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jonrkarr committed Jan 20, 2019
1 parent db50d5b commit bf49975c20f6a3e7639af72e71710c6163685ed6
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version: 2
jobs:
build:
working_directory: /root/project
docker:
- image: karrlab/wc_env_dependencies:latest

steps:
# Clone repository
- checkout

# Load packages from cache
- restore_cache:
keys:
- v1-{{ arch }}-{{ .Branch }}-{{ checksum "/etc/docker-image-tag" }}-{{ checksum "requirements.txt" }}

# Python 3 installation tasks
- run:
name: Install pkg_utils (Python 3)
command: pip3 install -U --process-dependency-links git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
- run:
name: Install karr_lab_build_utils (Python 3)
command: pip3 install -U --process-dependency-links git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils[all]
- run:
name: Install package configuration files including credentials
command: karr_lab_build_utils3 download-install-package-config-files
- run:
name: Install and upgrade requirements (Python 3)
command: |
set +e
karr_lab_build_utils3 install-requirements
karr_lab_build_utils3 upgrade-karr-lab-packages
- run:
name: Install package (Python 3)
command: pip3 install -U --process-dependency-links -e .[all]

# Save packages to cache
- save_cache:
key: v1-{{ arch }}-{{ .Branch }}-{{ checksum "/etc/docker-image-tag" }}-{{ checksum "requirements.txt" }}
paths:
- /usr/local/lib/python3.6/site-packages

# Test code
- run:
name: Test code
command: |
set +e
karr_lab_build_utils3 run-tests --with-xunit --with-coverage
TEST_EXIT_CODE_PY3=$?
# Calculate exit code and save to file for reading by the next step
if [[ $TEST_EXIT_CODE_PY3 -eq 0 ]]; then
echo "0" > TEST_EXIT_CODE
exit 0
else
echo "0" > TEST_EXIT_CODE
exit 1
fi
# Generate reports, archive results, and send notifications
- run:
name: Generate reports, archive results, and send notifications
when: always
command: |
if [[ -f TEST_EXIT_CODE ]]; then
INSTALLATION_EXIT_CODE=0
TEST_EXIT_CODE=$(<TEST_EXIT_CODE)
else
INSTALLATION_EXIT_CODE=1
TEST_EXIT_CODE=1
fi
karr_lab_build_utils3 do-post-test-tasks $INSTALLATION_EXIT_CODE $TEST_EXIT_CODE
- store_test_results:
path: /root/project/tests/reports
- store_artifacts:
path: /root/project/tests/reports
destination: reports
- store_artifacts:
path: /root/.wc/log
destination: log
- store_artifacts:
path: /root/project/docs/_build/html
destination: docs

# workflows:
# version: 2
# build:
# jobs:
# - build:
# context: karr_lab
@@ -0,0 +1,51 @@
# compiled files
*.pyc

# python cache
__pycache__/

#distribution files
/build/
/dist/
/sdists/
*.egg-info

# test reports
tests/reports

# coverage file
.coverage*
htmlcov/
.tox/

# profiling data
prof/

# .rst-formatted README
README.rst

# compiled documentation
docs/source
docs/_build
docs/.doctrees/

# pytest .cache directory
.cache/
.pytest_cache/

# passwords
tests/fixtures/secret/

# IDE configuration
.idea/
.spyderproject
.ropeproject

# temporary files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
.~lock.*
Thumbs.db
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downstream_dependencies:
- wc_sim
email_notifications:
- jonrkarr@gmail.com
- arthur.p.goldberg@mssm.edu
21 LICENSE
@@ -0,0 +1,21 @@
The MIT License (MIT)

Copyright (c) 2019 Karr Lab

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
@@ -0,0 +1,12 @@
# description
README.rst

# version
include desim/VERSION

# license
include LICENSE

# requirements
include requirements.txt
include requirements.optional.txt
@@ -1,2 +1,30 @@
[//]: # ( [![PyPI package](https://img.shields.io/pypi/v/desim.svg)](https://pypi.python.org/pypi/desim) )
[![Documentation](https://readthedocs.org/projects/desim/badge/?version=latest)](https://docs.karrlab.org/desim)
[![Test results](https://circleci.com/gh/KarrLab/desim.svg?style=shield)](https://circleci.com/gh/KarrLab/desim)
[![Test coverage](https://coveralls.io/repos/github/KarrLab/desim/badge.svg)](https://coveralls.io/github/KarrLab/desim)
[![Code analysis](https://api.codeclimate.com/v1/badges/b44357806d2f36820c7a/maintainability)](https://codeclimate.com/github/KarrLab/desim)
[![License](https://img.shields.io/github/license/KarrLab/desim.svg)](LICENSE)
![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/desim/README.md?pixel)

# desim
Python framework for discrete event simulation

Write an overview

## Installation
1. Install dependencies
2. Install this package
```
pip install git+git://github.com/KarrLab/desim#egg=desim
```

## Documentation
Please see the [API documentation](https://docs.karrlab.org/desim).

## License
The package is released under the [MIT license](LICENSE).

## Development team
This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, USA.

## Questions and comments
Please contact the [Karr Lab](https://www.karrlab.org) with any questions or comments.
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0.0.1
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import pkg_resources

# read version
with open(pkg_resources.resource_filename('desim', 'VERSION'), 'r') as file:
__version__ = file.read().strip()
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About
=====

----------------------
License
----------------------

The software is released under the MIT license

.. literalinclude:: ../LICENSE
:language: text

----------------------
Development team
----------------------

This package was developed by the `Karr Lab <https://www.karrlab.org/>`_ at the Icahn School of Medicine at Mount Sinai in New York, USA.

----------------------
Acknowledgements
----------------------

----------------------
Questions and comments
----------------------

Please contact the `Karr Lab <https://www.karrlab.org/>`_ with any questions or comments.

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