py-modelrunner 0.18.3__tar.gz → 0.19.1__tar.gz

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/.github/workflows/build.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.12']
+        python-version: ['3.9', '3.13']
 
     steps:
     - uses: actions/checkout@v4

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/.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-0.18.3 → py_modelrunner-0.19.1}/.github/workflows/coverage_report.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v4

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/.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: '3.9'
 
     - name: Install dependencies
       run: |

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/.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-0.18.3 → py_modelrunner-0.19.1}/.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.9"
   apt_packages:
     - graphviz
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: py-modelrunner
-Version: 0.18.3
+Version: 0.19.1
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT
@@ -14,12 +14,12 @@ 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
-Requires-Python: <3.13,>=3.8
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: <3.14,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: jinja2>=3
@@ -39,6 +39,7 @@ 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-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/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 3.9+ and should run on all common
 platforms. 
 
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/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-0.19.1/modelrunner/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.19.1'
+__version_tuple__ = version_tuple = (0, 19, 1)
+
+__commit_id__ = commit_id = 'gb76984877'

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/modelrunner/model/parameters.py

@@ -19,8 +19,9 @@ from __future__ import annotations
 import copy
 import logging
 import warnings
+from collections.abc import Container, Iterator
 from dataclasses import dataclass, field
-from typing import Any, Callable, Container, Dict, Iterator, List, Optional, Union
+from typing import Any, Callable, Optional, Union
 
 import numpy as np
 
@@ -279,8 +280,8 @@ class HideParameter:
         pass
 
 
-ParameterListType = List[Union[Parameter, HideParameter]]
-ParameterInputType = Optional[Dict[str, Any]]
+ParameterListType = list[Union[Parameter, HideParameter]]
+ParameterInputType = Optional[dict[str, Any]]
 
 
 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-0.18.3 → py_modelrunner-0.19.1}/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

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/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
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/run/launch.py

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

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/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

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/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-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/backend/hdf.py

@@ -8,8 +8,9 @@ Requires the optional :mod:`h5py` module.
 
 from __future__ import annotations
 
+from collections.abc import Collection, Sequence
 from pathlib import Path
-from typing import Any, Collection, Sequence
+from typing import Any
 
 import h5py
 import numpy as np

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/backend/memory.py

@@ -6,7 +6,8 @@
 from __future__ import annotations
 
 import copy
-from typing import Any, Collection, Sequence
+from collections.abc import Collection, Sequence
+from typing import Any
 
 import numpy as np
 from numpy.typing import ArrayLike, DTypeLike

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/backend/text_base.py

@@ -6,9 +6,10 @@ from __future__ import annotations
 
 import io
 from abc import ABCMeta, abstractmethod
+from collections.abc import Sequence
 from io import StringIO
 from pathlib import Path
-from typing import Any, Sequence
+from typing import Any
 
 import numpy as np
 from numpy.lib.recfunctions import (

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/backend/zarr.py

@@ -8,8 +8,9 @@ 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
@@ -60,9 +61,15 @@ class ZarrStorage(StorageBase):
             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":

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/base.py

@@ -24,7 +24,8 @@ from __future__ import annotations
 
 import logging
 from abc import ABCMeta, abstractmethod
-from typing import TYPE_CHECKING, Any, Collection, Literal, Sequence
+from collections.abc import Collection, Sequence
+from typing import TYPE_CHECKING, Any, Literal
 
 import numcodecs
 import numpy as np

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/group.py

@@ -4,7 +4,8 @@
 
 from __future__ import annotations
 
-from typing import Any, Collection, Iterator
+from collections.abc import Collection, Iterator
+from typing import Any
 
 import numpy as np
 from numpy.typing import ArrayLike, DTypeLike

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/trajectory.py

@@ -11,8 +11,9 @@
 
 from __future__ import annotations
 
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Any, Iterator, Literal
+from typing import Any, Literal
 
 import numpy as np
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/modelrunner/storage/utils.py

@@ -9,8 +9,9 @@ import codecs
 import inspect
 import pickle
 from collections import defaultdict
+from collections.abc import Sequence
 from importlib import import_module
-from typing import TYPE_CHECKING, Any, Callable, Literal, Sequence, Union, overload
+from typing import TYPE_CHECKING, Any, Callable, Literal, Union, overload
 
 import numpy as np
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/py_modelrunner.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: py-modelrunner
-Version: 0.18.3
+Version: 0.19.1
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT
@@ -14,12 +14,12 @@ 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
-Requires-Python: <3.13,>=3.8
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: <3.14,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: jinja2>=3
@@ -39,6 +39,7 @@ 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-0.18.3 → py_modelrunner-0.19.1}/pyproject.toml

@@ -6,7 +6,7 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.8,<3.13"
+requires-python = ">=3.9,<3.14"
 dynamic = ["version"]
 
 classifiers = [
@@ -17,11 +17,11 @@ classifiers = [
     "Topic :: Utilities",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 
 # Requirements for setuptools
@@ -77,7 +77,7 @@ namespaces = false
 write_to = "modelrunner/_version.py"
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py39"
 exclude = ["scripts/templates"]
 
 [tool.ruff.format]
@@ -113,7 +113,7 @@ section-order = ["future", "standard-library", "third-party", "first-party", "se
 self = ["modelrunner", "helpers"]
 
 [tool.black]
-target_version = ["py38"]
+target_version = ["py39"]
 
 [tool.isort]
 profile = "black"
@@ -136,7 +136,7 @@ filterwarnings = [
 omit = ['*/test*']
 
 [tool.mypy]
-python_version = "3.8"
+python_version = "3.10"
 plugins = "numpy.typing.mypy_plugin"
 warn_return_any = true
 warn_unused_configs = true

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/tests/helpers/asserts.py

@@ -2,7 +2,8 @@
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
 
-from typing import Any, Sequence
+from collections.abc import Sequence
+from typing import Any
 
 import numpy as np
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/tests/helpers/storage.py

@@ -6,7 +6,7 @@
 from __future__ import annotations
 
 import importlib
-from typing import Any, Callable, List, Optional, TypeVar
+from typing import Any, Callable, Optional, TypeVar
 
 import numpy as np
 

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/tests/model/test_parameters.py

@@ -6,7 +6,6 @@ import itertools
 import logging
 import math
 import pickle
-from typing import List
 
 import numpy as np
 import pytest

{py_modelrunner-0.18.3 → py_modelrunner-0.19.1}/tests/test_examples.py

@@ -6,7 +6,6 @@ import os
 import subprocess as sp
 import sys
 from pathlib import Path
-from typing import List
 
 import pytest
 

py_modelrunner-0.18.3/modelrunner/_version.py

@@ -1,16 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple, Union
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '0.18.3'
-__version_tuple__ = version_tuple = (0, 18, 3)