From dc8aadd790f93ebde660a00d411f94c2c3152162 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 25 Mar 2024 22:36:23 +0000 Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- setup.cfg | 9 ++------- src/config.py | 1 + src/contact_models/task_create_contact_params.py | 2 +- .../create_contact_model_group_ids.py | 6 +++--- .../create_group_transition_probs.py | 1 + src/create_initial_states/create_vaccination_priority.py | 1 + src/create_initial_states/task_build_full_params.py | 6 +++--- .../task_create_background_characteristics.py | 1 + src/plotting/task_plot_decomposition.py | 1 + src/plotting/task_plot_incidences_by_group.py | 1 + src/plotting/task_plot_share_known_cases.py | 1 + src/policies/domain_level_policy_blocks.py | 1 + src/policies/policy_tools.py | 1 + src/policies/single_policy_functions.py | 1 + src/policies/task_create_work_multiplier_series.py | 1 + src/prepare_data/task_prepare_rki_data.py | 1 + src/simulation/scenario_simulation_inputs.py | 1 + src/testing/rapid_tests.py | 1 + src/testing/testing_models.py | 1 + 19 files changed, 24 insertions(+), 14 deletions(-) diff --git a/setup.cfg b/setup.cfg index cb983100..92c84a8c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -5,20 +5,15 @@ 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 = >=3.8 include_package_data = True package_dir = = . diff --git a/src/config.py b/src/config.py index f295ac96..7ca63541 100644 --- a/src/config.py +++ b/src/config.py @@ -6,6 +6,7 @@ REMOVE EVERYTHING THAT IMPORTS THE VARIABLE YOU CHANGED. """ + import warnings from pathlib import Path diff --git a/src/contact_models/task_create_contact_params.py b/src/contact_models/task_create_contact_params.py index 4d67a7a8..a4c7050f 100644 --- a/src/contact_models/task_create_contact_params.py +++ b/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 diff --git a/src/create_initial_states/create_contact_model_group_ids.py b/src/create_initial_states/create_contact_model_group_ids.py index d2b636e3..72d2ea95 100644 --- a/src/create_initial_states/create_contact_model_group_ids.py +++ b/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 diff --git a/src/create_initial_states/create_group_transition_probs.py b/src/create_initial_states/create_group_transition_probs.py index babcf27f..87ae8e59 100644 --- a/src/create_initial_states/create_group_transition_probs.py +++ b/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 diff --git a/src/create_initial_states/create_vaccination_priority.py b/src/create_initial_states/create_vaccination_priority.py index 364a4323..fdd84553 100644 --- a/src/create_initial_states/create_vaccination_priority.py +++ b/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 diff --git a/src/create_initial_states/task_build_full_params.py b/src/create_initial_states/task_build_full_params.py index f7e20eba..c373fd5c 100644 --- a/src/create_initial_states/task_build_full_params.py +++ b/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 diff --git a/src/create_initial_states/task_create_background_characteristics.py b/src/create_initial_states/task_create_background_characteristics.py index b97f2314..b39ac007 100644 --- a/src/create_initial_states/task_create_background_characteristics.py +++ b/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 diff --git a/src/plotting/task_plot_decomposition.py b/src/plotting/task_plot_decomposition.py index e7734a76..8f889546 100644 --- a/src/plotting/task_plot_decomposition.py +++ b/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 diff --git a/src/plotting/task_plot_incidences_by_group.py b/src/plotting/task_plot_incidences_by_group.py index 8f305254..bd3b46d4 100644 --- a/src/plotting/task_plot_incidences_by_group.py +++ b/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 diff --git a/src/plotting/task_plot_share_known_cases.py b/src/plotting/task_plot_share_known_cases.py index 91c1d64f..e23f0813 100644 --- a/src/plotting/task_plot_share_known_cases.py +++ b/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 diff --git a/src/policies/domain_level_policy_blocks.py b/src/policies/domain_level_policy_blocks.py index 4894c28b..ac37daae 100644 --- a/src/policies/domain_level_policy_blocks.py +++ b/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 diff --git a/src/policies/policy_tools.py b/src/policies/policy_tools.py index 9d1b8a5d..23a8f1cc 100644 --- a/src/policies/policy_tools.py +++ b/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 diff --git a/src/policies/single_policy_functions.py b/src/policies/single_policy_functions.py index 19e0016f..94e0bc73 100644 --- a/src/policies/single_policy_functions.py +++ b/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 diff --git a/src/policies/task_create_work_multiplier_series.py b/src/policies/task_create_work_multiplier_series.py index ce10c68b..81f2403a 100644 --- a/src/policies/task_create_work_multiplier_series.py +++ b/src/policies/task_create_work_multiplier_series.py @@ -8,6 +8,7 @@ people still go to work. """ + import warnings from zipfile import ZipFile diff --git a/src/prepare_data/task_prepare_rki_data.py b/src/prepare_data/task_prepare_rki_data.py index 6e288bbf..7657fac4 100644 --- a/src/prepare_data/task_prepare_rki_data.py +++ b/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 diff --git a/src/simulation/scenario_simulation_inputs.py b/src/simulation/scenario_simulation_inputs.py index 50abe265..6b5edeb7 100644 --- a/src/simulation/scenario_simulation_inputs.py +++ b/src/simulation/scenario_simulation_inputs.py @@ -9,6 +9,7 @@ - rapid_test_reaction_models """ + from functools import partial import pandas as pd diff --git a/src/testing/rapid_tests.py b/src/testing/rapid_tests.py index 6d295d8e..8d2b8d2d 100644 --- a/src/testing/rapid_tests.py +++ b/src/testing/rapid_tests.py @@ -1,4 +1,5 @@ """Functions for rapid tests.""" + import warnings import numpy as np diff --git a/src/testing/testing_models.py b/src/testing/testing_models.py index 87c6f8c6..5a7c5226 100644 --- a/src/testing/testing_models.py +++ b/src/testing/testing_models.py @@ -1,4 +1,5 @@ """PCR testing model for sid.""" + import warnings import numpy as np