[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: v6.0.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=25']
@@ -17,7 +17,7 @@ repos:
         args: [--branch, main]
     -   id: trailing-whitespace
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
     -   id: python-check-blanket-noqa
     -   id: python-check-mock-methods
@@ -28,37 +28,37 @@ repos:
     -   id: rst-inline-touching-normal
     -   id: text-unicode-replacement-char
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.0
+    rev: v3.21.2
     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: v3.16.0
     hooks:
     -   id: reorder-python-imports
         types: [python]
 -   repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.19.0
+    rev: v3.2.0
     hooks:
     -   id: setup-cfg-fmt
--   repo: https://github.com/psf/black
-    rev: 21.10b0
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
     hooks:
     -   id: black
         types: [python]
 - 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/asottile/blacken-docs
-    rev: v1.11.0
+    rev: 1.20.0
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black]
 -   repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.3.0
     hooks:
     -   id: flake8
         types: [python]
@@ -77,16 +77,16 @@ repos:
             Pygments,
         ]
 -   repo: https://github.com/PyCQA/doc8
-    rev: 0.9.1
+    rev: v2.0.0
     hooks:
     -   id: doc8
 -   repo: https://github.com/econchick/interrogate
-    rev: 1.5.0
+    rev: 1.7.0
     hooks:
     -   id: interrogate
         args: [-v, --fail-under=25, src, tests]
 -   repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
+    rev: "0.51"
     hooks:
     -   id: check-manifest
 -   repo: meta

docs/source/conf.py

@@ -9,7 +9,6 @@
 import os
 import sys
 
-
 sys.path.insert(0, os.path.abspath("../.."))
 
 

setup.cfg

@@ -5,20 +5,14 @@ long_description = file: README.rst
 long_description_content_type = text/x-rst
 author = Janos Gabler, Tobias Raabe, Klara Röhrl
 license = MIT
-license_file = LICENSE
+license_files = LICENSE
 classifiers =
-    License :: OSI Approved :: MIT License
     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
-    Programming Language :: Python :: 3.10
 
 [options]
 packages = find:
-python_requires = >=3.6.1
+python_requires = >=3.10
 include_package_data = True
 package_dir =
     = .

src/__init__.py

@@ -1,6 +1,5 @@
 from src import simulation
 
-
 try:
     from ._version import version as __version__
 except ImportError:

src/config.py

@@ -6,6 +6,7 @@
 REMOVE EVERYTHING THAT IMPORTS THE VARIABLE YOU CHANGED.
 
 """
+
 import warnings
 from pathlib import Path
 

src/contact_models/contact_model_functions.py

@@ -6,7 +6,6 @@
 
 from src.shared import from_epochs_to_timestamps
 
-
 IS_POSITIVE_CASE = (
     "knows_infectious | (knows_immune & symptomatic) "
     "| (knows_immune & (cd_received_test_result_true >= -13))"

src/contact_models/task_create_contact_params.py

@@ -351,7 +351,7 @@ def measure_of_diff_btw_distributions(params, old_distribution, desired_total):
     """
     assert (params.index == old_distribution.index).all()
     params_deviation = params["value"].to_numpy() - old_distribution.to_numpy()
-    params_penalty = (params_deviation ** 2).sum()
+    params_penalty = (params_deviation**2).sum()
     actual_total = params.index.to_numpy() @ params["value"].to_numpy()
     total_contacts_penalty = (desired_total - actual_total) ** 2
     cost = total_contacts_penalty + params_penalty

src/create_initial_states/create_contact_model_group_ids.py

@@ -93,9 +93,9 @@ class with 23 individuals of the same age. Classes meet their peers and 3 pairs
     df[educ_group_cols] = df[educ_group_cols].astype("category")
 
     # the stays_home_when_schools_close variable is not used yet.
-    df[
-        "stays_home_when_schools_close"
-    ] = _identify_adult_staying_home_when_schools_close(df)
+    df["stays_home_when_schools_close"] = (
+        _identify_adult_staying_home_when_schools_close(df)
+    )
 
     df = df.drop(columns=["pos_in_group", "one", "group_size"])
     return df

src/create_initial_states/create_group_transition_probs.py

@@ -3,6 +3,7 @@
 This module is copied from sid commit 206886a14eeb3257deb71db91aba4e7fb2385fc2.
 
 """
+
 import string
 
 import numpy as np

src/create_initial_states/create_vaccination_priority.py

@@ -91,6 +91,7 @@
 - shares of each group: https://bit.ly/3cb5uUQ
 
 """
+
 import numpy as np
 import pandas as pd
 

src/create_initial_states/task_build_full_params.py

@@ -368,9 +368,9 @@ def _add_rapid_test_reaction_params(params):
 
     """
     params = params.copy(deep=True)
-    params.loc[
-        ("rapid_test_demand", "reaction", "hh_contacts_multiplier"), "value"
-    ] = 0.7
+    params.loc[("rapid_test_demand", "reaction", "hh_contacts_multiplier"), "value"] = (
+        0.7
+    )
     params.loc[
         ("rapid_test_demand", "reaction", "not_hh_contacts_multiplier"), "value"
     ] = 0.15

src/create_initial_states/task_create_background_characteristics.py

@@ -1,4 +1,5 @@
 """Create a synthetic population that is representative of Germany."""
+
 from pathlib import Path
 
 import numpy as np

src/plotting/msm_plots.py

@@ -7,7 +7,6 @@
 
 from src.plotting.plotting import format_date_axis
 
-
 plt.rcParams.update(
     {
         "axes.spines.right": False,

src/plotting/task_create_empirical_dataset.py

@@ -5,7 +5,6 @@
 from src.config import BLD
 from src.config import SRC
 
-
 _DEPENDENCIES = {
     "rki": BLD / "data" / "processed_time_series" / "rki.pkl",
     "cosmo_ever_rapid_test": SRC

src/plotting/task_plot_decomposition.py

@@ -1,4 +1,5 @@
 """This module holds the code to compute marginal contributions and shapley values."""
+
 from typing import Dict
 
 import matplotlib
@@ -21,7 +22,6 @@
 from src.simulation.scenario_config import get_available_scenarios
 from src.simulation.scenario_config import get_named_scenarios
 
-
 _CHANNEL_SCENARIOS_TO_MEMBERS = {
     "spring_baseline": frozenset(["rapid_tests", "vaccinations", "seasonality"]),
     "spring_without_rapid_tests_and_no_vaccinations": frozenset(["seasonality"]),

src/plotting/task_plot_incidences_by_group.py

@@ -1,4 +1,5 @@
 """For each available scenario plot the incidences in each of the age groups."""
+
 import matplotlib.pyplot as plt
 import pandas as pd
 import pytask
@@ -15,7 +16,6 @@
     create_path_to_scenario_outcome_time_series,
 )
 
-
 _DEPENDENCIES = {
     "calculate_moments.py": SRC / "calculate_moments.py",
     "plotting.py": SRC / "plotting" / "plotting.py",

src/plotting/task_plot_scenario_comparisons.py

@@ -25,7 +25,6 @@
 from src.simulation.scenario_config import get_available_scenarios
 from src.simulation.scenario_config import get_named_scenarios
 
-
 _MODULE_DEPENDENCIES = {
     "plotting.py": SRC / "plotting" / "plotting.py",
     "policy_tools.py": SRC / "policies" / "policy_tools.py",

src/plotting/task_plot_share_known_cases.py

@@ -1,4 +1,5 @@
 """Create plots, illustrating the share known cases over time."""
+
 import matplotlib.pyplot as plt
 import pandas as pd
 import pytask

src/plotting/task_plot_vaccinated_shares.py

@@ -15,7 +15,6 @@
 from src.simulation.scenario_config import get_available_scenarios
 from src.simulation.scenario_config import get_named_scenarios
 
-
 NAMED_SCENARIOS = get_named_scenarios()
 AVAILABLE_SCENARIOS = get_available_scenarios(NAMED_SCENARIOS)
 VACCINATION_SCENARIOS = sorted(

src/policies/domain_level_policy_blocks.py

@@ -15,6 +15,7 @@
 The functions here expect that the domain names are part of contact model names.
 
 """
+
 from functools import partial
 
 from src.policies.single_policy_functions import mixed_educ_policy

src/policies/policy_tools.py

@@ -1,4 +1,5 @@
 """Tools to work with policy dictionaries without accidentally modifying them."""
+
 import itertools
 
 import pandas as pd

src/policies/single_policy_functions.py

@@ -12,6 +12,7 @@
 All other arguments must be documented.
 
 """
+
 import numpy as np
 import pandas as pd
 from scipy.interpolate import interp1d

src/policies/task_create_work_multiplier_series.py

@@ -8,6 +8,7 @@
       people still go to work.
 
 """
+
 import warnings
 from zipfile import ZipFile
 

src/policies/task_plot_multipliers.py

@@ -18,7 +18,6 @@
 from src.simulation.seasonality import create_seasonality_series
 from src.testing.shared import get_piecewise_linear_interpolation
 
-
 _DEPENDENCIES = {
     # modules
     "plotting.py": SRC / "plotting" / "plotting.py",

src/prepare_data/shared.py

@@ -4,7 +4,6 @@
 import pandas as pd
 from sid.contacts import _sum_preserving_round
 
-
 # ---------------------------------- Contact Models ----------------------------------
 
 

src/prepare_data/task_prepare_mossong_data.py

@@ -7,7 +7,6 @@
 from src.shared import create_age_groups
 from src.shared import load_dataset
 
-
 LOCATIONS = [
     "cnt_home",
     "cnt_work",

src/prepare_data/task_prepare_rki_data.py

@@ -13,6 +13,7 @@
 - https://covid19-de-stats.sourceforge.io/rki-fall-tabelle.html
 
 """
+
 from datetime import datetime
 from datetime import timedelta
 
@@ -22,7 +23,6 @@
 
 from src.config import BLD
 
-
 DROPPPED_COLUMNS = [
     "IdBundesland",
     "Landkreis",

src/prepare_data/task_prepare_vaccination_data.py

@@ -12,7 +12,6 @@
 from src.config import POPULATION_GERMANY
 from src.plotting.plotting import style_plot
 
-
 plt.rcParams.update(
     {
         "axes.spines.right": False,

src/prepare_data/task_prepare_virus_variant_data.py

@@ -5,7 +5,6 @@
 from src.config import SRC
 from src.testing.shared import get_date_from_year_and_week
 
-
 STRAIN_FILES = {
     "rki_strains": BLD / "data" / "virus_strains" / "rki_strains.csv",
     "virus_shares_dict": BLD / "data" / "virus_strains" / "virus_shares_dict.pkl",

src/shared.py

@@ -4,7 +4,6 @@
 import pandas as pd
 from sid.contacts import _sum_preserving_round
 
-
 # ---------------------------------- Contact Models ----------------------------------
 
 

src/simulation/scenario_simulation_inputs.py

@@ -9,6 +9,7 @@
     - rapid_test_reaction_models
 
 """
+
 from functools import partial
 
 import pandas as pd

src/simulation/task_process_simulation_outputs.py

@@ -14,7 +14,6 @@
 from src.simulation.scenario_config import INCIDENCE_OUTCOMES
 from src.simulation.scenario_config import NON_INCIDENCE_OUTCOMES
 
-
 _MODULE_DEPENDENCIES = {
     "calculate_moments.py": SRC / "calculate_moments.py",
     "load_simulation_inputs.py": SRC / "simulation" / "load_simulation_inputs.py",

src/testing/rapid_tests.py

@@ -1,4 +1,5 @@
 """Functions for rapid tests."""
+
 import warnings
 
 import numpy as np

src/testing/testing_models.py

@@ -1,4 +1,5 @@
 """PCR testing model for sid."""
+
 import warnings
 
 import numpy as np

tests/test_params_scenarios.py

@@ -12,7 +12,6 @@
 )
 from src.testing.shared import get_piecewise_linear_interpolation
 
-
 SCENARIO_FUNCS = [func for name, func in get_params_scenarios()]
 
 

tests/test_testing_models.py

@@ -6,7 +6,6 @@
 from src.testing.testing_models import allocate_tests
 from src.testing.testing_models import process_tests
 
-
 DATE = pd.Timestamp("2020-10-10")