KIM-EDN encoder and decoder

edn

Extensible data notation [eed-n]

edn is an extensible data notation. A superset of edn is used by Clojure to represent programs, and it is used by KIM and other applications as a data format.

kim-edn

The KIM infrastructure embraces a subset of edn as a standard data format. The primary purpose of this data format choice is to serve as a notational superset to JSON with the enhancements being that it (1) allows for comments and (2) treats commas as whitespace enabling easier templating.

The subset of edn allowed is constrained to:

• Booleans
• Strings
• Integers
• Floating point numbers
• Vectors (or arrays)
• Maps (or hash, dicts, hashmaps, etc.)

Exceptions:

• nil is not allowed, this includes JSON's null which is not allowed. Instead consider:
  1. using an empty string ("") as the value,
  2. using the number 0 as the value,
  3. or omitting a key-value pair.
• Symbols are not allowed
• Keywords are not allowed
• Lists are not allowed, please use vectors instead
• Sets are not allowed
• Tagged elements are not allowed

kim-edn has been adapted and updated from the Python json module. It exposes an API familiar to users of the standard library. (See pickle, or marshal, or json modules.)

Encoding basic Python object hierarchies::

    >>> import kim_edn
    >>> kim_edn.dumps(["short-name", {"source-value": ["hcp"]}])
    '["short-name" {"source-value" ["hcp"]}]'

    >>> print(kim_edn.dumps("\"P6_3/mmc"))
    "\"P6_3/mmc"

    >>> print(kim_edn.dumps('\\'))
    "\\"

    >>> print(kim_edn.dumps({"domain": "openkim.org", "data-method": "computation", "author": "John Doe"}, sort_keys=True))
    {"author" "John Doe" "data-method" "computation" "domain" "openkim.org"}

    >>> from io import StringIO
    >>> io = StringIO()
    >>> kim_edn.dump(['streaming API'], io)
    >>> io.getvalue()
    '["streaming API"]'

Pretty printing::

    >>> import kim_edn
    >>> print(kim_edn.dumps({"domain": "openkim.org", "data-method": "computation", "author": "John Doe"}, sort_keys=True, indent=4))
    {
        "author" "John Doe"
        "data-method" "computation"
        "domain" "openkim.org"
    }

Decoding KIM-EDN::

    >>> import kim_edn
    >>> obj = ["a", {"source-value": 6.9790981921, "source-unit": "angstrom"}]
    >>> kim_edn.loads('["a", {"source-value": 6.9790981921, "source-unit": "angstrom"}]') == obj
    True
    >>> kim_edn.load('["a", {"source-value": 6.9790981921, "source-unit": "angstrom"}]') == obj
    True
    >>> kim_edn.loads('"\\"foo\\bar"') == '"foo\x08ar'
    True
    >>> kim_edn.load(kim_edn.dumps(obj)) == obj
    True
    >>> from io import StringIO
    >>> io = StringIO('["openkim.org"]')
    >>> kim_edn.load(io)[0] == 'openkim.org'
    True

Decoding Commented KIM-EDN::

    >>> obj = {"property-id": "tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass"}
    >>> c_str = '{\n  ; property-id\n  "property-id"           "tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass" ; property id containing the unique ID of the property.\n }'
    >>> kim_edn.load(c_str) == obj
    True

Specializing KIM-EDN object decoding::

    >>> import kim_edn
    >>> def as_complex(dct):
    ...     if '__complex__' in dct:
    ...         return complex(dct['real'], dct['imag'])
    ...     return dct
    ...
    >>> kim_edn.loads('{"__complex__": true, "real": 1, "imag": 2}',
    ...     object_hook=as_complex)
    (1+2j)
    >>> from decimal import Decimal
    >>> kim_edn.loads('1.1', parse_float=Decimal) == Decimal('1.1')
    True

Specializing KIM-EDN object encoding::

    >>> import kim_edn
    >>> def encode_complex(obj):
    ...     if isinstance(obj, complex):
    ...         return [obj.real, obj.imag]
    ...     msg = 'Object of type {} is not '.format(obj.__class__.__name__)
    ...     msg += 'KIM-EDN serializable'
    ...     raise TypeError(msg)
    ...
    >>> kim_edn.dumps(2 + 1j, default=encode_complex)
    '[2.0 1.0]'
    >>> kim_edn.KIMEDNEncoder(default=encode_complex).encode(2 + 1j)
    '[2.0 1.0]'
    >>> ''.join(kim_edn.KIMEDNEncoder(default=encode_complex).iterencode(2 + 1j))
    '[2.0 1.0]'

Using kim_edn.tool from the shell to validate and pretty-print::

    $ echo '{"kim_edn" "obj"}' | python -m kim_edn.tool
    {
        "kim_edn" "obj"
    }

    $ echo '{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal"}' | python -m kim_edn.tool
    {
        "property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal"
    }

    $ echo '{"foo": ["bar", "baz"]}' | python -m kim_edn.tool
    {
        "foo" [
            "bar"
            "baz"
        ]
    }

    $ echo '{"foo" ["bar" "baz"]}' | python -m kim_edn.tool
    {
        "foo" [
            "bar"
            "baz"
        ]
    }

    $ echo '{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-potential-energy-hexagonal-crystal" "instance-id" 1 "space-group" {"source-value" "P6_3/mmc"} "basis-atom-coordinates" {"source-value" [[0, 0, 0][0.5, 0, 0.5]]}}' | python -m kim_edn.tool
    {
        "property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-potential-energy-hexagonal-crystal"
        "instance-id" 1
        "space-group" {
            "source-value" "P6_3/mmc"
        }
        "basis-atom-coordinates" {
            "source-value" [
                [
                    0
                    0
                    0
                ]
                [
                    0.5
                    0
                    0.5
                ]
            ]
        }
    }

Note:

This module's encoders and decoders preserve input and output order by default. Order is only lost if the underlying containers are unordered.

Encoders and Decoders

KIM-EDN decoder (KIMEDNDecoder) object, performs the following translations in decoding by default:

KIM-EDN encoder (KIMEDNEncoder) for OpenKIM Python data structures, supports the following objects and types by default:

Installing kim-edn

Requirements

You need Python 3.6 or later to run kim-edn. You can have multiple Python versions (2.x and 3.x) installed on the same system without problems.

To install Python 3 for different Linux flavors, macOS and Windows, packages are available at
https://www.python.org/getit/

Using pip

pip is the most popular tool for installing Python packages, and the one included with modern versions of Python.

kim-edn can be installed with pip:

pip install kim-edn

Note:

Depending on your Python installation, you may need to use pip3 instead of pip.

pip3 install kim-edn

Depending on your configuration, you may have to run pip like this:

python3 -m pip install kim-edn

Using pip (GIT Support)

pip currently supports cloning over git

pip install git+https://github.com/openkim/kim-edn.git

For more information and examples, see the pip install reference.

Using conda

conda is the package management tool for Anaconda Python installations.

Installing kim-edn from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, kim-edn can be installed with conda:

conda install kim-edn

or with mamba:

mamba install kim-edn

It is possible to list all of the versions of kim-edn available on your platform with conda:

conda search kim-edn --channel conda-forge

or with mamba:

mamba search kim-edn --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search kim-edn --channel conda-forge

# List packages depending on `kim-edn`:
mamba repoquery whoneeds kim-edn --channel conda-forge

# List dependencies of `kim-edn`:
mamba repoquery depends kim-edn --channel conda-forge

References

This module has been adapted and updated from the python json module to comply with the subset of edn format used in KIM.

Copyright

Copyright © 2001-2024 Python Software Foundation. All rights reserved.

Copyright (c) 2019-2024, Regents of the University of Minnesota. All Rights Reserved.

Contributing

Contributors:
      Yaser Afshar