py-modelrunner 0.20.0__tar.gz → 0.20.1__tar.gz

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py-modelrunner
-Version: 0.20.0
+Version: 0.20.1
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/modelrunner/_version.py

@@ -18,7 +18,7 @@ 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)
+__version__ = version = '0.20.1'
+__version_tuple__ = version_tuple = (0, 20, 1)
 
-__commit_id__ = commit_id = 'ga172a6158'
+__commit_id__ = commit_id = 'g25228fdcb'

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/modelrunner/run/job.py

@@ -54,7 +54,7 @@ DEFAULT_CONFIG = [
         "qsub",
         str,
         "The job submission method.",
-        choices=["background", "foreground", "qsub", "srun"],
+        choices=["background", "foreground", "qsub", "sbatch", "srun"],
     ),
     Parameter(
         "partition", "", str, "The partition to which the job will be submitted."
@@ -159,8 +159,8 @@ def submit_job(
             working directory for remote jobs.
         method (str):
             Specifies the submission method. Currently `background`, `foreground`,
-            'srun', and `qsub` are supported. The special value `auto` reads the method
-            from the `config` argument.
+            'sbatch', and `qsub` are supported. The special value `auto` reads the
+            method from the `config` argument.
         use_modelrunner (bool):
             If True, `script` is envoked with the modelrunner library, e.g. by calling
             `python -m modelrunner {script}`.
@@ -267,7 +267,7 @@ def submit_job(
     script_content = Template(script_template).render(script_args)
     logger.debug("Script: `%s`", script_content)
 
-    if method in {"qsub", "srun"}:
+    if method in {"qsub", "srun", "sbatch"}:
         # submit job to queue
         proc = sp.Popen(
             [method],

py_modelrunner-0.20.1/modelrunner/run/templates/sbatch.jinja

@@ -0,0 +1,42 @@
+#!/bin/bash -l
+
+{% if LOG_FOLDER is defined %}
+# Standard output and error
+#SBATCH --output={{ LOG_FOLDER }}/{{ JOB_NAME }}.out.txt
+#SBATCH --error={{ LOG_FOLDER }}/{{ JOB_NAME }}.err.txt
+{% endif %}
+# Preserve environment variables:
+#SBATCH --export=ALL
+#SBATCH --job-name={{ JOB_NAME }}
+# Queue (Partition):
+{% if CONFIG['partition'] is defined %}
+#SBATCH -p {{ CONFIG['partition'] }}
+{% endif %}
+# Set max. runtime
+{% if CONFIG['time'] is defined %}
+#SBATCH --time={{ TIME }}
+{% endif %}
+#SBATCH --time=12:00:00
+
+hostname
+echo $JOB_ID
+
+{% if CONFIG.num_threads is number %}
+# set the number of threads to use
+export MKL_NUM_THREADS={{ CONFIG.num_threads }}
+export NUMBA_NUM_THREADS={{ CONFIG.num_threads }}
+export NUMEXPR_NUM_THREADS={{ CONFIG.num_threads }}
+export OMP_NUM_THREADS={{ CONFIG.num_threads }}
+export OPENBLAS_NUM_THREADS={{ CONFIG.num_threads }}
+{% endif %}
+
+{% if OUTPUT_FOLDER is defined and OUTPUT_FOLDER %}
+mkdir -p {{ OUTPUT_FOLDER }}
+{% endif %}
+
+# Run the program
+{% if USE_MODELRUNNER is defined and USE_MODELRUNNER %}
+{{ CONFIG.python_bin }} -m modelrunner {{ MODEL_FILE }} {{ JOB_ARGS }}
+{% else %}
+{{ CONFIG.python_bin }} {{ MODEL_FILE }} {{ JOB_ARGS }}
+{% endif %}

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/modelrunner/run/templates/srun.jinja

@@ -12,6 +12,11 @@
 {% if CONFIG['partition'] is defined %}
 #SBATCH -p {{ CONFIG['partition'] }}
 {% endif %}
+# Set max. runtime
+{% if CONFIG['time'] is defined %}
+#SBATCH --time={{ TIME }}
+{% endif %}
+#SBATCH --time=12:00:00
 
 hostname
 echo $JOB_ID

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/modelrunner/storage/trajectory.py

@@ -124,7 +124,9 @@ class TrajectoryWriter:
                 shape: tuple[int, ...] = data.shape
                 self._item_type = "array"
             else:
-                raise NotImplementedError("Trajectories must be arrays for zarr3")
+                raise NotImplementedError(
+                    f"Trajectories must be arrays for zarr3, not {data.__class__}"
+                )
             self._trajectory.create_dynamic_array("data", shape=shape, dtype=dtype)
             self._trajectory.create_dynamic_array("time", shape=(), dtype=float)
             self._trajectory.write_attrs(None, {"item_type": self._item_type})

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/py_modelrunner.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py-modelrunner
-Version: 0.20.0
+Version: 0.20.1
 Summary: Python classes for organizing (HPC) simulations
 Author-email: David Zwicker <david.zwicker@ds.mpg.de>
 License: MIT

{py_modelrunner-0.20.0 → py_modelrunner-0.20.1}/py_modelrunner.egg-info/SOURCES.txt

@@ -62,6 +62,7 @@ modelrunner/run/compatibility/version2.py
 modelrunner/run/templates/background.jinja
 modelrunner/run/templates/foreground.jinja
 modelrunner/run/templates/qsub.jinja
+modelrunner/run/templates/sbatch.jinja
 modelrunner/run/templates/srun.jinja
 modelrunner/storage/__init__.py
 modelrunner/storage/access_modes.py
@@ -86,6 +87,8 @@ py_modelrunner.egg-info/SOURCES.txt
 py_modelrunner.egg-info/dependency_links.txt
 py_modelrunner.egg-info/not-zip-safe
 py_modelrunner.egg-info/requires.txt
+py_modelrunner.egg-info/scm_file_list.json
+py_modelrunner.egg-info/scm_version.json
 py_modelrunner.egg-info/top_level.txt
 scripts/create_compatibility_files.py
 scripts/format_code.sh

py_modelrunner-0.20.1/py_modelrunner.egg-info/scm_file_list.json

@@ -0,0 +1,212 @@
+{
+  "files": [
+    ".gitignore",
+    "README.md",
+    "requirements.txt",
+    "pyproject.toml",
+    "requirements_full.txt",
+    "LICENSE",
+    ".readthedocs.yaml",
+    "modelrunner/.gitignore",
+    "modelrunner/config.py",
+    "modelrunner/utils.py",
+    "modelrunner/__main__.py",
+    "modelrunner/py.typed",
+    "modelrunner/__init__.py",
+    "modelrunner/run/job.py",
+    "modelrunner/run/results.py",
+    "modelrunner/run/__main__.py",
+    "modelrunner/run/launch.py",
+    "modelrunner/run/__init__.py",
+    "modelrunner/run/templates/srun.jinja",
+    "modelrunner/run/templates/qsub.jinja",
+    "modelrunner/run/templates/foreground.jinja",
+    "modelrunner/run/templates/background.jinja",
+    "modelrunner/run/templates/sbatch.jinja",
+    "modelrunner/run/compatibility/triage.py",
+    "modelrunner/run/compatibility/version1.py",
+    "modelrunner/run/compatibility/version0.py",
+    "modelrunner/run/compatibility/version2.py",
+    "modelrunner/run/compatibility/__init__.py",
+    "modelrunner/storage/base.py",
+    "modelrunner/storage/access_modes.py",
+    "modelrunner/storage/utils.py",
+    "modelrunner/storage/trajectory.py",
+    "modelrunner/storage/group.py",
+    "modelrunner/storage/attributes.py",
+    "modelrunner/storage/tools.py",
+    "modelrunner/storage/__init__.py",
+    "modelrunner/storage/backend/zarr.py",
+    "modelrunner/storage/backend/memory.py",
+    "modelrunner/storage/backend/_zarr3.py",
+    "modelrunner/storage/backend/yaml.py",
+    "modelrunner/storage/backend/json.py",
+    "modelrunner/storage/backend/text_base.py",
+    "modelrunner/storage/backend/utils.py",
+    "modelrunner/storage/backend/_zarr2.py",
+    "modelrunner/storage/backend/hdf.py",
+    "modelrunner/storage/backend/__init__.py",
+    "modelrunner/model/parameters.py",
+    "modelrunner/model/base.py",
+    "modelrunner/model/factory.py",
+    "modelrunner/model/__init__.py",
+    ".github/workflows/release_pip.yml",
+    ".github/workflows/coverage_report.yml",
+    ".github/workflows/build.yml",
+    ".github/workflows/check_docs.yml",
+    "scripts/tests_coverage.sh",
+    "scripts/tests_debug.sh",
+    "scripts/requirements.txt",
+    "scripts/tests_run.sh",
+    "scripts/run_tests.py",
+    "scripts/tests_codestyle.sh",
+    "scripts/format_code.sh",
+    "scripts/tests_all.sh",
+    "scripts/performance_hdf5_zarr.py",
+    "scripts/tests_types.sh",
+    "scripts/tests_parallel.sh",
+    "scripts/create_compatibility_files.py",
+    "examples/script_minimal.py",
+    "examples/script_many_classes.py",
+    "examples/io_yaml.py",
+    "examples/script_custom_func.py",
+    "examples/model_storage_output.py",
+    "examples/submit_function.py",
+    "examples/io_json.py",
+    "examples/model_class.py",
+    "examples/script_model_class.py",
+    "examples/submit_shebang.py",
+    "examples/read_many.py",
+    "examples/script_function.py",
+    "examples/model_decorator.py",
+    "examples/model_function.py",
+    "examples/io_hdf.py",
+    "examples/submit_many_func.py",
+    "examples/submit_many_iter.py",
+    "tests/test_version.py",
+    "tests/conftest.py",
+    "tests/requirements.txt",
+    "tests/test_config.py",
+    "tests/test_examples.py",
+    "tests/test_main.py",
+    "tests/helpers/asserts.py",
+    "tests/helpers/storage.py",
+    "tests/helpers/__init__.py",
+    "tests/run/test_job.py",
+    "tests/run/test_run_main.py",
+    "tests/run/test_results.py",
+    "tests/run/scripts/function.py",
+    "tests/run/scripts/print.py",
+    "tests/run/scripts/fail.py",
+    "tests/run/scripts/custom.jinja",
+    "tests/run/scripts/script.py",
+    "tests/storage/test_register_action.py",
+    "tests/storage/test_group.py",
+    "tests/storage/test_storage_generic.py",
+    "tests/storage/test_trajectory.py",
+    "tests/storage/test_storage_special.py",
+    "tests/storage/test_utils.py",
+    "tests/model/test_model.py",
+    "tests/model/test_parameters.py",
+    "tests/model/scripts/make_model_class.py",
+    "tests/model/scripts/make_model.py",
+    "tests/model/scripts/make_model_marked.py",
+    "tests/model/scripts/function.py",
+    "tests/model/scripts/function_marked.py",
+    "tests/model/scripts/function_main.py",
+    "tests/model/scripts/empty.py",
+    "tests/compatibility/test_compatibility.py",
+    "tests/compatibility/1/object.yaml",
+    "tests/compatibility/1/array.yaml",
+    "tests/compatibility/1/array_col.pkl",
+    "tests/compatibility/1/array.json",
+    "tests/compatibility/1/object.pkl",
+    "tests/compatibility/1/array_col.yaml",
+    "tests/compatibility/1/array.zarr",
+    "tests/compatibility/1/dict.json",
+    "tests/compatibility/1/array.pkl",
+    "tests/compatibility/1/array_col.zarr",
+    "tests/compatibility/1/_object.zarr",
+    "tests/compatibility/1/_dict.zarr",
+    "tests/compatibility/1/dict.pkl",
+    "tests/compatibility/1/object.json",
+    "tests/compatibility/1/dict.yaml",
+    "tests/compatibility/1/array_col.json",
+    "tests/compatibility/2/nested.hdf",
+    "tests/compatibility/2/array.yaml",
+    "tests/compatibility/2/array_col.zip",
+    "tests/compatibility/2/array.zip",
+    "tests/compatibility/2/array_col.pkl",
+    "tests/compatibility/2/array.json",
+    "tests/compatibility/2/array_col.yaml",
+    "tests/compatibility/2/nested.json",
+    "tests/compatibility/2/dict.json",
+    "tests/compatibility/2/dict.zip",
+    "tests/compatibility/2/nested.pkl",
+    "tests/compatibility/2/array.pkl",
+    "tests/compatibility/2/dict.hdf",
+    "tests/compatibility/2/nested.yaml",
+    "tests/compatibility/2/array_col.hdf",
+    "tests/compatibility/2/dict.pkl",
+    "tests/compatibility/2/nested.zip",
+    "tests/compatibility/2/array.hdf",
+    "tests/compatibility/2/dict.yaml",
+    "tests/compatibility/2/array_col.json",
+    "tests/compatibility/3/model_nested.hdf",
+    "tests/compatibility/3/nested.hdf",
+    "tests/compatibility/3/model_array.yaml",
+    "tests/compatibility/3/array.yaml",
+    "tests/compatibility/3/model_array.hdf",
+    "tests/compatibility/3/model_dict.hdf",
+    "tests/compatibility/3/array_col.zip",
+    "tests/compatibility/3/array.zip",
+    "tests/compatibility/3/array_col.pkl",
+    "tests/compatibility/3/model_dict.json",
+    "tests/compatibility/3/array.json",
+    "tests/compatibility/3/model_array.json",
+    "tests/compatibility/3/model_array_col.hdf",
+    "tests/compatibility/3/model_nested.json",
+    "tests/compatibility/3/model_dict.yaml",
+    "tests/compatibility/3/array_col.yaml",
+    "tests/compatibility/3/model_dict.pkl",
+    "tests/compatibility/3/nested.json",
+    "tests/compatibility/3/dict.json",
+    "tests/compatibility/3/dict.zip",
+    "tests/compatibility/3/model_array_col.yaml",
+    "tests/compatibility/3/model_nested.pkl",
+    "tests/compatibility/3/nested.pkl",
+    "tests/compatibility/3/model_nested.zip",
+    "tests/compatibility/3/array.pkl",
+    "tests/compatibility/3/dict.hdf",
+    "tests/compatibility/3/nested.yaml",
+    "tests/compatibility/3/model_array_col.pkl",
+    "tests/compatibility/3/model_array_col.zip",
+    "tests/compatibility/3/array_col.hdf",
+    "tests/compatibility/3/model_nested.yaml",
+    "tests/compatibility/3/dict.pkl",
+    "tests/compatibility/3/model_array_col.json",
+    "tests/compatibility/3/nested.zip",
+    "tests/compatibility/3/model_dict.zip",
+    "tests/compatibility/3/array.hdf",
+    "tests/compatibility/3/model_array.zip",
+    "tests/compatibility/3/dict.yaml",
+    "tests/compatibility/3/model_array.pkl",
+    "tests/compatibility/3/array_col.json",
+    "tests/compatibility/0/result.yaml",
+    "tests/compatibility/0/result.json",
+    "tests/compatibility/0/result.hdf",
+    "tests/compatibility/0/result.pkl",
+    "docs/Makefile",
+    "docs/requirements.txt",
+    "docs/build_all.sh",
+    "docs/source/conf.py",
+    "docs/source/.gitignore",
+    "docs/source/installation.rst",
+    "docs/source/index.rst",
+    "docs/source/sphinx_simplify_typehints.py",
+    "docs/source/run_autodoc.py",
+    "docs/source/examples.rst",
+    "docs/source/parse_examples.py",
+    "docs/source/user_manual.rst"
+  ]
+}

py_modelrunner-0.20.1/py_modelrunner.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.20.1",
+  "distance": 0,
+  "node": "g25228fdcb2126acc0b18bf32a0dfd86b2b8223e6",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-07-17"
+}