py-modelrunner 0.18.1__tar.gz → 0.18.3__tar.gz

{py_modelrunner-0.18.1 → py_modelrunner-0.18.3}/.github/workflows/build.yml

@@ -12,10 +12,10 @@ jobs:
         python-version: ['3.8', '3.12']
 
     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-0.18.1 → py_modelrunner-0.18.3}/.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-0.18.1 → py_modelrunner-0.18.3}/.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-0.18.1 → py_modelrunner-0.18.3}/.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-0.18.1 → py_modelrunner-0.18.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py-modelrunner
-Version: 0.18.1
+Version: 0.18.3
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT
@@ -30,7 +30,7 @@ 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 +49,6 @@ 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-0.18.1 → py_modelrunner-0.18.3}/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-0.18.1 → py_modelrunner-0.18.3}/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-0.18.1 → py_modelrunner-0.18.3}/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-0.18.3}/docs/source/run_autodoc.py

@@ -4,15 +4,16 @@ 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):
-    """reads in a file, replaces the given data using python formatting and
-    writes back the result to a file.
+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.
 
     Args:
         infile (str):
@@ -22,26 +23,25 @@ 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
 
-    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(
@@ -67,7 +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-0.18.1 → py_modelrunner-0.18.3}/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'
@@ -50,25 +48,28 @@ 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):
-    """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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/examples/read_many.py

@@ -1,17 +1,16 @@
 #!/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>
 """
 
-import os
+from pathlib import Path
 
 from modelrunner import ResultCollection, make_model_class
 
 
 def multiply(a: float = 1, b: float = 2):
-    """Multiply two numbers"""
+    """Multiply two numbers."""
     return a * b
 
 
@@ -20,11 +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-0.18.1 → py_modelrunner-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/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-0.18.3}/examples/submit_many_func.py

@@ -1,21 +1,19 @@
 #!/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>
 """
 
-
 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-0.18.3}/examples/submit_many_iter.py

@@ -1,21 +1,19 @@
 #!/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>
 """
 
-
 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-0.18.3}/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-0.18.3}/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-0.18.3}/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 = '0.18.3'
+__version_tuple__ = version_tuple = (0, 18, 3)