| Name | aiida-amber JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | None |
| Summary | AiiDA plugin that wraps amber molecular dynamics executables |
| upload_time | 2024-05-20 19:43:26 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
aiida
plugin
amber
aiida-amber
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[![Build Status][ci-badge]][ci-link]
[![Coverage Status][cov-badge]][cov-link]
[![Docs status][docs-badge]][docs-link]
[![PyPI version][pypi-badge]][pypi-link]
# aiida-amber
AiiDA plugin that wraps amber molecular dynamics executables
This plugin is the default output of the
[AiiDA plugin cutter](https://github.com/aiidateam/aiida-plugin-cutter),
intended to help developers get started with their AiiDA plugins.
## Repository contents
* [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration
* [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and builds documentation at every new commit
* [`publish-on-pypi.yml`](.github/workflows/publish-on-pypi.yml): automatically deploy git tags to PyPI - just generate a [PyPI API token](https://pypi.org/help/#apitoken) for your PyPI account and add it to the `pypi_token` secret of your github repository
* [`aiida_amber/`](aiida_amber/): The main source code of the plugin package
* [`data/`](aiida_amber/data/): A new `DiffParameters` data class, used as input to the `DiffCalculation` `CalcJob` class
* [`calculations.py`](aiida_amber/calculations.py): A new `DiffCalculation` `CalcJob` class
* [`cli.py`](aiida_amber/cli.py): Extensions of the `verdi data` command line interface for the `DiffParameters` class
* [`helpers.py`](aiida_amber/helpers.py): Helpers for setting up an AiiDA code for `diff` automatically
* [`parsers.py`](aiida_amber/parsers.py): A new `Parser` for the `DiffCalculation`
* [`docs/`](docs/): A documentation template ready for publication on [Read the Docs](http://aiida-diff.readthedocs.io/en/latest/)
* [`examples/`](examples/): An example of how to submit a calculation using this plugin
* [`tests/`](tests/): Basic regression tests using the [pytest](https://docs.pytest.org/en/latest/) framework (submitting a calculation, ...). Install `pip install -e .[testing]` and run `pytest`.
* [`.gitignore`](.gitignore): Telling git which files to ignore
* [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`
* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)
* [`LICENSE`](LICENSE): License for your plugin
* [`README.md`](README.md): This file
* [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
* [`pyproject.toml`](setup.json): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
See also the following video sequences from the 2019-05 AiiDA tutorial:
* [run aiida-diff example calculation](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=403s)
* [aiida-diff CalcJob plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=685s)
* [aiida-diff Parser plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=936s)
* [aiida-diff computer/code helpers](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1238s)
* [aiida-diff input data (with validation)](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1353s)
* [aiida-diff cli](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1621s)
* [aiida-diff tests](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1931s)
* [Adding your plugin to the registry](https://www.youtube.com/watch?v=760O2lDB-TM&t=112s)
* [pre-commit hooks](https://www.youtube.com/watch?v=760O2lDB-TM&t=333s)
For more information, see the [developer guide](https://aiida-diff.readthedocs.io/en/latest/developer_guide) of your plugin.
## Features
* Add input files using `SinglefileData`:
```python
SinglefileData = DataFactory('singlefile')
inputs['file1'] = SinglefileData(file='/path/to/file1')
inputs['file2'] = SinglefileData(file='/path/to/file2')
```
* Specify command line options via a python dictionary and `DiffParameters`:
```python
d = { 'ignore-case': True }
DiffParameters = DataFactory('amber')
inputs['parameters'] = DiffParameters(dict=d)
```
* `DiffParameters` dictionaries are validated using [voluptuous](https://github.com/alecthomas/voluptuous).
Find out about supported options:
```python
DiffParameters = DataFactory('amber')
print(DiffParameters.schema.schema)
```
## Installation
```shell
pip install aiida-amber
verdi quicksetup # better to set up a new profile
verdi plugin list aiida.calculations # should now show your calclulation plugins
```
## Usage
Here goes a complete example of how to submit a test calculation using this plugin.
A quick demo of how to submit a calculation:
```shell
verdi daemon start # make sure the daemon is running
cd examples
./example_01.py # run test calculation
verdi process list -a # check record of calculation
```
The plugin also includes verdi commands to inspect its data types:
```shell
verdi data amber list
verdi data amber export <PK>
```
## Development
```shell
git clone https://github.com/jkalayan/aiida-amber .
cd aiida-amber
pip install --upgrade pip
pip install -e .[pre-commit,testing] # install extra dependencies
pre-commit install # install pre-commit hooks
pytest -v # discover and run all tests
```
See the [developer guide](http://aiida-amber.readthedocs.io/en/latest/developer_guide/index.html) for more information.
## License
MIT
## Contact
jas.kalayan@stfc.ac.uk
[ci-badge]: https://github.com/jkalayan/aiida-amber/workflows/ci/badge.svg?branch=master
[ci-link]: https://github.com/jkalayan/aiida-amber/actions
[cov-badge]: https://coveralls.io/repos/github/jkalayan/aiida-amber/badge.svg?branch=master
[cov-link]: https://coveralls.io/github/jkalayan/aiida-amber?branch=master
[docs-badge]: https://readthedocs.org/projects/aiida-amber/badge
[docs-link]: http://aiida-amber.readthedocs.io/
[pypi-badge]: https://badge.fury.io/py/aiida-amber.svg
[pypi-link]: https://badge.fury.io/py/aiida-amber
Raw data
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Install `pip install -e .[testing]` and run `pytest`.\n* [`.gitignore`](.gitignore): Telling git which files to ignore\n* [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`\n* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)\n* [`LICENSE`](LICENSE): License for your plugin\n* [`README.md`](README.md): This file\n* [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)\n* [`pyproject.toml`](setup.json): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)\n\nSee also the following video sequences from the 2019-05 AiiDA tutorial:\n\n * [run aiida-diff example calculation](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=403s)\n * [aiida-diff CalcJob plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=685s)\n * [aiida-diff Parser plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=936s)\n * [aiida-diff computer/code helpers](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1238s)\n * [aiida-diff input data (with validation)](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1353s)\n * [aiida-diff cli](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1621s)\n * [aiida-diff tests](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1931s)\n * [Adding your plugin to the registry](https://www.youtube.com/watch?v=760O2lDB-TM&t=112s)\n * [pre-commit hooks](https://www.youtube.com/watch?v=760O2lDB-TM&t=333s)\n\nFor more information, see the [developer guide](https://aiida-diff.readthedocs.io/en/latest/developer_guide) of your plugin.\n\n\n## Features\n\n * Add input files using `SinglefileData`:\n ```python\n SinglefileData = DataFactory('singlefile')\n inputs['file1'] = SinglefileData(file='/path/to/file1')\n inputs['file2'] = SinglefileData(file='/path/to/file2')\n ```\n\n * Specify command line options via a python dictionary and `DiffParameters`:\n ```python\n d = { 'ignore-case': True }\n DiffParameters = DataFactory('amber')\n inputs['parameters'] = DiffParameters(dict=d)\n ```\n\n * `DiffParameters` dictionaries are validated using [voluptuous](https://github.com/alecthomas/voluptuous).\n Find out about supported options:\n ```python\n DiffParameters = DataFactory('amber')\n print(DiffParameters.schema.schema)\n ```\n\n## Installation\n\n```shell\npip install aiida-amber\nverdi quicksetup # better to set up a new profile\nverdi plugin list aiida.calculations # should now show your calclulation plugins\n```\n\n\n## Usage\n\nHere goes a complete example of how to submit a test calculation using this plugin.\n\nA quick demo of how to submit a calculation:\n```shell\nverdi daemon start # make sure the daemon is running\ncd examples\n./example_01.py # run test calculation\nverdi process list -a # check record of calculation\n```\n\nThe plugin also includes verdi commands to inspect its data types:\n```shell\nverdi data amber list\nverdi data amber export <PK>\n```\n\n## Development\n\n```shell\ngit clone https://github.com/jkalayan/aiida-amber .\ncd aiida-amber\npip install --upgrade pip\npip install -e .[pre-commit,testing] # install extra dependencies\npre-commit install # install pre-commit hooks\npytest -v # discover and run all tests\n```\n\nSee the [developer guide](http://aiida-amber.readthedocs.io/en/latest/developer_guide/index.html) for more information.\n\n## License\n\nMIT\n## Contact\n\njas.kalayan@stfc.ac.uk\n\n\n[ci-badge]: https://github.com/jkalayan/aiida-amber/workflows/ci/badge.svg?branch=master\n[ci-link]: https://github.com/jkalayan/aiida-amber/actions\n[cov-badge]: https://coveralls.io/repos/github/jkalayan/aiida-amber/badge.svg?branch=master\n[cov-link]: https://coveralls.io/github/jkalayan/aiida-amber?branch=master\n[docs-badge]: https://readthedocs.org/projects/aiida-amber/badge\n[docs-link]: http://aiida-amber.readthedocs.io/\n[pypi-badge]: https://badge.fury.io/py/aiida-amber.svg\n[pypi-link]: https://badge.fury.io/py/aiida-amber\n\n",
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