From 022a2571532ffe796f73dc8020304716ba7a267d Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 10:55:03 +0200
Subject: [PATCH 1/7] Prevent SciPy deprecation warning for
`estimate_gradients_2d_global` (#475)
* Prevent SciPy deprecation warning
Currently, I see:
```
~/pipefunc/.venv/lib/python3.13/site-packages/adaptive/learner/learner2D.py:52: DeprecationWarning: `scipy.interpolate.interpnd.estimate_gradients_2d_global` is deprecated along with the `scipy.interpolate.interpnd` namespace. `scipy.interpolate.interpnd.estimate_gradients_2d_global` will be removed in SciPy 1.16.0, and the `scipy.interpolate.interpnd` namespace will be removed in SciPy 2.0.0.
gradients = interpolate.interpnd.estimate_gradients_2d_global(
```
* Use CloughTocher2DInterpolator
---
adaptive/learner/learner2D.py | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/adaptive/learner/learner2D.py b/adaptive/learner/learner2D.py
index 017a9da3..15864a80 100644
--- a/adaptive/learner/learner2D.py
+++ b/adaptive/learner/learner2D.py
@@ -11,7 +11,7 @@
import cloudpickle
import numpy as np
from scipy import interpolate
-from scipy.interpolate import LinearNDInterpolator
+from scipy.interpolate import CloughTocher2DInterpolator, LinearNDInterpolator
from adaptive.learner.base_learner import BaseLearner
from adaptive.learner.triangulation import simplex_volume_in_embedding
@@ -49,9 +49,7 @@ def deviations(ip: LinearNDInterpolator) -> list[np.ndarray]:
The deviation per triangle.
"""
values = ip.values / (np.ptp(ip.values, axis=0).max() or 1)
- gradients = interpolate.interpnd.estimate_gradients_2d_global(
- ip.tri, values, tol=1e-6
- )
+ gradients = CloughTocher2DInterpolator(ip.tri, values, tol=1e-6).grad
simplices = ip.tri.simplices
p = ip.tri.points[simplices]
From 5167fe0c5cfafd85aa5cc3d6a7c9018b978aacae Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 11:16:58 +0200
Subject: [PATCH 2/7] Use `uv` as Nox backend and several related improvements
(#476)
---
.github/workflows/coverage.yml | 8 +++---
.github/workflows/matchers/pytest.json | 18 ------------
.github/workflows/nox.yml | 12 ++++----
.github/workflows/typeguard.yml | 8 +++---
README.md | 4 +--
noxfile.py | 40 +++++++++++++++++---------
pyproject.toml | 11 ++++++-
7 files changed, 52 insertions(+), 49 deletions(-)
delete mode 100644 .github/workflows/matchers/pytest.json
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index ab393048..4c177878 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -11,10 +11,10 @@ jobs:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
- python-version: 3.11
- - name: Install dependencies
- run: pip install nox
+ python-version: 3.13
+ - name: Install uv
+ uses: astral-sh/setup-uv@v6
- name: Test with nox
- run: nox -e coverage
+ run: uv run --group nox nox -e coverage
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v4
diff --git a/.github/workflows/matchers/pytest.json b/.github/workflows/matchers/pytest.json
deleted file mode 100644
index 3e5d8d5b..00000000
--- a/.github/workflows/matchers/pytest.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "problemMatcher": [
- {
- "owner": "python",
- "pattern": [
- {
- "regexp": "^\\s*File\\s\\\"(.*)\\\",\\sline\\s(\\d+),\\sin\\s(.*)$",
- "file": 1,
- "line": 2
- },
- {
- "regexp": "^\\s*raise\\s(.*)\\(\\'(.*)\\'\\)$",
- "message": 2
- }
- ]
- }
- ]
-}
diff --git a/.github/workflows/nox.yml b/.github/workflows/nox.yml
index 499b48c4..f021d3b2 100644
--- a/.github/workflows/nox.yml
+++ b/.github/workflows/nox.yml
@@ -12,7 +12,7 @@ jobs:
fail-fast: false
matrix:
platform: [ubuntu-latest, macos-latest, windows-latest]
- python-version: ["3.9", "3.10", "3.11", "3.12"]
+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
steps:
- uses: actions/checkout@v4
@@ -20,11 +20,9 @@ jobs:
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- - name: Register Python problem matcher
- run: echo "::add-matcher::.github/workflows/matchers/pytest.json"
- - name: Install dependencies
- run: pip install nox pytest-github-actions-annotate-failures
+ - name: Install uv
+ uses: astral-sh/setup-uv@v6
- name: Test with nox using minimal dependencies
- run: nox -e "pytest-${{ matrix.python-version }}(all_deps=False)"
+ run: uv run --group nox nox -e "pytest_min_deps-${{ matrix.python-version }}"
- name: Test with nox with all dependencies
- run: nox -e "pytest-${{ matrix.python-version }}(all_deps=True)"
+ run: uv run --group nox nox -e "pytest_all_deps-${{ matrix.python-version }}"
diff --git a/.github/workflows/typeguard.yml b/.github/workflows/typeguard.yml
index a95ac4f2..3689442b 100644
--- a/.github/workflows/typeguard.yml
+++ b/.github/workflows/typeguard.yml
@@ -12,8 +12,8 @@ jobs:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
- python-version: "3.11"
- - name: Install dependencies
- run: pip install nox
+ python-version: "3.13"
+ - name: Install uv
+ uses: astral-sh/setup-uv@v6
- name: Test with nox
- run: nox -e pytest_typeguard
+ run: uv run --group nox nox -e pytest_typeguard
diff --git a/README.md b/README.md
index c7b2fcad..dcfd4ff8 100644
--- a/README.md
+++ b/README.md
@@ -160,12 +160,12 @@ jupyter labextension install @pyviz/jupyterlab_pyviz
## :wrench: Development
-Clone the repository and run `pip install -e ".[notebook,testing,other]"` to add a link to the cloned repo into your Python path:
+Clone the repository and run `pip install -e ".[notebook,test,other]"` to add a link to the cloned repo into your Python path:
```bash
git clone git@github.com:python-adaptive/adaptive.git
cd adaptive
-pip install -e ".[notebook,testing,other]"
+pip install -e ".[notebook,test,other]"
```
We recommend using a Conda environment or a virtualenv for package management during Adaptive development.
diff --git a/noxfile.py b/noxfile.py
index 55544435..6a6114bb 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -1,31 +1,45 @@
"""Nox configuration file."""
+import os
+
import nox
+nox.options.default_venv_backend = "uv"
+
+python = ["3.9", "3.10", "3.11", "3.12", "3.13"]
+num_cpus = os.cpu_count() or 1
+xdist = ("-n", "auto") if num_cpus > 2 else ()
+
+
+@nox.session(python=python)
+def pytest_min_deps(session: nox.Session) -> None:
+ """Run pytest with no optional dependencies."""
+ session.install(".[test]")
+ session.run("coverage", "erase")
+ session.run("pytest", *xdist)
+
-@nox.session(python=["3.9", "3.10", "3.11", "3.12"])
-@nox.parametrize("all_deps", [True, False])
-def pytest(session: nox.Session, all_deps: bool) -> None:
- """Run pytest with optional dependencies."""
- session.install(".[testing,other]" if all_deps else ".[testing]")
+@nox.session(python=python)
+def pytest_all_deps(session: nox.Session) -> None:
+ """Run pytest with "other" optional dependencies."""
+ session.install(".[test,other]")
session.run("coverage", "erase")
- session.run("pytest")
+ session.run("pytest", *xdist)
-@nox.session(python="3.11")
+@nox.session(python="3.13")
def pytest_typeguard(session: nox.Session) -> None:
"""Run pytest with typeguard."""
- session.install(".[testing,other]")
+ session.install(".[test,other]")
session.run("coverage", "erase")
- session.run("pytest", "--typeguard-packages=adaptive")
+ session.run("pytest", "--typeguard-packages=adaptive", *xdist)
-@nox.session(python="3.11")
+@nox.session(python="3.13")
def coverage(session: nox.Session) -> None:
"""Generate coverage report."""
- session.install("coverage")
- session.install(".[testing,other]")
- session.run("pytest")
+ session.install(".[test,other]")
+ session.run("pytest", *xdist)
session.run("coverage", "report")
session.run("coverage", "xml")
diff --git a/pyproject.toml b/pyproject.toml
index 8dbe2c89..5e59cad3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,15 +47,18 @@ notebook = [
"matplotlib",
"plotly",
]
-testing = [
+test = [
"flaky",
"pytest",
"pytest-cov",
"pytest-randomly",
"pytest-timeout",
+ "pytest-xdist",
"pre_commit",
"typeguard",
+ "coverage",
]
+dev = ["adaptive[test,nox,notebook,other]"]
[project.urls]
homepage = "https://adaptive.readthedocs.io/"
@@ -66,6 +69,12 @@ repository = "https://github.com/python-adaptive/adaptive"
content-type = "text/markdown"
file = "README.md"
+[dependency-groups]
+nox = [
+ "nox",
+ "pytest-github-actions-annotate-failures",
+]
+
[tool.setuptools.packages.find]
include = ["adaptive.*", "adaptive"]
From d25e7e7656c6cabcd6978ca0cb4de358e745bf60 Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 12:40:51 +0200
Subject: [PATCH 3/7] Follow SPEC 0 and drop support for Python 3.9 and 3.10
(#477)
---
.github/workflows/nox.yml | 2 +-
adaptive/learner/average_learner.py | 2 +-
adaptive/learner/average_learner1D.py | 3 +-
adaptive/learner/balancing_learner.py | 20 ++---
adaptive/learner/base_learner.py | 3 +-
adaptive/learner/data_saver.py | 3 +-
adaptive/learner/integrator_learner.py | 3 +-
adaptive/learner/learner1D.py | 44 ++++------
adaptive/learner/learner2D.py | 3 +-
adaptive/learner/sequence_learner.py | 10 +--
adaptive/runner.py | 89 +++++++--------------
adaptive/tests/algorithm_4.py | 2 +-
adaptive/tests/test_average_learner1d.py | 2 +-
adaptive/tests/test_notebook_integration.py | 8 +-
adaptive/types.py | 16 ++--
adaptive/utils.py | 4 +-
docs/environment.yml | 2 +-
docs/source/algorithms_and_examples.md | 2 +-
docs/source/tutorial/tutorial.LearnerND.md | 2 +-
environment.yml | 2 +-
noxfile.py | 2 +-
pyproject.toml | 11 ++-
22 files changed, 81 insertions(+), 154 deletions(-)
diff --git a/.github/workflows/nox.yml b/.github/workflows/nox.yml
index f021d3b2..a03b2d7b 100644
--- a/.github/workflows/nox.yml
+++ b/.github/workflows/nox.yml
@@ -12,7 +12,7 @@ jobs:
fail-fast: false
matrix:
platform: [ubuntu-latest, macos-latest, windows-latest]
- python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+ python-version: ["3.11", "3.12", "3.13"]
steps:
- uses: actions/checkout@v4
diff --git a/adaptive/learner/average_learner.py b/adaptive/learner/average_learner.py
index c3d4892b..3252530b 100644
--- a/adaptive/learner/average_learner.py
+++ b/adaptive/learner/average_learner.py
@@ -1,7 +1,7 @@
from __future__ import annotations
+from collections.abc import Callable
from math import sqrt
-from typing import Callable
import cloudpickle
import numpy as np
diff --git a/adaptive/learner/average_learner1D.py b/adaptive/learner/average_learner1D.py
index 9678b4f6..cb844f01 100644
--- a/adaptive/learner/average_learner1D.py
+++ b/adaptive/learner/average_learner1D.py
@@ -3,10 +3,9 @@
import math
import sys
from collections import defaultdict
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
from copy import deepcopy
from math import hypot
-from typing import Callable
import numpy as np
import scipy.stats
diff --git a/adaptive/learner/balancing_learner.py b/adaptive/learner/balancing_learner.py
index e9a4a661..b8a340f9 100644
--- a/adaptive/learner/balancing_learner.py
+++ b/adaptive/learner/balancing_learner.py
@@ -1,13 +1,12 @@
from __future__ import annotations
import itertools
-import sys
from collections import defaultdict
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
from contextlib import suppress
from functools import partial
from operator import itemgetter
-from typing import Any, Callable, Union, cast
+from typing import Any, Literal, TypeAlias, cast
import numpy as np
@@ -16,13 +15,6 @@
from adaptive.types import Int, Real
from adaptive.utils import cache_latest, named_product, restore
-if sys.version_info >= (3, 10):
- from typing import TypeAlias
-else:
- from typing_extensions import TypeAlias
-
-from typing import Literal
-
try:
import pandas
@@ -38,11 +30,9 @@ def dispatch(child_functions: list[Callable], arg: Any) -> Any:
STRATEGY_TYPE: TypeAlias = Literal["loss_improvements", "loss", "npoints", "cycle"]
-CDIMS_TYPE: TypeAlias = Union[
- Sequence[dict[str, Any]],
- tuple[Sequence[str], Sequence[tuple[Any, ...]]],
- None,
-]
+CDIMS_TYPE: TypeAlias = (
+ Sequence[dict[str, Any]] | tuple[Sequence[str], Sequence[tuple[Any, ...]]] | None
+)
class BalancingLearner(BaseLearner):
diff --git a/adaptive/learner/base_learner.py b/adaptive/learner/base_learner.py
index 73720dd5..f5ef73ec 100644
--- a/adaptive/learner/base_learner.py
+++ b/adaptive/learner/base_learner.py
@@ -1,8 +1,9 @@
from __future__ import annotations
import abc
+from collections.abc import Callable
from contextlib import suppress
-from typing import TYPE_CHECKING, Any, Callable, TypeVar
+from typing import TYPE_CHECKING, Any, TypeVar
import cloudpickle
diff --git a/adaptive/learner/data_saver.py b/adaptive/learner/data_saver.py
index a6980738..644691a5 100644
--- a/adaptive/learner/data_saver.py
+++ b/adaptive/learner/data_saver.py
@@ -2,7 +2,8 @@
import functools
from collections import OrderedDict
-from typing import Any, Callable
+from collections.abc import Callable
+from typing import Any
from adaptive.learner.base_learner import BaseLearner, LearnerType
from adaptive.utils import copy_docstring_from
diff --git a/adaptive/learner/integrator_learner.py b/adaptive/learner/integrator_learner.py
index 0fc97df6..d6ee9ef1 100644
--- a/adaptive/learner/integrator_learner.py
+++ b/adaptive/learner/integrator_learner.py
@@ -3,9 +3,10 @@
import sys
from collections import defaultdict
+from collections.abc import Callable
from math import sqrt
from operator import attrgetter
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
import cloudpickle
import numpy as np
diff --git a/adaptive/learner/learner1D.py b/adaptive/learner/learner1D.py
index bf04743b..6cd88b4a 100644
--- a/adaptive/learner/learner1D.py
+++ b/adaptive/learner/learner1D.py
@@ -3,10 +3,9 @@
import collections.abc
import itertools
import math
-import sys
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
from copy import copy, deepcopy
-from typing import TYPE_CHECKING, Any, Callable, Optional, Union
+from typing import TYPE_CHECKING, Any, TypeAlias
import cloudpickle
import numpy as np
@@ -24,12 +23,6 @@
partial_function_from_dataframe,
)
-if sys.version_info >= (3, 10):
- from typing import TypeAlias
-else:
- from typing_extensions import TypeAlias
-
-
try:
import pandas
@@ -42,28 +35,21 @@
# -- types --
# Commonly used types
- Interval: TypeAlias = Union[tuple[float, float], tuple[float, float, int]]
- NeighborsType: TypeAlias = SortedDict[float, list[Optional[float]]]
+ Interval: TypeAlias = tuple[float, float] | tuple[float, float, int]
+ NeighborsType: TypeAlias = SortedDict[float, list[float | None]]
# Types for loss_per_interval functions
XsType0: TypeAlias = tuple[float, float]
- YsType0: TypeAlias = Union[tuple[float, float], tuple[np.ndarray, np.ndarray]]
- XsType1: TypeAlias = tuple[
- Optional[float], Optional[float], Optional[float], Optional[float]
- ]
- YsType1: TypeAlias = Union[
- tuple[Optional[float], Optional[float], Optional[float], Optional[float]],
- tuple[
- Optional[np.ndarray],
- Optional[np.ndarray],
- Optional[np.ndarray],
- Optional[np.ndarray],
- ],
- ]
- XsTypeN: TypeAlias = tuple[Optional[float], ...]
- YsTypeN: TypeAlias = Union[
- tuple[Optional[float], ...], tuple[Optional[np.ndarray], ...]
- ]
+ YsType0: TypeAlias = tuple[float, float] | tuple[np.ndarray, np.ndarray]
+ XsType1: TypeAlias = tuple[float | None, float | None, float | None, float | None]
+ YsType1: TypeAlias = (
+ tuple[float | None, float | None, float | None, float | None]
+ | tuple[
+ np.ndarray | None, np.ndarray | None, np.ndarray | None, np.ndarray | None
+ ]
+ )
+ XsTypeN: TypeAlias = tuple[float | None, ...]
+ YsTypeN: TypeAlias = tuple[float | None, ...] | tuple[np.ndarray | None, ...]
__all__ = [
@@ -598,7 +584,7 @@ def tell(self, x: float, y: Float | Sequence[Float] | np.ndarray) -> None:
)
# either it is a float/int, if not, try casting to a np.array
- if not isinstance(y, (float, int)):
+ if not isinstance(y, float | int):
y = np.asarray(y, dtype=float)
# Add point to the real data dict
diff --git a/adaptive/learner/learner2D.py b/adaptive/learner/learner2D.py
index 15864a80..49b9cef5 100644
--- a/adaptive/learner/learner2D.py
+++ b/adaptive/learner/learner2D.py
@@ -3,10 +3,9 @@
import itertools
import warnings
from collections import OrderedDict
-from collections.abc import Iterable
+from collections.abc import Callable, Iterable
from copy import copy
from math import sqrt
-from typing import Callable
import cloudpickle
import numpy as np
diff --git a/adaptive/learner/sequence_learner.py b/adaptive/learner/sequence_learner.py
index c307744f..e8d83af5 100644
--- a/adaptive/learner/sequence_learner.py
+++ b/adaptive/learner/sequence_learner.py
@@ -1,8 +1,7 @@
from __future__ import annotations
-import sys
from copy import copy
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, TypeAlias
import cloudpickle
from sortedcontainers import SortedDict, SortedSet
@@ -16,8 +15,7 @@
)
if TYPE_CHECKING:
- from collections.abc import Sequence
- from typing import Callable
+ from collections.abc import Callable, Sequence
try:
import pandas
@@ -27,10 +25,6 @@
except ModuleNotFoundError:
with_pandas = False
-if sys.version_info >= (3, 10):
- from typing import TypeAlias
-else:
- from typing_extensions import TypeAlias
PointType: TypeAlias = tuple[Int, Any]
diff --git a/adaptive/runner.py b/adaptive/runner.py
index 4f877096..592fca4a 100644
--- a/adaptive/runner.py
+++ b/adaptive/runner.py
@@ -8,77 +8,48 @@
import itertools
import pickle
import platform
-import sys
import time
import traceback
import warnings
+from collections.abc import Callable
from contextlib import suppress
from datetime import datetime, timedelta
from importlib.util import find_spec
-from typing import TYPE_CHECKING, Any, Callable, Literal, Optional, Union
+from typing import TYPE_CHECKING, Any, Literal, TypeAlias
import loky
-from adaptive import (
- BalancingLearner,
- DataSaver,
- IntegratorLearner,
- SequenceLearner,
-)
+from adaptive import BalancingLearner, DataSaver, IntegratorLearner, SequenceLearner
from adaptive.learner.base_learner import LearnerType
from adaptive.notebook_integration import in_ipynb, live_info, live_plot
from adaptive.utils import SequentialExecutor
-ExecutorTypes: TypeAlias = Union[
- concurrent.ProcessPoolExecutor,
- concurrent.ThreadPoolExecutor,
- SequentialExecutor,
- loky.reusable_executor._ReusablePoolExecutor,
-]
-FutureTypes: TypeAlias = Union[concurrent.Future, asyncio.Future, asyncio.Task]
-
if TYPE_CHECKING:
import holoviews
-if sys.version_info >= (3, 10):
- from typing import TypeAlias
-else:
- from typing_extensions import TypeAlias
-
-
with_ipyparallel = find_spec("ipyparallel") is not None
with_distributed = find_spec("distributed") is not None
with_mpi4py = find_spec("mpi4py") is not None
if TYPE_CHECKING:
- ExecutorTypes = Optional[()]
- FutureTypes = Optional[()]
-
- if with_distributed:
- import distributed
-
- ExecutorTypes = Optional[
- Union[
- ExecutorTypes, distributed.Client, distributed.cfexecutor.ClientExecutor
- ]
- ]
-
- if with_mpi4py:
- import mpi4py.futures
-
- ExecutorTypes = Optional[Union[ExecutorTypes, mpi4py.futures.MPIPoolExecutor]]
-
- if with_ipyparallel:
- import ipyparallel
- from ipyparallel.client.asyncresult import AsyncResult
+ import distributed
+ import ipyparallel
+ import mpi4py.futures
+
+ ExecutorTypes: TypeAlias = (
+ concurrent.ProcessPoolExecutor
+ | concurrent.ThreadPoolExecutor
+ | SequentialExecutor
+ | loky.reusable_executor._ReusablePoolExecutor
+ | distributed.Client
+ | distributed.cfexecutor.ClientExecutor
+ | mpi4py.futures.MPIPoolExecutor
+ | ipyparallel.Client
+ | ipyparallel.client.view.ViewExecutor
+ )
+ FutureTypes: TypeAlias = concurrent.Future | asyncio.Future
- ExecutorTypes = Optional[
- Union[
- ExecutorTypes, ipyparallel.Client, ipyparallel.client.view.ViewExecutor
- ]
- ]
- FutureTypes = Optional[Union[FutureTypes, AsyncResult]]
with suppress(ModuleNotFoundError):
import uvloop
@@ -203,7 +174,7 @@ def __init__(
self._max_tasks = ntasks
- self._pending_tasks: dict[concurrent.Future, int] = {}
+ self._pending_tasks: dict[FutureTypes, int] = {}
# if we instantiate our own executor, then we are also responsible
# for calling 'shutdown'
@@ -292,7 +263,8 @@ def _process_futures(
pid = self._pending_tasks.pop(fut)
try:
y = fut.result()
- t = time.time() - fut.start_time # total execution time
+ # total execution time
+ t = time.time() - fut.start_time # type: ignore[union-attr]
except Exception as e:
self._tracebacks[pid] = traceback.format_exc()
self._to_retry[pid] = self._to_retry.get(pid, 0) + 1
@@ -508,12 +480,12 @@ def _run(self) -> None:
try:
while not self.goal(self.learner):
futures = self._get_futures()
- done, _ = concurrent.wait(futures, return_when=first_completed)
- self._process_futures(done)
+ done, _ = concurrent.wait(futures, return_when=first_completed) # type: ignore[arg-type]
+ self._process_futures(done) # type: ignore[arg-type]
finally:
remaining = self._remove_unfinished()
if remaining:
- concurrent.wait(remaining)
+ concurrent.wait(remaining) # type: ignore[arg-type]
# Some futures get their result set, despite being cancelled.
# see https://github.com/python-adaptive/adaptive/issues/319
with_result = {f for f in remaining if not f.cancelled() and f.done()}
@@ -835,13 +807,12 @@ async def _run(self) -> None:
try:
while not self.goal(self.learner):
futures = self._get_futures()
- kw = {"loop": self.ioloop} if sys.version_info[:2] < (3, 10) else {}
- done, _ = await asyncio.wait(futures, return_when=first_completed, **kw) # type: ignore[arg-type]
+ done, _ = await asyncio.wait(futures, return_when=first_completed) # type: ignore[arg-type,type-var]
self._process_futures(done)
finally:
remaining = self._remove_unfinished()
if remaining:
- await asyncio.wait(remaining)
+ await asyncio.wait(remaining) # type: ignore[type-var]
self._cleanup()
def elapsed_time(self) -> float:
@@ -1062,9 +1033,7 @@ def _get_ncores(
import mpi4py.futures
if with_ipyparallel and isinstance(ex, ipyparallel.client.view.ViewExecutor):
return len(ex.view)
- elif isinstance(
- ex, (concurrent.ProcessPoolExecutor, concurrent.ThreadPoolExecutor)
- ):
+ elif isinstance(ex, concurrent.ProcessPoolExecutor | concurrent.ThreadPoolExecutor):
return ex._max_workers # type: ignore[union-attr]
elif isinstance(ex, loky.reusable_executor._ReusablePoolExecutor):
return ex._max_workers # type: ignore[union-attr]
@@ -1119,7 +1088,7 @@ def stop_after(*, seconds=0, minutes=0, hours=0) -> Callable[[LearnerType], bool
class _TimeGoal:
def __init__(self, dt: timedelta | datetime | int | float):
- self.dt = dt if isinstance(dt, (timedelta, datetime)) else timedelta(seconds=dt)
+ self.dt = dt if isinstance(dt, timedelta | datetime) else timedelta(seconds=dt)
self.start_time = None
def __call__(self, _):
diff --git a/adaptive/tests/algorithm_4.py b/adaptive/tests/algorithm_4.py
index 27832298..8741fdc5 100644
--- a/adaptive/tests/algorithm_4.py
+++ b/adaptive/tests/algorithm_4.py
@@ -3,8 +3,8 @@
from __future__ import annotations
from collections import defaultdict
+from collections.abc import Callable
from fractions import Fraction
-from typing import Callable
import numpy as np
from numpy.testing import assert_allclose
diff --git a/adaptive/tests/test_average_learner1d.py b/adaptive/tests/test_average_learner1d.py
index c0148c5e..a9be7fce 100644
--- a/adaptive/tests/test_average_learner1d.py
+++ b/adaptive/tests/test_average_learner1d.py
@@ -21,7 +21,7 @@ def almost_equal_dicts(a, b):
if (
v1 is None
or v2 is None
- or isinstance(v1, (tuple, list))
+ or isinstance(v1, tuple | list)
and any(x is None for x in chain(v1, v2))
):
assert v1 == v2
diff --git a/adaptive/tests/test_notebook_integration.py b/adaptive/tests/test_notebook_integration.py
index 3e4ddb29..2fb266f2 100644
--- a/adaptive/tests/test_notebook_integration.py
+++ b/adaptive/tests/test_notebook_integration.py
@@ -1,7 +1,5 @@
from __future__ import annotations
-import os
-import sys
from typing import TYPE_CHECKING
import pytest
@@ -16,13 +14,9 @@
except ImportError:
with_notebook_dependencies = False
-# XXX: remove when is fixed https://github.com/ipython/ipykernel/issues/468
-skip_because_of_bug = os.name == "nt" and sys.version_info[:2] == (3, 8)
-
@pytest.mark.skipif(
- not with_notebook_dependencies or skip_because_of_bug,
- reason="notebook dependencies are not installed",
+ not with_notebook_dependencies, reason="notebook dependencies are not installed"
)
def test_private_api_used_in_live_info():
"""We are catching all errors in
diff --git a/adaptive/types.py b/adaptive/types.py
index 367445ee..e2869d46 100644
--- a/adaptive/types.py
+++ b/adaptive/types.py
@@ -1,17 +1,11 @@
-import sys
-from typing import Union
+from typing import TypeAlias
import numpy as np
-if sys.version_info >= (3, 10):
- from typing import TypeAlias
-else:
- from typing_extensions import TypeAlias
-
-Float: TypeAlias = Union[float, np.float64]
-Bool: TypeAlias = Union[bool, np.bool_]
-Int: TypeAlias = Union[int, np.int_]
-Real: TypeAlias = Union[Float, Int]
+Float: TypeAlias = float | np.float64
+Bool: TypeAlias = bool | np.bool_
+Int: TypeAlias = int | np.int_
+Real: TypeAlias = Float | Int
__all__ = ["Float", "Bool", "Int", "Real"]
diff --git a/adaptive/utils.py b/adaptive/utils.py
index ff80f62f..2a1680ca 100644
--- a/adaptive/utils.py
+++ b/adaptive/utils.py
@@ -7,11 +7,11 @@
import os
import pickle
import warnings
-from collections.abc import Awaitable, Iterator, Sequence
+from collections.abc import Awaitable, Callable, Iterator, Sequence
from contextlib import contextmanager
from functools import wraps
from itertools import product
-from typing import TYPE_CHECKING, Any, Callable, TypeVar
+from typing import TYPE_CHECKING, Any, TypeVar
import cloudpickle
diff --git a/docs/environment.yml b/docs/environment.yml
index 3e99ae62..caa8badc 100644
--- a/docs/environment.yml
+++ b/docs/environment.yml
@@ -4,7 +4,7 @@ channels:
- conda-forge
dependencies:
- - python=3.10
+ - python=3.11
- sortedcollections=2.1.0
- scipy=1.10.1
- holoviews=1.18.3
diff --git a/docs/source/algorithms_and_examples.md b/docs/source/algorithms_and_examples.md
index eda3c2ff..0aff9f1f 100644
--- a/docs/source/algorithms_and_examples.md
+++ b/docs/source/algorithms_and_examples.md
@@ -4,7 +4,7 @@ jupytext:
extension: .md
format_name: myst
format_version: 0.13
- jupytext_version: 1.14.5
+ jupytext_version: 1.17.1
kernelspec:
display_name: python3
name: python3
diff --git a/docs/source/tutorial/tutorial.LearnerND.md b/docs/source/tutorial/tutorial.LearnerND.md
index 46f94870..37705b79 100644
--- a/docs/source/tutorial/tutorial.LearnerND.md
+++ b/docs/source/tutorial/tutorial.LearnerND.md
@@ -4,7 +4,7 @@ jupytext:
extension: .md
format_name: myst
format_version: 0.13
- jupytext_version: 1.14.5
+ jupytext_version: 1.17.1
kernelspec:
display_name: python3
name: python3
diff --git a/environment.yml b/environment.yml
index a31560f1..1dfb8c86 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
- conda-forge
dependencies:
- - python=3.9
+ - python=3.13
- sortedcontainers
- sortedcollections
- scipy
diff --git a/noxfile.py b/noxfile.py
index 6a6114bb..71a2217a 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -6,7 +6,7 @@
nox.options.default_venv_backend = "uv"
-python = ["3.9", "3.10", "3.11", "3.12", "3.13"]
+python = ["3.11", "3.12", "3.13"]
num_cpus = os.cpu_count() or 1
xdist = ("-n", "auto") if num_cpus > 2 else ()
diff --git a/pyproject.toml b/pyproject.toml
index 5e59cad3..5c7186e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,15 +8,14 @@ dynamic = ["version"]
description = "Parallel active learning of mathematical functions"
maintainers = [{ name = "Adaptive authors" }]
license = { text = "BSD" }
-requires-python = ">=3.9"
+requires-python = ">=3.11"
classifiers = [
"Development Status :: 4 - Beta",
"License :: OSI Approved :: BSD License",
"Intended Audience :: Science/Research",
- "Programming Language :: Python :: 3.9",
- "Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
+ "Programming Language :: Python :: 3.13",
]
dependencies = [
"scipy",
@@ -24,7 +23,6 @@ dependencies = [
"sortedcontainers >= 2.0",
"cloudpickle",
"loky >= 2.9",
- "typing_extensions; python_version < '3.10'",
"versioningit",
]
@@ -100,11 +98,11 @@ output = ".coverage.xml"
[tool.mypy]
ignore_missing_imports = true
-python_version = "3.9"
+python_version = "3.11"
[tool.ruff]
line-length = 88
-target-version = "py39"
+target-version = "py311"
[tool.ruff.lint]
select = ["B", "C", "E", "F", "W", "T", "B9", "I", "UP"]
@@ -118,6 +116,7 @@ ignore = [
"PLW0603", # Using the global statement to update `X` is discouraged
"D401", # First line of docstring should be in imperative mood
"E501", # Line too long
+ "B905", # `zip()` without an explicit `strict=` parameter
]
[tool.ruff.lint.mccabe]
From 240fb89f3e6713d2224db281b17ef2704484cd47 Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 13:21:21 +0200
Subject: [PATCH 4/7] Enable runtime type checking in tests with typeguard
(#478)
Re-enables the `typeguard` job that I disabled 2 years ago in https://github.com/python-adaptive/adaptive/pull/415.
---
.github/workflows/typeguard.yml | 7 +--
adaptive/_types.py | 24 +++++++++++
adaptive/learner/balancing_learner.py | 8 ++--
adaptive/learner/learner1D.py | 48 ++++++++++-----------
adaptive/learner/sequence_learner.py | 4 +-
adaptive/runner.py | 24 +++--------
adaptive/tests/test_average_learner.py | 4 --
adaptive/tests/test_average_learner1d.py | 4 --
adaptive/tests/test_balancing_learner.py | 2 +-
adaptive/tests/test_learner1d.py | 4 --
adaptive/tests/test_notebook_integration.py | 4 --
11 files changed, 62 insertions(+), 71 deletions(-)
create mode 100644 adaptive/_types.py
diff --git a/.github/workflows/typeguard.yml b/.github/workflows/typeguard.yml
index 3689442b..c89a4442 100644
--- a/.github/workflows/typeguard.yml
+++ b/.github/workflows/typeguard.yml
@@ -1,8 +1,9 @@
name: typeguard
-# TODO: enable this once typeguard=4 is released and issues are fixed.
-# on:
-# - push
+on:
+ pull_request:
+ push:
+ branches: [main]
jobs:
typeguard:
diff --git a/adaptive/_types.py b/adaptive/_types.py
new file mode 100644
index 00000000..3f56bf59
--- /dev/null
+++ b/adaptive/_types.py
@@ -0,0 +1,24 @@
+# Only used for static type checkers, should only be imported in `if TYPE_CHECKING` block
+# Workaround described in https://github.com/agronholm/typeguard/issues/456
+
+import concurrent.futures as concurrent
+from typing import TypeAlias
+
+import distributed
+import ipyparallel
+import loky
+import mpi4py.futures
+
+from adaptive.utils import SequentialExecutor
+
+ExecutorTypes: TypeAlias = (
+ concurrent.ProcessPoolExecutor
+ | concurrent.ThreadPoolExecutor
+ | SequentialExecutor
+ | loky.reusable_executor._ReusablePoolExecutor
+ | distributed.Client
+ | distributed.cfexecutor.ClientExecutor
+ | mpi4py.futures.MPIPoolExecutor
+ | ipyparallel.Client
+ | ipyparallel.client.view.ViewExecutor
+)
diff --git a/adaptive/learner/balancing_learner.py b/adaptive/learner/balancing_learner.py
index b8a340f9..1b59d2b3 100644
--- a/adaptive/learner/balancing_learner.py
+++ b/adaptive/learner/balancing_learner.py
@@ -269,17 +269,17 @@ def ask(
return self._ask_and_tell(n)
def tell(self, x: tuple[Int, Any], y: Any) -> None:
- index, x = x
+ index, x_ = x
self._ask_cache.pop(index, None)
self._loss.pop(index, None)
self._pending_loss.pop(index, None)
- self.learners[index].tell(x, y)
+ self.learners[index].tell(x_, y)
def tell_pending(self, x: tuple[Int, Any]) -> None:
- index, x = x
+ index, x_ = x
self._ask_cache.pop(index, None)
self._loss.pop(index, None)
- self.learners[index].tell_pending(x)
+ self.learners[index].tell_pending(x_)
def _losses(self, real: bool = True) -> list[float]:
losses = []
diff --git a/adaptive/learner/learner1D.py b/adaptive/learner/learner1D.py
index 6cd88b4a..d805f396 100644
--- a/adaptive/learner/learner1D.py
+++ b/adaptive/learner/learner1D.py
@@ -5,7 +5,7 @@
import math
from collections.abc import Callable, Sequence
from copy import copy, deepcopy
-from typing import TYPE_CHECKING, Any, TypeAlias
+from typing import Any, TypeAlias
import cloudpickle
import numpy as np
@@ -31,25 +31,21 @@
except ModuleNotFoundError:
with_pandas = False
-if TYPE_CHECKING:
- # -- types --
- # Commonly used types
- Interval: TypeAlias = tuple[float, float] | tuple[float, float, int]
- NeighborsType: TypeAlias = SortedDict[float, list[float | None]]
+# Commonly used types
+Interval: TypeAlias = tuple[float, float] | tuple[float, float, int]
+NeighborsType: TypeAlias = SortedDict[float, list[float | None]]
- # Types for loss_per_interval functions
- XsType0: TypeAlias = tuple[float, float]
- YsType0: TypeAlias = tuple[float, float] | tuple[np.ndarray, np.ndarray]
- XsType1: TypeAlias = tuple[float | None, float | None, float | None, float | None]
- YsType1: TypeAlias = (
- tuple[float | None, float | None, float | None, float | None]
- | tuple[
- np.ndarray | None, np.ndarray | None, np.ndarray | None, np.ndarray | None
- ]
- )
- XsTypeN: TypeAlias = tuple[float | None, ...]
- YsTypeN: TypeAlias = tuple[float | None, ...] | tuple[np.ndarray | None, ...]
+# Types for loss_per_interval functions
+XsType0: TypeAlias = tuple[float, float]
+YsType0: TypeAlias = tuple[float, float] | tuple[np.ndarray, np.ndarray]
+XsType1: TypeAlias = tuple[float | None, float | None, float | None, float | None]
+YsType1: TypeAlias = (
+ tuple[float | None, float | None, float | None, float | None]
+ | tuple[np.ndarray | None, np.ndarray | None, np.ndarray | None, np.ndarray | None]
+)
+XsTypeN: TypeAlias = tuple[float | None, ...]
+YsTypeN: TypeAlias = tuple[float | None, ...] | tuple[np.ndarray | None, ...]
__all__ = [
@@ -110,18 +106,18 @@ def abs_min_log_loss(xs: XsType0, ys: YsType0) -> Float:
@uses_nth_neighbors(1)
def triangle_loss(xs: XsType1, ys: YsType1) -> Float:
assert len(xs) == 4
- xs = [x for x in xs if x is not None] # type: ignore[assignment]
- ys = [y for y in ys if y is not None] # type: ignore[assignment]
+ x = [x for x in xs if x is not None]
+ y = [y for y in ys if y is not None]
- if len(xs) == 2: # we do not have enough points for a triangle
- return xs[1] - xs[0] # type: ignore[operator]
+ if len(x) == 2: # we do not have enough points for a triangle
+ return x[1] - x[0] # type: ignore[operator]
- N = len(xs) - 2 # number of constructed triangles
- if isinstance(ys[0], collections.abc.Iterable):
- pts = [(x, *y) for x, y in zip(xs, ys)] # type: ignore[misc]
+ N = len(x) - 2 # number of constructed triangles
+ if isinstance(y[0], collections.abc.Iterable):
+ pts = [(x, *y) for x, y in zip(x, y)] # type: ignore[misc]
vol = simplex_volume_in_embedding
else:
- pts = list(zip(xs, ys))
+ pts = list(zip(x, y))
vol = volume
return sum(vol(pts[i : i + 3]) for i in range(N)) / N
diff --git a/adaptive/learner/sequence_learner.py b/adaptive/learner/sequence_learner.py
index e8d83af5..2209ff87 100644
--- a/adaptive/learner/sequence_learner.py
+++ b/adaptive/learner/sequence_learner.py
@@ -134,13 +134,13 @@ def remove_unfinished(self) -> None:
self.pending_points = set()
def tell(self, point: PointType, value: Any) -> None:
- index, point = point
+ index, _ = point
self.data[index] = value
self.pending_points.discard(index)
self._to_do_indices.discard(index)
def tell_pending(self, point: PointType) -> None:
- index, point = point
+ index, _ = point
self.pending_points.add(index)
self._to_do_indices.discard(index)
diff --git a/adaptive/runner.py b/adaptive/runner.py
index 592fca4a..53ed79a1 100644
--- a/adaptive/runner.py
+++ b/adaptive/runner.py
@@ -24,32 +24,18 @@
from adaptive.notebook_integration import in_ipynb, live_info, live_plot
from adaptive.utils import SequentialExecutor
+FutureTypes: TypeAlias = concurrent.Future | asyncio.Future
+
if TYPE_CHECKING:
import holoviews
+ from ._types import ExecutorTypes
+
with_ipyparallel = find_spec("ipyparallel") is not None
with_distributed = find_spec("distributed") is not None
with_mpi4py = find_spec("mpi4py") is not None
-if TYPE_CHECKING:
- import distributed
- import ipyparallel
- import mpi4py.futures
-
- ExecutorTypes: TypeAlias = (
- concurrent.ProcessPoolExecutor
- | concurrent.ThreadPoolExecutor
- | SequentialExecutor
- | loky.reusable_executor._ReusablePoolExecutor
- | distributed.Client
- | distributed.cfexecutor.ClientExecutor
- | mpi4py.futures.MPIPoolExecutor
- | ipyparallel.Client
- | ipyparallel.client.view.ViewExecutor
- )
- FutureTypes: TypeAlias = concurrent.Future | asyncio.Future
-
with suppress(ModuleNotFoundError):
import uvloop
@@ -906,7 +892,7 @@ def _info_text(runner, separator: str = "\n"):
info.append(("# of samples", runner.learner.nsamples))
with suppress(Exception):
- info.append(("latest loss", f'{runner.learner._cache["loss"]:.3f}'))
+ info.append(("latest loss", f"{runner.learner._cache['loss']:.3f}"))
width = 30
formatted_info = [f"{k}: {v}".ljust(width) for i, (k, v) in enumerate(info)]
diff --git a/adaptive/tests/test_average_learner.py b/adaptive/tests/test_average_learner.py
index d9493339..d0176858 100644
--- a/adaptive/tests/test_average_learner.py
+++ b/adaptive/tests/test_average_learner.py
@@ -1,5 +1,4 @@
import random
-from typing import TYPE_CHECKING
import flaky
import numpy as np
@@ -7,9 +6,6 @@
from adaptive.learner import AverageLearner
from adaptive.runner import simple
-if TYPE_CHECKING:
- pass
-
def f_unused(seed):
raise NotImplementedError("This function shouldn't be used.")
diff --git a/adaptive/tests/test_average_learner1d.py b/adaptive/tests/test_average_learner1d.py
index a9be7fce..619358e8 100644
--- a/adaptive/tests/test_average_learner1d.py
+++ b/adaptive/tests/test_average_learner1d.py
@@ -1,5 +1,4 @@
from itertools import chain
-from typing import TYPE_CHECKING
import numpy as np
@@ -10,9 +9,6 @@
simple_run,
)
-if TYPE_CHECKING:
- pass
-
def almost_equal_dicts(a, b):
assert a.keys() == b.keys()
diff --git a/adaptive/tests/test_balancing_learner.py b/adaptive/tests/test_balancing_learner.py
index 905a55e0..c50b2105 100644
--- a/adaptive/tests/test_balancing_learner.py
+++ b/adaptive/tests/test_balancing_learner.py
@@ -35,7 +35,7 @@ def test_distribute_first_points_over_learners(strategy):
learner = BalancingLearner(learners, strategy=strategy)
points = learner.ask(initial_points)[0]
- learner.tell_many(points, points)
+ learner.tell_many(points, [x for i, x in points])
points, _ = learner.ask(100)
i_learner, xs = zip(*points)
diff --git a/adaptive/tests/test_learner1d.py b/adaptive/tests/test_learner1d.py
index 1f28d7a1..e83629f3 100644
--- a/adaptive/tests/test_learner1d.py
+++ b/adaptive/tests/test_learner1d.py
@@ -2,7 +2,6 @@
import random
import time
-from typing import TYPE_CHECKING
import flaky
import numpy as np
@@ -11,9 +10,6 @@
from adaptive.learner.learner1D import curvature_loss_function
from adaptive.runner import BlockingRunner, simple
-if TYPE_CHECKING:
- pass
-
def flat_middle(x):
x *= 1e7
diff --git a/adaptive/tests/test_notebook_integration.py b/adaptive/tests/test_notebook_integration.py
index 2fb266f2..45ee1c8c 100644
--- a/adaptive/tests/test_notebook_integration.py
+++ b/adaptive/tests/test_notebook_integration.py
@@ -1,11 +1,7 @@
from __future__ import annotations
-from typing import TYPE_CHECKING
-
import pytest
-if TYPE_CHECKING:
- pass
try:
import ipykernel.iostream
import zmq
From 462c531b2ff1299993e0e3c4344160f4a470c4c0 Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 13:41:52 +0200
Subject: [PATCH 5/7] Bump `mypy` and `ruff` in `pre-commit` (#479)
---
.pre-commit-config.yaml | 8 ++++----
adaptive/learner/average_learner1D.py | 6 ++----
adaptive/learner/balancing_learner.py | 4 +---
adaptive/learner/data_saver.py | 2 +-
adaptive/learner/learner1D.py | 3 ++-
adaptive/learner/learner2D.py | 2 +-
adaptive/learner/learnerND.py | 3 +--
adaptive/learner/triangulation.py | 3 +--
adaptive/notebook_integration.py | 11 ++++-------
adaptive/runner.py | 2 +-
example-notebook.ipynb | 14 ++++++--------
11 files changed, 24 insertions(+), 34 deletions(-)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5a0a4184..2715666e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.6.0
+ rev: v5.0.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
@@ -9,13 +9,13 @@ repos:
- id: debug-statements
- id: check-ast
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: "v0.3.5"
+ rev: "v0.11.9"
hooks:
- id: ruff
args: ["--fix"]
- id: ruff-format
- repo: https://github.com/nbQA-dev/nbQA
- rev: 1.8.5
+ rev: 1.9.1
hooks:
- id: nbqa-black
additional_dependencies: [jupytext, black]
@@ -23,7 +23,7 @@ repos:
args: ["ruff", "--fix", "--ignore=E402,B018,F704"]
additional_dependencies: [jupytext, ruff]
- repo: https://github.com/pre-commit/mirrors-mypy
- rev: "v1.9.0"
+ rev: "v1.15.0"
hooks:
- id: mypy
exclude: ipynb_filter.py|docs/source/conf.py
diff --git a/adaptive/learner/average_learner1D.py b/adaptive/learner/average_learner1D.py
index cb844f01..82c76f5d 100644
--- a/adaptive/learner/average_learner1D.py
+++ b/adaptive/learner/average_learner1D.py
@@ -499,8 +499,7 @@ def tell_many( # type: ignore[override]
# but ignore it going forward.
if not np.prod([x >= self.bounds[0] and x <= self.bounds[1] for _, x in xs]):
raise ValueError(
- "x value out of bounds, "
- "remove x or enlarge the bounds of the learner"
+ "x value out of bounds, remove x or enlarge the bounds of the learner"
)
# Create a mapping of points to a list of samples
@@ -533,8 +532,7 @@ def tell_many_at_point(self, x: Real, seed_y_mapping: dict[int, Real]) -> None:
# Check x is within the bounds
if not np.prod(x >= self.bounds[0] and x <= self.bounds[1]):
raise ValueError(
- "x value out of bounds, "
- "remove x or enlarge the bounds of the learner"
+ "x value out of bounds, remove x or enlarge the bounds of the learner"
)
# If x is a new point:
diff --git a/adaptive/learner/balancing_learner.py b/adaptive/learner/balancing_learner.py
index 1b59d2b3..43f7dc1f 100644
--- a/adaptive/learner/balancing_learner.py
+++ b/adaptive/learner/balancing_learner.py
@@ -106,9 +106,7 @@ def __init__(
self._cdims_default = cdims
if len({learner.__class__ for learner in self.learners}) > 1:
- raise TypeError(
- "A BalacingLearner can handle only one type" " of learners."
- )
+ raise TypeError("A BalacingLearner can handle only one type of learners.")
self.strategy: STRATEGY_TYPE = strategy
diff --git a/adaptive/learner/data_saver.py b/adaptive/learner/data_saver.py
index 644691a5..2deafe2c 100644
--- a/adaptive/learner/data_saver.py
+++ b/adaptive/learner/data_saver.py
@@ -162,7 +162,7 @@ def _set_data(
self.learner._set_data(learner_data)
def __getstate__(self) -> tuple[LearnerType, Callable, OrderedDict]:
- return (
+ return ( # type: ignore[return-value]
self.learner,
self.arg_picker,
self.extra_data,
diff --git a/adaptive/learner/learner1D.py b/adaptive/learner/learner1D.py
index d805f396..68583422 100644
--- a/adaptive/learner/learner1D.py
+++ b/adaptive/learner/learner1D.py
@@ -761,8 +761,9 @@ def _ask_points_without_adding(self, n: int) -> tuple[list[float], list[float]]:
ival is not None
and self._loss(self.losses_combined, ival) >= self._loss(quals, qual)
):
+ assert ival is not None
i += 1
- quals[(*ival, 2)] = loss_ival / 2
+ quals[(ival[0], ival[1], 2)] = loss_ival / 2
else:
quals.pop(qual, None)
*xs, n = qual
diff --git a/adaptive/learner/learner2D.py b/adaptive/learner/learner2D.py
index 49b9cef5..a4b2a812 100644
--- a/adaptive/learner/learner2D.py
+++ b/adaptive/learner/learner2D.py
@@ -448,7 +448,7 @@ def __init__(
self.aspect_ratio = 1
self._bounds_points = list(itertools.product(*bounds))
- self._stack.update({p: np.inf for p in self._bounds_points})
+ self._stack.update(dict.fromkeys(self._bounds_points, np.inf))
self.function = function # type: ignore
self._ip = self._ip_combined = None
diff --git a/adaptive/learner/learnerND.py b/adaptive/learner/learnerND.py
index c4af7ddc..d0300143 100644
--- a/adaptive/learner/learnerND.py
+++ b/adaptive/learner/learnerND.py
@@ -1098,8 +1098,7 @@ def _get_iso(self, level=0.0, which="surface"):
if which == "surface":
if self.ndim != 3 or self.vdim != 1:
raise Exception(
- "Isosurface plotting is only supported"
- " for a 3D input and 1D output"
+ "Isosurface plotting is only supported for a 3D input and 1D output"
)
get_surface = True
get_line = False
diff --git a/adaptive/learner/triangulation.py b/adaptive/learner/triangulation.py
index 03455e3b..26a5ebc2 100644
--- a/adaptive/learner/triangulation.py
+++ b/adaptive/learner/triangulation.py
@@ -336,8 +336,7 @@ def __init__(self, coords):
vectors = subtract(coords[1:], coords[0])
if matrix_rank(vectors) < dim:
raise ValueError(
- "Initial simplex has zero volumes "
- "(the points are linearly dependent)"
+ "Initial simplex has zero volumes (the points are linearly dependent)"
)
self.vertices = list(coords)
diff --git a/adaptive/notebook_integration.py b/adaptive/notebook_integration.py
index 782bc855..5eb5c6d2 100644
--- a/adaptive/notebook_integration.py
+++ b/adaptive/notebook_integration.py
@@ -16,8 +16,7 @@ def notebook_extension(*, _inline_js=True):
"""Enable ipywidgets, holoviews, and asyncio notebook integration."""
if not in_ipynb():
raise RuntimeError(
- '"adaptive.notebook_extension()" may only be run '
- "from a Jupyter notebook."
+ '"adaptive.notebook_extension()" may only be run from a Jupyter notebook.'
)
global _holoviews_enabled, _ipywidgets_enabled
@@ -116,8 +115,7 @@ def live_plot(runner, *, plotter=None, update_interval=2, name=None, normalize=T
"""
if not _holoviews_enabled:
raise RuntimeError(
- "Live plotting is not enabled; did you run "
- "'adaptive.notebook_extension()'?"
+ "Live plotting is not enabled; did you run 'adaptive.notebook_extension()'?"
)
import holoviews as hv
@@ -202,8 +200,7 @@ def live_info(runner, *, update_interval=0.5):
"""
if not _holoviews_enabled:
raise RuntimeError(
- "Live plotting is not enabled; did you run "
- "'adaptive.notebook_extension()'?"
+ "Live plotting is not enabled; did you run 'adaptive.notebook_extension()'?"
)
import ipywidgets
@@ -268,7 +265,7 @@ def _info_html(runner):
info.append(("# of samples", runner.learner.nsamples))
with suppress(Exception):
- info.append(("latest loss", f'{runner.learner._cache["loss"]:.3f}'))
+ info.append(("latest loss", f"{runner.learner._cache['loss']:.3f}"))
table = "\n".join(_table_row(i, k, v) for i, (k, v) in enumerate(info))
diff --git a/adaptive/runner.py b/adaptive/runner.py
index 53ed79a1..b9812505 100644
--- a/adaptive/runner.py
+++ b/adaptive/runner.py
@@ -1157,7 +1157,7 @@ def auto_goal(
if isinstance(learner, DataSaver):
assert learner is not None
return auto_goal(
- learner=learner.learner,
+ learner=learner.learner, # type: ignore[arg-type]
loss=loss,
npoints=npoints,
end_time=end_time,
diff --git a/example-notebook.ipynb b/example-notebook.ipynb
index 4f49415f..429239c6 100644
--- a/example-notebook.ipynb
+++ b/example-notebook.ipynb
@@ -23,16 +23,15 @@
"metadata": {},
"outputs": [],
"source": [
- "import adaptive\n",
- "\n",
- "adaptive.notebook_extension()\n",
- "\n",
"import random\n",
"from functools import partial\n",
"\n",
- "# Import modules that are used in multiple cells\n",
"import holoviews as hv\n",
- "import numpy as np"
+ "import numpy as np\n",
+ "\n",
+ "import adaptive\n",
+ "\n",
+ "adaptive.notebook_extension()"
]
},
{
@@ -489,8 +488,7 @@
" print(\"WARINING: The runner hasn't reached it goal yet!\")\n",
"\n",
"print(\n",
- " f\"The integral value is {learner.igral} \"\n",
- " f\"with a corresponding error of {learner.err}\"\n",
+ " f\"The integral value is {learner.igral} with a corresponding error of {learner.err}\"\n",
")\n",
"learner.plot()"
]
From 1eae4ae7eb0f411a989d35644bcc4dad112a050f Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 13:49:58 +0200
Subject: [PATCH 6/7] Update changelog to v1.4.0 (#480)
---
CHANGELOG.md | 59 +++++++++++++++++++++++++++++++++++++++++-----------
1 file changed, 47 insertions(+), 12 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e497b099..339c9db0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,46 @@
# 🗞️ Changelog
-## [v1.3.0](https://github.com/python-adaptive/adaptive/tree/v1.3.0) (2024-04-10)
+## [v1.4.0](https://github.com/python-adaptive/adaptive/tree/v1.3.0) (2025-05-13)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v1.3.2...v.1.4.0)
+
+**Merged pull requests:**
+
+- Bump `mypy` and `ruff` in `pre-commit` [\#479](https://github.com/python-adaptive/adaptive/pull/479) ([basnijholt](https://github.com/basnijholt))
+- Enable runtime type checking in tests with typeguard [\#478](https://github.com/python-adaptive/adaptive/pull/478) ([basnijholt](https://github.com/basnijholt))
+- Follow SPEC 0 and drop support for Python 3.9 and 3.10 [\#477](https://github.com/python-adaptive/adaptive/pull/477) ([basnijholt](https://github.com/basnijholt))
+- Use `uv` as Nox backend and several related improvements [\#476](https://github.com/python-adaptive/adaptive/pull/476) ([basnijholt](https://github.com/basnijholt))
+- Prevent SciPy deprecation warning for `estimate_gradients_2d_global` [\#475](https://github.com/python-adaptive/adaptive/pull/475) ([basnijholt](https://github.com/basnijholt))
+
+## [v1.3.2](https://github.com/python-adaptive/adaptive/tree/v1.3.2) (2025-03-03)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v1.3.1...v1.3.2)
+
+**Closed issues:**
+
+- Runner slows down visual studio code on linux [\#471](https://github.com/python-adaptive/adaptive/issues/471)
+
+**Merged pull requests:**
+
+- Fix readthedocs.yml [\#474](https://github.com/python-adaptive/adaptive/pull/474) ([basnijholt](https://github.com/basnijholt))
+- Remove async activation magic in notebook\_integration.py [\#473](https://github.com/python-adaptive/adaptive/pull/473) ([basnijholt](https://github.com/basnijholt))
+
+## [v1.3.1](https://github.com/python-adaptive/adaptive/tree/v1.3.1) (2025-01-07)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v1.3.0...v1.3.1)
+
+**Merged pull requests:**
+
+- Fix scipy deprecation warning for LinearNDInterpolator [\#465](https://github.com/python-adaptive/adaptive/pull/465) ([eendebakpt](https://github.com/eendebakpt))
+- Remove Azure Pipelines badge in README.md [\#462](https://github.com/python-adaptive/adaptive/pull/462) ([basnijholt](https://github.com/basnijholt))
+
+## [v1.3.0](https://github.com/python-adaptive/adaptive/tree/v1.3.0) (2024-05-31)
[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v1.2.0...v1.3.0)
**Merged pull requests:**
+- Release v1.3.0 [\#459](https://github.com/python-adaptive/adaptive/pull/459) ([basnijholt](https://github.com/basnijholt))
- Replace deprecated numpy aliases [\#458](https://github.com/python-adaptive/adaptive/pull/458) ([eendebakpt](https://github.com/eendebakpt))
- Remove `SKOptLearner` because `scikit-optimize` is unmaintained [\#404](https://github.com/python-adaptive/adaptive/pull/404) ([basnijholt](https://github.com/basnijholt))
@@ -27,8 +62,8 @@
- \[pre-commit.ci\] pre-commit autoupdate [\#447](https://github.com/python-adaptive/adaptive/pull/447) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
- Use ruff-format instead of black [\#446](https://github.com/python-adaptive/adaptive/pull/446) ([basnijholt](https://github.com/basnijholt))
- Bump versions to compatible packages in `docs/environment.yml` [\#445](https://github.com/python-adaptive/adaptive/pull/445) ([basnijholt](https://github.com/basnijholt))
-- Add `AsyncRunner.block\_until\_done` [\#444](https://github.com/python-adaptive/adaptive/pull/444) ([basnijholt](https://github.com/basnijholt))
-- Add `live\_info\_terminal`, closes \#436 [\#441](https://github.com/python-adaptive/adaptive/pull/441) ([basnijholt](https://github.com/basnijholt))
+- Add `AsyncRunner.block_until_done` [\#444](https://github.com/python-adaptive/adaptive/pull/444) ([basnijholt](https://github.com/basnijholt))
+- Add `live_info_terminal`, closes \#436 [\#441](https://github.com/python-adaptive/adaptive/pull/441) ([basnijholt](https://github.com/basnijholt))
- \[pre-commit.ci\] pre-commit autoupdate [\#434](https://github.com/python-adaptive/adaptive/pull/434) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
- Add benchmarks page for Learner1D and Learner2D functions [\#405](https://github.com/python-adaptive/adaptive/pull/405) ([basnijholt](https://github.com/basnijholt))
@@ -51,7 +86,7 @@
## [v1.0.0](https://github.com/python-adaptive/adaptive/tree/v1.0.0) (2023-05-15)
-[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.15.1...v1.0.0)
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.15.0...v1.0.0)
**Closed issues:**
@@ -90,13 +125,13 @@
- Add nbQA for notebook and docs linting [\#361](https://github.com/python-adaptive/adaptive/pull/361) ([basnijholt](https://github.com/basnijholt))
- Fix HoloViews opts deprecation warnings [\#357](https://github.com/python-adaptive/adaptive/pull/357) ([basnijholt](https://github.com/basnijholt))
-## [v0.15.1](https://github.com/python-adaptive/adaptive/tree/v0.15.1) (2022-12-02)
+## [v0.15.0](https://github.com/python-adaptive/adaptive/tree/v0.15.0) (2022-12-02)
-[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.15.0...v0.15.1)
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.15.1...v0.15.0)
-## [v0.15.0](https://github.com/python-adaptive/adaptive/tree/v0.15.0) (2022-12-02)
+## [v0.15.1](https://github.com/python-adaptive/adaptive/tree/v0.15.1) (2022-12-02)
-[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.14.2...v0.15.0)
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.14.2...v0.15.1)
**Closed issues:**
@@ -290,7 +325,7 @@
- bump pre-commit filter dependencies [\#293](https://github.com/python-adaptive/adaptive/pull/293) ([basnijholt](https://github.com/basnijholt))
- fix docs [\#291](https://github.com/python-adaptive/adaptive/pull/291) ([basnijholt](https://github.com/basnijholt))
- update to miniver 0.7.0 [\#290](https://github.com/python-adaptive/adaptive/pull/290) ([basnijholt](https://github.com/basnijholt))
-- add `runner.live\_plot\(\)` in README example [\#288](https://github.com/python-adaptive/adaptive/pull/288) ([basnijholt](https://github.com/basnijholt))
+- add `runner.live_plot()` in README example [\#288](https://github.com/python-adaptive/adaptive/pull/288) ([basnijholt](https://github.com/basnijholt))
- Update pre commit [\#287](https://github.com/python-adaptive/adaptive/pull/287) ([basnijholt](https://github.com/basnijholt))
- Use m2r2 [\#286](https://github.com/python-adaptive/adaptive/pull/286) ([basnijholt](https://github.com/basnijholt))
- temporarily pin scikit-learn\<=0.23.1 [\#285](https://github.com/python-adaptive/adaptive/pull/285) ([basnijholt](https://github.com/basnijholt))
@@ -382,6 +417,7 @@
- add \_RequireAttrsABCMeta and make the BaseLearner use it [\#222](https://github.com/python-adaptive/adaptive/pull/222) ([basnijholt](https://github.com/basnijholt))
- 2D: add triangle\_loss [\#221](https://github.com/python-adaptive/adaptive/pull/221) ([basnijholt](https://github.com/basnijholt))
- 2D: add interpolated\_on\_grid method [\#216](https://github.com/python-adaptive/adaptive/pull/216) ([basnijholt](https://github.com/basnijholt))
+- add scatter\_or\_line argument to Learner1D.plot [\#215](https://github.com/python-adaptive/adaptive/pull/215) ([basnijholt](https://github.com/basnijholt))
- WIP: raise an error when using a lambda and default executor [\#210](https://github.com/python-adaptive/adaptive/pull/210) ([basnijholt](https://github.com/basnijholt))
## [v0.10.0-dev](https://github.com/python-adaptive/adaptive/tree/v0.10.0-dev) (2019-10-07)
@@ -408,7 +444,6 @@
**Merged pull requests:**
- pass value\_scale to the LearnerND's loss\_per\_simplex function [\#219](https://github.com/python-adaptive/adaptive/pull/219) ([basnijholt](https://github.com/basnijholt))
-- add scatter\_or\_line argument to Learner1D.plot [\#215](https://github.com/python-adaptive/adaptive/pull/215) ([basnijholt](https://github.com/basnijholt))
- remove MPI4PY\_MAX\_WORKERS where it's not used [\#209](https://github.com/python-adaptive/adaptive/pull/209) ([basnijholt](https://github.com/basnijholt))
- use jupyter\_sphinx v0.2.0 from conda instead of my branch [\#204](https://github.com/python-adaptive/adaptive/pull/204) ([basnijholt](https://github.com/basnijholt))
- Authors [\#202](https://github.com/python-adaptive/adaptive/pull/202) ([basnijholt](https://github.com/basnijholt))
@@ -524,7 +559,7 @@
- Gracefully handle exceptions when evaluating the function to be learned [\#125](https://github.com/python-adaptive/adaptive/issues/125)
- Allow BalancingLearner to return arbitrary number of points from 'choose\_points' [\#124](https://github.com/python-adaptive/adaptive/issues/124)
- Increase the default refresh rate for 'live\_plot' [\#120](https://github.com/python-adaptive/adaptive/issues/120)
-- remove default number of points to choose in `choose\_points` [\#118](https://github.com/python-adaptive/adaptive/issues/118)
+- remove default number of points to choose in `choose_points` [\#118](https://github.com/python-adaptive/adaptive/issues/118)
- Consider using Gaussian process optimization as a learner [\#115](https://github.com/python-adaptive/adaptive/issues/115)
- Make `distributed.Client` work with automatic scaling of the cluster [\#104](https://github.com/python-adaptive/adaptive/issues/104)
- Improve plotting for learners [\#83](https://github.com/python-adaptive/adaptive/issues/83)
@@ -611,7 +646,7 @@
- Remove public 'fname' learner attribute [\#17](https://github.com/python-adaptive/adaptive/issues/17)
- Release v0.7.0 [\#14](https://github.com/python-adaptive/adaptive/issues/14)
- \(Learner1D\) improve time complexity [\#13](https://github.com/python-adaptive/adaptive/issues/13)
-- Typo in documentation for` adaptive.learner.learner2D.uniform\_loss\(ip\)` [\#12](https://github.com/python-adaptive/adaptive/issues/12)
+- Typo in documentation for` adaptive.learner.learner2D.uniform_loss(ip)` [\#12](https://github.com/python-adaptive/adaptive/issues/12)
- \(LearnerND\) fix plotting of scaled domains [\#11](https://github.com/python-adaptive/adaptive/issues/11)
- suggested points lie outside of domain [\#7](https://github.com/python-adaptive/adaptive/issues/7)
- DEVELOPMENT IS ON GITLAB: https://gitlab.kwant-project.org/qt/adaptive [\#5](https://github.com/python-adaptive/adaptive/issues/5)
From d0aab31298ffeb1c4825bad40b9ac3294ea4aa80 Mon Sep 17 00:00:00 2001
From: Bas Nijholt <bas@nijho.lt>
Date: Tue, 13 May 2025 14:16:32 +0200
Subject: [PATCH 7/7] Fix several deprecation warnings (#481)
---
adaptive/learner/learner2D.py | 6 +++++-
adaptive/learner/learnerND.py | 7 ++++---
2 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/adaptive/learner/learner2D.py b/adaptive/learner/learner2D.py
index a4b2a812..cb179a22 100644
--- a/adaptive/learner/learner2D.py
+++ b/adaptive/learner/learner2D.py
@@ -287,6 +287,10 @@ def custom_loss(ip: LinearNDInterpolator) -> np.ndarray:
return custom_loss
+def _cross_2d(x, y):
+ return x[..., 0] * y[..., 1] - x[..., 1] * y[..., 0]
+
+
def choose_point_in_triangle(triangle: np.ndarray, max_badness: int) -> np.ndarray:
"""Choose a new point in inside a triangle.
@@ -310,7 +314,7 @@ def choose_point_in_triangle(triangle: np.ndarray, max_badness: int) -> np.ndarr
The x and y coordinate of the suggested new point.
"""
a, b, c = triangle
- area = 0.5 * np.cross(b - a, c - a)
+ area = 0.5 * _cross_2d(b - a, c - a)
triangle_roll = np.roll(triangle, 1, axis=0)
edge_lengths = np.linalg.norm(triangle - triangle_roll, axis=1)
i = edge_lengths.argmax()
diff --git a/adaptive/learner/learnerND.py b/adaptive/learner/learnerND.py
index d0300143..33bbbbb0 100644
--- a/adaptive/learner/learnerND.py
+++ b/adaptive/learner/learnerND.py
@@ -726,9 +726,10 @@ def _compute_loss(self, simplex):
if self.nth_neighbors == 0:
# compute the loss on the scaled simplex
- return float(
- self.loss_per_simplex(vertices, values, self._output_multiplier)
- )
+ loss = self.loss_per_simplex(vertices, values, self._output_multiplier)
+ if isinstance(loss, np.ndarray):
+ return float(loss.item())
+ return float(loss)
# We do need the neighbors
neighbors = self.tri.get_opposing_vertices(simplex)