datalab-server 0.5.3rc6__tar.gz

datalab_server-0.5.3rc6/PKG-INFO

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+Metadata-Version: 2.4
+Name: datalab-server
+Version: 0.5.3rc6
+Author: Joshua Bocarsly
+Author-email: Matthew Evans <dev@datalab.industries>, datalab development team <dev@datalab-org.io>
+License-Expression: MIT
+Project-URL: homepage, https://github.com/datalab-org/datalab
+Project-URL: repository, https://github.com/datalab-org/datalab
+Project-URL: documentation, https://docs.datalab-org.io
+Project-URL: changelog, https://github.com/datalab-org/datalab/releases
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Information Technology
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: <3.12,>=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: bokeh<3.0,~=2.4
+Requires-Dist: matplotlib~=3.8
+Requires-Dist: periodictable~=1.7
+Requires-Dist: pydantic[dotenv,email]<2.0
+Requires-Dist: pint~=0.24
+Requires-Dist: pandas[excel]~=2.2
+Provides-Extra: server
+Requires-Dist: pymongo<4.11,~=4.7; extra == "server"
+Requires-Dist: Flask~=3.0; extra == "server"
+Requires-Dist: Flask-Login~=0.6; extra == "server"
+Requires-Dist: Flask-Cors~=5.0; extra == "server"
+Requires-Dist: Flask-Dance~=7.1; extra == "server"
+Requires-Dist: Flask-PyMongo~=2.3; extra == "server"
+Requires-Dist: Flask-Mail~=0.10; extra == "server"
+Requires-Dist: Flask-Compress~=1.15; extra == "server"
+Requires-Dist: Werkzeug~=3.0; extra == "server"
+Requires-Dist: python-dotenv~=1.0; extra == "server"
+Requires-Dist: pillow~=11.0; extra == "server"
+Requires-Dist: pyjwt~=2.9; extra == "server"
+Requires-Dist: invoke~=2.2; extra == "server"
+Requires-Dist: paramiko~=3.4; extra == "server"
+Provides-Extra: apps
+Requires-Dist: scipy~=1.13; extra == "apps"
+Requires-Dist: nmrglue~=0.10; extra == "apps"
+Requires-Dist: navani>=0.1.11; extra == "apps"
+Requires-Dist: pybaselines~=1.1; extra == "apps"
+Requires-Dist: rosettasciio<0.4,~=0.3; extra == "apps"
+Requires-Dist: python-dateutil~=2.9; extra == "apps"
+Provides-Extra: app-plugins-git
+Requires-Dist: datalab-app-plugin-insitu; extra == "app-plugins-git"
+Provides-Extra: chat
+Requires-Dist: langchain<0.3,>=0.2.6; extra == "chat"
+Requires-Dist: langchain-openai~=0.1; extra == "chat"
+Requires-Dist: langchain-anthropic~=0.1; extra == "chat"
+Requires-Dist: tiktoken~=0.7; extra == "chat"
+Requires-Dist: transformers~=4.42; extra == "chat"
+Provides-Extra: deploy
+Requires-Dist: gunicorn~=23.0; extra == "deploy"
+Provides-Extra: all
+Requires-Dist: datalab-server[apps,chat,server]; extra == "all"
+
+# <div align="center"><i>datalab</i></div>
+
+<div align="center" style="padding-bottom: 5px">
+<a href="https://demo.datalab-org.io"><img src="https://img.shields.io/badge/try_it_out!-public_demo_server-orange?logo=firefox"></a>
+</div>
+
+<div align="center">
+<a href="https://github.com/datalab-org/datalab/releases"><img src="https://badgen.net/github/release/datalab-org/datalab?icon=github&color=blue"></a>
+<a href="https://github.com/datalab-org/datalab#MIT-1-ov-file"><img src="https://badgen.net/github/license/datalab-org/datalab?icon=license&color=purple"></a>
+</div>
+
+<div align="center">
+<a href="https://github.com/datalab-org/datalab/actions/workflows/ci.yml"><img src="https://img.shields.io/github/actions/workflow/status/datalab-org/datalab/ci.yml?logo=github"></a>
+<a href="https://cloud.cypress.io/projects/4kqx5i/runs"><img src="https://img.shields.io/endpoint?url=https://cloud.cypress.io/badge/simple/4kqx5i/main&style=flat&logo=cypress"></a>
+<a href="https://the-datalab.readthedocs.io/en/latest/?badge=latest"><img src="https://img.shields.io/readthedocs/the-datalab?logo=readthedocs"></a>
+</div>
+
+<div align="center">
+<a href="https://github.com/datalab-org/datalab-ansible-terraform">
+  <img alt="Static Badge" src="https://img.shields.io/badge/Ansible-playbook-white?logo=ansible">
+</a>
+<a href="https://pypi.org/project/datalab-api">
+  <img alt="PyPI - Version" src="https://img.shields.io/pypi/v/datalab-api?logo=pypi&label=Python%20API">
+</a>
+</div>
+
+<div align="center">
+<a href="https://join.slack.com/t/datalab-world/shared_invite/zt-2h58ev3pc-VV496~5je~QoT2TgFIwn4g"><img src="https://img.shields.io/badge/Slack-chat_with_us-yellow?logo=slack"></a>
+</div>
+
+This repository contains the code for the *datalab* data management system, targeted (broadly) at materials chemistry labs but with customisability and extensability in mind.
+
+The main aim of *datalab* is to provide a platform for capturing the significant amounts of long-tail experimental data and metadata produced in a typical lab, and enable storage, filtering and future data re-use by humans and machines.
+The platform provides researchers with a way to record sample- and cell-specific metadata, attach and sync raw data from instruments, and perform analysis and visualisation of many characterisation techniques in the browser (XRD, NMR, electrochemical cycling, TEM, TGA, Mass Spec, Raman).
+Importantly, *datalab* stores a network of interconnected research objects in the lab, such that individual pieces of data are stored with the context needed to make them scientifically useful.
+
+The system was originally developed in and is currently deployed for the
+[Grey Group](https://www.ch.cam.ac.uk/group/grey/)
+in the Department of Chemistry at the University of Cambridge,
+with several instances deployed for members in the
+[*datalab* federation](https://github.com/datalab-org/datalab-federation).
+
+
+<div align="center">
+<video width="400" controls src="https://github.com/datalab-org/datalab/assets/7916000/0065cdd6-a5f0-4391-b192-0137fe208acc">
+</video>
+</div>
+
+## Features
+
+*datalab* consists of two main components:
+
+- a Flask-based Python web server (`pydatalab`) that communicates with a MongoDB
+  database backend and can perform simple analysis and ETL of particular data types,
+- a Vue 3 web application for a GUI that can be used to record information on
+  samples alongside raw data files and analysis documents.
+
+
+### Server
+
+- A REST API for accessing data and analysis related to chemical samples,
+  inventory and their connections, with ergonomic access provided via the
+  [*datalab* Python API](https://github.com/datalab-org/datalab-api).
+- OAuth2-based user authentication via GitHub or ORCID and simple user role
+  management.
+- Real-time data streaming and syncing with remote data sources (e.g., instrumentation, archives and file stores).
+
+### UI
+
+- A simple, intuitive UI for recording sample-based metadata and relationships with
+  other samples (batches, derivatives, _etc._), alongside synthesis parameters and raw data.
+- Basic analysis and plotting of live and archived data attached to a sample, _e.g._,
+  characterisation via XRD or NMR, electrochemical cycling data and images (see "Data blocks" section for a complete list).
+- Interactive network visualisation of the connections between samples and inventory.
+
+## Development status
+
+*datalab* remains under active development, and the API, data models and UI may change significantly between versions without prior notice.
+Where possible, breaking changes will be listed in the release notes for every pre-v1 release.
+
+## Installation
+
+Installation, usage and deployment instructions can be found in
+[INSTALL.md](./INSTALL.md) and in the [online documentation](https://the-datalab.readthedocs.io).
+
+## License
+
+This software is released under the conditions of the MIT license.
+Please see [LICENSE](./LICENSE) for the full text of the license.
+
+## Contributions
+
+This software was conceived and developed by:
+
+- [Prof Joshua Bocarsly](https://jdbocarsly.github.io) ([Department of Chemistry, University of Houston](https://www.uh.edu/nsm/chemistry), previously [Department of Chemistry, University of Cambridge](https://www.ch.cam.ac.uk/))
+- [Dr Matthew Evans](https://ml-evs.science) ([MODL-IMCN,
+  UCLouvain](https://uclouvain.be/en/research-institutes/imcn/modl) & [Matgenix](https://matgenix.com))
+
+with contributions and testing performed by other members of the Grey Group.
+
+A full list of code contributions can be found on [GitHub](https://github.com/datalab-org/datalab/graphs/contributors).
+
+## Contact
+
+We are available for consultations on setting up and managing *datalab* deployments, as well as collaborating on or sponsoring additions of new features and techniques.
+Please contact Josh or Matthew on their academic emails, or join the [public *datalab* Slack workspace](https://join.slack.com/t/datalab-world/shared_invite/zt-2h58ev3pc-VV496~5je~QoT2TgFIwn4g).
+
+## Funding
+
+This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement 957189 (DOI: [10.3030/957189](https://doi.org/10.3030/957189)), the [Battery Interface Genome - Materials Acceleration Platform (BIG-MAP)](https://www.big-map.eu), as an external stakeholder project.
+
+<div align="center">
+<img href="https://big-map.org" src="https://big-map.github.io/big-map-registry/static/img/big-map-white-transparent.png" width=100>
+</div>

datalab_server-0.5.3rc6/README.md

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+# <div align="center"><i>datalab</i></div>
+
+<div align="center" style="padding-bottom: 5px">
+<a href="https://demo.datalab-org.io"><img src="https://img.shields.io/badge/try_it_out!-public_demo_server-orange?logo=firefox"></a>
+</div>
+
+<div align="center">
+<a href="https://github.com/datalab-org/datalab/releases"><img src="https://badgen.net/github/release/datalab-org/datalab?icon=github&color=blue"></a>
+<a href="https://github.com/datalab-org/datalab#MIT-1-ov-file"><img src="https://badgen.net/github/license/datalab-org/datalab?icon=license&color=purple"></a>
+</div>
+
+<div align="center">
+<a href="https://github.com/datalab-org/datalab/actions/workflows/ci.yml"><img src="https://img.shields.io/github/actions/workflow/status/datalab-org/datalab/ci.yml?logo=github"></a>
+<a href="https://cloud.cypress.io/projects/4kqx5i/runs"><img src="https://img.shields.io/endpoint?url=https://cloud.cypress.io/badge/simple/4kqx5i/main&style=flat&logo=cypress"></a>
+<a href="https://the-datalab.readthedocs.io/en/latest/?badge=latest"><img src="https://img.shields.io/readthedocs/the-datalab?logo=readthedocs"></a>
+</div>
+
+<div align="center">
+<a href="https://github.com/datalab-org/datalab-ansible-terraform">
+  <img alt="Static Badge" src="https://img.shields.io/badge/Ansible-playbook-white?logo=ansible">
+</a>
+<a href="https://pypi.org/project/datalab-api">
+  <img alt="PyPI - Version" src="https://img.shields.io/pypi/v/datalab-api?logo=pypi&label=Python%20API">
+</a>
+</div>
+
+<div align="center">
+<a href="https://join.slack.com/t/datalab-world/shared_invite/zt-2h58ev3pc-VV496~5je~QoT2TgFIwn4g"><img src="https://img.shields.io/badge/Slack-chat_with_us-yellow?logo=slack"></a>
+</div>
+
+This repository contains the code for the *datalab* data management system, targeted (broadly) at materials chemistry labs but with customisability and extensability in mind.
+
+The main aim of *datalab* is to provide a platform for capturing the significant amounts of long-tail experimental data and metadata produced in a typical lab, and enable storage, filtering and future data re-use by humans and machines.
+The platform provides researchers with a way to record sample- and cell-specific metadata, attach and sync raw data from instruments, and perform analysis and visualisation of many characterisation techniques in the browser (XRD, NMR, electrochemical cycling, TEM, TGA, Mass Spec, Raman).
+Importantly, *datalab* stores a network of interconnected research objects in the lab, such that individual pieces of data are stored with the context needed to make them scientifically useful.
+
+The system was originally developed in and is currently deployed for the
+[Grey Group](https://www.ch.cam.ac.uk/group/grey/)
+in the Department of Chemistry at the University of Cambridge,
+with several instances deployed for members in the
+[*datalab* federation](https://github.com/datalab-org/datalab-federation).
+
+
+<div align="center">
+<video width="400" controls src="https://github.com/datalab-org/datalab/assets/7916000/0065cdd6-a5f0-4391-b192-0137fe208acc">
+</video>
+</div>
+
+## Features
+
+*datalab* consists of two main components:
+
+- a Flask-based Python web server (`pydatalab`) that communicates with a MongoDB
+  database backend and can perform simple analysis and ETL of particular data types,
+- a Vue 3 web application for a GUI that can be used to record information on
+  samples alongside raw data files and analysis documents.
+
+
+### Server
+
+- A REST API for accessing data and analysis related to chemical samples,
+  inventory and their connections, with ergonomic access provided via the
+  [*datalab* Python API](https://github.com/datalab-org/datalab-api).
+- OAuth2-based user authentication via GitHub or ORCID and simple user role
+  management.
+- Real-time data streaming and syncing with remote data sources (e.g., instrumentation, archives and file stores).
+
+### UI
+
+- A simple, intuitive UI for recording sample-based metadata and relationships with
+  other samples (batches, derivatives, _etc._), alongside synthesis parameters and raw data.
+- Basic analysis and plotting of live and archived data attached to a sample, _e.g._,
+  characterisation via XRD or NMR, electrochemical cycling data and images (see "Data blocks" section for a complete list).
+- Interactive network visualisation of the connections between samples and inventory.
+
+## Development status
+
+*datalab* remains under active development, and the API, data models and UI may change significantly between versions without prior notice.
+Where possible, breaking changes will be listed in the release notes for every pre-v1 release.
+
+## Installation
+
+Installation, usage and deployment instructions can be found in
+[INSTALL.md](./INSTALL.md) and in the [online documentation](https://the-datalab.readthedocs.io).
+
+## License
+
+This software is released under the conditions of the MIT license.
+Please see [LICENSE](./LICENSE) for the full text of the license.
+
+## Contributions
+
+This software was conceived and developed by:
+
+- [Prof Joshua Bocarsly](https://jdbocarsly.github.io) ([Department of Chemistry, University of Houston](https://www.uh.edu/nsm/chemistry), previously [Department of Chemistry, University of Cambridge](https://www.ch.cam.ac.uk/))
+- [Dr Matthew Evans](https://ml-evs.science) ([MODL-IMCN,
+  UCLouvain](https://uclouvain.be/en/research-institutes/imcn/modl) & [Matgenix](https://matgenix.com))
+
+with contributions and testing performed by other members of the Grey Group.
+
+A full list of code contributions can be found on [GitHub](https://github.com/datalab-org/datalab/graphs/contributors).
+
+## Contact
+
+We are available for consultations on setting up and managing *datalab* deployments, as well as collaborating on or sponsoring additions of new features and techniques.
+Please contact Josh or Matthew on their academic emails, or join the [public *datalab* Slack workspace](https://join.slack.com/t/datalab-world/shared_invite/zt-2h58ev3pc-VV496~5je~QoT2TgFIwn4g).
+
+## Funding
+
+This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement 957189 (DOI: [10.3030/957189](https://doi.org/10.3030/957189)), the [Battery Interface Genome - Materials Acceleration Platform (BIG-MAP)](https://www.big-map.eu), as an external stakeholder project.
+
+<div align="center">
+<img href="https://big-map.org" src="https://big-map.github.io/big-map-registry/static/img/big-map-white-transparent.png" width=100>
+</div>

datalab_server-0.5.3rc6/docs/.pages

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+nav:
+    - index.md
+    - INSTALL.md
+    - deployment.md
+    - config.md
+    - schemas
+    - blocks
+    - CHANGELOG.md