Cleanup

noxfile.py

@@ -1,3 +1,5 @@
+"""Nox Test Sessions."""
+
 from __future__ import annotations
 
 import argparse
@@ -8,14 +10,12 @@
 
 DIR = Path(__file__).parent.resolve()
 
-nox.options.sessions = ["lint", "tests"]  # "pylint",
+nox.options.sessions = ["lint", "pylint", "tests"]
 
 
 @nox.session
 def lint(session: nox.Session) -> None:
-    """
-    Run the linter.
-    """
+    """Run the linter."""
     session.install("pre-commit")
     session.run(
         "pre-commit", "run", "--all-files", "--show-diff-on-failure", *session.posargs
@@ -25,9 +25,7 @@ def lint(session: nox.Session) -> None:
 # TODO: turn this on eventually
 @nox.session
 def pylint(session: nox.Session) -> None:
-    """
-    Run PyLint.
-    """
+    """Run PyLint."""
     # This needs to be installed into the package environment, and is slower
     # than a pre-commit check
     session.install(".", "pylint")
@@ -36,19 +34,14 @@ def pylint(session: nox.Session) -> None:
 
 @nox.session
 def tests(session: nox.Session) -> None:
-    """
-    Run the unit and regular tests.
-    """
+    """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.
-    """
-
+    """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(
@@ -87,10 +80,7 @@ def docs(session: nox.Session) -> None:
 
 @nox.session
 def build_api_docs(session: nox.Session) -> None:
-    """
-    Build (regenerate) API docs.
-    """
-
+    """Build (regenerate) API docs."""
     session.install("sphinx")
     session.chdir("docs")
     session.run(
@@ -106,10 +96,7 @@ def build_api_docs(session: nox.Session) -> None:
 
 @nox.session
 def build(session: nox.Session) -> None:
-    """
-    Build an SDist and wheel.
-    """
-
+    """Build an SDist and wheel."""
     build_path = DIR.joinpath("build")
     if build_path.exists():
         shutil.rmtree(build_path)

pyproject.toml

@@ -29,16 +29,17 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-  "numpy",
-  "scipy>1.10",
+  "asdf",
+  "dustmaps",
   "astropy",
-  "matplotlib",
+  "astroquery",
   "gala",
   "galstreams",
+  "matplotlib",
+  "numba",
+  "numpy",
   "pyia",
-  "astroquery",
-  "dustmaps",
-  "asdf",
+  "scipy>1.10",
   "ugali",
 ]
 
@@ -81,6 +82,7 @@ addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
 xfail_strict = true
 filterwarnings = [
   "error",
+  "ignore:numpy.ndarray size changed",
 ]
 log_cli_level = "INFO"
 testpaths = [
@@ -123,41 +125,27 @@ disallow_incomplete_defs = true
 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
-]
+extend-select = ["ALL"]
 ignore = [
+  "ANN101",  # Missing type annotation for self in method
+  "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
+  "BLE001",  # Using bare `except`
+  "COM812",  # Missing trailing comma
+  "D107",  # Missing docstring in `__init__`
+  "D203",  # 1 blank line required before class docstring
+  "D213",  # Multi-line docstring summary should start at the second line
+  "ERA001",  # Commented-out code
+  "FIX002",  # Line contains TODO
+  "N8",  # Naming conventions
+  "N999",  # Invalid module name
   "PD",  # Pandas
   "PLR",    # Design related pylint codes
+  "TD002",  # Missing author in TODO
+  "TD003",  # Missing issue link on the line following this TODO
   # TODO: fix these and remove
   "ARG001",  # Unused function argument `X`
   "ARG003",  # Unused method argument `X`
-  "E711",  # Comparison to `None` should be `cond is None`
-  "E731",  # Do not assign a `lambda` expression, use a `def`
-  "EM101",  # Exception must not use a string literal, assign to variable first
   "F821",  # Undefined name `X`
-  "PT018",  # Assertion should be broken down into multiple parts
-  "RET504",  # Unnecessary assignment `return` statement
   "RET505",  # Unnecessary `else` after `return`
   "SIM118",  # Use `key in dict` instead of `key in dict.keys()`
   "T201",  # `print` found
@@ -167,8 +155,11 @@ isort.required-imports = ["from __future__ import annotations"]
 # typing-modules = ["cats._compat.typing"]
 
 [tool.ruff.lint.per-file-ignores]
-"tests/**" = ["T20"]
+"docs/conf.py" = ["A001", "D100", "INP001"]
+"scripts/**" = ["INP001"]
+"tests/**" = ["ANN", "D1", "INP", "S101", "T20"]
 "noxfile.py" = ["T20"]
+"__init__.py" = ["F403"]
 # TODO: fix these and remove
 "src/cats/pawprint/tests/mwe.py" = ["F821"]
 
@@ -181,7 +172,11 @@ similarities.ignore-imports = "yes"
 messages_control.disable = [
   "design",
   "fixme",
-  "line-too-long",
-  "missing-module-docstring",
   "wrong-import-position",
+  # TODO: fix these and remove
+  "attribute-defined-outside-init",
+  "duplicate-code",
+  "invalid-name",
+  "no-member",
+  "unused-variable",
 ]

src/cats/combine_pm_cmd.py → scripts/combine_pm_cmd.py

@@ -1,39 +1,26 @@
+"""Combine PM and CMD cuts."""
+
 from __future__ import annotations
 
+from typing import Any
+
 import astropy.table as at
-import matplotlib as mpl
+import matplotlib.pyplot as plt
 import pandas as pd
 
-from cats.cmd.CMD import Isochrone
-from cats.pawprint.pawprint import Footprint2D, Pawprint
-
-plt = mpl.pyplot
-
-plt.rc(
-    "xtick",
-    top=True,
-    direction="in",
-    labelsize=15,
-)
-plt.rc(
-    "ytick",
-    right=True,
-    direction="in",
-    labelsize=15,
-)
-plt.rc(
-    "font",
-    family="Arial",
-)
+from cats.cmd import Isochrone
+from cats.pawprint import Footprint2D, Pawprint
+
+plt.rc("xtick", top=True, direction="in", labelsize=15)
+plt.rc("ytick", right=True, direction="in", labelsize=15)
+plt.rc("font", family="Arial")
 
 
 def generate_isochrone_vertices(
-    cat,
-    sky_poly,
-    pm_poly,
-    config,
-):
-    """
+    cat: Any, sky_poly: Any, pm_poly: Any, config: Any
+) -> Any:
+    """Generate Isochrone Vertices.
+
     Use the generated class to make a new polygon for the given catalog in CMD
     space given a sky and PM polygon.
     """
@@ -63,26 +50,17 @@ def generate_isochrone_vertices(
     return o.simpleSln(0.1, 15, mass_thresh=0.83)[0]
 
 
-def generate_pm_vertices(
-    cat,
-    sky_poly,
-    cmd_poly,
-    config,
-):
-    """
+def generate_pm_vertices() -> list[list[float]]:
+    """Generate Proper Motion Vertices.
+
     Use the generated class to make a new polygon for the given catalog in PM
     space given a sky and CMD polygon.
     """
-    pm_poly = [
-        [-7.0, 0.0],
-        [-5.0, 0.0],
-        [-5.0, 1.6],
-        [-7.0, -1.6],
-    ]
-    return pm_poly
+    return [[-7.0, 0.0], [-5.0, 0.0], [-5.0, 1.6], [-7.0, -1.6]]
 
 
-def load_sky_region(fn):
+def load_sky_region(fn: Any) -> tuple[list[float], list[float]]:
+    """Load Sky Region."""
     sky_print = [
         [-5, -2],
         [+5, -2],
@@ -94,12 +72,13 @@ def load_sky_region(fn):
 
 
 def main() -> int:
+    """Run Script."""
     # load in config file, catalog from filename
     config = pd.read_json("config.json")
     cat = at.Table.read(config.streaminfo.cat_fn)
 
     # load in file with the sky footprint.
-    sky_poly, bg_poly = load_sky_region(config.streaminfo.sky_print)
+    sky_poly, _ = load_sky_region(config.streaminfo.sky_print)
 
     # have an initial selection for the PM region that is very wide
     # this could also be stored in a footprint

src/cats/__init__.py

@@ -1,12 +1,16 @@
-"""
-Copyright (c) 2023 CATS. All rights reserved.
+"""Copyright (c) 2023 CATS. All rights reserved.
 
 cats: Community Atlas of Tidal Streams
 """
 
-
 from __future__ import annotations
 
-from ._version import version as __version__
+__all__ = [
+    # Constants
+    "__version__",
+    # Modules
+    "data",
+    "frames",
+]
 
-__all__ = ["__version__"]
+from ._version import version as __version__

src/cats/_version.pyi

@@ -1,4 +1,2 @@
-from __future__ import annotations
-
 version: str
 version_tuple: tuple[int, int, int] | tuple[int, int, int, str, str]