVERWRITE_CLI = Overwrite.force,
 ) -> None:
     """

tools/dataclass_parser.py

@@ -155,11 +155,11 @@ def factory(
         const: Any = UNDEFINED,
         default: Any | None = UNDEFINED,
         dest: str = UNDEFINED,
-        help: str = UNDEFINED,
+        help: str = UNDEFINED,  # noqa: A002
         metavar: str = UNDEFINED,
         nargs: str | int | None = UNDEFINED,
         required: bool = UNDEFINED,
-        type: Callable[[Any], Any] = UNDEFINED,
+        type: Callable[[Any], Any] = UNDEFINED,  # noqa: A002
     ) -> Self:
         """Factory method."""
         return cls(
@@ -187,11 +187,11 @@ def add_option(
     choices: Container[Any] = UNDEFINED,
     const: Any = UNDEFINED,
     dest: str = UNDEFINED,
-    help: str = UNDEFINED,
+    help: str = UNDEFINED,  # noqa: A002
     metavar: str = UNDEFINED,
     nargs: str | int | None = UNDEFINED,
     required: bool = UNDEFINED,
-    type: Callable[[Any], Any] = UNDEFINED,
+    type: Callable[[Any], Any] = UNDEFINED,  # noqa: A002
     **field_kws: Any,  # noqa: ARG001
 ) -> Any:
     """Add option."""
@@ -268,7 +268,7 @@ def _get_dataclass_annotations_and_options(
 ) -> dict[str, tuple[Any, Option]]:
     annotations = get_type_hints(cls, include_extras=True)
 
-    assert is_dataclass(cls)
+    assert is_dataclass(cls)  # noqa: S101
     cls_fields = fields(cls)
 
     out: dict[str, tuple[Any, Any]] = {}

tools/noxtools.py

@@ -296,7 +296,7 @@ def write_hashes(hash_path: str | Path, hashes: dict[str, Any]) -> None:
 def _get_file_hash(path: str | Path, buff_size: int = 65536) -> str:
     import hashlib
 
-    md5 = hashlib.md5()
+    md5 = hashlib.md5()  # noqa: S324
     with Path(path).open("rb") as f:
         while data := f.read(buff_size):  # pylint: disable=while-used
             md5.update(data)