[pre-commit.ci] auto fixes from pre-commit.com hooks

pre-commit-ci[bot] · pre-commit-ci[bot] · commit 7f4726c37457 · 2025-11-24T22:12:26.000Z
for more information, see https://pre-commit.ci
diff --git a/docs/source/_static/images/make_infectiousness_period.ipynb b/docs/source/_static/images/make_infectiousness_period.ipynb
@@ -125,9 +125,7 @@
    ],
    "source": [
     "dist_mean = 2 * 0.12 + 4 * 0.29 + 6 * 0.47 + 10 * 0.12\n",
-    "dist_var = (\n",
-    "    2 ** 2 * 0.12 + 4 ** 2 * 0.29 + 6 ** 2 * 0.47 + 10 ** 2 * 0.12 - dist_mean ** 2\n",
-    ")\n",
+    "dist_var = 2**2 * 0.12 + 4**2 * 0.29 + 6**2 * 0.47 + 10**2 * 0.12 - dist_mean**2\n",
     "dist_std = np.sqrt(dist_var)\n",
     "dist_mean, dist_std"
    ]
diff --git a/docs/source/_static/images/make_time_until_death.ipynb b/docs/source/_static/images/make_time_until_death.ipynb
@@ -41,7 +41,7 @@
    "source": [
     "mean = 11.74\n",
     "std = 8.79\n",
-    "var = 8.79 ** 2\n",
+    "var = 8.79**2\n",
     "\n",
     "print(mean, std)"
    ]
diff --git a/docs/source/_static/images/make_time_until_icu_recovery.ipynb b/docs/source/_static/images/make_time_until_icu_recovery.ipynb
@@ -41,7 +41,7 @@
    "source": [
     "mean = 18.8\n",
     "std = 12.21\n",
-    "var = std ** 2\n",
+    "var = std**2\n",
     "\n",
     "print(mean, std)"
    ]
diff --git a/setup.cfg b/setup.cfg
@@ -7,19 +7,14 @@ url = https://github.com/covid-19-impact-lab/sid
 author = Janos Gabler, Tobias Raabe, Klara Roehrl
 author_email = janos.gabler@gmail.com
 license = MIT
-license_file = LICENSE
+license_files = LICENSE
 platforms = any
 classifiers =
     Development Status :: 3 - Alpha
     Intended Audience :: Science/Research
-    License :: OSI Approved :: MIT License
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
     Topic :: Scientific/Engineering
 project_urls =
     Changelog = https://sid-dev.readthedocs.io/en/latest/changes.html
@@ -41,7 +36,7 @@ install_requires =
     python-snappy
     seaborn
     tqdm
-python_requires = >=3.6
+python_requires = >=3.10
 include_package_data = True
 package_dir =
     =src
diff --git a/src/sid/colors.py b/src/sid/colors.py
@@ -3,6 +3,7 @@
 https://github.com/covid-19-impact-lab/utilities/blob/master/utilities/colors.py.""
 
 """
+
 import numpy as np
 import seaborn as sns
 from matplotlib.colors import LinearSegmentedColormap
diff --git a/src/sid/config.py b/src/sid/config.py
@@ -1,4 +1,5 @@
 """This module contains configuration values for sid."""
+
 from pathlib import Path
 
 import numpy as np
diff --git a/src/sid/contacts.py b/src/sid/contacts.py
@@ -1,4 +1,5 @@
 """This module contains everything related to contacts and matching."""
+
 import itertools
 from typing import Any
 from typing import Dict
diff --git a/src/sid/events.py b/src/sid/events.py
@@ -1,4 +1,5 @@
 """This module contains the code to calculate infections by events."""
+
 import pandas as pd
 from sid.config import DTYPE_VIRUS_STRAIN
 from sid.virus_strains import combine_first_factorized_infections
diff --git a/src/sid/initial_conditions.py b/src/sid/initial_conditions.py
@@ -4,6 +4,7 @@
 beginning of a simulation and can used to create patterns which match the real data.
 
 """
+
 import itertools
 import math
 from typing import Any
@@ -456,9 +457,9 @@ def _sample_factorized_virus_strains_for_infections(
             sampled_virus_strains = np.random.choice(
                 virus_strain_factors, p=probabilities, size=n_infected
             )
-            spread_out_virus_strains.loc[
-                spread_out_infections[column], column
-            ] = sampled_virus_strains
+            spread_out_virus_strains.loc[spread_out_infections[column], column] = (
+                sampled_virus_strains
+            )
 
     return spread_out_virus_strains
 
diff --git a/src/sid/matching_probabilities.py b/src/sid/matching_probabilities.py
@@ -1,4 +1,5 @@
 """Functions to work with transition matrices for assortative matching."""
+
 import string
 import warnings
 from typing import List
diff --git a/src/sid/msm.py b/src/sid/msm.py
@@ -15,6 +15,7 @@
        of Asset Prices. Econometrica, 61(4), 929-952.
 
 """
+
 import functools
 
 import numpy as np
@@ -156,7 +157,7 @@ def _msm(
     moment_errors = flat_simulated_moments - flat_empirical_moments
 
     root_contribs = np.sqrt(np.diagonal(weighting_matrix)) * moment_errors
-    value = np.sum(root_contribs ** 2)
+    value = np.sum(root_contribs**2)
 
     out = {
         "value": value,
diff --git a/src/sid/parse_model.py b/src/sid/parse_model.py
@@ -1,4 +1,5 @@
 """This module contains the code the parse input data."""
+
 import copy
 import pprint
 import warnings
diff --git a/src/sid/pathogenesis.py b/src/sid/pathogenesis.py
@@ -4,6 +4,7 @@
 countdown lengths. Currently, most of it is deterministic.
 
 """
+
 import numpy as np
 import pandas as pd
 from sid.config import DTYPE_DRAW_COURSE_OF_DISEASE
diff --git a/src/sid/policies.py b/src/sid/policies.py
@@ -1,4 +1,5 @@
 """This module contains the code to for applying contact policies."""
+
 import itertools
 from typing import Any
 from typing import Dict
diff --git a/src/sid/seasonality.py b/src/sid/seasonality.py
@@ -1,4 +1,5 @@
 """This module contains the code related to seasonality."""
+
 import itertools
 from typing import Any
 from typing import Callable
diff --git a/src/sid/testing.py b/src/sid/testing.py
@@ -1,4 +1,5 @@
 """This module holds the interface for the testing models."""
+
 import itertools
 from typing import Any
 from typing import Dict
diff --git a/src/sid/testing_demand.py b/src/sid/testing_demand.py
@@ -1,4 +1,5 @@
 """Contains the code for calculating the demand for tests."""
+
 import itertools
 from typing import Any
 from typing import Dict
diff --git a/src/sid/time.py b/src/sid/time.py
@@ -13,6 +13,7 @@
 estimation to reduce memory consumption.
 
 """
+
 from functools import partial
 
 import pandas as pd
diff --git a/src/sid/update_states.py b/src/sid/update_states.py
@@ -289,7 +289,7 @@ def _get_waning_immunity_coefficients(
         ("immunity", "immunity_waning", f"slope_after_maximum_{event}"), "value"
     ]
 
-    slope_before_maximum = maximum_immunity / (time_to_reach_maximum ** 3)
+    slope_before_maximum = maximum_immunity / (time_to_reach_maximum**3)
     intercept_after_maximum = (
         maximum_immunity - slope_after_maximum * time_to_reach_maximum
     )
diff --git a/src/sid/vaccination.py b/src/sid/vaccination.py
@@ -1,4 +1,5 @@
 """This module contains the code for vaccinating individuals."""
+
 import itertools
 from typing import Any
 from typing import Dict
diff --git a/src/sid/validation.py b/src/sid/validation.py
@@ -1,4 +1,5 @@
 """This module contains routines to validate inputs to functions."""
+
 import inspect
 import warnings
 from typing import Callable

Original file line number	Diff line number	Diff line change
`@@ -41,7 +41,7 @@`
`41`	`41`	`"source": [`
`42`	`42`	`"mean = 11.74\n",`
`43`	`43`	`"std = 8.79\n",`
`44`		`- "var = 8.79 ** 2\n",`
	`44`	`+ "var = 8.79**2\n",`
`45`	`45`	`"\n",`
`46`	`46`	`"print(mean, std)"`
`47`	`47`	`]`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""This module contains configuration values for sid."""`
	`2`	`+`
`2`	`3`	`from pathlib import Path`
`3`	`4`
`4`	`5`	`import numpy as np`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""This module contains everything related to contacts and matching."""`
	`2`	`+`
`2`	`3`	`import itertools`
`3`	`4`	`from typing import Any`
`4`	`5`	`from typing import Dict`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""This module contains the code to calculate infections by events."""`
	`2`	`+`
`2`	`3`	`import pandas as pd`
`3`	`4`	`from sid.config import DTYPE_VIRUS_STRAIN`
`4`	`5`	`from sid.virus_strains import combine_first_factorized_infections`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""Functions to work with transition matrices for assortative matching."""`
	`2`	`+`
`2`	`3`	`import string`
`3`	`4`	`import warnings`
`4`	`5`	`from typing import List`