updated repos with copied code

.github/workflows/pytest.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+
+    services:
+      mongodb:
+        image: mongo
+        ports:
+          - 27017:27017
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@main
+      with:
+        ref: main
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@main
+      with:
+        python-version: '3.10'
+
+    - name: Install project and dependencies
+      run: pip install ".[cobra, copasi, smoldyn, tellurium]"
+
+    - name: Install additional dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install nbconvert pytest pytest-cov
+
+    - name: Test with pytest
+      run: |
+        pytest --cov=core_processes

.gitignore

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+.python-version
+__pycache__/
+.idea/
+*.ipynb_checkpoints/
+dist/
+.DS_Store
+*.egg-info/

AUTHORS.md

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+# Authors of Bigraph Schema
+
+The maintainers of the Process-Bigraph project are:
+
+* Ryan Spangler (@prismofeverything)
+* Eran Agmon  (@eagmon)

CLA.md

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+# Individual Contributor License Agreement
+
+Thank you for your interest in Vivarium Core. To clarify the
+intellectual property license granted with Contributions from any person
+or entity, each Contribution must indicate each Contributor's agreement
+with the license terms below. This agreement is for your protection as a
+Contributor as well as the protection of the Vivarium Core authors
+(Authors) and Vivarium Core's users. It does not change your rights to
+use your own Contributions for any other purpose.
+
+You accept and agree to the following terms and conditions for Your
+Contributions (present and future) that you submit to the Authors.
+Except for the license granted herein to the Authors and recipients of
+software distributed by the Authors, You reserve all right, title, and
+interest in and to Your Contributions.
+
+1. Definitions
+
+   "You" (or "Your") shall mean the copyright owner or legal entity
+   authorized by the copyright owner that is making this Agreement with
+   the Authors. For legal entities, the entity making a Contribution and
+   all other entities that control, are controlled by, or are under
+   common control with that entity are considered to be a single
+   Contributor. For the purposes of this definition, "control" means (i)
+   the power, direct or indirect, to cause the direction or management
+   of such entity, whether by contract or otherwise, or (ii) ownership
+   of fifty percent (50%) or more of the outstanding shares, or (iii)
+   beneficial ownership of such entity.
+
+   "Contribution" shall mean any original work of authorship, including
+   any modifications or additions to an existing work, that is
+   intentionally submitted by You to the Authors for inclusion in, or
+   documentation of, any of the products owned or managed by the Authors
+   (the "Work"). For the purposes of this definition, "submitted" means
+   any form of electronic, verbal, or written communication sent to the
+   Authors or their representatives, including but not limited to
+   communication on electronic mailing lists, source code control
+   systems, and issue tracking systems that are managed by, or on behalf
+   of, the Authors for the purpose of discussing and improving the Work,
+   but excluding communication that is conspicuously marked or otherwise
+   designated in writing by You as "Not a Contribution."
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+   this Agreement, You hereby grant to the Authors and to recipients
+   of software distributed by the Authors a perpetual, worldwide,
+   non-exclusive, no-charge, royalty-free, irrevocable copyright license
+   to reproduce, prepare derivative works of, publicly display, publicly
+   perform, sublicense, and distribute Your Contributions and such
+   derivative works.
+
+3. Grant of Patent License. Subject to the terms and conditions of this
+   Agreement, You hereby grant to the Authors and to recipients of
+   software distributed by the Authors a perpetual, worldwide,
+   non-exclusive, no-charge, royalty-free, irrevocable (except as stated
+   in this section) patent license to make, have made, use, offer to
+   sell, sell, import, and otherwise transfer the Work, where such
+   license applies only to those patent claims licensable by You that
+   are necessarily infringed by Your Contribution(s) alone or by
+   combination of Your Contribution(s) with the Work to which such
+   Contribution(s) was submitted. If any entity institutes patent
+   litigation against You or any other entity (including a cross-claim
+   or counterclaim in a lawsuit) alleging that your Contribution, or the
+   Work to which you have contributed, constitutes direct or
+   contributory patent infringement, then any patent licenses granted to
+   that entity under this Agreement for that Contribution or Work shall
+   terminate as of the date such litigation is filed.
+
+4. You represent that you are legally entitled to grant the above
+   license. If your employer(s) has rights to intellectual property that
+   you create that includes your Contributions, you represent that you
+   have received permission to make Contributions on behalf of that
+   employer, that your employer has waived such rights for your
+   Contributions to the Authors, or that your employer has executed a
+   separate Corporate CLA with the Authors.
+
+5. You represent that each of Your Contributions is Your original
+   creation (see section 7 for submissions on behalf of others). You
+   represent that Your Contribution submissions include complete details
+   of any third-party license or other restriction (including, but not
+   limited to, related patents and trademarks) of which you are
+   personally aware and which are associated with any part of Your
+   Contributions.
+
+6. You are not expected to provide support for Your Contributions,
+   except to the extent You desire to provide support. You may provide
+   support for free, for a fee, or not at all. Unless required by
+   applicable law or agreed to in writing, You provide Your
+   Contributions on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
+   OF ANY KIND, either express or implied, including, without
+   limitation, any warranties or conditions of TITLE, NON- INFRINGEMENT,
+   MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE.
+
+7. Should You wish to submit work that is not Your original creation,
+   You may submit it to the Authors separately from any Contribution,
+   identifying the complete details of its source and of any license or
+   other restriction (including, but not limited to, related patents,
+   trademarks, and license agreements) of which you are personally
+   aware, and conspicuously marking the work as "Submitted on behalf of
+   a third-party: [named here]".
+
+8. You agree to notify the Authors of any facts or circumstances of
+   which you become aware that would make these representations
+   inaccurate in any respect.
+
+-----------------------------------------------------------------------
+
+End of Contributor License Agreement
+
+-----------------------------------------------------------------------
+
+The text of this agreement was adapted from the Apache Software
+Foundation's [Individual Contributor License
+Agreement](https://apache.org/licenses/icla.pdf).

CODE_OF_CONDUCT.md

@@ -0,0 +1,137 @@
+# Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in
+our community a harassment-free experience for everyone, regardless of
+age, body size, visible or invisible disability, ethnicity, sex
+characteristics, gender identity and expression, level of experience,
+education, socio-economic status, nationality, personal appearance,
+race, caste, color, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open,
+welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our
+  mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political
+  attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our
+standards of acceptable behavior and will take appropriate and fair
+corrective action in response to any behavior that they deem
+inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other
+contributions that are not aligned to this Code of Conduct, and will
+communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also
+applies when an individual is officially representing the community in
+public spaces. Examples of representing our community include using an
+official e-mail address, posting via an official social media account,
+or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may
+be reported to the Authors at the email addresses in
+[`AUTHORS.md`](AUTHORS.md). All complaints will be reviewed and
+investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security
+of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in
+determining the consequences for any action they deem in violation of
+this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior
+deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders,
+providing clarity around the nature of the violation and an explanation
+of why the behavior was inappropriate. A public apology may be
+requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, for a specified period of
+time. This includes avoiding interactions in community spaces as well as
+external channels like social media. Violating these terms may lead to a
+temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards,
+including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No
+public or private interaction with the people involved, including
+unsolicited interaction with those enforcing the Code of Conduct, is
+allowed during this period. Violating these terms may lead to a
+permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of
+individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction
+within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

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+# Contributing to Process-Bigraph
+
+## Making a Contribution
+
+Thank you for your interest in contributing to Vivarium Core! Here's how
+you can get started:
+
+1. Review the [Contributor License Agreement](CLA.md) (CLA). Whenever
+   you submit a contribution to Vivarium Core, you are agreeing to the
+   CLA, which grants us rights to use your contribution. You don't need
+   to do anything special to "sign" the CLA. Instead, opening a pull
+   request indicates your agreement to the CLA.
+2. [Optional] If you want to make a contribution that isn't covered by
+   an existing issue, go ahead an open a new one!
+3. Once you have found or created an issue that describes the
+   contribution you want to make, wait to get feedback from the project
+   maintainers.
+4. If the project maintainers agree that your proposal makes sense, you
+   can fork the repository, make your changes, and open a pull request.
+   If you haven't done this before, check out [GitHub's guide to open
+   source
+   contributions](https://docs.github.com/en/get-started/quickstart/contributing-to-projects).
+5. Wait to get feedback from the project maintainers and then address
+   any review comments they leave. Once your pull request is approved,
+   the project maintainers will merge it.
+
+## Contacting Us
+
+* To request features or report bugs, please open an
+  [issue](https://github.com/vivarium-collective/process-bigraph/issues).
+* To ask questions or request help, please open a [discussion
+  thread](https://github.com/vivarium-collective/process-bigraph/discussions).
+* To contact the maintainers privately, for example to report a
+  violation of our [code of conduct](CODE_OF_CONDUCT.md) or to notify us
+  of a security issue, you can use the contact information in the
+  [`AUTHORS.md` file](AUTHORS.md).
+
+## Code of Conduct
+
+We expect kindness and respect in all interactions with the Vivarium
+Collective community. Harassing or insulting behavior is not welcome and will
+result in enforcement actions. Please review our [code of
+conduct](CODE_OF_CONDUCT.md), which describes our expectations and
+enforcement actions in more detail.

Dockerfile

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+# TODO: Make this work for Smoldyn to be platform-agnostic
+
+FROM python:3.10-bullseye
+
+# Implement the next two lines for use in Cloud
+# RUN useradd -m simuser
+
+# USER simuser
+
+WORKDIR /app
+
+COPY . /app
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    wget \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN echo 'deb http://download.opensuse.org/repositories/home:/dilawar/Debian_11/ /' | tee /etc/apt/sources.list.d/home:dilawar.list
+RUN curl -fsSL https://download.opensuse.org/repositories/home:dilawar/Debian_11/Release.key | gpg --dearmor | tee /etc/apt/trusted.gpg.d/home_dilawar.gpg > /dev/null
+RUN apt update
+RUN apt install smoldyn
+
+RUN pip install --upgrade pip \
+    && pip install . ipython
+    # && pytest
+
+CMD ["ipython3"]