From 955cbcfc1616c56c9c1acdbcb77d6d2d2b4450bd Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 18 Mar 2024 20:23:28 +0100 Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#496) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-prettier: v3.0.3 → v4.0.0-alpha.8](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.3...v4.0.0-alpha.8) - [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.3.3) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- docs/extensions/function_images.py | 1 + src/scirpy/io/_convert_anndata.py | 1 + src/scirpy/ir_dist/__init__.py | 1 + src/scirpy/pl/base.py | 1 + src/scirpy/tests/test_workflow.py | 1 + src/scirpy/util/__init__.py | 12 ++++-------- src/scirpy/util/graph/_fr_size_aware_layout.py | 4 +--- 8 files changed, 12 insertions(+), 13 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8a7e1b8b6..0327ca61c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,12 +7,12 @@ default_stages: minimum_pre_commit_version: 2.16.0 repos: - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.3 + rev: v4.0.0-alpha.8 hooks: - id: prettier exclude: '^\.conda' - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.1.14 + rev: v0.3.3 hooks: - id: ruff types_or: [python, pyi, jupyter] diff --git a/docs/extensions/function_images.py b/docs/extensions/function_images.py index f8cbca0f3..1effd4409 100644 --- a/docs/extensions/function_images.py +++ b/docs/extensions/function_images.py @@ -2,6 +2,7 @@ Adapted from scanpy (c) Philipp Angerer """ + import re from pathlib import Path from typing import Any diff --git a/src/scirpy/io/_convert_anndata.py b/src/scirpy/io/_convert_anndata.py index a298a3f35..0268924bf 100644 --- a/src/scirpy/io/_convert_anndata.py +++ b/src/scirpy/io/_convert_anndata.py @@ -1,4 +1,5 @@ """Convert IrCells to AnnData and vice-versa""" + from collections.abc import Iterable from importlib.metadata import version from typing import cast diff --git a/src/scirpy/ir_dist/__init__.py b/src/scirpy/ir_dist/__init__.py index 696b6413d..de7ac389f 100644 --- a/src/scirpy/ir_dist/__init__.py +++ b/src/scirpy/ir_dist/__init__.py @@ -1,4 +1,5 @@ """Compute distances between immune receptor sequences""" + import itertools from collections.abc import Sequence from typing import Literal, Optional, Union diff --git a/src/scirpy/pl/base.py b/src/scirpy/pl/base.py index 5c5802c15..2957b7328 100644 --- a/src/scirpy/pl/base.py +++ b/src/scirpy/pl/base.py @@ -1,4 +1,5 @@ """Base plotting functions""" + import itertools from collections.abc import Sequence from typing import Literal, Optional, Union diff --git a/src/scirpy/tests/test_workflow.py b/src/scirpy/tests/test_workflow.py index d8b04c539..c7e5083db 100644 --- a/src/scirpy/tests/test_workflow.py +++ b/src/scirpy/tests/test_workflow.py @@ -8,6 +8,7 @@ The tests need to be quick in order not to overload the bioconda CI, but AIRR-compliance mandates to have these tests. """ + import pandas as pd import pandas.testing as pdt import pytest diff --git a/src/scirpy/util/__init__.py b/src/scirpy/util/__init__.py index 6dddd59d8..f232b2e08 100644 --- a/src/scirpy/util/__init__.py +++ b/src/scirpy/util/__init__.py @@ -59,13 +59,11 @@ class DataHandler: @overload @staticmethod - def default(data: None) -> None: - ... + def default(data: None) -> None: ... @overload @staticmethod - def default(data: "DataHandler.TYPE") -> "DataHandler": - ... + def default(data: "DataHandler.TYPE") -> "DataHandler": ... @staticmethod def default(data): @@ -119,12 +117,10 @@ def _check_chain_indices(self): index_chains(self.adata, airr_key=self._airr_key, key_added=self._chain_idx_key) @overload - def get_obs(self, columns: str) -> pd.Series: - ... + def get_obs(self, columns: str) -> pd.Series: ... @overload - def get_obs(self, columns: Sequence[str]) -> pd.DataFrame: - ... + def get_obs(self, columns: Sequence[str]) -> pd.DataFrame: ... def get_obs(self, columns): """\ diff --git a/src/scirpy/util/graph/_fr_size_aware_layout.py b/src/scirpy/util/graph/_fr_size_aware_layout.py index 0d27525d6..ca6d80fed 100644 --- a/src/scirpy/util/graph/_fr_size_aware_layout.py +++ b/src/scirpy/util/graph/_fr_size_aware_layout.py @@ -117,9 +117,7 @@ def layout_fr_size_aware( dimensionality_node_positions = np.array(list(node_positions.values())).shape[1] assert ( dimensionality_node_positions == dimensionality - ), "The dimensionality of values of `node_positions` (d={}) must match the dimensionality of `origin`/ `scale` (d={})!".format( - dimensionality_node_positions, dimensionality - ) + ), f"The dimensionality of values of `node_positions` (d={dimensionality_node_positions}) must match the dimensionality of `origin`/ `scale` (d={dimensionality})!" is_valid = _is_within_bbox(list(node_positions.values()), origin=origin, scale=scale) if not np.all(is_valid):