ipyoptimade 1.2.2
Jupyter client for searching structures through OPTIMADE API
Requires Python: >=3.9

# OPTIMADE Jupyter widgets and Voilà application

[![MaterialsCloud](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/CasperWA/voila-optimade-client/develop/docs/resources/mcloud_badge.json)](https://materialscloud.org/optimadeclient/)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/aiidalab/ipyoptimade/main?urlpath=%2Fvoila%2Frender%2Foptimade-client.ipynb)
[![codecov](https://codecov.io/gh/aiidalab/ipyoptimade/branch/main/graph/badge.svg)](https://codecov.io/gh/aiidalab/ipyoptimade)
[![PyPI - Version](https://img.shields.io/pypi/v/ipyoptimade?color=4CC61E)](https://pypi.org/project/ipyoptimade/)

Query for and import structures from [OPTIMADE](https://www.optimade.org) providers (COD, MaterialsCloud, NoMaD, Materials Project, ODBX, OQMD, and more ...).
The package provides a Jupyter widget for querying OPTIMADE providers and an example Voilà application to stack widgets into an web application.

Current supported OPTIMADE API versions: `1.1.0`, `1.0.0`, `1.0.0-rc.2`, `1.0.0-rc.1`, `0.10.1`

Install with

```bash
pip install ipyoptimade
```

## 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 ipyoptimade 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

To run the application locally, you need to have Jupyter installed.
You can then run the application by opening the notebook [`optimade-client.ipynb`](optimade-client.ipynb) in Jupyter and running all cells.
If you have the `voila` package installed, you can also run the application in Voilà by clicking the Voilà button in the Jupyter notebook toolbar.

## Configuration (Voilà)

For running the application (in Voilà) on Binder, the configuration file [`jupyter_config.json`](ipyoptimade/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`](ipyoptimade/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 `ipyoptimade_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).

## Development

Install with

```bash
pip install -e .[dev]
pre-commit install
```

Set

```
export ipyoptimade_DEBUG=1
```

to automatically open and show the debug & error messages in the `OptimadeLog()` widget.

Test voila with

```bash
voila optimade-client.ipynb
```

If dependencies are updated, update `requirements.txt` file that is used for the Docker image used in binder. The command to update the file is included at the top of `requirements.txt`.

### Making a new release

To create a new release, clone the repository, install development dependencies with `pip install -e '.[dev]'`, and then execute `bumpver update [--major|--minor|--patch] [--tag-num --tag [alpha|beta|rc]]`.
This will:

1. Create a tagged release with bumped version and push it to the repository.
2. Trigger a GitHub actions workflow that creates a GitHub release and publishes it on PyPI.

Additional notes:

- Use the `--dry` option to preview the release change.
- The release tag (e.g. a/b/rc) is determined from the last release.
  Use the `--tag` option to switch the release tag.
- This package follows [semantic versioning](https://semver.org/).

## License

MIT. The terms of the license can be found in the [LICENSE](LICENSE) file.

## Acknowledgements

<!-- prettier-ignore -->
| | |
|---|---|
| [![BIG-MAP](https://avatars1.githubusercontent.com/u/72801303?s=200&v=4)](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

casper+github@welzel.nu  
aiidalab@materialscloud.org