py-modelrunner 0.19.0__tar.gz → 0.20.0__tar.gz

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/.github/workflows/build.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.13']
+        python-version: ['3.12', '3.14']
 
     steps:
     - uses: actions/checkout@v4

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/.github/workflows/check_docs.yml

@@ -7,6 +7,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: ammaraskar/sphinx-action@master
+    - uses: ammaraskar/sphinx-action@8.0.2
       with:
         docs-folder: "docs/"

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/.github/workflows/coverage_report.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
 
     steps:
     - uses: actions/checkout@v4

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/.github/workflows/release_pip.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.12'
 
     - name: Install dependencies
       run: |

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/.gitignore

@@ -2,6 +2,7 @@
 .pydevproject
 .project
 tests/coverage
+debug
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -140,4 +141,4 @@ dmypy.json
 .pyre/
 
 # JetBrains
-.idea/
+.idea/

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.12"
   apt_packages:
     - graphviz
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: py-modelrunner
-Version: 0.19.0
+Version: 0.20.0
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT
@@ -14,24 +14,22 @@ Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Utilities
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: <3.14,>=3.8
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: jinja2>=3
 Requires-Dist: numpy>=1.18.0
 Requires-Dist: tqdm>=4.45
-Requires-Dist: numcodecs>=0.10
+Requires-Dist: numcodecs>=0.16
 Provides-Extra: all
 Requires-Dist: h5py>=3.5; extra == "all"
 Requires-Dist: pandas>=1.3; extra == "all"
 Requires-Dist: PyYAML>=5; extra == "all"
-Requires-Dist: zarr<3,>=2; extra == "all"
+Requires-Dist: zarr<4,>=3; extra == "all"
 Provides-Extra: test
 Requires-Dist: black>=19; extra == "test"
 Requires-Dist: isort>=5.1; extra == "test"
@@ -40,6 +38,7 @@ Requires-Dist: pytest-cov>=2.8; extra == "test"
 Requires-Dist: pytest-xdist>=1.30; extra == "test"
 Requires-Dist: py-pde>=0.33; extra == "test"
 Requires-Dist: mypy>=0.770; extra == "test"
+Dynamic: license-file
 
 # py-modelrunner
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/docs/source/conf.py

@@ -241,7 +241,7 @@ intersphinx_mapping = {
     "h5py": ("https://docs.h5py.org/en/latest", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
     "napari": ("https://napari.org/", None),
-    "numba": ("https://numba.pydata.org/numba-doc/latest/", None),
+    "numba": ("https://numba.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "pde": ("https://py-pde.readthedocs.io/en/latest", None),
     "python": ("https://docs.python.org/3/", None),

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/docs/source/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ############
 
-This `py-modelrunner` package is developed for python 3.8+ and should run on all common
+This `py-modelrunner` package is developed for python 3.11+ and should run on all common
 platforms. 
 
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/docs/source/run_autodoc.py

@@ -38,9 +38,11 @@ def replace_in_file(infile: Path, replacements, outfile=None):
 
 
 def main(package="modelrunner"):
+    logger = logging.getLogger("autodoc")
+
     # remove old files
     for path in Path(OUTPUT_PATH).glob("*.rst"):
-        logging.info("Remove file `%s`", path)
+        logger.info("Remove file `%s`", path)
         path.unlink()
 
     # run sphinx-apidoc
@@ -68,7 +70,7 @@ def main(package="modelrunner"):
 
     # replace unwanted information
     for path in Path(OUTPUT_PATH).glob("*.rst"):
-        logging.info("Patch file `%s`", path)
+        logger.info("Patch file `%s`", path)
         replace_in_file(path, REPLACEMENTS)
 
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/docs/source/sphinx_simplify_typehints.py

@@ -4,6 +4,7 @@ import collections
 import re
 
 from modelrunner import Parameterized
+from modelrunner.model.parameters import sphinx_display_parameters
 
 # simple (literal) replacement rules
 REPLACEMENTS = collections.OrderedDict(
@@ -39,36 +40,6 @@ def process_signature(
     return signature, return_annotation
 
 
-def sphinx_display_parameters(app, what, name, obj, options, lines):
-    """Helper function to display parameters in sphinx documentation.
-
-    Example:
-        This function should be connected to the 'autodoc-process-docstring'
-        event like so:
-
-            app.connect('autodoc-process-docstring', sphinx_display_parameters)
-    """
-    if (
-        what == "class"
-        and issubclass(obj, Parameterized)
-        and any(":param parameters:" in line for line in lines)
-    ):
-        # parse parameters
-        parameters = obj.get_parameters(sort=False)
-        if parameters:
-            lines.append(".. admonition::")
-            lines.append(f"   Parameters of {obj.__name__}:")
-            lines.append("   ")
-            for p in parameters.values():
-                lines.append(f"   {p.name}")
-                text = p.description.splitlines()
-                text.append(f"(Default value: :code:`{p.default_value!r}`)")
-                text = ["     " + t for t in text]
-                lines.extend(text)
-                lines.append("")
-            lines.append("")
-
-
 def setup(app):
     """Set up hooks for this sphinx plugin."""
     app.connect("autodoc-process-signature", process_signature)

py_modelrunner-0.20.0/modelrunner/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.20.0'
+__version_tuple__ = version_tuple = (0, 20, 0)
+
+__commit_id__ = commit_id = 'ga172a6158'

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/config.py

@@ -12,8 +12,9 @@ from __future__ import annotations
 
 import collections
 import contextlib
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Any, Sequence
+from typing import Any
 
 from .model.parameters import DeprecatedParameter, Parameter
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/model/base.py

@@ -9,8 +9,9 @@ import argparse
 import json
 import logging
 from abc import ABCMeta, abstractmethod
+from collections.abc import Sequence
 from datetime import datetime
-from typing import TYPE_CHECKING, Any, Sequence
+from typing import TYPE_CHECKING, Any
 
 from ..storage import ModeType, StorageGroup, open_storage
 from ..utils import is_serial_or_mpi_root

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/model/factory.py

@@ -7,7 +7,8 @@ from __future__ import annotations
 
 import functools
 import inspect
-from typing import TYPE_CHECKING, Any, Callable, Literal, TypeVar, get_args, get_origin
+from collections.abc import Callable
+from typing import TYPE_CHECKING, Any, Literal, TypeVar, get_args, get_origin
 
 from ..storage import ModeType
 from .base import ModelBase

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/model/parameters.py

@@ -19,8 +19,9 @@ from __future__ import annotations
 import copy
 import logging
 import warnings
+from collections.abc import Callable, Container, Iterator
 from dataclasses import dataclass, field
-from typing import Any, Callable, Container, Dict, Iterator, List, Optional, Union
+from typing import Any
 
 import numpy as np
 
@@ -279,8 +280,8 @@ class HideParameter:
         pass
 
 
-ParameterListType = List[Union[Parameter, HideParameter]]
-ParameterInputType = Optional[Dict[str, Any]]
+ParameterListType = list[Parameter | HideParameter]
+ParameterInputType = dict[str, Any] | None
 
 
 class Parameterized:
@@ -644,3 +645,33 @@ def get_all_parameters(data: str = "name") -> dict[str, Any]:
 
         result[cls_name] = parameters
     return result
+
+
+def sphinx_display_parameters(app, what, name, obj, options, lines):
+    """Helper function to display parameters in sphinx documentation.
+
+    Example:
+        This function should be connected to the 'autodoc-process-docstring'
+        event like so:
+
+            app.connect('autodoc-process-docstring', sphinx_display_parameters)
+    """
+    if (
+        what == "class"
+        and issubclass(obj, Parameterized)
+        and any(":param parameters:" in line for line in lines)
+    ):
+        # parse parameters
+        parameters = obj.get_parameters(sort=False)
+        if parameters:
+            lines.append(".. admonition::")
+            lines.append(f"   Parameters of {obj.__name__}:")
+            lines.append("   ")
+            for p in parameters.values():
+                lines.append(f"   {p.name}")
+                text = p.description.splitlines()
+                text.append(f"(Default value: :code:`{p.default_value!r}`)")
+                text = ["     " + t for t in text]
+                lines.extend(text)
+                lines.append("")
+            lines.append("")

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/run/compatibility/triage.py

@@ -7,8 +7,9 @@ from __future__ import annotations
 
 import json
 import logging
+from collections.abc import Mapping
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Mapping, Union
+from typing import TYPE_CHECKING, Any, Union
 
 from ...model import ModelBase
 from ..results import Result
@@ -146,12 +147,12 @@ def _get_format_version(path: Path, label: str) -> int | None:
         store = normalize_zarr_store(path, mode="r")
         if store is None:
             raise RuntimeError
-        with zarr.open_group(store, mode="r") as root:
-            format_version = _find_version(root, label)
-            if format_version is None and label != "data":
-                format_version = _find_version(root, "data")
-                if format_version is not None:
-                    label = "data"
+        root = zarr.open_group(store, mode="r")
+        format_version = _find_version(root, label)
+        if format_version is None and label != "data":
+            format_version = _find_version(root, "data")
+            if format_version is not None:
+                label = "data"
 
     else:
         raise RuntimeError

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/run/compatibility/version0.py

@@ -6,8 +6,9 @@
 from __future__ import annotations
 
 import json
+from collections.abc import Mapping
 from pathlib import Path
-from typing import Any, Mapping
+from typing import Any
 
 import numpy as np
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/run/compatibility/version1.py

@@ -7,9 +7,8 @@ from __future__ import annotations
 
 import json
 import warnings
-from abc import ABCMeta
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, TypeVar, Union
+from typing import TYPE_CHECKING, Any, TypeVar
 
 import numpy as np
 
@@ -20,7 +19,7 @@ from .triage import guess_format, normalize_zarr_store
 if TYPE_CHECKING:
     import zarr
 
-    zarrElement = Union[zarr.Group, zarr.Array]
+    zarrElement = zarr.Group | zarr.Array
 
 
 class NoData:
@@ -119,7 +118,7 @@ class StateBase:
             raise TypeError(f"Do not know how to load `{cls_name}`")
 
     @classmethod
-    def _from_zarr(cls, zarr_element: zarrElement, *, index=...) -> StateBase:
+    def _from_zarr(cls, zarr_element: zarrElement, *, index=...) -> StateBase:  # type: ignore
         """Create instance of correct subclass from data stored in zarr."""
         # determine the class that knows how to read this data
         cls_name = zarr_element.attrs["__class__"]

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/run/job.py

@@ -14,8 +14,9 @@ import shlex
 import subprocess as sp
 import sys
 import warnings
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Iterable, Literal
+from typing import Any, Literal
 
 from tqdm.auto import tqdm
 
@@ -365,7 +366,7 @@ def submit_jobs(
 
     # build the list of all varying arguments
     p_vary_list = [
-        dict(zip(p_vary.keys(), values))
+        dict(zip(p_vary.keys(), values, strict=False))
         for values in itertools.product(*p_vary.values())
     ]
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/run/launch.py

@@ -9,8 +9,8 @@ import importlib.util
 import inspect
 import logging
 import os.path
+from collections.abc import Callable, Sequence
 from pathlib import Path
-from typing import Callable, Sequence
 
 from ..model import ModelBase, cleared_default_model, factory, make_model_class
 from .results import Result

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/run/results.py

@@ -10,8 +10,9 @@ import inspect
 import itertools
 import logging
 import warnings
+from collections.abc import Collection, Iterator
 from pathlib import Path
-from typing import Any, Collection, Iterator, List
+from typing import Any
 
 import numpy as np
 from tqdm.auto import tqdm
@@ -248,7 +249,7 @@ storage_actions.register(
 )
 
 
-class ResultCollection(List[Result]):
+class ResultCollection(list[Result]):
     """Represents a collection of results."""
 
     @classmethod
@@ -410,7 +411,7 @@ class ResultCollection(List[Result]):
         group_values = [self.parameters[name] for name in args]
 
         for group_value in itertools.product(*group_values):
-            group_parameters = dict(zip(args, group_value))
+            group_parameters = dict(zip(args, group_value, strict=False))
             subset = self.filtered(**group_parameters)
             if len(subset) > 0:
                 yield group_parameters, subset

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/storage/access_modes.py

@@ -6,7 +6,7 @@ from __future__ import annotations
 
 import warnings
 from dataclasses import dataclass
-from typing import ClassVar, Literal, Union
+from typing import ClassVar, Literal
 
 FileMode = Literal[
     "r",  # open as readable
@@ -137,7 +137,7 @@ access_truncate = AccessMode(
     dynamic_append=True,
 )
 
-ModeType = Union[str, AccessMode]
+ModeType = str | AccessMode
 
 
 class AccessError(RuntimeError):

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/storage/attributes.py

@@ -5,11 +5,12 @@
 from __future__ import annotations
 
 import json
-from typing import Any, Dict, Mapping
+from collections.abc import Mapping
+from typing import Any
 
 from .utils import decode_binary, encode_binary
 
-Attrs = Dict[str, Any]
+Attrs = dict[str, Any]
 AttrsLike = Mapping[str, Any]
 
 

{py_modelrunner-0.19.0 → py_modelrunner-0.20.0}/modelrunner/storage/backend/__init__.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import importlib
-from typing import List, Type
 
 from ..base import StorageBase
 from .json import JSONStorage

py_modelrunner-0.19.0/modelrunner/storage/backend/zarr.py → py_modelrunner-0.20.0/modelrunner/storage/backend/_zarr2.py

@@ -8,19 +8,24 @@ Requires the optional :mod:`zarr` module.
 from __future__ import annotations
 
 import shutil
+from collections.abc import Collection, Sequence
 from pathlib import Path
-from typing import Any, Collection, Sequence, Union
+from typing import Any, Union
 
 import numpy as np
 import zarr
 from numpy.typing import ArrayLike, DTypeLike
-from zarr._storage.store import Store
+
+zarr_version = int(zarr.__version__.split(".", 1)[0])
+assert zarr_version == 2
+
+from zarr.storage import Store
 
 from ..access_modes import ModeType
 from ..attributes import AttrsLike
 from ..base import StorageBase
 
-zarrElement = Union[zarr.Group, zarr.Array]
+zarrElement = zarr.Group | zarr.Array
 
 
 class ZarrStorage(StorageBase):
@@ -55,14 +60,20 @@ class ZarrStorage(StorageBase):
                 if self.mode.file_mode == "r":
                     self._logger.info("DirectoryStore is always opened writable")
 
-                self._store = zarr.DirectoryStore(path)
+                self._store = zarr.storage.LocalStore(path)
 
             elif path.suffix == ".zip":
                 # create a ZipStore
                 file_mode = self.mode.file_mode
-                if path.exists() and file_mode == "w":
+                if file_mode == "x":
+                    if path.exists():
+                        raise OSError("File `{path}` already exists")
+                    else:
+                        file_mode = "w"
+                elif file_mode == "w" and path.exists():
                     self._logger.info("Delete file `%s`", path)
                     path.unlink()
+
                 self._store = zarr.storage.ZipStore(path, mode=file_mode)
 
             elif path.suffix == ".sqldb":
@@ -70,7 +81,7 @@ class ZarrStorage(StorageBase):
                 if self.mode.file_mode == "w" and path.exists():
                     self._logger.info("Delete file `%s`", path)
                     path.unlink()
-                self._store = zarr.SQLiteStore(path)
+                self._store = zarr.storage.SQLiteStore(path)
 
         elif isinstance(store_or_path, Store):
             # use already opened zarr storage
@@ -135,7 +146,7 @@ class ZarrStorage(StorageBase):
             return self._root.keys()  # type: ignore
 
     def is_group(self, loc: Sequence[str], *, ignore_cls: bool = False) -> bool:
-        return isinstance(self[loc], zarr.hierarchy.Group)
+        return isinstance(self[loc], zarr.Group)
 
     def _create_group(self, loc: Sequence[str]) -> None:
         parent, name = self._get_parent(loc)