[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v5.0.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=500']
@@ -18,7 +18,7 @@ repos:
         args: [--branch, main]
     -   id: trailing-whitespace
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0  # Use the ref you want to point at
+    rev: v1.10.0  # Use the ref you want to point at
     hooks:
     -   id: python-check-blanket-noqa
     -   id: python-check-mock-methods
@@ -32,31 +32,31 @@ repos:
     -   id: text-unicode-replacement-char
         exclude_types: [jupyter]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.0
+    rev: v3.19.0
     hooks:
     -   id: pyupgrade
         args: [--py36-plus]
--   repo: https://github.com/asottile/reorder_python_imports
-    rev: v2.6.0
+-   repo: https://github.com/asottile/reorder-python-imports
+    rev: v3.14.0
     hooks:
     -   id: reorder-python-imports
         types: [python]
 -   repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.17.0
+    rev: v2.7.0
     hooks:
     -   id: setup-cfg-fmt
 -   repo: https://github.com/psf/black
-    rev: 21.9b0
+    rev: 24.10.0
     hooks:
     -   id: black
         types: [python]
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.11.0
+    rev: 1.19.1
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black]
 -   repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
+    rev: 7.1.1
     hooks:
     -   id: flake8
         types: [python]
@@ -76,29 +76,29 @@ repos:
             Pygments,
         ]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.1.1
+  rev: 1.9.1
   hooks:
     -   id: nbqa-black
     -   id: nbqa-pyupgrade
     -   id: nbqa-isort
 -   repo: https://github.com/PyCQA/doc8
-    rev: 0.9.1
+    rev: v1.1.2
     hooks:
     -   id: doc8
 -   repo: https://github.com/econchick/interrogate
-    rev: 1.5.0
+    rev: 1.7.0
     hooks:
     -   id: interrogate
         args: [-v, --fail-under=78, src]
         pass_filenames: false
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
+    rev: v2.3.0
     hooks:
     -   id: codespell
         exclude: \.ipynb
         args: [-L effekt, -L unparseable]
 -   repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
+    rev: "0.50"
     hooks:
     -   id: check-manifest
 -   repo: meta

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"
    ]

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)"
    ]

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)"
    ]

setup.cfg

@@ -7,7 +7,7 @@ url = https://github.com/covid-19-impact-lab/sid
 author = Janos Gabler, Tobias Raabe, Klara Roehrl
 author_email = [email protected]
 license = MIT
-license_file = LICENSE
+license_files = LICENSE
 platforms = any
 classifiers =
     Development Status :: 3 - Alpha
@@ -16,10 +16,6 @@ classifiers =
     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 +37,7 @@ install_requires =
     python-snappy
     seaborn
     tqdm
-python_requires = >=3.6
+python_requires = >=3.9
 include_package_data = True
 package_dir =
     =src

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

src/sid/config.py

@@ -1,4 +1,5 @@
 """This module contains configuration values for sid."""
+
 from pathlib import Path
 
 import numpy as np

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

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

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
 

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

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,

src/sid/parse_model.py

@@ -1,4 +1,5 @@
 """This module contains the code the parse input data."""
+
 import copy
 import pprint
 import warnings

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

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

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

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

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

src/sid/time.py

@@ -13,6 +13,7 @@
 estimation to reduce memory consumption.
 
 """
+
 from functools import partial
 
 import pandas as pd

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
     )

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

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