mdadash 0.0.1__tar.gz

mdadash-0.0.1/AUTHORS.md

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+# Authors
+
+mdadash was created by Pardhav Maradani in 2026.
+
+All contributing authors are listed in this file below.
+The repository history at https://github.com/MDAnalysis/mdadash
+and the CHANGELOG show individual code contributions.
+
+## Chronological list of authors
+
+<!--
+The rules for this file:
+  * Authors are sorted chronologically, earliest to latest
+  * Please format it each entry as "Preferred name <GitHub username>"
+  * Your preferred name is whatever you wish to go by --
+    it does *not* have to be your legal name!
+  * Please start a new section for each new year
+  * Don't ever delete anything
+-->
+
+**2026**
+
+- Pardhav Maradani <@PardhavMaradani>

mdadash-0.0.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+The rules for this file:
+  * entries are sorted newest-first.
+  * summarize sets of changes - don't reproduce every git log comment here.
+  * don't ever delete anything.
+  * keep the format consistent:
+    * do not use tabs but use spaces for formatting
+    * 79 char width
+    * YYYY-MM-DD date format (following ISO 8601)
+  * accompany each entry with github issue/PR number (Issue #xyz)
+-->
+
+## [Unreleased]
+
+### Authors
+
+<!-- GitHub usernames of contributors to this release -->
+
+PardhavMaradani
+
+### Added
+
+<!-- New added features -->
+
+- Added overall project structure (PR #3)
+- Added async jupyter kernel support (PR #4)
+- Added more tests and enabled code coverage (PR #5)
+- Add basic connectivity between frontend and backend (PR #6)
+
+### Fixed
+
+<!-- Bug fixes -->
+
+### Changed
+
+<!-- Changes in existing functionality -->
+
+### Deprecated
+
+<!-- Soon-to-be removed features -->
+
+### Removed
+
+<!-- Removed features -->

mdadash-0.0.1/CODE_OF_CONDUCT.md

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+The MDAnalysis *Code of Conduct* sets the rules for the behavior of
+every member in the MDAnalysis community so that everyone can
+experience a welcoming, supportive, and productive environment that is
+free from harassment. As a [NumFOCUS][NF] sponsored
+project, MDAnalysis follows the [NumFOCUS Code of Conduct][NF-conduct].
+
+**Table of Contents**
+
+- [MDAnalysis Code of Conduct](#numfocus-code-of-conduct)
+- [How to Report](#how-to-report)
+- [Who Will Receive Your Report](#who-will-receive-your-report)
+- [Diversity, Equity, and Inclusion Statement](#diversity-equity-and-inclusion-statement)
+- [Acknowledgment](#acknowledgment)
+
+## MDANALYSIS CODE OF CONDUCT
+You can find the whole document here: [https://numfocus.org/code-of-conduct][NF-conduct].
+
+### THE SHORT VERSION
+MDAnalysis and NumFOCUS are dedicated to providing a harassment-free community for everyone,
+regardless of gender, sexual orientation, gender identity and expression, disability,
+physical appearance, body size, race, or religion. We do not tolerate harassment of
+community members in any form.
+
+Be kind to others. Do not insult or put down others. Behave professionally. Remember
+that harassment and sexist, racist, or exclusionary jokes are not appropriate for MDAnalysis
+or NumFOCUS.
+
+All communication should be appropriate for a professional audience including people of
+many different backgrounds. Sexual language and imagery is not appropriate.
+
+Thank you for helping make this a welcoming, friendly community for all.
+
+### THE LONG VERSION
+You can find the long version of the Code of Conduct on the NumFOCUS website:
+[https://numfocus.org/code-of-conduct][NF-conduct].
+
+## HOW TO REPORT
+If you feel that the Code of Conduct has been violated, feel free to submit a report, by
+using the [NumFOCUS Code of Conduct Reporting Form](https://numfocus.typeform.com/to/ynjGdT?typeform-source=numfocus.org).
+
+### REPORTING AT MDANALYSIS EVENTS AND MEETUPS
+If you are attending an MDAnalysis event or meetup and wish to make a report that requires
+an appropriate immediate response, you may contact the ombudspersons (who will identify
+themselves at the event) or other event staff/meetup organizers. If you would prefer not to
+do that, please [submit a report](#how-to-report) to NumFOCUS, but please note it may not be
+possible for the [NumFOCUS Code of Conduct Working Group](#who-will-receive-your-report) to
+respond immediately. 
+
+Ombudspeople and event staff/meetup organizers will be happy to help participants contact
+venue security or local law enforcement, provide escorts, or otherwise assist those
+experiencing harassment to feel safe for the duration of the event/meetup.
+
+## WHO WILL RECEIVE YOUR REPORT
+Your report will be received and handled by the NumFOCUS Code of Conduct Working Group; trained,
+and experienced contributors with diverse backgrounds. The group is making decisions independently
+from the MDAnalysis project, PyData, NumFOCUS or any other organization. 
+
+You can learn more about the current group members, as well as the reporting procedure [HERE][NF-conduct].
+
+### ENFORCEMENT
+Based on recommendations for next steps as determined by the NumFOCUS Code of Conduct Working Group,
+the MDAnalysis project will remain responsible for making the final decision and implementing any
+resulting actions. See the [MDAnalysis team](https://www.mdanalysis.org/pages/team/#roles) page on
+the MDAnalysis website for a current list of the **MDAnalysis Code of Conduct Committee** members.
+
+Once a resolution has been agreed upon, but before it is enacted, the MDAnalysis Code of Conduct
+Committee will contact the original reporter and any other affected parties and explain the proposed
+resolution. We will ask if this resolution is acceptable and note feedback for the record. We are,
+however, not required to act on this feedback.
+
+## DIVERSITY, EQUITY, AND INCLUSION STATEMENT
+MDAnalysis strives to ensure a welcoming, inclusive space for all. As a [NumFOCUS][NF] sponsored project,
+we fully support their [*Diversity & Inclusion in Scientific Computing*](https://numfocus.org/programs/diversity-inclusion)
+(DISC) mission and abide by their Diversity Statement:
+
+> *"NumFOCUS welcomes and encourages participation in our community by people of all backgrounds and identities.
+> We are committed to promoting and sustaining a culture that values mutual respect, tolerance, and learning,
+> and we work together as a community to help each other live out these values."*
+
+## ACKNOWLEDGMENT
+
+Original text courtesy of [*NumFOCUS*](https://numfocus.org/code-of-conduct), modified by MDAnalysis.
+
+All content on this page is licensed under a [*Creative Commons Attribution*](http://creativecommons.org/licenses/by/3.0/)
+license. 
+
+[NF]: https://numfocus.org/
+[NF-conduct]: https://numfocus.org/code-of-conduct
+

mdadash-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 MDAnalysis
+
+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.

mdadash-0.0.1/MANIFEST.in

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+include LICENSE
+include MANIFEST.in
+include AUTHORS.md CHANGELOG.md CODE_OF_CONDUCT.md README.md
+
+graft mdadash
+global-exclude *.py[cod] __pycache__ *.so
+
+prune mdadash/frontend/node_modules
+recursive-exclude mdadash/frontend/node_modules *
+recursive-include mdadash/frontend/dist *
+prune mdadash/frontend/coverage
+recursive-exclude mdadash/frontend/coverage *
+recursive-exclude mdadash/backend/tests *.npz

mdadash-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: mdadash
+Version: 0.0.1
+Summary: Dashboard for tracking and analyzing live MD simulations with streaming.
+Author-email: Pardhav Maradani <pardhav.maradani@gmail.com>
+Maintainer-email: Pardhav Maradani <pardhav.maradani@gmail.com>
+License-Expression: MIT
+Project-URL: source, https://github.com/MDAnalysis/mdadash
+Keywords: streaming monitoring mdanalysis molecular-dynamics-simulations
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: fastapi>=0.136.3
+Requires-Dist: imdclient>=0.2.3
+Requires-Dist: ipykernel>=7.2.0
+Requires-Dist: MDAnalysis>=2.10.0
+Requires-Dist: python-socketio>=5.16.2
+Requires-Dist: uvicorn>=0.47.0
+Provides-Extra: dev
+Requires-Dist: nodejs; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-xdist>=2.5; extra == "test"
+Requires-Dist: pytest-cov>=3.0; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Dynamic: license-file
+
+# mdadash
+
+[//]: # "Badges"
+
+| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since] [![Documentation Status][badge_docs]][url_docs] |
+| :----------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov]                                                                                                 |
+| **Community**      | [![License: MIT License][badge_license]][url_license] [![Powered by MDAnalysis][badge_mda]][url_mda]                                                                                        |
+
+[badge_actions]: https://github.com/MDAnalysis/mdadash/actions/workflows/gh-ci.yaml/badge.svg
+[badge_codecov]: https://codecov.io/gh/MDAnalysis/mdadash/branch/main/graph/badge.svg
+[badge_commits_since]: https://img.shields.io/github/commits-since/MDAnalysis/mdadash/latest
+[badge_docs]: https://readthedocs.org/projects/mdadash/badge/?version=latest
+[badge_license]: https://img.shields.io/badge/License-MIT-yellow.svg
+[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
+[badge_release]: https://img.shields.io/github/release-pre/MDAnalysis/mdadash.svg
+[url_actions]: https://github.com/MDAnalysis/mdadash/actions?query=branch%3Amain+workflow%3Agh-ci
+[url_codecov]: https://codecov.io/gh/MDAnalysis/mdadash/branch/main
+[url_docs]: https://mdadash.readthedocs.io/en/latest/?badge=latest
+[url_latest_release]: https://github.com/MDAnalysis/mdadash/releases
+[url_license]: https://opensource.org/licenses/MIT
+[url_mda]: https://www.mdanalysis.org
+
+Dashboard for tracking and analyzing live MD simulations with streaming.
+
+mdadash is bound by a [Code of Conduct](https://github.com/MDAnalysis/mdadash/blob/main/CODE_OF_CONDUCT.md).
+
+### Installation
+
+To build mdadash from source,
+we highly recommend using virtual environments.
+If possible, we strongly recommend that you use
+[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
+Below we provide instructions both for `conda` and
+for `pip`.
+
+#### With conda
+
+Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+
+Create a virtual environment and activate it:
+
+```sh
+conda create --name mdadash
+conda activate mdadash
+```
+
+Install the development, testing and documentation dependencies:
+
+```sh
+conda env update --name mdadash --file devtools/conda-envs/dev_env.yaml
+conda env update --name mdadash --file devtools/conda-envs/test_env.yaml
+conda env update --name mdadash --file docs/requirements.yaml
+```
+
+Build this package from source:
+
+```sh
+pip install -e .
+```
+
+If you want to update your dependencies (which can be risky!), run:
+
+```sh
+conda update --all
+```
+
+And when you are finished, you can exit the virtual environment with:
+
+```sh
+conda deactivate
+```
+
+#### With pip
+
+To build the package from source, run:
+
+```sh
+pip install .
+```
+
+If you want to create a development environment, install
+the dependencies required for tests and docs with:
+
+```sh
+pip install ".[dev,test,doc]"
+```
+
+### Run
+
+> The frontend code needs to be built before running the backend server. This can be done as follows:
+
+```sh
+cd mdadash/frontend
+npm install
+npm run build
+```
+
+To run the dashboard server:
+
+```sh
+mdadash
+```
+
+To see the options available:
+
+```sh
+mdadash --help
+```
+
+### Development
+
+#### Frontend
+
+Developer instruction for `frontend` code can be found [here](mdadash/frontend/README.md).
+
+#### Backend
+
+- Use the `editable` installation above (`pip install -e .`)
+
+### Tests
+
+#### Frontend
+
+```sh
+npm run test:unit --prefix mdadash/frontend -- --run
+```
+
+#### Backend
+
+```sh
+pytest -v
+```
+
+### Code Coverage
+
+#### Frontend
+
+```sh
+cd mdadash/frontend
+npx vitest --run --coverage
+```
+
+The coverage details will be shown on the console. Open `coverage/index.html` to view the interactive coverage report in the browser.
+
+#### Backend
+
+To see coverage output on the console:
+
+```sh
+pytest -v --cov=mdadash
+```
+
+To write coverage output to `html` file:
+
+```sh
+pytest -v --cov=mdadash --cov-report=html
+```
+
+Open `htmlcov/index.html` to view the coverage report in the browser.
+
+### Build
+
+To build this package:
+
+```sh
+rm -rf mdadash.egg-info dist && python -m build
+```
+
+To verify the created wheel:
+
+```sh
+uv run --refresh --with path.to.whl mdadash
+```
+
+To check the created distribution:
+
+```sh
+twine check dist/*
+```
+
+### Verify GitHub actions locally
+
+GitHub actions can be verified locally using [act](https://github.com/nektos/act).
+
+> Note that this requires [Docker](https://www.docker.com). Running on Mac needs an additional param `--container-architecture linux/arm64`. To bypass the repo name check, you can pass `--env GITHUB_REPOSITORY=MDAnalysis/mdadash`. Both these can be set in `~/.actrc` as well.
+
+To list the jobs:
+
+```sh
+act -l
+```
+
+To run a job (eg: `pylint_check`):
+
+```sh
+act -j pylint_check
+```
+
+To run all jobs:
+
+```sh
+act
+```
+
+### Docs
+
+Setting up the docs environment:
+
+```sh
+conda env update --name mdadash --file docs/requirements.yaml
+```
+
+Building docs locally:
+
+```sh
+cd docs
+make clean && make html
+```
+
+Open `docs/_build/html/index.html` to view the docs in the browser.
+
+### Copyright
+
+The mdadash source code is hosted at https://github.com/MDAnalysis/mdadash
+and is available under the [MIT License](https://opensource.org/licenses/MIT) (see the file [LICENSE](https://github.com/MDAnalysis/mdadash/blob/main/LICENSE)).
+
+Copyright (c) 2026, MDAnalysis
+
+#### Acknowledgements
+
+Project based on the
+[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
+Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using mdadash in published work.