Address disabled Ruff checks

[pp-mo]

QA checks which we expect later to review + possibly remove.

The ultimate goal is to have few or no 'ignored' Ruff checks.
But for now, a few are accepted as "permanent", in fact the same as the Iris ones : see below

The main (lint) controls are in the pyproject.toml "[tool.ruff.lint]" section e.g. these lines (as-after #568)

So-far chosen permanent disables :

• flake8-commas (COM) # https://docs.astral.sh/ruff/rules/#flake8-commas-com

  • COM812 Trailing comma missing.
  • COM819 Trailing comma prohibited.

• flake8-implicit-str-concat (ISC) # https://docs.astral.sh/ruff/rules/single-line-implicit-string-concatenation/

  • ISC001 Implicitly concatenate string literals on one line.

Note: interactions

The select key specifically includes "D212 : Multi-line docstring summary should start at the first line",
because this conflicts with "D213 : Multi-line docstring summary should start at the second line",
so it is explicitly added to the select : select = ["ALL". "D212"]

There are other possible conflicts like this, too, in which case "ALL" does not enable either rule.
See list of conflicting rules and linter rule selection

---

Remaining temporarily disabled checks :

• flake8-builtins-a

  • A001
  • A002

• flake8-annotations (ANN)

  • ANN001
  • ANN002
  • ANN003
  • ANN101
  • ANN102
  • ANN201
  • ANN202
  • ANN204
  • ANN205

• flake8-unused-arguments (ARG)

  • ARG001
  • ARG002
  • ARG005

• flake8-bugbear (B)

  • B007
  • B018
  • B028
  • B904

• flake8-blind-except (BLE)

  • BLE001

• flake8-comprehensions (C4)

  • C408
  • C901

• pydocstyle (D)

  • D100", # Missing docstring in public module
  • D101", # Missing docstring in public class
  • D102", # Missing docstring in public method
  • D103", # Missing docstring in public function
  • D105", # Missing docstring in magic method
  • D200", # One-line docstring should fit on one line
  • D202", # No blank lines allowed after function docstring
  • D205", # 1 blank line required between summary line and description
  • D212", # Multi-line docstring summary should start at the second line
  • D300", # Use triple double quotes """
  • D301", # Use r""" if any backslashes in a docstring
  • D400", # First line should end with a period
  • D401", # First line of docstring should be in imperative mood
  • D406", # Section name should end with a newline
  • D407", # Missing dashed underline after section

• flake8-datetimez (DTZ)

  • DTZ001
  • DTZ006

• flake8-errmsg (EM)

  • EM101
  • EM102
  • EM103

• eradicate (ERA)

  • ERA001

• flake8-boolean-trap (FBT)

  • FBT001
  • FBT002
  • FBT003

• flake8-fixme (FIX)

  • FIX002
  • FIX003

• isort (I)

  • I001", # Import block is un-sorted or un-formatted

• pep8-naming (N)

  • N801
  • N802
  • N803
  • N806
  • N999

• Numpy-specific rules (NPY)

  • NPY002

• Perflint (PERF)

  • PERF203
  • PERF401

• Refactor (R)

  • PLR0402
  • PLR0912
  • PLR0913
  • PLR0915
  • PLR1714
  • PLR2004
  • PLR5501

• Warning (W)

  • PLW0602
  • PLW2901

• flake8-pytest-style (PT)

  • PT009
  • PT027

• flake8-use-pathlib (PTH)

  • PTH100
  • PTH107
  • PTH110
  • PTH111
  • PTH112
  • PTH113
  • PTH118
  • PTH120
  • PTH122
  • PTH123

• flake8-pyi (PYI)

  • PYI024

• flake8-return (RET)

  • RET503
  • RET504
  • RET505
  • RET506

• flake8-raise (RSE)

  • RSE102

• Ruff-specific rules (RUF)

  • RUF005
  • RUF012
  • RUF015

• flake8-bandit (S)

  • S101
  • S110
  • S603
  • S607

• flake8-simplify (SIM)

  • SIM102
  • SIM108
  • SIM115
  • SIM117
  • SIM118

• flake8-self (SLF)

  • SLF001

• flake8-print (T20)

  • T201

• flake8-todos (TD)

  • TD001
  • TD002
  • TD003
  • TD004
  • TD005
  • TD006

• tryceratops (TRY)

  • TRY003
  • TRY004
  • TRY301

• pyupgrade (UP)

  • UP009
  • UP018
  • UP027
  • UP031
  • UP032