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‎.gitignore

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# compiled Python files
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*.egg-info/
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__pycache__/
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*.pyc
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# compiled documentation
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docs/.doctrees/
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docs/_raw_sources/
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docs/_sources/

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, religion, or sexual identity
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and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the
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overall community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or
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advances of any kind
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* Public or private harassment
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* Publishing others' private information, such as a physical or email
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address, without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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[[email protected]](mailto:[email protected]).
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series
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of actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or
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permanent ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within
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the community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/version/2/0/code_of_conduct.html).
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The Community Impact Guidelines were inspired by [Mozilla's Code of Conduct Enforcement ladder](https://github.com/mozilla/diversity).
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Answers to common questions about this code of conduct are available at
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https://www.contributor-covenant.org/faq. Translations of this code of conduct are available at
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https://www.contributor-covenant.org/translations.

‎CONTRIBUTING.md

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# Contributing to BioSimulators-utils
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We enthusiastically welcome contributions to BioSimulators-utils!
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## Coordinating contributions
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Before getting started, please contact the lead developers at [[email protected]](mailto:[email protected]) to coordinate your planned contributions with other ongoing efforts. Please also use GitHub issues to announce your plans to the community so that other developers can provide input into your plans and coordinate their own work. As the development community grows, we will institute additional infrastructure as needed such as a leadership committee and regular online meetings.
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## Repository organization
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This repository follows standard Python conventions:
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* `README.md`: Overview of this repository
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* `biosimulators_utils/`: Source code for this package
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* `tests/`: Unit tests for this package
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* `setup.py`: pip installation script for this package
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* `setup.cfg`: Configuration for the pip installation script
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* `requirements.txt`: Dependencies of this package
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* `requirements.optional.txt`: Optional dependencies of this package
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* `MANIFEST.in`: List of files to include when BioSimulators-utils is packaged for distribution through PyPI
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* `LICENSE`: License for this package
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* `CONTRIBUTING.md`: Guide to contributing to this package (this document)
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* `CODE_OF_CONDUCT.md`: Code of conduct for developers of this package
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## Coding convention
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This repository follows standard Python style conventions:
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* Class names: `UpperCamelCase`
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* Function names: `lower_snake_case`
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* Variable names: `lower_snake_case`
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## Documentation convention
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BioSimulators-utils is documented using [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html) and the [napoleon Sphinx plugin](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html). The documentation can be compiled with [Sphinx](https://www.sphinx-doc.org/) by running the following commands:
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```
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python -m pip install -r docs-src/requirements.txt
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sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
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sphinx-build docs-src docs
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```
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## Submitting changes
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Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features.
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## Releasing new versions
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Contact [[email protected]](mailto:[email protected]) to request release of new changes.
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## Reporting issues
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Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_utils/issues) to report any issues to the development community.
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## Getting help
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Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_utils/issues) to post questions or contact the lead developers at [[email protected]](mailto:[email protected]).

‎LICENSE

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The MIT License (MIT)
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Copyright (c) 2020 Center for Reproducible Biomedical Modeling
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎MANIFEST.in

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# description
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include README.rst
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# license
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include LICENSE
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# requirements
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include requirements.txt
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include requirements.optional.txt

‎README.md

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[![Build](https://github.com/biosimulators/Biosimulators_utils/workflows/Build/badge.svg)](https://github.com/biosimulators/Biosimulators_utils/actions?query=workflow:"Build")
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[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_utils/branch/master/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_utils)
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[![License](https://img.shields.io/github/license/biosimulators/Biosimulators_utils.svg)](LICENSE)
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![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/Biosimulators_utils/README.md?pixel)
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# BioSimulators-utils
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Utilities for building standardized command-line interfaces for biosimulation tools that support the [Simulation Experiment Description Markup Language](https://sed-ml.org/) (SED-ML) and the [COMBINE/OMEX format](https://combinearchive.org/).
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## Contents
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* [Installation](#installation)
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* [API documentation](#api-documentation)
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* [License](#license)
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* [Development team](#development-team)
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* [Contributing to BioSimulators-utils](#contributing-to-biosimulators-utils)
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* [Acknowledgements](#acknowledgements)
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* [Questions and comments](#questions-and-comments)
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## Installation
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Requirements
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* Python >= 3.7
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* pip
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### Install latest release from PyPI
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```
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pip install biosimulators-utils
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```
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### Install latest revision from GitHub
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```
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pip install git+https://github.com/biosimulators/Biosimulators_utils.git#biosimulators_utils
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```
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## API documentation
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API documentation is available [here](https://biosimulators.github.io/Biosimulators_utils/).
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## License
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This package is released under the [MIT license](LICENSE).
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## Development team
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This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York and the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org).
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## Contributing to BioSimulators-utils
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We enthusiastically welcome contributions to BioSimulators-utils! Please see the [guide to contributing](CONTRIBUTING.md) and the [developer's code of conduct](CODE_OF_CONDUCT.md).
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## Acknowledgements
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This work was supported by National Institutes of Health award P41EB023912.
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## Questions and comments
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Please contact the [BioSimulators Team](mailto:[email protected]) with any questions or comments.

‎biosimulators_utils/__init__.py

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‎biosimulators_utils/_version.py

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__version__ = '0.0.1'

‎docs-src/about.rst

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About BioSimulators-utils
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=============================
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License
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-------
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This package is released under the `MIT License <https://github.com/biosimulators/Biosimulators_utils/blob/dev/LICENSE>`_.
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Development team
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----------------
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This package was developed by the `Karr Lab <https://www.karrlab.org>`_ at the Icahn School of Medicine at Mount Sinai and the `Center for Reproducible Biomedical Modeling <https://reproduciblebiomodels.org/>`_.
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Contributing to BioSimulators-utils
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-----------------------------------
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We enthusiastically welcome contributions to BioSimulators-utils! Please see the `guide to contributing <https://github.com/biosimulators/Biosimulators_utils/blob/dev/CONTRIBUTING.md>`_ and the `developer's code of conduct <https://github.com/biosimulators/Biosimulators_utils/blob/dev/CODE_OF_CONDUCT.md>`_.
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Acknowledgements
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----------------
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This work was supported by National Institutes of Health award P41EB023912.
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Questions and comments
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-------------------------
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Please contact the `BioSimulators Team <mailto:[email protected]>`_ with any questions or comments.

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