aiida-grouppathx 0.2.0

AiiDA plugin provides the GroupPathX class

aiida-grouppathx

AiiDA plugin provides the GroupPathX class.

This plugin was kickstarted using AiiDA plugin cutter, intended to help developers get started with their AiiDA plugins.

Features and usage

This package is provides a enhanced version of GroupPath - GroupPathX. The main feature is that it allows nodes stored under a group to be named by an alias. This way, one can address a specific Node as GroupPath('mygroup/structure1'). In addition, a show_tree method is provided for visualising the content of a specific GroupPathX, similiar to the command line tool tree that works on the file system. The goal is to provide a way for managing data with an interface what is similar to a file system based approach.

tree aiida_grouppathx

aiida_grouppathx
├── __init__.py
├── pathx.py
└── __pycache__
   ├── __init__.cpython-38.pyc
   └── pathx.cpython-38.pyc

In analogy:

from aiida_grouppathx import GroupPathX
path = GroupPathX('group1')
path.get_or_create_group()
path['group2'].get_or_create_group()
path.add_node(Int(1).store(), 'int1')
path['group2'].add_node(Int(1).store(), 'int2')

path.show_tree()

gives

group1
├── group2
│   └── int2 *
└── int1 *

where the * highlights that a leaf is a Node rather than a group. This kind of mark up can be customised, for example, to show the status of workflow nodes.

def decorate_name(path):
    if path.is_node:
        return ' ' + str(path.get_node())
path.show_tree(decorate_name)

gives:

group1
├── group2
│   └── int2  uuid: de79d244-d3bb-4f61-9d3a-b3f09e1afb72 (pk: 7060) value: 1
└── int1  uuid: e2f70643-0c25-4ae5-929a-a3e055969d10 (pk: 7059) value: 1

Multiple decorators can be combined

from aiida_grouppathx import decorate_with_group_names, decorate_with_label decorate_with_uuid_first_n

path.show_tree(decorate_with_group_names, decorate_with_label, decorate_with_uuid_first_n())

output:

group1
├── group2
│   └── int2 group1/group2 |  | de79d244-d3b
└── int1 group1 |  | e2f70643-0c2

The stored nodes can be access through:

group1['group2/int2'].get_node()  # Gives node de89d2
group1.browse.group2.int2().get_node()  # Also gives node de89d2

and also

path.browse.<tab>
path.browse.int1()     # To access the `group1/int1` path
path.browse.int1().get_node()     # To access the `group1/int1` node

Please see the pathx.py for the extended methods, and the official documentation for the concept of GroupPath.

The package does not change how Group and Node operates in the AiiDA. It is only built on top of the existing system as an alternative way to access the underlying data.

Installation

pip install aiida-grouppathx
verdi quicksetup  # better to set up a new profile

Development

git clone https://github.com/zhubonan/aiida-grouppathx .
cd aiida-grouppathx
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 for more information.

License

MIT

Contact

[e-mail]