py-modelrunner 0.18.2__tar.gz → 0.19.0__tar.gz

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/.github/workflows/build.yml

@@ -9,13 +9,13 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/.github/workflows/check_docs.yml

@@ -6,7 +6,7 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: ammaraskar/sphinx-action@master
       with:
         docs-folder: "docs/"

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/.github/workflows/coverage_report.yml

@@ -11,9 +11,9 @@ jobs:
         python-version: [3.8]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/.github/workflows/release_pip.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
 

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py-modelrunner
-Version: 0.18.2
+Version: 0.19.0
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT
@@ -19,7 +19,8 @@ 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,>=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: jinja2>=3
@@ -30,7 +31,7 @@ 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>=2; extra == "all"
+Requires-Dist: zarr<3,>=2; extra == "all"
 Provides-Extra: test
 Requires-Dist: black>=19; extra == "test"
 Requires-Dist: isort>=5.1; extra == "test"
@@ -49,8 +50,6 @@ Requires-Dist: mypy>=0.770; extra == "test"
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/py-modelrunner.svg)](https://anaconda.org/conda-forge/py-modelrunner)
 [![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
 [![codecov](https://codecov.io/gh/zwicker-group/py-modelrunner/branch/main/graph/badge.svg)](https://codecov.io/gh/zwicker-group/py-modelrunner)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-
 
 
 This package provides python classes for handling and running physical simulations.

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/README.md

@@ -7,8 +7,6 @@
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/py-modelrunner.svg)](https://anaconda.org/conda-forge/py-modelrunner)
 [![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
 [![codecov](https://codecov.io/gh/zwicker-group/py-modelrunner/branch/main/graph/badge.svg)](https://codecov.io/gh/zwicker-group/py-modelrunner)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-
 
 
 This package provides python classes for handling and running physical simulations.

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/docs/source/conf.py

@@ -15,19 +15,19 @@
 import os.path
 import sys
 
-sys.path.insert(0, os.path.abspath("../.."))
+sys.path.insert(0, os.path.abspath("../.."))  # noqa: PTH100
 sys.path.insert(0, ".")
 
 from datetime import date
 
-import sphinx_simplify_typehints  # @UnresolvedImport @UnusedImport
+import sphinx_simplify_typehints
 
 # -- Project information -----------------------------------------------------
 
 project = "py-modelrunner"
 module_name = "modelrunner"
 author = "David Zwicker"
-copyright = f"{date.today().year}, {author}"  # @ReservedAssignment
+copyright = f"{date.today().year}, {author}"  # noqa: A001
 
 # The short X.Y version
 import modelrunner

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/docs/source/run_autodoc.py

@@ -4,13 +4,14 @@ import glob
 import logging
 import os
 import subprocess as sp
+from pathlib import Path
 
 logging.basicConfig(level=logging.INFO)
 
 OUTPUT_PATH = "packages"
 
 
-def replace_in_file(infile, replacements, outfile=None):
+def replace_in_file(infile: Path, replacements, outfile=None):
     """Reads in a file, replaces the given data using python formatting and writes back
     the result to a file.
 
@@ -26,21 +27,21 @@ def replace_in_file(infile, replacements, outfile=None):
     if outfile is None:
         outfile = infile
 
-    with open(infile) as fp:
+    with infile.open() as fp:
         content = fp.read()
 
     for key, value in replacements.items():
         content = content.replace(key, value)
 
-    with open(outfile, "w") as fp:
+    with outfile.open("w") as fp:
         fp.write(content)
 
 
 def main(package="modelrunner"):
     # remove old files
-    for path in glob.glob(f"{OUTPUT_PATH}/*.rst"):
+    for path in Path(OUTPUT_PATH).glob("*.rst"):
         logging.info("Remove file `%s`", path)
-        os.remove(path)
+        path.unlink()
 
     # run sphinx-apidoc
     sp.check_call(
@@ -66,7 +67,7 @@ def main(package="modelrunner"):
     }
 
     # replace unwanted information
-    for path in glob.glob(f"{OUTPUT_PATH}/*.rst"):
+    for path in Path(OUTPUT_PATH).glob("*.rst"):
         logging.info("Patch file `%s`", path)
         replace_in_file(path, REPLACEMENTS)
 

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/docs/source/sphinx_simplify_typehints.py

@@ -48,22 +48,25 @@ def sphinx_display_parameters(app, what, name, obj, options, lines):
 
             app.connect('autodoc-process-docstring', sphinx_display_parameters)
     """
-    if what == "class" and issubclass(obj, Parameterized):
-        if 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("")
+    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):

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/examples/read_many.py

@@ -4,7 +4,7 @@
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
 
-import os
+from pathlib import Path
 
 from modelrunner import ResultCollection, make_model_class
 
@@ -19,11 +19,11 @@ if __name__ == "__main__":
     model = make_model_class(multiply)
 
     # write data
-    os.makedirs("data")
+    Path("data").mkdir(parents=True)
     for n, a in enumerate(range(5, 10)):
         result = model({"a": a}).get_result()
         result.to_file(f"data/test_{n}.json")
 
     # read data
     rc = ResultCollection.from_folder("data")
-    print(rc.dataframe)
+    print(rc.as_dataframe())

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/examples/submit_many_func.py

@@ -8,7 +8,6 @@ argument by something more suitable; see the documentation.
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
 
-
 from modelrunner import make_model, submit_jobs
 
 

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/examples/submit_many_iter.py

@@ -8,7 +8,6 @@ argument by something more suitable; see the documentation.
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
 
-
 from modelrunner import make_model, submit_job
 
 

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.18.2'
-__version_tuple__ = version_tuple = (0, 18, 2)
+__version__ = version = '0.19.0'
+__version_tuple__ = version_tuple = (0, 19, 0)

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/config.py

@@ -69,14 +69,14 @@ class Config(collections.UserDict):
         """Load configuration from yaml file."""
         import yaml
 
-        with open(path) as fp:
+        with Path(path).open() as fp:
             self.update(yaml.safe_load(fp))
 
     def save(self, path: str | Path):
         """Save configuration to yaml file."""
         import yaml
 
-        with open(path, "w") as fp:
+        with Path(path).open("w") as fp:
             yaml.dump(self.to_dict(), fp)
 
     def __getitem__(self, key: str):
@@ -124,7 +124,7 @@ class Config(collections.UserDict):
         Returns:
             dict: A representation of the configuration in a normal :class:`dict`.
         """
-        return {k: v for k, v in self.items()}
+        return dict(self.items())
 
     def __repr__(self) -> str:
         """Represent the configuration as a string."""

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/model/base.py

@@ -17,7 +17,10 @@ from ..utils import is_serial_or_mpi_root
 from .parameters import DeprecatedParameter, HideParameter, Parameterized
 
 if TYPE_CHECKING:
-    from ..run.results import Result  # @UnusedImport
+    from ..run.results import Result
+
+_base_logger = logging.getLogger(__name__.rsplit(".", 1)[0])
+""":class:`logging.Logger`: Base logger for models."""
 
 
 class ModelBase(Parameterized, metaclass=ABCMeta):
@@ -27,6 +30,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
     """str: the name of the model"""
     description: str | None = None
     """str: a longer description of the model"""
+    _logger: logging.Logger  # logger instance to output information
 
     def __init__(
         self,
@@ -63,7 +67,12 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
         self.output = output  # TODO: also allow already opened storages
         self.mode = mode
         self._storage: open_storage | None = None
-        self._logger = logging.getLogger(self.__class__.__name__)
+
+    def __init_subclass__(cls, **kwargs):
+        """Initialize class-level attributes of subclasses."""
+        super().__init_subclass__(**kwargs)
+        # create logger for this specific field class
+        cls._logger = _base_logger.getChild(cls.__qualname__)
 
     @property
     def storage(self) -> StorageGroup:
@@ -97,7 +106,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
         Returns:
             :class:`Result`: The result after the model is run
         """
-        from ..run.results import Result  # @Reimport
+        from ..run.results import Result
 
         if data is None:
             data = self()
@@ -112,7 +121,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
             result:
                 The result data. If omitted, the model is run to obtain results
         """
-        from ..run.results import Result  # @Reimport
+        from ..run.results import Result
 
         if self.output is None:
             raise RuntimeError("Output file needs to be specified")

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/model/factory.py

@@ -14,7 +14,7 @@ from .base import ModelBase
 from .parameters import NoValue, Parameter
 
 if TYPE_CHECKING:
-    from ..run.results import Result  # @UnusedImport
+    from ..run.results import Result
 
 _DEFAULT_MODEL: Callable | ModelBase | None = None
 """Stores the default model that will be used automatically."""

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/model/parameters.py

@@ -26,6 +26,9 @@ import numpy as np
 
 from ..utils import hybridmethod, import_class
 
+_logger = logging.getLogger(__name__)
+""":class:`logging.Logger`: Logger instance."""
+
 
 class NoValueType:
     """Special value to indicate no value for a parameter."""
@@ -129,8 +132,10 @@ class Parameter:
                 )
 
             if not valid_default:
-                logging.warning(
-                    f"Default value `{self.name}` is not of type `{self.cls.__name__}`"
+                _logger.warning(
+                    "Default value `%s` is not of type `%s`",
+                    self.name,
+                    self.cls.__name__,
                 )
 
     def __getstate__(self):
@@ -254,8 +259,6 @@ class Parameter:
 class DeprecatedParameter(Parameter):
     """A parameter that can still be used normally but is deprecated."""
 
-    pass
-
 
 class HideParameter:
     """A helper class that allows hiding parameters of the parent classes.
@@ -314,7 +317,7 @@ class Parameterized:
                 parameters, include_deprecated=True, check_validity=strict
             )
 
-    def __init_subclass__(cls, **kwargs) -> None:  # @NoSelf
+    def __init_subclass__(cls, **kwargs) -> None:
         """Register all subclasses to reconstruct them later."""
         # normalize the parameters_default attribute to be a list of `Parameter`
         if hasattr(cls, "parameters_default") and isinstance(
@@ -470,7 +473,7 @@ class Parameterized:
         return result
 
     @classmethod
-    def get_parameter_default(cls, name):  # @NoSelf
+    def get_parameter_default(cls, name):
         """Return the default value for the parameter with `name`
 
         Args:
@@ -551,7 +554,7 @@ class Parameterized:
                 yield template.format(**data)
 
     @hybridmethod
-    def show_parameters(  # @NoSelf
+    def show_parameters(
         cls,
         description: bool = False,
         sort: bool = False,

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/run/compatibility/triage.py

@@ -125,13 +125,13 @@ def _get_format_version(path: Path, label: str) -> int | None:
     # check for compatibility
     fmt = guess_format(path)
     if fmt == "json":
-        with open(path) as fp:
+        with path.open() as fp:
             format_version = _find_version(json.load(fp), label)
 
     elif fmt == "yaml":
         import yaml
 
-        with open(path) as fp:
+        with path.open() as fp:
             format_version = _find_version(yaml.safe_load(fp), label)
 
     elif fmt == "hdf":

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/run/compatibility/version0.py

@@ -79,14 +79,14 @@ def result_from_file_v0(path: Path, **kwargs) -> Result:
     """
     fmt = guess_format(path)
     if fmt == "json":
-        with open(path) as fp:
+        with path.open() as fp:
             content = json.load(fp)
         return _Result_from_simple_objects(content, **kwargs)
 
     elif fmt == "yaml":
         import yaml
 
-        with open(path) as fp:
+        with path.open() as fp:
             content = yaml.safe_load(fp)
         return _Result_from_simple_objects(content, **kwargs)
 

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/run/compatibility/version1.py

@@ -26,13 +26,11 @@ if TYPE_CHECKING:
 class NoData:
     """Helper class that marks data omission."""
 
-    ...
-
 
 TState = TypeVar("TState", bound="StateBase")
 
 
-class StateBase(metaclass=ABCMeta):
+class StateBase:
     """Base class for specifying the state of a simulation.
 
     A state contains values of all degrees of freedom of a physical system (called the
@@ -224,19 +222,19 @@ def result_from_file_v1(store: Path, *, label: str = "data", **kwargs) -> Result
     """
     fmt = guess_format(store)
     if fmt == "json":
-        with open(store) as fp:
+        with store.open() as fp:
             content = json.load(fp)
         return _Result_from_simple_objects(content, **kwargs)
 
     elif fmt == "yaml":
         import yaml
 
-        with open(store) as fp:
+        with store.open() as fp:
             content = yaml.safe_load(fp)
         return _Result_from_simple_objects(content, **kwargs)
 
     elif fmt == "zarr":
-        import zarr  # @Reimport
+        import zarr
 
         zarr_store = normalize_zarr_store(store, mode="r")
         root = zarr.open_group(zarr_store, mode="r")

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/run/job.py

@@ -28,12 +28,12 @@ def escape_string(obj) -> str:
     return shlex.quote(str(obj))
 
 
-def ensure_directory_exists(folder):
+def ensure_directory_exists(folder: str | Path) -> None:
     """Creates a folder if it not already exists."""
     if folder == "":
         return
     try:
-        os.makedirs(folder)
+        Path(folder).mkdir(parents=True)
     except OSError as err:
         if err.errno != errno.EEXIST:
             raise
@@ -199,7 +199,7 @@ def submit_job(
     else:
         template_path = Path(template)
     logger.info("Load template `%s`", template_path)
-    with open(template_path) as fp:
+    with template_path.open() as fp:
         script_template = fp.read()
 
     # prepare submission script

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/run/launch.py

@@ -9,6 +9,7 @@ import importlib.util
 import inspect
 import logging
 import os.path
+from pathlib import Path
 from typing import Callable, Sequence
 
 from ..model import ModelBase, cleared_default_model, factory, make_model_class
@@ -35,7 +36,7 @@ def run_function_with_cmd_args(
 
 
 @cleared_default_model
-def run_script(script_path: str, model_args: Sequence[str]) -> Result:
+def run_script(script_path: str | Path, model_args: Sequence[str]) -> Result:
     """Helper function that runs a model script.
 
     The function detects models automatically by trying several methods until one yields
@@ -59,7 +60,7 @@ def run_script(script_path: str, model_args: Sequence[str]) -> Result:
     logger = logging.getLogger("modelrunner")
 
     # load the script as a module
-    filename = os.path.basename(script_path)
+    filename = Path(script_path).name
     spec = importlib.util.spec_from_file_location("model_code", script_path)
     if spec is None:
         raise OSError(f"Could not find job script `{script_path}`")

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/run/results.py

@@ -11,7 +11,7 @@ import itertools
 import logging
 import warnings
 from pathlib import Path
-from typing import Any, Iterator, List
+from typing import Any, Collection, Iterator, List
 
 import numpy as np
 from tqdm.auto import tqdm
@@ -276,11 +276,11 @@ class ResultCollection(List[Result]):
             progress (bool):
                 Flag indicating whether a progress bar is shown
         """
-        logger = logging.getLogger(cls.__name__)
+        logger = logging.getLogger("modelrunner." + cls.__name__)
 
         folder = Path(folder)
         if not folder.is_dir():
-            logger.warning(f"{folder} is not a directory")
+            logger.warning("%s is not a directory", folder)
 
         # iterate over all files and load them as a Result
         results = []
@@ -293,7 +293,7 @@ class ResultCollection(List[Result]):
                         err.args = (str(err) + f"\nError reading file `{path}`",)
                         raise
                     else:
-                        logger.warning(f"Error reading file `{path}`")
+                        logger.warning("Error reading file `%s`", path)
                 else:
                     results.append(result)
 
@@ -303,7 +303,7 @@ class ResultCollection(List[Result]):
                 logger.warning("Did not find any files")
             else:
                 logger.warning(
-                    f"Did not find any files. Is pattern `{pattern}` too restrictive?"
+                    "Did not find any files. Is pattern `%s` too restrictive?", pattern
                 )
 
         return cls(results)
@@ -316,6 +316,7 @@ class ResultCollection(List[Result]):
     def __add__(self, other: ResultCollection) -> ResultCollection:  # type: ignore
         if isinstance(other, ResultCollection):
             return ResultCollection(super().__add__(other))
+        return None
 
     @property
     def same_model(self) -> bool:
@@ -441,22 +442,21 @@ class ResultCollection(List[Result]):
                 seen.append(result.parameters)
         return self.__class__(unique_results)
 
-    @property
-    def dataframe(self):
-        """Create a pandas dataframe summarizing the data."""
-        # deprecated on 2023-10-19
-        warnings.warn("Property `dataframe` deprecated; use method `as_dataframe`")
-        return self.as_dataframe()
-
-    def as_dataframe(self, *, enforce_same_model: bool = True):
+    def as_dataframe(
+        self, *, enforce_same_model: bool = True, drop_keys: Collection | None = None
+    ):
         """Create a pandas dataframe summarizing the data.
 
         Args:
             enforce_same_model (bool):
                 If True, forces all model results to derive from the same model
+            drop_keys (sequence):
+                A list of items that will not be included in the final data frame
         """
         import pandas as pd
 
+        drop_keys = set() if drop_keys is None else set(drop_keys)
+
         if enforce_same_model and not self.same_model:
             raise RuntimeError("Results are not from the same model")
 
@@ -476,10 +476,14 @@ class ResultCollection(List[Result]):
                 df_data["result"] = data
             elif isinstance(data, dict):
                 for key, value in data.items():
+                    if key in drop_keys:
+                        continue
                     if np.isscalar(value):
                         df_data[key] = value
                     elif isinstance(value, (list, tuple, np.ndarray)):
                         df_data[key] = np.asarray(value)
+                    else:
+                        df_data[key] = value
             else:
                 raise RuntimeError("Do not know how to interpret result")
             return df_data

{py_modelrunner-0.18.2 → py_modelrunner-0.19.0}/modelrunner/storage/__init__.py

@@ -13,7 +13,7 @@
 from .access_modes import AccessError, ModeType
 from .attributes import Attrs
 from .backend import *
-from .base import StorageBase  # @Reimport
+from .base import StorageBase
 from .group import StorageGroup
 from .tools import StorageID, open_storage
 from .trajectory import Trajectory, TrajectoryWriter