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https://github.com/casperwa/voila-optimade-client
Import structures in AiiDA lab using OPTIMADE
https://github.com/casperwa/voila-optimade-client
Last synced: about 1 month ago
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Import structures in AiiDA lab using OPTIMADE
- Host: GitHub
- URL: https://github.com/casperwa/voila-optimade-client
- Owner: CasperWA
- License: mit
- Created: 2019-01-07T10:13:51.000Z (almost 6 years ago)
- Default Branch: develop
- Last Pushed: 2024-10-09T06:38:34.000Z (3 months ago)
- Last Synced: 2024-11-23T08:42:20.585Z (about 1 month ago)
- Language: Python
- Homepage:
- Size: 1.47 MB
- Stars: 3
- Watchers: 2
- Forks: 7
- Open Issues: 46
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# OPTIMADE client (in Voilà)
[](https://materialscloud.org/optimadeclient/)
[](https://mybinder.org/v2/gh/CasperWA/voila-optimade-client/develop?urlpath=%2Fvoila%2Frender%2FOPTIMADE-Client.ipynb)
Query for and import structures from [OPTIMADE](https://www.optimade.org) providers (COD, MaterialsCloud, NoMaD, Materials Project, ODBX, OQMD, and more ...).
Current supported OPTIMADE API versions: `1.0.0`, `1.0.0-rc.2`, `1.0.0-rc.1`, `0.10.1`
## Run the client
This Jupyter-based app is intended to run either:
- In [AiiDAlab](https://aiidalab.materialscloud.org) as well as inside a [Quantum Mobile](https://materialscloud.org/work/quantum-mobile) Virtual Machine;
- As a [MaterialsCloud tool](https://materialscloud.org/optimadeclient/);
- As a standalone [MyBinder application](https://mybinder.org/v2/gh/CasperWA/voila-optimade-client/develop?urlpath=%2Fvoila%2Frender%2FOPTIMADE-Client.ipynb); or
- As a standalone local application (see more information about this below).
For AiiDAlab, use the App Store in the [Home App](https://github.com/aiidalab/aiidalab-home) to install it.
## Usage
### AiiDAlab
To use the OPTIMADE structure importer in your own AiiDAlab application write the following:
```python
from aiidalab_widget_base import OptimadeQueryWidget
from aiidalab_widgets_base.viewers import StructureDataViewer
from ipywidgets import dlink
structure_query = OptimadeQueryWidget()
structure_viewer = StructureDataViewer()
# Save to `_` in order to suppress output
_ = dlink((structure_query, 'structure'), (structure_viewer, 'structure'))
display(structure_query)
display(structure_viewer)
```
This will immediately display a query widget with a dropdown of current structure databases that implements the OPTIMADE API.
Then you can filter to find a family of structures according to elements, number of elements, chemical formula, and more.
See the [OPTIMADE API specification](https://github.com/Materials-Consortia/OPTiMaDe/blob/master/optimade.rst) for the full list of filter options and their description.
In order to delve deeper into the details of a particular structure, you can also import and display `OptimadeResultsWidget`.
See the notebook [`OPTIMADE-Client.ipynb`](OPTIMADE-Client.ipynb) for an example of how to set up a general purpose OPTIMADE importer.
#### Embedded
The query widget may also be embedded into another app.
For this a more "minimalistic" version of the widget can be used by passing `embedded=True` upon initiating the widget, i.e., `structure_query = OptimadeQueryWidget(embedded=True)`.
Everything else works the same - so you would still have to link up the query widget to the rest of your app.
### General Jupyter notebook
The package's widgets can be used in any general Jupyter notebook as well as AiiDAlab.
Example:
```python
from optimade_client import
OptimadeQueryProviderWidget,
OptimadeQueryFilterWidget,
OptimadeSummaryWidget
from ipywidgets import dlink
database_selector = OptimadeQueryProviderWidget()
structure_query = OptimadeQueryFilterWidget()
structure_viewer = OptimadeSummaryWidget()
# Save to `_` in order to suppress output
_ = dlink((database_selector, 'database'), (structure_query, 'database'))
_ = dlink((structure_query, 'structure'), (structure_viewer, 'entity'))
display(database_selector, structure_query, structure_viewer)
```
This will use the package's own structure viewer and summary widget.
Note, the `OptimadeQueryWidget` mentioned above is a special wrapper widget in AiiDAlab for the `OptimadeQueryProviderWidget` and `OptimadeQueryFilterWidget` widgets.
### Running application locally
First, you will need to install the package either from [PyPI](https://pypi.org/project/optimade-client) or by retrieving the git repository hosted on [GitHub](https://github.com/CasperWA/voila-optimade-client).
#### PyPI
```shell
pip install optimade-client[server]
```
#### GitHub
```shell
git clone https://github.com/CasperWA/voila-optimade-client.git
cd voila-optimade-client
pip install .[server]
```
Note, it is important to install the `server` extra in order to also install the `voila` package (and the `ase` package for a wider variety of download formats).
To now run the application (notebook) [`OPTIMADE-Client.ipynb`](OPTIMADE-Client.ipynb) you can simply run the command `optimade-client` in a terminal and go to the printed URL (usually ) or pass the `--open-browser` option to let the program try to automatically open your default browser.
The application will be run in Voilà using Voilà's own `tornado`-based server.
The configuration will automatically be copied to Jupyter's configuration directory before starting the server.
```shell
optimade-client
```
For a list of all options that can be passed to `optimade-client` use the `-h/--help` option.
## Contribute
If you wish to contribute to the application, you can install it in "editable" mode by using the `-e` flag: `pip install -e .[dev]`.
It is recommended that you use the GitHub-route mentioned above.
You should also install `pre-commit` in the cloned git repository by running:
```shell
pre-commit install
```
To start making contributions, fork the repository and create PRs.
## Configuration (Voilà)
For running the application (in Voilà) on Binder, the configuration file [`jupyter_config.json`](optimade_client/jupyter_config.json) can be used.
If you wish to start the Voilà server locally with the same configuration, either copy the [`jupyter_config.json`](optimade_client/jupyter_config.json) file to your Jupyter config directory, renaming it to `voila.json` or pass the configurations when you start the server using the CLI.
> **Note**: `jupyter_config.json` is automatically copied over as `voila.json` when running the application using the `optimade-client` command.
Locate your Jupyter config directory:
```shell
jupyter --config-dir
/path/to/jupyter/config/dir
```
Example of passing configurations when you start the Voilà server using the CLI:
```shell
voila --enable_nbextensions=True --VoilaExecutePreprocessor.timeout=180 "OPTIMADE-Client.ipynb"
```
To see the full list of configurations you can call `voila` and pass `--help-all`.
### Running with "development" providers (Materials Cloud-specific)
Set the environment variable `OPTIMADE_CLIENT_DEVELOPMENT_MODE` to `1` (the integer version for `True` (`1`) or `False` (`0`)) in order to force the use of development servers for providers (currently only relevant for Materials Cloud).
## License
MIT. The terms of the license can be found in the [LICENSE](LICENSE) file.
## Acknowledgements
| | |
|---|---|
| [](https://www.big-map.eu/) | [BIG-MAP](https://www.big-map.eu/); This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 957189. The project is part of [BATTERY 2030+](https://battery2030.eu/), the large-scale European research initiative for inventing the sustainable batteries of the future. |
## Contact