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[NDSL] Add functionality to pre-commit #983

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c68d1d9
add functionality to pre-commit
Aug 16, 2024
4972596
reviewer's comments
Aug 16, 2024
b273757
remove unneccessary exceptions
Aug 16, 2024
6810c93
change black and flake8 to ruff
Aug 16, 2024
12f7aef
have codespell ignore in a file
Aug 16, 2024
0c01ec8
remove flake
Aug 16, 2024
4077fa4
use ruff isort
Aug 16, 2024
781f957
tmp
Oct 7, 2024
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61 changes: 33 additions & 28 deletions GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/.pre-commit-config.yaml
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Expand Up @@ -4,22 +4,18 @@ default_language_version:
files: pyMoist

repos:
- repo: https://github.com/psf/black
rev: 20.8b1
hooks:
- id: black
additional_dependencies: ["click==8.0.4"]

- repo: https://github.com/pre-commit/mirrors-isort
rev: v5.4.2
hooks:
- id: isort
description: Group and sort Python imports
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@romanc romanc Aug 16, 2024

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we should also be able to get rid of isort if we go with ruff

args: ["--profile", "black"]

- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.4.1
hooks:
- id: mypy
description: Perform static type analysis of Python code
name: mypy-pyMoist
args: [
--ignore-missing-imports,
Expand All @@ -35,31 +31,40 @@ repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v2.3.0
hooks:
- id: check-added-large-files
- id: check-ast
- id: check-case-conflict
- id: check-merge-conflict
- id: check-toml
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace

- repo: https://github.com/pycqa/flake8
rev: 3.9.2
- repo: https://github.com/codespell-project/codespell
rev: v2.3.0
hooks:
- id: codespell
name: codespell
description: Check for spelling errors
entry: codespell
args: ["--ignore-words","GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/ignored_codespell.txt"]

- repo: https://github.com/pycqa/pydocstyle
rev: 6.3.0
hooks:
- id: flake8
name: flake8
language_version: python3
args: [
"--exclude=docs",
"--ignore=W503,E302,E203,F841",
"--max-line-length=88"
]
exclude: |
(?x)^(
.*/__init__.py |
)$
- id: flake8
name: flake8 __init__.py files
files: "__init__.py"
# ignore unused import error in __init__.py files
args: [
"--exclude=docs",
"--ignore=W503,E302,E203,F841,F401",
"--max-line-length=88",]
- id: pydocstyle
name: pydocstyle
description: Check docstrings in Python code for compliance with conventions
entry: pydocstyle
types: [python]
args: ["--ignore=D101,D102,D103,D105,D107,D203,D213,D406,D407"]

- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.6.0
hooks:
# Run the linter.
- id: ruff
args: [ --fix ]
# Run the formatter.
- id: ruff-format
1 change: 1 addition & 0 deletions GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/ignored_codespell.txt
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@@ -0,0 +1 @@
THIRDPARTY
13 changes: 5 additions & 8 deletions GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/aer_activation.py
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Expand Up @@ -67,7 +67,6 @@ def aer_activation_stencil(
None
"""
with computation(PARALLEL), interval(...):

# Compute nwfa
# Fortran AeroProps aero_kap is aero_hygroscopicity
nfaux = 0.0
Expand Down Expand Up @@ -194,9 +193,7 @@ def aer_activation_stencil(
) # [1/m]
gamma = (constants.RGASJMOL * tk) / (wpe * constants.WMOLMASS) + (
constants.WMOLMASS * constants.HEATVAP * constants.HEATVAP
) / (
constants.CPAIR * plo * constants.AMOLMASS * tk
) # [m^3/kg]
) / (constants.CPAIR * plo * constants.AMOLMASS * tk) # [m^3/kg]
dum = sqrt(alpha * wupdraft / g) # [1/m]
zeta = 2.0 * a * dum / 3.0 # [1]

Expand All @@ -208,18 +205,18 @@ def aer_activation_stencil(
sm = (2.0 / sqrt(bibar[0, 0, 0][n])) * (
a / (3.0 * rg[0, 0, 0][n])
) ** 1.5 # [1]
eta = dum ** 3 / (
eta = dum**3 / (
constants.TWOPI * constants.DENH2O * gamma * ni[0, 0, 0][n]
) # [1]
f1 = 0.5 * exp(2.50 * xlogsigm ** 2) # [1]
f1 = 0.5 * exp(2.50 * xlogsigm**2) # [1]
f2 = 1.0 + 0.25 * xlogsigm # [1]
smax = (
smax
+ (
f1 * (zeta / eta) ** 1.5
+ f2 * (sm ** 2 / (eta + 3.0 * zeta)) ** 0.75
+ f2 * (sm**2 / (eta + 3.0 * zeta)) ** 0.75
)
/ sm ** 2
/ sm**2
) # [1] - eq. (6)
n += 1

Expand Down
4 changes: 2 additions & 2 deletions ...gcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/numerical_recipes.py
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Expand Up @@ -162,7 +162,7 @@ def Erf(x: Float) -> Float:
"""
erf = 0.0
if x < 0.0e00:
erf = -1.0 * GammP(0.5, x ** 2)
erf = -1.0 * GammP(0.5, x**2)
else:
erf = GammP(0.5, x ** 2)
erf = GammP(0.5, x**2)
return erf
6 changes: 3 additions & 3 deletions ...cm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/radiation_coupling.py
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Expand Up @@ -61,14 +61,14 @@ def cloud_effective_radius_ice(
1.0e-3 * (radconstants.MAPL_TICE - TE) ** 1.5
)
BB = min(max(BB, -6.0), -2.0)
RADIUS = 377.4 + 203.3 * BB + 37.91 * BB ** 2 + 2.3696 * BB ** 3
RADIUS = 377.4 + 203.3 * BB + 37.91 * BB**2 + 2.3696 * BB**3
RADIUS = min(150.0e-6, max(5.0e-6, 1.0e-6 * RADIUS))
else:
# Ice cloud effective radius ----- [Sun, 2001]
TC = TE - radconstants.MAPL_TICE
ZFSR = 1.2351 + 0.0105 * TC
AA = 45.8966 * (WC ** 0.2214)
BB = 0.79570 * (WC ** 0.2535)
AA = 45.8966 * (WC**0.2214)
BB = 0.79570 * (WC**0.2535)
RADIUS = ZFSR * (AA + BB * (TE - 83.15))
RADIUS = min(150.0e-6, max(5.0e-6, 1.0e-6 * RADIUS * 0.64952))
return RADIUS
Expand Down
2 changes: 0 additions & 2 deletions ...m_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/redistribute_clouds.py
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Expand Up @@ -19,7 +19,6 @@ def redist_clouds(
QV: FloatField,
TE: FloatField,
):

with computation(PARALLEL), interval(...):
# Constants from MAPL.h
alhlbcp = radconstants.ALHLBCP
Expand Down Expand Up @@ -95,7 +94,6 @@ def __init__(
stencil_factory: StencilFactory,
quantity_factory: QuantityFactory,
) -> None:

self._redist_clouds = stencil_factory.from_dims_halo(
func=redist_clouds,
compute_dims=[X_DIM, Y_DIM, Z_DIM],
Expand Down
6 changes: 6 additions & 0 deletions GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/ruff.toml
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@@ -0,0 +1,6 @@
[lint]
ignore = ["F841"]

[lint.per-file-ignores]
# Ignore `E402` (import violations) in all `__init__.py` files
"__init__.py" = ["F401"]