py-modelrunner 0.18.1__tar.gz → 0.18.2__tar.gz

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py-modelrunner
-Version: 0.18.1
+Version: 0.18.2
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/docs/source/parse_examples.py

@@ -12,7 +12,7 @@ OUTPUT = ROOT / "docs" / "source" / "examples"
 
 
 def main():
-    """parse all examples and write them in a special example module"""
+    """Parse all examples and write them in a special example module."""
     # create the output directory
     OUTPUT.mkdir(parents=True, exist_ok=True)
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/docs/source/run_autodoc.py

@@ -11,8 +11,8 @@ OUTPUT_PATH = "packages"
 
 
 def replace_in_file(infile, replacements, outfile=None):
-    """reads in a file, replaces the given data using python formatting and
-    writes back the result to a file.
+    """Reads in a file, replaces the given data using python formatting and writes back
+    the result to a file.
 
     Args:
         infile (str):
@@ -22,7 +22,6 @@ def replace_in_file(infile, replacements, outfile=None):
         outfile (str):
             Output file to which the data is written. If it is omitted, the
             input file will be overwritten instead
-
     """
     if outfile is None:
         outfile = infile

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/docs/source/sphinx_simplify_typehints.py

@@ -1,6 +1,4 @@
-"""
-Simple sphinx plug-in that simplifies  type information in function signatures
-"""
+"""Simple sphinx plug-in that simplifies  type information in function signatures."""
 
 import collections
 import re
@@ -32,7 +30,7 @@ REPLACEMENTS_REGEX = {
 def process_signature(
     app, what: str, name: str, obj, options, signature, return_annotation
 ):
-    """Process signature by applying replacement rules"""
+    """Process signature by applying replacement rules."""
     if signature is not None:
         for key, value in REPLACEMENTS.items():
             signature = signature.replace(key, value)
@@ -42,7 +40,7 @@ def process_signature(
 
 
 def sphinx_display_parameters(app, what, name, obj, options, lines):
-    """helper function to display parameters in sphinx documentation
+    """Helper function to display parameters in sphinx documentation.
 
     Example:
         This function should be connected to the 'autodoc-process-docstring'
@@ -69,6 +67,6 @@ def sphinx_display_parameters(app, what, name, obj, options, lines):
 
 
 def setup(app):
-    """set up hooks for this sphinx plugin"""
+    """Set up hooks for this sphinx plugin."""
     app.connect("autodoc-process-signature", process_signature)
     app.connect("autodoc-process-docstring", sphinx_display_parameters)

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/io_hdf.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows reading and writing data using HDF files.
+"""This example shows reading and writing data using HDF files.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -11,7 +10,7 @@ from modelrunner import Result, run_function_with_cmd_args
 
 
 def number_range(start: float = 1, length: int = 3):
-    """create an ascending list of numbers"""
+    """Create an ascending list of numbers."""
     return start + np.arange(length)
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/io_json.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows reading and writing data using JSON files.
+"""This example shows reading and writing data using JSON files.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -9,7 +8,7 @@ from modelrunner import Result, run_function_with_cmd_args
 
 
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/io_yaml.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows reading and writing data using JSON files.
+"""This example shows reading and writing data using JSON files.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -9,7 +8,7 @@ from modelrunner import Result, run_function_with_cmd_args
 
 
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/model_class.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows defining a custom model class by subclassing.
+"""This example shows defining a custom model class by subclassing.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/model_decorator.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows defining a custom model class using a decorator on a function.
+"""This example shows defining a custom model class using a decorator on a function.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/model_function.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows defining a custom model class using a function.
+"""This example shows defining a custom model class using a function.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/model_storage_output.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows defining a custom model that stores additional data
+"""This example shows defining a custom model that stores additional data.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/read_many.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows how a collection of results can be read.
+"""This example shows how a collection of results can be read.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -11,7 +10,7 @@ from modelrunner import ResultCollection, make_model_class
 
 
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/script_custom_func.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3 -m modelrunner
-"""
-This example shows how a function is turned into a model using decorators.
+"""This example shows how a function is turned into a model using decorators.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -9,11 +8,11 @@ import modelrunner
 
 
 def do_not_calculate(a=1, b=2):
-    """This function should not be run"""
+    """This function should not be run."""
     raise RuntimeError("This must not run")
 
 
 @modelrunner.make_model
 def calculate(a=1, b=2):
-    """This function has been marked as a model"""
+    """This function has been marked as a model."""
     print(a * b)

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/script_function.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example shows how a function is turned into a model explicitly.
+"""This example shows how a function is turned into a model explicitly.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -9,7 +8,7 @@ from modelrunner import run_function_with_cmd_args
 
 
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/script_many_classes.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
-"""
-This example displays a minimal script containing two model classes 
+"""This example displays a minimal script containing two model classes.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/script_minimal.py

@@ -1,11 +1,10 @@
 #!/usr/bin/env python3 -m modelrunner
-"""
-This example displays a minimal script defining a model using a `main` function. 
+"""This example displays a minimal script defining a model using a `main` function.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
 
 
 def main(a=1, b=2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     print(a * b)

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/script_model_class.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3 -m modelrunner
-"""
-This example displays a minimal script containing a model class. 
+"""This example displays a minimal script containing a model class.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/submit_function.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python3
-"""
-This example shows how to submit a model to a queuing system.
+"""This example shows how to submit a model to a queuing system.
 
 Note that the method `foreground` just runs the script locally, thus not really queuing. To
 actually queue a job on a high performance computing cluster, replace the `method`
-argument by something more suitable; see the documentation. 
+argument by something more suitable; see the documentation.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -14,7 +13,7 @@ from modelrunner import make_model, submit_job
 
 @make_model
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/submit_many_func.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python3
-"""
-This example shows how to submit the same model with multiple parameters.
+"""This example shows how to submit the same model with multiple parameters.
 
 Note that the method `foreground` just runs the script locally, thus not really queuing. To
 actually queue a job on a high performance computing cluster, replace the `method`
-argument by something more suitable; see the documentation. 
+argument by something more suitable; see the documentation.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -15,7 +14,7 @@ from modelrunner import make_model, submit_jobs
 
 @make_model
 def main(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/submit_many_iter.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python3
-"""
-This example shows how to submit the same model with multiple parameters.
+"""This example shows how to submit the same model with multiple parameters.
 
 Note that the method `foreground` just runs the script locally, thus not really queuing. To
 actually queue a job on a high performance computing cluster, replace the `method`
-argument by something more suitable; see the documentation. 
+argument by something more suitable; see the documentation.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -15,7 +14,7 @@ from modelrunner import make_model, submit_job
 
 @make_model
 def main(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/examples/submit_shebang.py

@@ -1,15 +1,15 @@
 #!/usr/bin/env python3 -m modelrunner.run --output data.hdf5 --method foreground
-"""
-This example shows how to submit a model to a queuing system using the magic line above.
+"""This example shows how to submit a model to a queuing system using the magic line
+above.
 
 Note that the method `foreground` just runs the script locally, thus not really
 queuing. To actually queue a job on a high performance computing cluster, replace the
-`method` argument by something more suitable; see the documentation. 
+`method` argument by something more suitable; see the documentation.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
 
 
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/modelrunner/__main__.py

@@ -1,5 +1,4 @@
-"""
-Main module allowing to use the package to wrap existing code
+"""Main module allowing to use the package to wrap existing code.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -12,7 +11,7 @@ from modelrunner import Result, run_script
 
 
 def run_script_from_command_line() -> Result:
-    """helper function that runs a model from flags specified at the command line
+    """Helper function that runs a model from flags specified at the command line.
 
     The function detects models automatically by trying several methods until one yields
     a unique model to run:

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/modelrunner/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.18.1'
-__version_tuple__ = version_tuple = (0, 18, 1)
+__version__ = version = '0.18.2'
+__version_tuple__ = version_tuple = (0, 18, 2)

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/modelrunner/config.py

@@ -1,5 +1,4 @@
-"""
-Handles configuration variables
+"""Handles configuration variables.
 
 .. autosummary::
    :nosignatures:
@@ -20,7 +19,7 @@ from .model.parameters import DeprecatedParameter, Parameter
 
 
 class Config(collections.UserDict):
-    """class handling the package configuration"""
+    """Class handling the package configuration."""
 
     def __init__(
         self,
@@ -67,21 +66,21 @@ class Config(collections.UserDict):
         self.mode = mode
 
     def load(self, path: str | Path):
-        """load configuration from yaml file"""
+        """Load configuration from yaml file."""
         import yaml
 
         with open(path) as fp:
             self.update(yaml.safe_load(fp))
 
     def save(self, path: str | Path):
-        """save configuration to yaml file"""
+        """Save configuration to yaml file."""
         import yaml
 
         with open(path, "w") as fp:
             yaml.dump(self.to_dict(), fp)
 
     def __getitem__(self, key: str):
-        """retrieve item `key`"""
+        """Retrieve item `key`"""
         parameter = self.data[key]
         if isinstance(parameter, Parameter):
             return parameter.convert()
@@ -89,7 +88,7 @@ class Config(collections.UserDict):
             return parameter
 
     def __setitem__(self, key: str, value):
-        """update item `key` with `value`"""
+        """Update item `key` with `value`"""
         if self.mode == "insert":
             self.data[key] = value
 
@@ -107,20 +106,20 @@ class Config(collections.UserDict):
             raise ValueError(f"Unsupported configuration mode `{self.mode}`")
 
     def __delitem__(self, key: str):
-        """removes item `key`"""
+        """Removes item `key`"""
         if self.mode == "insert":
             del self.data[key]
         else:
             raise RuntimeError("Configuration is not in `insert` mode")
 
     def copy(self) -> Config:
-        """return a copy of the configuration"""
+        """Return a copy of the configuration."""
         obj = self.__class__(self._default, self.mode)
         obj.update(self)
         return obj
 
     def to_dict(self) -> dict[str, Any]:
-        """convert the configuration to a simple dictionary
+        """Convert the configuration to a simple dictionary.
 
         Returns:
             dict: A representation of the configuration in a normal :class:`dict`.
@@ -128,12 +127,12 @@ class Config(collections.UserDict):
         return {k: v for k, v in self.items()}
 
     def __repr__(self) -> str:
-        """represent the configuration as a string"""
+        """Represent the configuration as a string."""
         return f"{self.__class__.__name__}({repr(self.to_dict())})"
 
     @contextlib.contextmanager
     def __call__(self, values: dict[str, Any] | None = None, **kwargs):
-        """context manager temporarily changing the configuration
+        """Context manager temporarily changing the configuration.
 
         Args:
             values (dict): New configuration parameters

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/modelrunner/model/__init__.py

@@ -1,5 +1,4 @@
-"""
-Defines models that handle a simulation and its inputs
+"""Defines models that handle a simulation and its inputs.
 
 .. autosummary::
    :nosignatures:

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/modelrunner/model/base.py

@@ -1,5 +1,4 @@
-"""
-Base class describing a model
+"""Base class describing a model.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -14,6 +13,7 @@ from datetime import datetime
 from typing import TYPE_CHECKING, Any, Sequence
 
 from ..storage import ModeType, StorageGroup, open_storage
+from ..utils import is_serial_or_mpi_root
 from .parameters import DeprecatedParameter, HideParameter, Parameterized
 
 if TYPE_CHECKING:
@@ -21,7 +21,7 @@ if TYPE_CHECKING:
 
 
 class ModelBase(Parameterized, metaclass=ABCMeta):
-    """base class for describing models"""
+    """Base class for describing models."""
 
     name: str | None = None
     """str: the name of the model"""
@@ -36,7 +36,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
         mode: ModeType = "insert",
         strict: bool = False,
     ):
-        """initialize the parameters of the object
+        """Initialize the parameters of the object.
 
         Args:
             parameters (dict):
@@ -67,7 +67,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
 
     @property
     def storage(self) -> StorageGroup:
-        """:class:`StorageGroup`: Storage to which data can be written"""
+        """:class:`StorageGroup`: Storage to which data can be written."""
         if self._storage is None:
             if self.output is None:
                 raise RuntimeError("Output file needs to be specified")
@@ -75,17 +75,20 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
         return self._storage
 
     def close(self) -> None:
-        """close any opened storages"""
+        """Close any opened storages."""
         if self._storage is not None:
             self._storage.close()
         self._storage = None
 
     @abstractmethod
     def __call__(self):
-        """main method calculating the result. Needs to be specified by sub-class"""
+        """Main method calculating the result.
+
+        Needs to be specified by sub-class
+        """
 
     def get_result(self, data: Any = None) -> Result:
-        """get the result as a :class:`~model.Result` object
+        """Get the result as a :class:`~model.Result` object.
 
         Args:
             data:
@@ -103,7 +106,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
         return Result(self, data, info=info)
 
     def write_result(self, result: Result | None = None) -> None:
-        """write the result to the output file
+        """Write the result to the output file.
 
         Args:
             result:
@@ -127,7 +130,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
 
     @classmethod
     def _prepare_argparser(cls, name: str | None = None) -> argparse.ArgumentParser:
-        """create argument parser for setting parameters of this model
+        """Create argument parser for setting parameters of this model.
 
         Args:
             name (str):
@@ -167,7 +170,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
     def from_command_line(
         cls, args: Sequence[str] | None = None, name: str | None = None
     ) -> ModelBase:
-        """create model from command line parameters
+        """Create model from command line parameters.
 
         Args:
             args (list):
@@ -207,7 +210,7 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
     def run_from_command_line(
         cls, args: Sequence[str] | None = None, name: str | None = None
     ) -> Result:
-        """run model using command line parameters
+        """Run model using command line parameters.
 
         Args:
             args (list):
@@ -223,13 +226,13 @@ class ModelBase(Parameterized, metaclass=ABCMeta):
 
         # run the model
         result = mdl.get_result()
-        if mdl.output:
-            # write the results to a file
+
+        # write the results
+        if mdl.output and is_serial_or_mpi_root():
+            # Write the results to a file if `output` is specified and if we are on the
+            # root node of an MPI run (or a serial program). The second check is a
+            # safe-guard against writing data on sub-nodes during an MPI program.
             mdl.write_result(result=result)
-        # else:
-        #     # display the results on stdout
-        #     storage = MemoryStorage()
-        #     result.to_file(storage)
 
         # close the output file
         mdl.close()

{py_modelrunner-0.18.1 → py_modelrunner-0.18.2}/modelrunner/model/factory.py

@@ -1,5 +1,4 @@
-"""
-Functions for creating models and model classes from other input
+"""Functions for creating models and model classes from other input.
 
 .. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de>
 """
@@ -18,14 +17,14 @@ if TYPE_CHECKING:
     from ..run.results import Result  # @UnusedImport
 
 _DEFAULT_MODEL: Callable | ModelBase | None = None
-"""stores the default model that will be used automatically"""
+"""Stores the default model that will be used automatically."""
 
 
 TModel = TypeVar("TModel", Callable, ModelBase, None)
 
 
 def set_default(func_or_model: TModel) -> TModel:
-    """sets the function or model as the default model
+    """Sets the function or model as the default model.
 
     The last model that received this flag will be run automatically. This only affects
     the behavior when the script is run using `modelrunner` from the command line, e.g.,
@@ -47,7 +46,7 @@ TFunc = TypeVar("TFunc", bound=Any)
 
 
 def cleared_default_model(func: TFunc) -> TFunc:
-    """run the function with a cleared _DEFAULT_MODEL and restore it afterwards"""
+    """Run the function with a cleared _DEFAULT_MODEL and restore it afterwards."""
 
     @functools.wraps(func)
     def inner(*args, **kwargs):
@@ -63,7 +62,7 @@ def cleared_default_model(func: TFunc) -> TFunc:
 
 
 def make_model_class(func: Callable, *, default: bool = False) -> type[ModelBase]:
-    """create a model from a function by interpreting its signature
+    """Create a model from a function by interpreting its signature.
 
     Args:
         func (callable):
@@ -103,7 +102,7 @@ def make_model_class(func: Callable, *, default: bool = False) -> type[ModelBase
             parameters_default.append(parameter)
 
     def __call__(self, *args, **kwargs):
-        """call the function preserving the original signature"""
+        """Call the function preserving the original signature."""
         parameters = {}
         for i, (name, value) in enumerate(self.parameters.items()):
             if len(args) > i:
@@ -150,7 +149,7 @@ def make_model(
     mode: ModeType = "insert",
     default: bool = False,
 ) -> ModelBase:
-    """create model from a function and a dictionary of parameters
+    """Create model from a function and a dictionary of parameters.
 
     Args:
         func (callable):