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"jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" From fb2e2bb71f6bf4409a692ec88f449728f17050bf Mon Sep 17 00:00:00 2001 From: muxator Date: Fri, 6 Sep 2024 09:10:54 +0200 Subject: [PATCH 2/8] deps: update black 23.12.1 -> 24.8.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Before this change, "make safety" would complain of the following vulnerability: -> Vulnerability found in black version 23.12.1 Vulnerability ID: 66742 Affected spec: <24.3.0 ADVISORY: Affected versions of Black are vulnerable to Regular Expression Denial of Service (ReDoS) via the lines_with_leading_tabs_expanded function in the strings.py file. An attacker could exploit this vulnerability by crafting a malicious input that causes a denial of service. CVE-2024-21503 For more information about this vulnerability, visit https://data.safetycli.com/v/66742/97c To ignore this vulnerability, use PyUp vulnerability id 66742 in safety’s ignore command-line argument or add the ignore to your safety policy file. --- poetry.lock | 48 ++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 25 insertions(+), 25 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7c66c23f..3e5bf8c3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -279,33 +279,33 @@ chardet = ">=3.0.2" [[package]] name = "black" -version = "23.12.1" +version = "24.8.0" description = "The uncompromising code formatter." optional = false python-versions = ">=3.8" files = [ - {file = "black-23.12.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e0aaf6041986767a5e0ce663c7a2f0e9eaf21e6ff87a5f95cbf3675bfd4c41d2"}, - {file = "black-23.12.1-cp310-cp310-macosx_11_0_arm64.whl", hash = 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codecov = "^2.1.13" darglint = "^1.8.1" hypothesis = "^6.86.2" From 2a2d3d08d5744258536ab193772e902d63c7f374 Mon Sep 17 00:00:00 2001 From: Aldo Date: Fri, 6 Sep 2024 10:21:17 +0200 Subject: [PATCH 3/8] lint: remove Safety checks (not open source anymore) Safety (https://github.com/pyupio/safety) has become a purely commercial platform for all practical puposes. Versions < 3.0.1 are unsupported and have grave configurability issues. Let's remove the dependency altogether. See: https://github.com/bancaditalia/black-it/pull/82#issuecomment-2333497964 --- .github/workflows/lint.yml | 2 +- CONTRIBUTING.md | 1 - Makefile | 6 +- poetry.lock | 143 +------------------------------------ pyproject.toml | 1 - tox.ini | 8 +-- 6 files changed, 4 insertions(+), 157 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 0d674423..871d0728 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -36,4 +36,4 @@ jobs: run: tox -e check-copyright - name: Misc checks run: | - tox -e bandit,safety \ No newline at end of file + tox -e bandit diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3f52e803..d66a4461 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -66,7 +66,6 @@ We have various commands which are helpful during development. ``` make lint-all make static -make safety make bandit ``` diff --git a/Makefile b/Makefile index aab08496..c7006698 100644 --- a/Makefile +++ b/Makefile @@ -67,7 +67,7 @@ clean-test: ## remove test and coverage artifacts rm -fr coverage.xml .PHONY: lint-all -lint-all: black check-copyright ruff static bandit safety vulture darglint ## run all linters +lint-all: black check-copyright ruff static bandit vulture darglint ## run all linters .PHONY: lint-all-files lint-all-files: black-files ruff-files static-files bandit-files vulture-files darglint-files ## run all linters for specific files (specified with files="file1 file2 somedir ...") @@ -130,10 +130,6 @@ bandit-files: ## run bandit for specific files (specified with files="file1 file $(call check_defined, files) bandit $(files) -.PHONY: safety -safety: ## run safety - safety check - .PHONY: vulture vulture: ## run vulture vulture black_it scripts/whitelists/package_whitelist.py diff --git a/poetry.lock b/poetry.lock index 3e5bf8c3..03867d13 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1076,25 +1076,6 @@ optional = false python-versions = "*" files = [] -[[package]] -name = "dparse" -version = "0.6.3" -description = "A parser for Python dependency files" -optional = false -python-versions = ">=3.6" -files = [ - {file = "dparse-0.6.3-py3-none-any.whl", hash = "sha256:0d8fe18714056ca632d98b24fbfc4e9791d4e47065285ab486182288813a5318"}, - {file = "dparse-0.6.3.tar.gz", hash = "sha256:27bb8b4bcaefec3997697ba3f6e06b2447200ba273c0b085c3d012a04571b528"}, -] - -[package.dependencies] -packaging = "*" -tomli = {version = "*", markers = "python_version < \"3.11\""} - -[package.extras] -conda = ["pyyaml"] -pipenv = ["pipenv (<=2022.12.19)"] - [[package]] name = "dynetx" version = "0.3.2" @@ -2465,25 +2446,6 @@ files = [ {file = "MarkupSafe-2.1.5.tar.gz", hash = "sha256:d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b"}, ] -[[package]] -name = "marshmallow" -version = "3.22.0" -description = "A lightweight library for converting complex datatypes to and from native Python datatypes." -optional = false -python-versions = ">=3.8" -files = [ - 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[testenv:vulture] skipsdist = True skip_install = True From 5d96fb8c96103a47e8ca3983a4f245611a9ecab7 Mon Sep 17 00:00:00 2001 From: muxator Date: Tue, 10 Sep 2024 14:36:22 +0200 Subject: [PATCH 4/8] deps: update numpy and statsmodels in preparation to solving python3.12 incompatibilities The issue with numpy is documented here, and officially solved with numpy 1.26: https://numpy.org/devdocs/reference/distutils_status_migration.html The upgrade on statsmodel probaby uncovers a bug in its MacOS build: the values computed by MethodOfMomentsLoss are slightly different there, and lead to a different result in the test. 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scipy = "^1.10.1" diff --git a/tests/test_examples/test_main.py b/tests/test_examples/test_main.py index 9cbb41e2..6afa0194 100644 --- a/tests/test_examples/test_main.py +++ b/tests/test_examples/test_main.py @@ -17,6 +17,8 @@ """Test the main example.""" from __future__ import annotations +import sys + from tests.conftest import DEFAULT_SUBPROCESS_TIMEOUT, ROOT_DIR from tests.test_examples.base import BaseMainExampleTestClass @@ -33,6 +35,13 @@ class TestMainExample(BaseMainExampleTestClass): script_path = EXAMPLE_MAIN_SCRIPT_PATH timeout = DEFAULT_SUBPROCESS_TIMEOUT nb_batches = 5 + if sys.platform == "darwin": + # 2024-09-10: MethodOfMomentsLoss started giving slightly different + # values on MacOS when statsmodels was updated from 0.13 to 0.14. This + # captures the change, so that when a fix arrives upstream we can update + # the test again. + BEST_PARAMETERS_STR = "Best parameters found: [0.21 0.19 0.76]" + expected_lines: tuple[str, ...] = ( "PARAMS SAMPLED: 0", "METHOD: HaltonSampler", From 06a5cc83fb279875d19943d51745a941c22d51b4 Mon Sep 17 00:00:00 2001 From: muxator Date: Sat, 24 Feb 2024 10:41:54 +0100 Subject: [PATCH 5/8] env: introduce support for python 3.12, but drop support for python 3.8 due to SciPy As of 2024-02, Python 3.8 is still going to be supproted for 6 months (until 2024-10, see https://devguide.python.org/versions). At the same time, Python 3.12 was released four months ago, on 2023-10, and will be supported for five years. We cannot support both, because SciPy 1.10 does not work with python 3.12, and scipy 1.11 drops python 3.8. Having to make a choiche, it is probably better to go with the more recent versions, thus 3.8 has to go down the drain. This commit introduces some failures on the mypy check, that are going to be fixed in the next commit. --- .github/workflows/docs.yml | 4 +- .github/workflows/lint.yml | 2 +- .github/workflows/test.yml | 2 +- poetry.lock | 1039 ++++++++++++++++-------------------- pyproject.toml | 6 +- tox.ini | 6 +- 6 files changed, 470 insertions(+), 589 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index c01b1441..02293af1 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -25,7 +25,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: [3.9] timeout-minutes: 30 @@ -37,7 +37,7 @@ jobs: - name: Install dependencies run: | pip install tox - + # Install markdown-spellcheck sudo npm install -g markdown-spellcheck - name: Generate Documentation diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 871d0728..6264bf4b 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml 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a/pyproject.toml +++ b/pyproject.toml @@ -27,10 +27,10 @@ classifiers = [ 'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)', 'Natural Language :: English', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', 'Topic :: Scientific/Engineering' ] @@ -39,7 +39,7 @@ classifiers = [ "Pull Requests" = "https://github.com/bancaditalia/black-it/pulls" [tool.poetry.dependencies] -python = ">=3.8,<3.12" +python = ">=3.9,<3.13" ipywidgets = "^8.1.2" matplotlib = "^3.7.3" numpy = ">=1.24.4,<1.27.0" @@ -49,7 +49,7 @@ seaborn = "^0.12.2" statsmodels = "^0.14.1" tables = "^3.8.0" xgboost = "^1.7.6" -scipy = "^1.10.1" +scipy = "^1.11.4" joblib = "^1.3.2" gymnasium = "^0.27.1" diff --git a/tox.ini b/tox.ini index ca94059d..e5b93d81 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ [tox] isolated_build = True -envlist = bandit, check-copyright, black-check, vulture, mypy, py3{8,9,10,11}, docs +envlist = bandit, check-copyright, black-check, vulture, mypy, py3{9,10,11,12}, docs [tox:.package] # note tox will use the same python version as under what tox is installed to package @@ -29,12 +29,12 @@ commands = --cov-report=html \ --cov-report=term {posargs} -[testenv:py{38,39,310,311}] +[testenv:py{39,310,311,312}] commands = {[testenv]commands} # test environment for notebooks -[testenv:py{38,39,310,311}-nb] +[testenv:py{39,310,311,312}-nb] deps = pytest==7.4.2 mesa==2.1.1 From 2c83b4212f2ac5bfce2716de23299d2a5a0cc3de Mon Sep 17 00:00:00 2001 From: Aldo Date: Thu, 5 Sep 2024 11:56:28 +0200 Subject: [PATCH 6/8] lint: solve mypy errors introduced in the previous commit --- black_it/calibrator.py | 8 +++++--- black_it/loss_functions/gsl_div.py | 2 +- black_it/loss_functions/likelihood.py | 12 ++++++++---- black_it/plot/plot_results.py | 4 +++- black_it/samplers/xgboost.py | 6 +++--- black_it/search_space.py | 2 +- tests/test_samplers/test_xgboost.py | 7 ++++--- 7 files changed, 25 insertions(+), 16 deletions(-) diff --git a/black_it/calibrator.py b/black_it/calibrator.py index 40e8ffff..78854490 100644 --- a/black_it/calibrator.py +++ b/black_it/calibrator.py @@ -127,9 +127,11 @@ def __init__( # noqa: PLR0913 # initialize arrays self.params_samp = np.zeros((0, self.param_grid.dims)) self.losses_samp = np.zeros(0) - self.batch_num_samp = np.zeros(0, dtype=int) - self.method_samp = np.zeros(0, dtype=int) - self.series_samp = np.zeros((0, self.ensemble_size, self.N, self.D)) + self.batch_num_samp: NDArray[np.int64] = np.zeros(0, dtype=int) + self.method_samp: NDArray[np.int64] = np.zeros(0, dtype=int) + self.series_samp: NDArray[np.float64] = np.zeros( + (0, self.ensemble_size, self.N, self.D), + ) # initialize variables before calibration self.n_sampled_params = 0 diff --git a/black_it/loss_functions/gsl_div.py b/black_it/loss_functions/gsl_div.py index f70696bc..28af0cbc 100644 --- a/black_it/loss_functions/gsl_div.py +++ b/black_it/loss_functions/gsl_div.py @@ -270,7 +270,7 @@ def get_words(time_series: NDArray[np.float64], length: int) -> NDArray: "the chosen word length is too high", exception_class=ValueError, ) - tsw = np.zeros(shape=(tswlen,), dtype=np.int32) + tsw: NDArray[np.float64] = np.zeros(shape=(tswlen,), dtype=np.int32) for i in range(length): k = 10 ** (length - i - 1) diff --git a/black_it/loss_functions/likelihood.py b/black_it/loss_functions/likelihood.py index 39243941..bef9f3bf 100644 --- a/black_it/loss_functions/likelihood.py +++ b/black_it/loss_functions/likelihood.py @@ -18,7 +18,7 @@ from __future__ import annotations import warnings -from typing import TYPE_CHECKING, Callable +from typing import TYPE_CHECKING, Callable, cast import numpy as np @@ -82,9 +82,13 @@ def compute_loss( Returns: The loss value. """ - r = sim_data_ensemble.shape[0] # number of repetitions - s = sim_data_ensemble.shape[1] # simulation length - d = sim_data_ensemble.shape[2] # number of dimensions + sim_data_ensemble_shape: tuple[int, int, int] = cast( + tuple[int, int, int], + sim_data_ensemble.shape, + ) + r = sim_data_ensemble_shape[0] # number of repetitions + s = sim_data_ensemble_shape[1] # simulation length + d = sim_data_ensemble_shape[2] # time series dimension if self.coordinate_weights is not None: warnings.warn( # noqa: B028 diff --git a/black_it/plot/plot_results.py b/black_it/plot/plot_results.py index 68bceec2..a5d233f7 100644 --- a/black_it/plot/plot_results.py +++ b/black_it/plot/plot_results.py @@ -32,6 +32,8 @@ if TYPE_CHECKING: import os + from numpy.typing import NDArray + def _get_samplers_id_table(saving_folder: str | os.PathLike) -> dict[str, int]: """Get the id table of the samplers from the checkpoint. @@ -298,7 +300,7 @@ def plot_sampling_interact(saving_folder: str | os.PathLike) -> None: data_frame = pd.read_csv(calibration_results_file) max_bn = int(max(data_frame["batch_num_samp"])) - all_bns = np.arange(max_bn + 1, dtype=int) + all_bns: NDArray[np.int64] = np.arange(max_bn + 1, dtype=int) indices_bns = np.array_split(all_bns, min(max_bn, 3)) dict_bns = {} diff --git a/black_it/samplers/xgboost.py b/black_it/samplers/xgboost.py index 275cea5b..da9b6d07 100644 --- a/black_it/samplers/xgboost.py +++ b/black_it/samplers/xgboost.py @@ -28,9 +28,9 @@ if TYPE_CHECKING: from numpy.typing import NDArray -MAX_FLOAT32 = np.finfo(np.float32).max -MIN_FLOAT32 = np.finfo(np.float32).min -EPS_FLOAT32 = np.finfo(np.float32).eps +MAX_FLOAT32: float = cast(float, np.finfo(np.float32).max) +MIN_FLOAT32: float = cast(float, np.finfo(np.float32).min) +EPS_FLOAT32: float = cast(float, np.finfo(np.float32).eps) class XGBoostSampler(MLSurrogateSampler): diff --git a/black_it/search_space.py b/black_it/search_space.py index 41a55e1c..2e03e1bd 100644 --- a/black_it/search_space.py +++ b/black_it/search_space.py @@ -72,7 +72,7 @@ def __init__( self._param_grid: list[NDArray[np.float64]] = [] self._space_size = 1 for i in range(self.dims): - new_col = np.arange( + new_col: NDArray[np.float64] = np.arange( parameters_bounds[0][i], parameters_bounds[1][i] + 0.0000001, parameters_precision[i], diff --git a/tests/test_samplers/test_xgboost.py b/tests/test_samplers/test_xgboost.py index 23a36369..590f5527 100644 --- a/tests/test_samplers/test_xgboost.py +++ b/tests/test_samplers/test_xgboost.py @@ -15,6 +15,7 @@ # along with this program. If not, see . """This module contains tests for the xgboost sampler.""" import sys +from typing import cast import numpy as np @@ -34,9 +35,9 @@ else: expected_params = np.array([[0.24, 0.26], [0.37, 0.21], [0.43, 0.14], [0.11, 0.04]]) -MAX_FLOAT32 = np.finfo(np.float32).max -MIN_FLOAT32 = np.finfo(np.float32).min -EPS_FLOAT32 = np.finfo(np.float32).eps +MAX_FLOAT32: float = cast(float, np.finfo(np.float32).max) +MIN_FLOAT32: float = cast(float, np.finfo(np.float32).min) +EPS_FLOAT32: float = cast(float, np.finfo(np.float32).eps) def test_xgboost_2d() -> None: From 5a00cf46c4d2e6db2f394b647baf2498ff5862bf Mon Sep 17 00:00:00 2001 From: muxator Date: Sat, 24 Feb 2024 13:06:29 +0100 Subject: [PATCH 7/8] lint: since we moved to python 3.9, let's bump ruff's target to 3.9, too --- .ruff.toml | 4 ++-- black_it/calibrator.py | 3 ++- black_it/loss_functions/base.py | 5 ++++- black_it/plot/plot_results.py | 3 ++- black_it/samplers/halton.py | 4 +++- black_it/schedulers/base.py | 4 +++- black_it/schedulers/rl/rl_scheduler.py | 5 +++-- black_it/utils/json_pandas_checkpointing.py | 4 +++- black_it/utils/sqlite3_checkpointing.py | 4 +++- examples/models/economics/brock_hommes.py | 4 +++- examples/models/simple_models.py | 4 +++- tests/test_examples/base.py | 2 +- tests/test_plot/base.py | 5 ++++- tests/test_plot/test_plot_descriptive_statistics.py | 5 ++++- 14 files changed, 40 insertions(+), 16 deletions(-) diff --git a/.ruff.toml b/.ruff.toml index a2adefc2..141519ff 100644 --- a/.ruff.toml +++ b/.ruff.toml @@ -42,8 +42,8 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" # Whether to enable preview mode. When preview mode is enabled, Ruff will use unstable rules and fixes. preview = true -# Assume Python 3.8 -target-version = "py38" +# Assume Python 3.9 +target-version = "py39" [per-file-ignores] "examples/docker-sir.py" = ["INP001", "T201"] diff --git a/black_it/calibrator.py b/black_it/calibrator.py index 78854490..419bd4a5 100644 --- a/black_it/calibrator.py +++ b/black_it/calibrator.py @@ -22,7 +22,7 @@ import time import warnings from pathlib import Path -from typing import TYPE_CHECKING, Callable, Sequence, cast +from typing import TYPE_CHECKING, Callable, cast import numpy as np from joblib import Parallel, delayed # type: ignore[import] @@ -39,6 +39,7 @@ if TYPE_CHECKING: import os + from collections.abc import Sequence from numpy.typing import NDArray diff --git a/black_it/loss_functions/base.py b/black_it/loss_functions/base.py index 09152b69..4da740d6 100644 --- a/black_it/loss_functions/base.py +++ b/black_it/loss_functions/base.py @@ -18,13 +18,16 @@ from __future__ import annotations from abc import ABC, abstractmethod -from typing import Callable, Optional, Sequence +from typing import TYPE_CHECKING, Callable, Optional import numpy as np from numpy.typing import NDArray from black_it.utils.base import _assert +if TYPE_CHECKING: + from collections.abc import Sequence + TimeSeriesFilter = Optional[Callable[[NDArray[np.float64]], NDArray[np.float64]]] """A filter that receives a time series and returns its filtered version. Used by the BaseLoss constructor.""" diff --git a/black_it/plot/plot_results.py b/black_it/plot/plot_results.py index a5d233f7..ed42c167 100644 --- a/black_it/plot/plot_results.py +++ b/black_it/plot/plot_results.py @@ -19,7 +19,7 @@ import pickle # nosec B403 from pathlib import Path -from typing import TYPE_CHECKING, Collection +from typing import TYPE_CHECKING import matplotlib.pyplot as plt # type: ignore[import] import numpy as np @@ -31,6 +31,7 @@ if TYPE_CHECKING: import os + from collections.abc import Collection from numpy.typing import NDArray diff --git a/black_it/samplers/halton.py b/black_it/samplers/halton.py index e4550f0c..3cc1b5a2 100644 --- a/black_it/samplers/halton.py +++ b/black_it/samplers/halton.py @@ -18,7 +18,7 @@ from __future__ import annotations import itertools -from typing import TYPE_CHECKING, Iterator +from typing import TYPE_CHECKING import numpy as np @@ -26,6 +26,8 @@ from black_it.utils.base import check_arg, digitize_data if TYPE_CHECKING: + from collections.abc import Iterator + from numpy.typing import NDArray from black_it.search_space import SearchSpace diff --git a/black_it/schedulers/base.py b/black_it/schedulers/base.py index 1af5aa6a..0ae00730 100644 --- a/black_it/schedulers/base.py +++ b/black_it/schedulers/base.py @@ -19,11 +19,13 @@ import contextlib from abc import ABC, abstractmethod -from typing import TYPE_CHECKING, Generator, Sequence +from typing import TYPE_CHECKING from black_it.utils.seedable import BaseSeedable if TYPE_CHECKING: + from collections.abc import Generator, Sequence + import numpy as np from numpy.typing import NDArray diff --git a/black_it/schedulers/rl/rl_scheduler.py b/black_it/schedulers/rl/rl_scheduler.py index 3c88b814..5235df72 100644 --- a/black_it/schedulers/rl/rl_scheduler.py +++ b/black_it/schedulers/rl/rl_scheduler.py @@ -18,7 +18,7 @@ from __future__ import annotations import threading -from typing import TYPE_CHECKING, List, Sequence, cast +from typing import TYPE_CHECKING, cast import numpy as np @@ -27,6 +27,7 @@ from black_it.schedulers.base import BaseScheduler if TYPE_CHECKING: + from collections.abc import Sequence from queue import Queue from numpy._typing import NDArray @@ -103,7 +104,7 @@ def _add_or_get_bootstrap_sampler( return samplers, sampler_types[HaltonSampler] new_sampler = HaltonSampler(batch_size=1) - return tuple(list(samplers) + cast(List[BaseSampler], [new_sampler])), len( + return tuple(list(samplers) + cast(list[BaseSampler], [new_sampler])), len( samplers, ) diff --git a/black_it/utils/json_pandas_checkpointing.py b/black_it/utils/json_pandas_checkpointing.py index b740e6ad..ab7289b6 100644 --- a/black_it/utils/json_pandas_checkpointing.py +++ b/black_it/utils/json_pandas_checkpointing.py @@ -20,7 +20,7 @@ import json import pickle # nosec B403 from pathlib import Path -from typing import TYPE_CHECKING, Mapping +from typing import TYPE_CHECKING import numpy as np import pandas as pd # type: ignore[import] @@ -29,6 +29,8 @@ from black_it.utils.base import NumpyArrayEncoder, PathLike if TYPE_CHECKING: + from collections.abc import Mapping + from numpy.typing import NDArray from black_it.loss_functions.base import BaseLoss diff --git a/black_it/utils/sqlite3_checkpointing.py b/black_it/utils/sqlite3_checkpointing.py index bde439c5..27a5be82 100644 --- a/black_it/utils/sqlite3_checkpointing.py +++ b/black_it/utils/sqlite3_checkpointing.py @@ -23,12 +23,14 @@ import pickle # nosec B403 import sqlite3 from pathlib import Path -from typing import TYPE_CHECKING, Mapping, Sequence +from typing import TYPE_CHECKING import numpy as np from numpy.typing import NDArray if TYPE_CHECKING: + from collections.abc import Mapping, Sequence + from black_it.loss_functions.base import BaseLoss from black_it.samplers.base import BaseSampler from black_it.utils.base import PathLike diff --git a/examples/models/economics/brock_hommes.py b/examples/models/economics/brock_hommes.py index 5bab458f..ccdb64fb 100644 --- a/examples/models/economics/brock_hommes.py +++ b/examples/models/economics/brock_hommes.py @@ -17,12 +17,14 @@ """Implementation of the model in (Brock and Hommes, 1998).""" from __future__ import annotations -from typing import TYPE_CHECKING, Sequence +from typing import TYPE_CHECKING import numpy as np from scipy.special import softmax if TYPE_CHECKING: + from collections.abc import Sequence + from numpy.typing import NDArray diff --git a/examples/models/simple_models.py b/examples/models/simple_models.py index 32853314..9ee8ef6e 100644 --- a/examples/models/simple_models.py +++ b/examples/models/simple_models.py @@ -28,12 +28,14 @@ """ from __future__ import annotations -from typing import TYPE_CHECKING, Sequence +from typing import TYPE_CHECKING import numpy as np from scipy.stats import alpha, bernoulli if TYPE_CHECKING: + from collections.abc import Sequence + from numpy.typing import NDArray diff --git a/tests/test_examples/base.py b/tests/test_examples/base.py index 3c2a9510..6dd89c27 100644 --- a/tests/test_examples/base.py +++ b/tests/test_examples/base.py @@ -16,8 +16,8 @@ """Base module for example tests.""" import sys +from collections.abc import Sequence from pathlib import Path -from typing import Sequence import pytest diff --git a/tests/test_plot/base.py b/tests/test_plot/base.py index a009aedb..57203290 100644 --- a/tests/test_plot/base.py +++ b/tests/test_plot/base.py @@ -20,11 +20,14 @@ import logging from pathlib import Path from tempfile import TemporaryDirectory -from typing import Any, Callable, Sequence +from typing import TYPE_CHECKING, Any, Callable import matplotlib.pyplot as plt # type: ignore[import] from matplotlib.testing.compare import compare_images # type: ignore[import] +if TYPE_CHECKING: + from collections.abc import Sequence + class BasePlotTest: """Base test class for plotting functions.""" diff --git a/tests/test_plot/test_plot_descriptive_statistics.py b/tests/test_plot/test_plot_descriptive_statistics.py index 6092edb3..2a0cb857 100644 --- a/tests/test_plot/test_plot_descriptive_statistics.py +++ b/tests/test_plot/test_plot_descriptive_statistics.py @@ -17,7 +17,7 @@ """This test module contains tests for the plot_descriptive_statistics.py module.""" from __future__ import annotations -from typing import Any, Sequence +from typing import TYPE_CHECKING, Any import numpy as np @@ -26,6 +26,9 @@ from tests.test_plot.base import BasePlotTest from tests.utils.base import skip_on_windows +if TYPE_CHECKING: + from collections.abc import Sequence + @skip_on_windows() class TestTsStats(BasePlotTest): From 62bda988af807a15a97e4b1f5fb0728281799fbb Mon Sep 17 00:00:00 2001 From: Aldo Date: Thu, 5 Sep 2024 11:53:49 +0200 Subject: [PATCH 8/8] tox-nb: update nbmake to make it work on 3.12 --- poetry.lock | 2 +- pyproject.toml | 2 +- tox.ini | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 58823655..81f5252b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5521,4 +5521,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "fb8978e54bfb79c61c66694fc9d61ef468234ffcd4ca7456b5f6c75d2709b80d" +content-hash = "ee3d84b68404cda9bf032629517244a4283b75abb48588c8a32546440872fe7e" diff --git a/pyproject.toml b/pyproject.toml index 80daa597..1ad6ab41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,7 +73,7 @@ mkdocstrings = "^0.22.0" mkdocstrings-python-legacy = "^0.2.3" mknotebooks = "^0.8.0" mypy = "^1.5.1" -nbmake = "^1.4.3" +nbmake = "^1.5.4" ndlib = "^5.1.1" pydocstyle = "^6.3.0" pymdown-extensions = "^10.3" diff --git a/tox.ini b/tox.ini index e5b93d81..966f4ea4 100644 --- a/tox.ini +++ b/tox.ini @@ -38,7 +38,7 @@ commands = deps = pytest==7.4.2 mesa==2.1.1 - nbmake==1.4.3 + nbmake==1.5.4 commands = pytest examples/tests_on_toy_model.ipynb --nbmake --nbmake-timeout=300 [testenv:mypy]