[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
         args: [--remove]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.1
     hooks:
       - id: pyupgrade
         types: [file]
@@ -36,15 +36,15 @@ repos:
         types_or: [python, pyi]
 
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.2.0
     hooks:
       - id: black
         types: [file]
         types_or: [python, pyi]
         language_version: python3
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         types: [file]
@@ -59,7 +59,7 @@ repos:
 
   # Notebook tools
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         args:
@@ -68,7 +68,7 @@ repos:
           - "metadata.vscode metadata.language_info.version"
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.1
+    rev: 1.8.4
     hooks:
       - id: nbqa-black
         additional_dependencies: [black==22.6.0]
@@ -92,7 +92,7 @@ repos:
         additional_dependencies: [flake8-docstrings, flake8-print>=5.0.0]
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         name: "flake8 lint code"
@@ -104,7 +104,7 @@ repos:
           - "--count"
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         alias: flake8-docs
@@ -116,7 +116,7 @@ repos:
         additional_dependencies: [flake8-docstrings, darglint==1.8.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.9.0
     hooks:
       - id: mypy
         exclude: "docs|benchmark/|.*/tests?/.*"

benchmark/asv.conf.json

@@ -2,65 +2,56 @@
   // The version of the config file format.  Do not change, unless
   // you know what you are doing.
   "version": 1,
-
   // The name of the project being benchmarked
   "project": "pyglotaran",
-
   // The project's homepage
   "project_url": "https://github.com/glotaran/pyglotaran",
-
   // The URL or local path of the source code repository for the
   // project being benchmarked
   "repo": "..",
-
   // The Python project's subdirectory in your repo.  If missing or
   // the empty string, the project is assumed to be located at the root
   // of the repository.
   // "repo_subdir": "",
-
   // Customizable commands for building, installing, and
   // uninstalling the project. See asv.conf.json documentation.
   //
   // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
   // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
-  // "build_command": [
-  //     "python setup.py build",
-  //     "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
-  // ],
-
+  // FIX build command
+  // Ref.: https://github.com/airspeed-velocity/asv/issues/903#issuecomment-1276110657
+  "build_command": [
+    "python -m pip install build",
+    "python -m build --wheel -o {build_cache_dir} {build_dir}"
+  ],
   // List of branches to benchmark. If not provided, defaults to "master"
   // (for git) or "default" (for mercurial).
-  "branches": ["HEAD"], // for git
+  "branches": [
+    "HEAD"
+  ], // for git
   // "branches": ["default"],    // for mercurial
-
   // The DVCS being used.  If not set, it will be automatically
   // determined from "repo" by looking at the protocol in the URL
   // (if remote), or by looking for special directories, such as
   // ".git" (if local).
   "dvcs": "git",
-
   // The tool to use to create environments.  May be "conda",
   // "virtualenv" or other value depending on the plugins in use.
   // If missing or the empty string, the tool will be automatically
   // determined by looking for tools on the PATH environment
   // variable.
   "environment_type": "virtualenv",
-
   // timeout in seconds for installing any dependencies in environment
   // defaults to 10 min
   //"install_timeout": 600,
-
   // the base URL to show a commit for the project.
   "show_commit_url": "https://github.com/glotaran/pyglotaran/commit/",
-
   // The Pythons you'd like to test against.  If not provided, defaults
   // to the current version of Python used to run `asv`.
   //   "pythons": ["3.8", "3.9"],
-
   // The list of conda channel names to be searched for benchmark
   // dependency packages in the specified order
   // "conda_channels": ["conda-forge", "defaults"],
-
   // The matrix of dependencies to test.  Each key is the name of a
   // package (in PyPI) and the values are version numbers.  An empty
   // list or empty string indicates to just test against the default
@@ -76,7 +67,6 @@
   //     "six": ["", null],        // test with and without six installed
   //     "pip+emcee": [""],   // emcee is only available for install with pip.
   // },
-
   // Combinations of libraries/python versions can be excluded/included
   // from the set to test. Each entry is a dictionary containing additional
   // key-value pairs to include/exclude.
@@ -109,31 +99,24 @@
   //     // additional env if run on windows+conda
   //     {"platform": "win32", "environment_type": "conda", "python": "2.7", "libpython": ""},
   // ],
-
   // The directory (relative to the current directory) that benchmarks are
   // stored in.  If not provided, defaults to "benchmarks"
   // "benchmark_dir": "benchmarks",
-
   // The directory (relative to the current directory) to cache the Python
   // environments in.  If not provided, defaults to "env"
   "env_dir": ".asv/env",
-
   // The directory (relative to the current directory) that raw benchmark
   // results are stored in.  If not provided, defaults to "results".
   "results_dir": ".asv/results",
-
   // The directory (relative to the current directory) that the html tree
   // should be written to.  If not provided, defaults to "html".
   "html_dir": ".asv/html"
-
   // The number of characters to retain in the commit hashes.
   // "hash_length": 8,
-
   // `asv` will cache results of the recent builds in each
   // environment, making them faster to install next time.  This is
   // the number of builds to keep, per environment.
   // "build_cache_size": 2,
-
   // The commits after which the regression search in `asv publish`
   // should start looking for regressions. Dictionary whose keys are
   // regexps matching to benchmark names, and values corresponding to
@@ -146,7 +129,6 @@
   //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
   //    "another_benchmark": null,   // Skip regression detection altogether
   // },
-
   // The thresholds for relative change in results, after which `asv
   // publish` starts reporting regressions. Dictionary of the same
   // form as in ``regressions_first_commits``, with values

docs/remove_notebook_written_data.py

@@ -6,6 +6,7 @@
 If you use ``tox`` to run the tests (``tox`` or ``tox -e docs-notebooks``)
 this script will be run before the tests.
 """
+
 import shutil
 from pathlib import Path
 

glotaran/__init__.py

@@ -1,4 +1,5 @@
 """Glotaran package root."""
+
 from glotaran.deprecation.deprecation_utils import deprecate_submodule
 from glotaran.plugin_system.base_registry import load_plugins
 

glotaran/analysis/__init__.py

@@ -1,4 +1,5 @@
 """This package contains functions for model simulation and fitting."""
+
 from glotaran.deprecation.deprecation_utils import deprecate_submodule
 
 simulation = deprecate_submodule(

glotaran/builtin/__init__.py

@@ -1,4 +1,5 @@
 """This package contains builtin plugins."""
+
 from glotaran.deprecation.deprecation_utils import deprecate_submodule
 
 read_data_file = deprecate_submodule(

glotaran/builtin/io/netCDF/netCDF.py

@@ -1,4 +1,5 @@
 """Module containing the NetCDF4 Data IO plugin."""
+
 from __future__ import annotations
 
 # Needed to prevent a netCDF4 RuntimeWarning at import time

glotaran/builtin/io/sdt/sdt_file_reader.py

@@ -1,4 +1,5 @@
 """Module containing the SDT Data IO plugin."""
+
 from __future__ import annotations
 
 import warnings

glotaran/builtin/io/yml/utils.py

@@ -1,4 +1,5 @@
 """Utility module for ``glotaran.builtin.io.yml.yml``."""
+
 from __future__ import annotations
 
 from pathlib import Path

glotaran/builtin/io/yml/yml.py

@@ -1,4 +1,5 @@
 """Module containing the YAML Data and Project IO plugins."""
+
 from __future__ import annotations
 
 from dataclasses import replace

glotaran/builtin/megacomplexes/coherent_artifact/coherent_artifact_megacomplex.py

@@ -1,4 +1,5 @@
 """This package contains the kinetic megacomplex item."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

glotaran/builtin/megacomplexes/decay/decay_parallel_megacomplex.py

@@ -1,4 +1,5 @@
 """This package contains the decay megacomplex item."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

glotaran/builtin/megacomplexes/decay/decay_sequential_megacomplex.py

@@ -1,4 +1,5 @@
 """This package contains the decay megacomplex item."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

glotaran/builtin/megacomplexes/decay/initial_concentration.py

@@ -1,4 +1,5 @@
 """This package contains the initial concentration item."""
+
 from __future__ import annotations
 
 import numpy as np

glotaran/builtin/megacomplexes/decay/irf.py

@@ -1,6 +1,5 @@
 """This package contains irf items."""
 
-
 import numpy as np
 
 from glotaran.model import ModelError

glotaran/builtin/megacomplexes/decay/k_matrix.py

@@ -1,4 +1,5 @@
 """ K-Matrix """
+
 from __future__ import annotations
 
 import itertools

glotaran/deprecation/__init__.py

@@ -1,4 +1,5 @@
 """Deprecation helpers and place to put deprecated implementations till removing."""
+
 from glotaran.deprecation.deprecation_utils import GlotaranApiDeprecationWarning
 from glotaran.deprecation.deprecation_utils import GlotaranDeprecatedApiError
 from glotaran.deprecation.deprecation_utils import deprecate

glotaran/deprecation/modules/builtin_io_yml.py

@@ -1,4 +1,5 @@
 """Deprecation functions for the yaml parser."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

glotaran/deprecation/modules/test/__init__.py

@@ -1,4 +1,5 @@
 """Package with deprecation tests and helper functions."""
+
 from __future__ import annotations
 
 from pathlib import Path

glotaran/deprecation/modules/test/test_glotaran_root.py

@@ -1,4 +1,5 @@
 """Test deprecated imports from 'glotaran/__init__.py' """
+
 from __future__ import annotations
 
 from warnings import warn

glotaran/deprecation/test/dummy_package/__init__.py

@@ -1,4 +1,5 @@
 """Module containing a deprecated fake module."""
+
 from glotaran.deprecation.deprecation_utils import deprecate_submodule
 
 # just here to be tested

glotaran/io/prepare_dataset.py

@@ -1,4 +1,5 @@
 """Module containing dataset preparation functionality."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

glotaran/io/preprocessor/__init__.py

@@ -1,2 +1,3 @@
 """Tools for data pre-processing."""
+
 from glotaran.io.preprocessor.pipeline import PreProcessingPipeline

glotaran/io/preprocessor/pipeline.py

@@ -1,4 +1,5 @@
 """A pre-processor pipeline for data."""
+
 from __future__ import annotations
 
 from typing import Annotated

glotaran/io/preprocessor/preprocessor.py

@@ -1,4 +1,5 @@
 """A pre-processor pipeline for data."""
+
 from __future__ import annotations
 
 import abc

glotaran/model/__init__.py

@@ -1,4 +1,5 @@
 """The glotaran model package."""
+
 from glotaran.model.clp_constraint import OnlyConstraint
 from glotaran.model.clp_constraint import ZeroConstraint
 from glotaran.model.clp_penalties import EqualAreaPenalty

glotaran/model/clp_constraint.py

@@ -1,4 +1,5 @@
 """This module contains clp constraint items."""
+
 from __future__ import annotations
 
 from glotaran.model.interval_item import IntervalItem

glotaran/model/clp_relation.py

@@ -1,4 +1,5 @@
 """This module contains clp relation items."""
+
 from __future__ import annotations
 
 from glotaran.model.interval_item import IntervalItem

glotaran/model/dataset_group.py

@@ -1,4 +1,5 @@
 """This module contains the dataset group."""
+
 from __future__ import annotations
 
 from collections.abc import Mapping
@@ -25,9 +26,9 @@
 class DatasetGroupModel(ModelItem):
     """A group of datasets which will evaluated independently."""
 
-    residual_function: Literal[
-        "variable_projection", "non_negative_least_squares"
-    ] = "variable_projection"
+    residual_function: Literal["variable_projection", "non_negative_least_squares"] = (
+        "variable_projection"
+    )
     """The residual function to use."""
 
     link_clp: bool | None = None

glotaran/model/interval_item.py

@@ -1,4 +1,5 @@
 """This module contains the interval item."""
+
 from __future__ import annotations
 
 from glotaran.model.item import Item

glotaran/model/item.py

@@ -1,4 +1,5 @@
 """This module contains the items."""
+
 from __future__ import annotations
 
 import contextlib
@@ -333,9 +334,13 @@ def iterate_names_and_labels(
                 yield name, v if isinstance(v, str) else (name, v.label)  # type:ignore[misc]
 
         else:
-            yield name, value if isinstance(value, str) else (
-                name,
-                value.label,  # type:ignore[misc]
+            yield name, (
+                value
+                if isinstance(value, str)
+                else (
+                    name,
+                    value.label,  # type:ignore[misc]
+                )
             )