ready for release

CHANGELOG.rst

@@ -0,0 +1,4 @@
+
+**v1.0.0 - 02/22/19**
+
+ - Initial release

MANIFEST.in

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+include README.rst
+include CHANGELOG.rst
+include setup.py
+
+recursive-include src/vivarium_cluster_tools/ *.py
+

README.rst

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+Vivarium Cluster Tools
+=======================
+
+This package includes a tool that allows vivarium users to run simulations based on multiple scenarios conveniently.
+It requires an access to IHME cluster. To install this package, create or edit a file called ~/.pip/pip.conf which looks like this:
+
+    | [global]
+    | extra-index-url = http://dev-tomflem.ihme.washington.edu/simple
+    | trusted-host = dev-tomflem.ihme.washington.edu
+
+
+This file tells the pip package management system to check with IHME's internal
+pypi server for packages.
+
+You can then install this package with
+
+    | > source activate <env-name>
+    | > pip install vivarium-cluster-tools
+
+In addition, this tool needs redis client and cython.
+
+    | > conda install redis cython
+
+How to use
+-------------
+
+The Vivarium ecosystem uses YAML configuration files throughout, including vivarium-cluster-tools.
+To run the multiple scenarios, you need to make a separate branch file (YAML) in addition to a usual
+vivarium model specification YAML file. You can specify how to vary a certain parameter in this branch file.
+For example,
+
+::
+
+    input_draw_count: 25
+    random_seed_count: 10
+
+    branches:
+      - intervention_name:
+           intervention_coverage: [0, 1]
+           efficacy: [0, .5, 1]
+
+This branch shows that you want to have 25 different input draws, 10 different random seeds and 2 different
+intervention coverages and 3 different intervention efficacy. This implies 25*10*2*3=1500 different simulation
+scenarios. You can run all 1500 simulations by
+
+::
+
+    psimulate run /path/to/your/model_configuration /path/to/your/branch_file
+
+As an optional parameter, you can specify the name of project as well as result directory to save the outputs
+and logs. To specify those optional arguments,
+
+::
+
+    psimulate run /path/to/your/model_configuration /path/to/your/branch_file -p project_name -o /path/to/output/
+
+If your psimulate run has any failed jobs from the previous runs, you can restart failed jobs by specifying
+which output directory includes the partially completed jobs by,
+
+::
+
+    psimulate restart /path/to/the/previous/results/
+
+

setup.py

@@ -1,17 +1,19 @@
+import os
 from setuptools import setup, find_packages
 
+if __name__ == "__main__":
 
-setup(
-    name='vivarium_cluster_tools',
-    version='0.1',
-    packages=find_packages(where='src'),
-    package_dir={'': 'src'},
-    include_package_data=True,
-    entry_points="""
-        [console_scripts]
-        psimulate=vivarium_cluster_tools.cli:psimulate
-    """,
-    install_requires=[
+    base_dir = os.path.dirname(__file__)
+    src_dir = os.path.join(base_dir, "src")
+
+    about = {}
+    with open(os.path.join(src_dir, "vivarium_cluster_tools", "__about__.py")) as f:
+        exec(f.read(), about)
+
+    with open(os.path.join(base_dir, "README.rst")) as f:
+        long_description = f.read()
+
+    install_requires = [
         'pandas',
         'numpy',
         'pyyaml',
@@ -20,5 +22,28 @@
         'rq',
         'vivarium',
         'click',
-    ],
-)
+    ]
+
+    setup(
+        name=about['__title__'],
+        version=about['__version__'],
+
+        description=about['__summary__'],
+        long_description=long_description,
+        url=about["__uri__"],
+
+        author=about["__author__"],
+        author_email=about["__email__"],
+
+        package_dir={'': 'src'},
+        packages=find_packages(where='src'),
+        include_package_data=True,
+        entry_points="""
+            [console_scripts]
+            psimulate=vivarium_cluster_tools.cli:psimulate
+        """,
+
+        install_requires=install_requires,
+
+        zip_safe=False,
+    )

src/vivarium_cluster_tools/__about__.py

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+__all__ = [
+    "__title__", "__summary__", "__uri__", "__version__", "__author__",  "__email__",
+]
+
+__title__ = "vivarium_cluster_tools"
+__summary__ = "A set of tools for running simulation using vivarium on cluster."
+__uri__ = "https://stash.ihme.washington.edu/projects/CSTE/repos/vivarium_cluster_tools"
+
+__version__ = "1.0.0"
+
+__author__ = "The vivarium developers"
+__email__ = "[email protected]"