idmtools 0.0.0.dev0__py3-none-any.whl → 0.0.2__py3-none-any.whl

idmtools/utils/json.py

@@ -0,0 +1,82 @@
+"""
+JSON utilities for idmtools such as encoders and decoders.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+import json
+from enum import Enum
+from json import JSONEncoder
+from logging import getLogger
+from typing import List, Any, Dict, Union
+from uuid import UUID
+from idmtools.assets import AssetCollection, Asset
+from idmtools.core import EntityStatus
+from idmtools.entities import CommandLine
+from idmtools.entities.experiment import Experiment
+from idmtools.entities.itask import ITask
+from idmtools.entities.simulation import Simulation
+from idmtools.utils.entities import as_dict
+from datetime import datetime
+
+user_logger = getLogger('user')
+
+
+class IDMJSONEncoder(JSONEncoder):
+    """
+    IDMJSONEncoder handles encoding IDM specific items.
+
+    """
+
+    def default(self, o):
+        """
+        JSON Encode item.
+
+        Args:
+            o: Object to encode
+
+        Returns:
+            JSON encoded object
+        """
+        if isinstance(o, Enum):
+            return o.value
+        elif isinstance(o, EntityStatus):
+            return o.value
+        elif isinstance(o, Experiment):
+            return o.to_dict()
+        elif isinstance(o, Simulation):
+            return o.to_dict()
+        elif isinstance(o, ITask):
+            result = o.to_dict()
+            result["task_type"] = o.__class__.__name__
+            return result
+        elif isinstance(o, bytes):
+            return None
+        elif isinstance(o, (CommandLine, UUID)):
+            return str(o)
+        elif isinstance(o, Asset):
+            return as_dict(o, exclude=['content'])
+        elif isinstance(o, AssetCollection):
+            return o.assets
+        elif isinstance(o, (dict, int, list, str)):
+            return o
+        elif isinstance(o, datetime):
+            return str(o)
+
+
+def load_json_file(path: str) -> Union[Dict[Any, Any], List]:
+    """
+    Load a json object from a file.
+
+    Args:
+        path: Path to file
+
+    Returns:
+        Contents of file parsed by JSON
+    """
+    if not path:
+        return
+    try:
+        with open(path, 'r') as fp:
+            return json.load(fp)
+    except IOError as e:
+        user_logger.error(f"The file at {path} could not be loaded or parsed to JSON.\n{e}")

idmtools/utils/language.py

@@ -0,0 +1,107 @@
+"""
+Tools to format different outputs for human consumption.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+from collections.abc import Iterable
+from typing import Type
+
+
+def on_off(test) -> str:
+    """
+    Print on or off depending on boolean state of test.
+
+    Args:
+        test: Boolean/object to check state
+
+    Returns:
+        On or off
+    """
+    return "on" if test else "off"
+
+
+def pluralize(word, plural_suffix="s"):
+    """
+    Convert work to plural form.
+
+    Args:
+        word: Word
+        plural_suffix: plural suffix. Default to s
+
+    Returns:
+        Pluralized string
+    """
+    if isinstance(word, Iterable):
+        return plural_suffix if len(word) > 1 else ""
+    return plural_suffix if word > 1 else ""
+
+
+def verbose_timedelta(delta):
+    """
+    The verbose_timedelta provides ms accurate, human readable of a time delta.
+
+    Args:
+        delta:
+
+    Returns:
+        Time delta
+    """
+    if isinstance(delta, float):
+        if delta < 1:
+            return "0 seconds"
+        hours, remainder = divmod(delta, 3600)
+    else:
+        if delta.seconds < 1:
+            return "0 seconds"
+        hours, remainder = divmod(delta.seconds, 3600)
+
+    minutes, seconds = divmod(remainder, 60)
+    hstr = "%s hour%s" % (hours, "s"[hours == 1:])
+    mstr = "%s minute%s" % (minutes, "s"[minutes == 1:])
+    sstr = "{:.2f} second{}".format(seconds, "s"[seconds == 1:])
+    dhms = [hstr, mstr, sstr]
+    for x in range(len(dhms)):
+        if not dhms[x].startswith('0'):
+            dhms = dhms[x:]
+            break
+    dhms.reverse()
+    for x in range(len(dhms)):
+        if not dhms[x].startswith('0'):
+            dhms = dhms[x:]
+            break
+    dhms.reverse()
+    return ', '.join(dhms)
+
+
+def get_qualified_class_name(cls: Type) -> str:
+    """
+    Return the full class name for an object.
+
+    Args:
+        cls: Class object to get name
+
+    Returns:
+        Fully qualified class name
+    """
+    return f'{cls.__module__}.{cls.__name__}'
+
+
+def get_qualified_class_name_from_obj(obj: object) -> str:
+    """
+    Return the full class name from object.
+
+    Args:
+        obj: Object
+
+    Example:
+        ```
+        a = Platform('COMPS')
+        class_name = get_qualified_class_name(a)
+        print(class_name)
+        'idmtools_platform_comps.comps_platform.COMPSPlatform'
+        ```
+
+    Returns:
+        Full module path to class of object
+    """
+    return get_qualified_class_name(obj.__class__)

idmtools/utils/local_os.py

@@ -0,0 +1,40 @@
+"""
+Info to determine info about Operation Systems.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+import platform
+import getpass
+
+
+class LocalOS:
+    """
+    A Central class for representing values whose proper access methods may differ between platforms.
+    """
+
+    class UnknownOS(Exception):
+        """
+        Unknown os detected.
+        """
+        pass
+
+    os_mapping = {'windows': 'win',
+                  'linux': 'lin',
+                  'darwin': 'mac'}
+
+    _os = platform.system().lower()
+    if _os not in os_mapping:
+        raise UnknownOS("Operating system %s is not currently supported." % _os)
+
+    username = getpass.getuser()
+    name = os_mapping[_os]
+
+    @staticmethod
+    def is_window() -> bool:
+        """
+        Are we running on a windows system?
+
+        Returns:
+            True if on windows
+        """
+        return LocalOS.name == 'win'

idmtools/utils/time.py

@@ -0,0 +1,22 @@
+"""
+Timestamp function.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+
+
+def timestamp(time=None):
+    """
+    Return a timestamp.
+
+    Args:
+        time: A time object; if None provided, use now.
+
+    Returns:
+        A string timestamp in UTC, format YYYYMMDD_HHmmSS.
+    """
+    import datetime
+    if not time:
+        time = datetime.datetime.utcnow()
+    ts = time.strftime('%Y%m%d_%H%M%S')
+    return ts

idmtools-0.0.2.dist-info/METADATA

@@ -0,0 +1,120 @@
+Metadata-Version: 2.4
+Name: idmtools
+Version: 0.0.2
+Summary: Core tools for modeling
+Author-email: Zhaowei Du <zdu@idmod.org>, Sharon Chen <shchen@idmod.org>, Clinton Collins <ccollins@idmod.org>, Benoit Raybaud <braybaud@idmod.org>, Clark Kirkman IV <ckirkman@idmod.org>, Emily Claps <emily.claps@gatesfoundation.org>, Jen Schripsema <jschripsema@idmod.org>, Ross Carter <rcarter@idmod.org>, Mandy Izzo <mizzo@idmod.org>, Mary Fisher <mafisher@idmod.org>, Lauren George <lgeorge@idmod.org>
+License: Proprietary or specify if known
+Project-URL: Homepage, https://github.com/InstituteforDiseaseModeling/idmtools
+Project-URL: Documentation, https://idmtools.readthedocs.io
+Project-URL: Bug Tracker, https://github.com/InstituteforDiseaseModeling/idmtools/issues
+Keywords: modeling,IDM,IDMTools
+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: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.TXT
+Requires-Dist: backoff<2.3,>=1.10.0
+Requires-Dist: coloredlogs~=15.0
+Requires-Dist: diskcache~=5.4.0
+Requires-Dist: filelock
+Requires-Dist: more-itertools~=10.3.0
+Requires-Dist: numpy!=1.19.4
+Requires-Dist: pandas>=1.1.4
+Requires-Dist: pluggy~=1.5
+Requires-Dist: PyYAML<6.1,>=5.3.0
+Requires-Dist: tabulate<0.10,>=0.8.9
+Requires-Dist: tqdm<5,>=4.52.0
+Requires-Dist: jinja2~=3.1.3
+Requires-Dist: packaging<25.0,>=20.4
+Provides-Extra: test
+Requires-Dist: allure-pytest<2.16,>=2.8.34; extra == "test"
+Requires-Dist: junitparser>=4.0.2; extra == "test"
+Requires-Dist: livereload~=2.6.3; extra == "test"
+Requires-Dist: pytest>=7.4.4; extra == "test"
+Requires-Dist: pytest-cache>=1.0; extra == "test"
+Requires-Dist: pytest-cov>=2.11.1; extra == "test"
+Requires-Dist: pytest-html>=3.1.1; extra == "test"
+Requires-Dist: py>=1.11.0; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: pytest-timeout~=2.4.0; extra == "test"
+Requires-Dist: pytest-xdist~=3.8; extra == "test"
+Requires-Dist: flake8>=7.0; extra == "test"
+Requires-Dist: flake8-docstrings~=1.7; extra == "test"
+Requires-Dist: coverage>=7.13; extra == "test"
+Requires-Dist: twine>=3.4.1; extra == "test"
+Provides-Extra: notebooks
+Requires-Dist: docker>5.0; extra == "notebooks"
+Provides-Extra: packaging
+Provides-Extra: idm
+Requires-Dist: idmtools_platform_comps; extra == "idm"
+Requires-Dist: idmtools_cli; extra == "idm"
+Requires-Dist: idmtools_models; extra == "idm"
+Provides-Extra: full
+Requires-Dist: idmtools_platform_comps; extra == "full"
+Requires-Dist: idmtools_cli; extra == "full"
+Requires-Dist: idmtools_models; extra == "full"
+Requires-Dist: idmtools_platform_general; extra == "full"
+Requires-Dist: idmtools_platform_slurm; extra == "full"
+Requires-Dist: idmtools_platform_container; extra == "full"
+Provides-Extra: container
+Requires-Dist: idmtools_cli; extra == "container"
+Requires-Dist: idmtools_models; extra == "container"
+Requires-Dist: idmtools_platform_general; extra == "container"
+Requires-Dist: idmtools_platform_container; extra == "container"
+Provides-Extra: slurm
+Requires-Dist: idmtools_cli; extra == "slurm"
+Requires-Dist: idmtools_models; extra == "slurm"
+Requires-Dist: idmtools_platform_general; extra == "slurm"
+Requires-Dist: idmtools_platform_slurm; extra == "slurm"
+Dynamic: license-file
+
+![Staging: idmtools-core](https://github.com/InstituteforDiseaseModeling/idmtools/workflows/Staging:%20idmtools-core/badge.svg?branch=dev)
+
+# idmtools-core
+
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of Contents**
+
+- [Overview](#overview)
+- [Installing](#installing)
+- [Development Tips](#development-tips)
+- [Future Work](#future-work)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
+# Overview
+
+idmtools provides the APIS, logic, and other operations to provision, execute, analysis, and manage jobs running on an HPC cluster
+
+To see the full API documentation, see https://institutefordiseasemodeling.github.io/idmtools/idmtools_index.html
+
+
+# Installing
+
+```bash
+pip install idmtools --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+```
+
+# Development Tips
+
+There is a Makefile file available for most common development tasks. Here is a list of commands
+
+```bash
+clean       -   Clean up temproary files
+lint        -   Lint package and tests
+test        -   Run All tests
+coverage    -   Run tests and generate coverage report that is shown in browser
+```
+
+On Windows, you can use `pymake` instead of `make`
+
+# Future Work
+
+* Add new analyze api to platform
+    * Where does this go?
+    * Move current code to Comps
+    * Add support for platform specific bootstrap scripts

idmtools-0.0.2.dist-info/RECORD

@@ -0,0 +1,116 @@
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idmtools-0.0.2.dist-info/entry_points.txt

@@ -0,0 +1,9 @@
+[idmtools_experiment]
+idmtools_experiment = idmtools.entities.experiment:ExperimentSpecification
+
+[idmtools_hooks]
+idmtools_add_git_tag = idmtools.plugins.git_commit
+
+[idmtools_task]
+idmtools_task_command = idmtools.entities.command_task:CommandTaskSpecification
+idmtools_task_docker = idmtools.core.docker_task:DockerTaskSpecification

idmtools-0.0.2.dist-info/licenses/LICENSE.TXT

@@ -0,0 +1,3 @@
+idmtools is licensed under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License.
+
+To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode

idmtools-0.0.0.dev0.dist-info/METADATA

@@ -1,41 +0,0 @@
-Metadata-Version: 2.4
-Name: idmtools
-Version: 0.0.0.dev0
-Summary: Placeholder package for idmtools - reserved for future use
-Author-email: IDM <idmtools@idmod.org>
-License: Proprietary
-Project-URL: Homepage, https://github.com/InstituteforDiseaseModeling/idmtools
-Project-URL: Bug Tracker, https://github.com/InstituteforDiseaseModeling/idmtools/issues
-Keywords: placeholder,reserved,idmtools
-Classifier: Development Status :: 1 - Planning
-Classifier: Intended Audience :: Developers
-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: >=3.8
-Description-Content-Type: text/markdown
-
-# idmtools
-
-**PLACEHOLDER PACKAGE - NOT FOR USE**
-
-This package is a placeholder to reserve the name `idmtools` on PyPI.
-
-The actual package implementation will be released in the future.
-
-## Purpose
-
-This placeholder ensures the package name is reserved and prevents name squatting.
-
-## Status
-
-This is version 0.0.0.dev0 - a minimal placeholder release.
-
-## Future Release
-
-The full implementation of idmtools will be published when ready.
-
-For more information, visit: https://github.com/InstituteforDiseaseModeling/idmtools

idmtools-0.0.0.dev0.dist-info/RECORD

@@ -1,5 +0,0 @@
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-idmtools-0.0.0.dev0.dist-info/RECORD,,