idmtools 0.0.0.dev0__tar.gz → 0.0.3__tar.gz

idmtools-0.0.3/.bumpversion.cfg

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+[bumpversion]
+current_version = 3.0.0+nightly
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?P<release>\+\w+)?(\.(?P<build>\d+))?
+serialize = 
+	{major}.{minor}.{patch}{release}.{build}
+	{major}.{minor}.{patch}{release}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = prod
+first_value = prod
+values = 
+	prod
+	+nightly
+
+[bumpversion:file:./idmtools/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
+serialize = {major}.{minor}.{patch}{release}
+	{major}.{minor}.{patch}
+
+[bumpversion:file:./pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+serialize = {major}.{minor}.{patch}{release}
+	{major}.{minor}.{patch}

idmtools-0.0.3/LICENSE.TXT

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+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-0.0.3/MANIFEST.in

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+include README.md
+include LICENSE.TXT
+prune tests

idmtools-0.0.3/Makefile

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+PACKAGE_NAME=idmtools_core
+include $(abspath ../dev_scripts/package_general.mk)
+
+help:
+	help-from-makefile -f ../dev_scripts/package_general.mk -f ./Makefile
+
+update-dependent-libraries: ## update any libraries in repo that depend on core
+	$(PDS)update_core_version.py

idmtools-0.0.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: idmtools
+Version: 0.0.3
+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-0.0.3/README.md

@@ -0,0 +1,47 @@
+![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-0.0.3/idmtools/__init__.py

@@ -0,0 +1,27 @@
+"""idmtools core package.
+
+This init installs a system exception hook for idmtools.
+It also ensures the configuration is loaded.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+import sys
+from idmtools.core.exceptions import idmtools_error_handler
+from idmtools.config.idm_config_parser import IdmConfigParser   # noqa: F401
+
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ImportError:
+    # Python < 3.8
+    from importlib_metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("idmtools")  # Use your actual package name
+except PackageNotFoundError:
+    # Package not installed, use fallback
+    __version__ = "0.0.0+unknown"
+
+
+# only set exception hook if it has not been overridden
+if sys.excepthook == sys.__excepthook__:
+    sys.excepthook = idmtools_error_handler

idmtools-0.0.3/idmtools/analysis/__init__.py

@@ -0,0 +1,5 @@
+"""idmtools analyzer framework
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+# flake8: noqa F821

idmtools-0.0.3/idmtools/analysis/add_analyzer.py

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+"""idmtools add analyzer.
+
+More of an example.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+import os
+from idmtools.entities.ianalyzer import IAnalyzer, ANALYZABLE_ITEM
+
+
+class AddAnalyzer(IAnalyzer):
+    """
+    A simple base class to add analyzers.
+
+    Examples:
+        .. literalinclude:: ../../examples/analyzers/example_analysis_AddAnalyzer.py
+    """
+
+    def __init__(self, filenames=None, output_path='output'):
+        """
+        Initialize our analyzer.
+
+        Args:
+            filenames: Filename to fetch
+            output_path: Path to write output to
+        """
+        super().__init__()
+        self.output_path = output_path
+        self.filenames = filenames or []
+
+        # We only want the raw files -> disable parsing
+        self.parse = True
+
+    def filter(self, item: ANALYZABLE_ITEM) -> bool:
+        """
+        Determine whether the given item should be included by this analyzer.
+
+        This implementation accepts all items unconditionally.
+
+        Args:
+            item (ANALYZABLE_ITEM): The item to be evaluated.
+
+        Returns:
+            bool: Always returns True, meaning all items are accepted.
+        """
+        return True  # download them all!
+
+    def initialize(self):
+        """
+        Initialize our analyzer before running it.
+
+        We use this to create our output directory.
+
+        Returns:
+            None
+        """
+        self.output_path = os.path.join(self.working_dir, self.output_path)
+        os.makedirs(self.output_path, exist_ok=True)
+
+    def map(self, data, item: ANALYZABLE_ITEM):
+        """
+        Run this on each item and the files we retrieve.
+
+        Args:
+            data: Map of filesnames -> content
+            item: Item we are mapping
+
+        Returns:
+            Values added up
+        """
+        number = int(list(data.values())[0].split()[10])
+        result = number + 100
+        return result
+
+    # ck4, should we pass objects as the keys? e.g. Item-type, not just their id
+    def reduce(self, data):
+        """
+        Combine all the data we mapped.
+
+        Args:
+            data: Map of results in form Item -> map results
+
+        Returns:
+            Sum of all the results
+        """
+        # data is currently a dict with item_id: value  entries
+        value = sum(data.values())
+        print(value)
+        return value