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‎.dockerignore‎

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Dockerfile
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README.md

‎.github/workflows/ci.yml‎

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name: Build and push Docker image
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on:
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push:
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jobs:
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buildAndPushImage:
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name: Build and push Docker image
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/[email protected]
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# Build Docker image
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- id: get-timestamp
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name: Get timestamp
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run: |
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TIMESTAMP=$(date --rfc-3339=seconds | sed 's/ /T/')
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echo "::set-output name=timestamp::$TIMESTAMP"
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- name: Build Docker image
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uses: whoan/docker-build-with-cache-action@v5
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with:
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dockerfile: Dockerfile
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build_extra_args: "--compress=true --label org.opencontainers.image.revision=${{github.sha}} --label org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}"
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registry: ghcr.io
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stages_image_name: biosimulators/biosimulators-tutorials-stages
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image_name: biosimulators/biosimulators-tutorials-stages
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image_tag: ${{github.sha}}
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push_image_and_stages: true
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username: ${{ secrets.DOCKER_REGISTRY_USERNAME }}
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password: "${{ secrets.DOCKER_REGISTRY_TOKEN }}"
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- name: Label Docker image
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run: |
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docker image tag ghcr.io/biosimulators/biosimulators-tutorials-stages:${{github.sha}} ghcr.io/biosimulators/biosimulators-tutorials:${{github.sha}}
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docker image tag ghcr.io/biosimulators/biosimulators-tutorials-stages:${{github.sha}} ghcr.io/biosimulators/biosimulators-tutorials:latest
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# Test tutorials
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- name: Test tutorials
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run: |
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cwd=$(pwd)
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docker run \
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--rm \
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--entrypoint bash \
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--mount type=bind,source=${cwd},target=/app/Biosimulators_tutorials \
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ghcr.io/biosimulators/biosimulators-tutorials:latest \
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-c "
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pipenv run pip install nbmake pytest pytest-forked
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/bin/bash /xvfb-startup.sh pipenv run python -m pytest --forked --verbose --nbmake Biosimulators_tutorials/tutorials/
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"
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# Get version number
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- id: get-version-number
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name: Get version number
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if: startsWith(github.ref, 'refs/tags/')
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env:
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TAG: ${{ github.ref }}
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run: |
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version="${TAG/refs\/tags\//}"
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echo "::set-output name=version::$version"
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# Create GitHub release
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- name: Create GitHub release
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if: startsWith(github.ref, 'refs/tags/')
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: ${{ steps.get-version-number.outputs.version }}
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release_name: Release ${{ steps.get-version-number.outputs.version }}
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# Push Docker image
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- name: Push Docker image
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if: startsWith(github.ref, 'refs/tags/')
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env:
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VERSION: ${{ steps.get-version-number.outputs.version }}
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run: |
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docker image tag ghcr.io/biosimulators/biosimulators-tutorials:${{github.sha}} ghcr.io/biosimulators/biosimulators-tutorials:${VERSION}
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docker login ghcr.io \
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--username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
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--password ${{ secrets.DOCKER_REGISTRY_TOKEN }}
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docker push ghcr.io/biosimulators/biosimulators-tutorials:${{github.sha}}
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docker push ghcr.io/biosimulators/biosimulators-tutorials:latest
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docker push ghcr.io/biosimulators/biosimulators-tutorials:${VERSION}

‎.gitignore‎

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*.pyc
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__pycache__/

‎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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* Trolling, insulting or derogatory comments, and personal or political attacks
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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 the BioSimulators tutorials
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We enthusiastically welcome contributions to the BioSimulators tutorials!
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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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* `README.md`: Overview of this repository
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* `tutorials/`: Tutorials
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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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* `GOVERNANCE.md`: Governance structure for this package
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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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To release changes, contact the [lead developers](mailto:[email protected]) to request their release.
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Below are instructions for releasing a new version:
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1. Commit the changes to this repository.
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2. Add a tag for the new version by running `git tag { version }`.
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3. Push these commits and the new tag to GitHub by running `git push && git push --tags`.
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4. This push will trigger a GitHub action which will execute the following tasks:
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* Compile a Docker image for this package.
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* Push the Docker image to the GitHub Container Registry (GHCR).
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* Create a GitHub release for the version.
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## Reporting issues
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Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_tutorials/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_tutorials/issues) to post questions or contact the lead developers at [[email protected]](mailto:[email protected]).

‎Dockerfile‎

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FROM ghcr.io/biosimulators/biosimulators:0.0.3
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LABEL \
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org.opencontainers.image.title="BioSimulators Jupyter server" \
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org.opencontainers.image.description="Jupyter server in a Python environment with the validated simulation tools registered with BioSimulators" \
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org.opencontainers.image.url="https://github.com/biosimulators/Biosimulators_tutorials" \
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org.opencontainers.image.documentation="https://biosimulators.org/help" \
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org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_tutorials" \
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org.opencontainers.image.authors="BioSimulators Team <[email protected]>" \
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org.opencontainers.image.vendor="BioSimulators Team"
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RUN pip install \
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notebook \
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jupyterhub \
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jupyterlab \
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matplotlib \
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pyyaml
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ENV MPLBACKEND=
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ARG NB_USER=biosimulators
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ARG NB_UID=1000
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ENV USER ${NB_USER}
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ENV NB_UID ${NB_UID}
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ENV HOME=/home/${NB_USER}
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RUN adduser --disabled-password \
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--gecos "Default user" \
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--uid ${NB_UID} \
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${NB_USER}
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COPY tutorials/ ${HOME}
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RUN chown -R ${NB_UID} ${HOME}
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USER ${NB_USER}
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WORKDIR ${HOME}
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CMD /bin/bash /xvfb-startup.sh

‎GOVERNANCE.md‎

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# Project governance
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The project is governed by a committee of maintainers who collectively decide the direction of the project with input from the community. A list of the current maintainers is available in the [README](README.md).
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## Maintainer responsibilities
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Maintainers are people who care about the project and are responsible for helping it grow and improve. Maintainers must contribute to the project, as well as help review contributions from the community. Maintainers must also work collaboratively with each other.
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Maintainers have write access to this repository. Maintainers can merge their own contributions or contributions from others. Nevertheless, maintainers are encouraged to seek review from each other, particularly for significant changes.
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## Becoming a Maintainer
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To become a maintainer you need to demonstrate the following:
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* Participation in project discussions
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* Contribution of significant pull requests
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* Ability to write quality code, tests, examples, and/or documentation
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* Ability to collaborate with the maintainers
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* Understanding of the project's goals, organization, and conventions
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Prospective maintainers can request maintainer privileges by sending a message to the current maintainers at [email protected].
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## Project meetings
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Maintainers are expected to participate in the project's meetings, which occur online at 11am EST on Thursdays. Other members of the community are also welcome to attend the project's meetings to provide input and feedback on the project. Please contact the maintainers at [email protected] for the link for the project meetings.

‎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.

‎README.md‎

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![Logo](https://raw.githubusercontent.com/biosimulations/Biosimulations/dev/libs/shared/assets/src/assets/images/biosimulators-logo/logo-white.svg)
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# BioSimulators tutorials
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This repository contains Jupyter notebooks with tutorials for the Python APIs for the simulation tools registered with BioSimulators and a Jupyter notebook server for running the notebooks.
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## Getting started
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### Running the tutorials online with Binder
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The easiest way to run the tutorials is with Binder. Simply open https://mybinder.org/v2/gh/biosimulators/Biosimulators_tutorials/HEAD in your browser.
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### Running the tutorials on your own machine
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Run the following commands to launch a Jupyter notebook server at http://localhost:8888 for the tutorials in this repository:
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```
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docker pull ghcr.io/biosimulators/biosimulators_tutorials
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docker run -it --rm -p 8888:8888 ghcr.io/biosimulators/biosimulators_tutorials jupyter notebook --ip=0.0.0.0 --port=8888
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```
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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 as part of the [Center for Reproducible Biomodeling Modeling](https://reproduciblebiomodels.org).
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- [Bilal Shaikh](https://www.bshaikh.com)
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- [Jonathan Karr](https://www.karrlab.org)
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## Funding
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This package was developed with support from the National Institute for Bioimaging and Bioengineering (award P41EB023912).
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## Questions and comments
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Please contact us at [[email protected]](mailto:[email protected]) with any questions or comments.

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