[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '(^docs/conf.py|^user_data/External_tables/)'
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v6.0.0
       hooks:
           - id: trailing-whitespace
           - id: check-added-large-files
@@ -17,7 +17,7 @@ repos:
           - id: mixed-line-ending
             args: ['--fix=no']
     - repo: https://github.com/PyCQA/flake8
-      rev: 6.1.0  # pick a git hash / tag to point to
+      rev: 7.3.0  # pick a git hash / tag to point to
       hooks:
         - id: flake8
           additional_dependencies:
@@ -28,16 +28,16 @@ repos:
             - flake8-rst-docstrings
             - flake8-copyright
             - flake8-docstrings
-    - repo: https://github.com/psf/black
-      rev: 23.9.1
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 25.12.0
       hooks:
           - id: black
     - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
+      rev: 7.0.0
       hooks:
       - id: isort
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.11.1
+      rev: v3.21.2
       hooks:
       -   id: pyupgrade
           args: [--py38-plus]

devel/simple_memory_leak_test.py

@@ -1,6 +1,7 @@
 """
 This is a script that runs a very basic mock Core/Likelihood
 """
+
 import gc
 import numpy as np
 import tracemalloc

src/py21cmmc/analyse.py

@@ -2,6 +2,7 @@
 
 Also enables more transparent input/output of chains.
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 from os.path import join

src/py21cmmc/core.py

@@ -4,6 +4,7 @@
 
 TODO: Add description of the API of cores (and how to define new ones).
 """
+
 import copy
 import inspect
 import logging
@@ -627,13 +628,15 @@ def run(self, astro_params, cosmo_params, ctx):
         for i in range(N):
             muv, mhalo, lf = p21.compute_luminosity_function(
                 mturnovers=mturnovers if self.flag_options.USE_MINI_HALOS else None,
-                mturnovers_mini=mturnovers_mini
-                if self.flag_options.USE_MINI_HALOS
-                else None,
+                mturnovers_mini=(
+                    mturnovers_mini if self.flag_options.USE_MINI_HALOS else None
+                ),
                 redshifts=self.redshift,
-                astro_params=astro_params[i]
-                if not isinstance(astro_params, p21.AstroParams)
-                else astro_params,
+                astro_params=(
+                    astro_params[i]
+                    if not isinstance(astro_params, p21.AstroParams)
+                    else astro_params
+                ),
                 flag_options=self.flag_options,
                 cosmo_params=cosmo_params,
                 user_params=self.user_params,

src/py21cmmc/cosmoHammer.py

@@ -1,4 +1,5 @@
 """A set of extensions to the basic ``CosmoHammer`` package."""
+
 import emcee
 import gc
 import h5py

src/py21cmmc/ensemble.py

@@ -1,4 +1,5 @@
 """Patch of `emcee.Ensemble` to allow for some new features required for 21CMMC."""
+
 import emcee
 import logging
 import numpy as np

src/py21cmmc/likelihood.py

@@ -1,4 +1,5 @@
 """Module containing 21CMMC likelihoods."""
+
 import logging
 import numpy as np
 from cached_property import cached_property
@@ -1041,13 +1042,13 @@ def computeLikelihood(self, model):
                             elif i == 4:
                                 tot[index + j] = cl["te"][j]
                             elif i == 5:
-                                tot[
-                                    index + j
-                                ] = 0  # cl['tb'][j] class does not compute tb
+                                tot[index + j] = (
+                                    0  # cl['tb'][j] class does not compute tb
+                                )
                             elif i == 6:
-                                tot[
-                                    index + j
-                                ] = 0  # cl['eb'][j] class does not compute eb
+                                tot[index + j] = (
+                                    0  # cl['eb'][j] class does not compute eb
+                                )
 
                         index += my_clik.get_lmax()[i] + 1
 

src/py21cmmc/mcmc.py

@@ -1,4 +1,5 @@
 """High-level functions for running MCMC chains."""
+
 import logging
 import numpy as np
 import scipy.stats as stats