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Software Configuration

SoftwareConfiguration

Bases: UUIDBaseNode

Definition

The software_configuration sub-object includes software and the set of algorithms to execute computation or computational_process.

Can Be Added To:
Available sub-objects:
Attributes
keys type example description required vocab
software Software software used True
algorithms list[Algorithm] algorithms used
notes str miscellaneous information, or custom data structure (e.g.; JSON)
citation list[Citation] reference to a book, paper, or scholarly work
JSON Representation
{
   "node":["SoftwareConfiguration"],
   "uid":"_:f0dc3415-635d-4590-8b1f-cd65ad8ab3fe"
   "software":{
      "name":"SOMA",
      "node":["Software"],
      "source":"https://gitlab.com/InnocentBug/SOMA",
      "uid":"_:5bf9cb33-f029-4d1b-ba53-3602036e4f75",
      "uuid":"5bf9cb33-f029-4d1b-ba53-3602036e4f75",
      "version":"0.7.0"
   }
}
Source code in src/cript/nodes/subobjects/software_configuration.py 
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class SoftwareConfiguration(UUIDBaseNode):
    """
    ## Definition

    The [software_configuration](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=24)
    sub-object includes software and the set of algorithms to execute computation or computational_process.

    ---

    ## Can Be Added To:
    * [Computation](../../primary_nodes/computation)
    * [Computation_Process](../../primary_nodes/computation_process)

    ## Available sub-objects:
    * [Algorithm](../algorithm)
    * [Citation](../citation)

    ---

    ## Attributes

    | keys                                             | type            | example | description                                                      | required | vocab |
    |--------------------------------------------------|-----------------|---------|------------------------------------------------------------------|----------|-------|
    | software                                         | Software        |         | software used                                                    | True     |       |
    | algorithms                                       | list[Algorithm] |         | algorithms used                                                  |          |       |
    | notes                                            | str             |         | miscellaneous information, or custom data structure (e.g.; JSON) |          |       |
    | citation                                         | list[Citation]  |         | reference to a book, paper, or scholarly work                    |          |       |


    ## JSON Representation
    ```json
    {
       "node":["SoftwareConfiguration"],
       "uid":"_:f0dc3415-635d-4590-8b1f-cd65ad8ab3fe"
       "software":{
          "name":"SOMA",
          "node":["Software"],
          "source":"https://gitlab.com/InnocentBug/SOMA",
          "uid":"_:5bf9cb33-f029-4d1b-ba53-3602036e4f75",
          "uuid":"5bf9cb33-f029-4d1b-ba53-3602036e4f75",
          "version":"0.7.0"
       }
    }
    ```
    """

    @dataclass(frozen=True)
    class JsonAttributes(UUIDBaseNode.JsonAttributes):
        software: Optional[Union[Software, UIDProxy]] = None
        algorithm: List[Union[Algorithm, UIDProxy]] = field(default_factory=list)
        notes: str = ""
        citation: List[Union[Citation, UIDProxy]] = field(default_factory=list)

    _json_attrs: JsonAttributes = JsonAttributes()

    @beartype
    def __init__(self, software: Union[Software, UIDProxy], algorithm: Optional[List[Union[Algorithm, UIDProxy]]] = None, notes: str = "", citation: Union[List[Union[Citation, UIDProxy]], None] = None, **kwargs):
        """
        Create Software_Configuration sub-object


        Parameters
        ----------
        software : Software
            Software node used for the Software_Configuration
        algorithm : Union[List[Algorithm], None], optional
            algorithm used for the Software_Configuration, by default None
        notes : str, optional
            plain text notes, by default ""
        citation : Union[List[Citation], None], optional
            list of Citation sub-object, by default None

        Examples
        ---------
        >>> import cript
        >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
        >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)

        Returns
        -------
        None
            Create Software_Configuration sub-object
        """
        if algorithm is None:
            algorithm = []
        if citation is None:
            citation = []
        super().__init__(**kwargs)
        new_json_attrs = replace(self._json_attrs, software=software, algorithm=algorithm, notes=notes, citation=citation)
        self._update_json_attrs_if_valid(new_json_attrs)

    @property
    @beartype
    def software(self) -> Union[Software, None, UIDProxy]:
        """
        Software used

        Examples
        --------
        >>> import cript
        >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
        >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)
        >>> my_software_configuration.software = my_software

        Returns
        -------
        Union[Software, None]
            Software node used
        """
        return self._json_attrs.software

    @software.setter
    @beartype
    def software(self, new_software: Union[Software, None, UIDProxy]) -> None:
        """
        set the Software used

        Parameters
        ----------
        new_software : Union[Software, None]
            new Software node

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, software=new_software)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def algorithm(self) -> List[Union[Algorithm, UIDProxy]]:
        """
        list of Algorithms used

        Examples
        --------
        >>> import cript
        >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
        >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
        >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)
        >>> my_software_configuration.algorithm = [my_algorithm]

        Returns
        -------
        List[Algorithm]
            list of algorithms used
        """
        return self._json_attrs.algorithm.copy()

    @algorithm.setter
    @beartype
    def algorithm(self, new_algorithm: List[Union[Algorithm, UIDProxy]]) -> None:
        """
        set the list of Algorithms

        Parameters
        ----------
        new_algorithm : List[Algorithm]
            list of algorithms

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, algorithm=new_algorithm)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def notes(self) -> str:
        """
        miscellaneous information, or custom data structure (e.g.; JSON). Notes can be written in plain text or JSON

        Examples
        --------
        ### Plain Text
        ```json
        my_software_configuration.notes = "these are my awesome notes!"
        ```

        Examples
        -------
        >>> import cript
        >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
        >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)
        >>> my_software_configuration.notes = "{'notes subject': 'notes contents'}"

        Returns
        -------
        str
            notes
        """
        return self._json_attrs.notes

    @notes.setter
    @beartype
    def notes(self, new_notes: str) -> None:
        """
        set notes for Software_configuration

        Parameters
        ----------
        new_notes : str
            new notes in plain text or JSON

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, notes=new_notes)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def citation(self) -> List[Union[Citation, UIDProxy]]:
        """
        list of Citation sub-objects for the Software_Configuration

        Examples
        --------
        >>> import cript
        >>> title = (
        ...     "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: "
        ...     "Soft coarse grained Monte-Carlo Acceleration (SOMA)"
        ... )
        >>> my_reference = cript.Reference(
        ...     type="journal_article",
        ...     title=title,
        ...     author=["Ludwig Schneider", "Marcus Müller"],
        ...     journal="Computer Physics Communications",
        ...     publisher="Elsevier",
        ...     year=2019,
        ...     pages=[463, 476],
        ...     doi="10.1016/j.cpc.2018.08.011",
        ...     issn="0010-4655",
        ...     website="https://www.sciencedirect.com/science/article/pii/S0010465518303072",
        ... )
        >>> my_citation = Citation("reference", my_reference)
        >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
        >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)
        >>> my_software_configuration.citation = [my_citation]

        Returns
        -------
        List[Citation]
            list of Citations
        """
        return self._json_attrs.citation.copy()

    @citation.setter
    @beartype
    def citation(self, new_citation: List[Union[Citation, UIDProxy]]) -> None:
        """
        set the Citation sub-object

        Parameters
        ----------
        new_citation : List[Citation]
            new list of Citation sub-objects

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, citation=new_citation)
        self._update_json_attrs_if_valid(new_attrs)

__init__(software, algorithm=None, notes='', citation=None, **kwargs)

Create Software_Configuration sub-object

Parameters:

Name Type Description Default
software Software

Software node used for the Software_Configuration

 required
algorithm Union[List[Algorithm], None]

algorithm used for the Software_Configuration, by default None

 None
notes str

plain text notes, by default ""

 ''
citation Union[List[Citation], None]

list of Citation sub-object, by default None

 None

Examples:

>>> import cript
>>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
>>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)

Returns:

Type Description
None

Create Software_Configuration sub-object
Source code in src/cript/nodes/subobjects/software_configuration.py 
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@beartype
def __init__(self, software: Union[Software, UIDProxy], algorithm: Optional[List[Union[Algorithm, UIDProxy]]] = None, notes: str = "", citation: Union[List[Union[Citation, UIDProxy]], None] = None, **kwargs):
    """
    Create Software_Configuration sub-object


    Parameters
    ----------
    software : Software
        Software node used for the Software_Configuration
    algorithm : Union[List[Algorithm], None], optional
        algorithm used for the Software_Configuration, by default None
    notes : str, optional
        plain text notes, by default ""
    citation : Union[List[Citation], None], optional
        list of Citation sub-object, by default None

    Examples
    ---------
    >>> import cript
    >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
    >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)

    Returns
    -------
    None
        Create Software_Configuration sub-object
    """
    if algorithm is None:
        algorithm = []
    if citation is None:
        citation = []
    super().__init__(**kwargs)
    new_json_attrs = replace(self._json_attrs, software=software, algorithm=algorithm, notes=notes, citation=citation)
    self._update_json_attrs_if_valid(new_json_attrs)

algorithm(new_algorithm)

set the list of Algorithms

Parameters:

Name Type Description Default
new_algorithm List[Algorithm]

list of algorithms

 required

Returns:

Type Description
None
Source code in src/cript/nodes/subobjects/software_configuration.py 
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@algorithm.setter
@beartype
def algorithm(self, new_algorithm: List[Union[Algorithm, UIDProxy]]) -> None:
    """
    set the list of Algorithms

    Parameters
    ----------
    new_algorithm : List[Algorithm]
        list of algorithms

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, algorithm=new_algorithm)
    self._update_json_attrs_if_valid(new_attrs)

citation(new_citation)

set the Citation sub-object

Parameters:

Name Type Description Default
new_citation List[Citation]

new list of Citation sub-objects

 required

Returns:

Type Description
None
Source code in src/cript/nodes/subobjects/software_configuration.py 
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@citation.setter
@beartype
def citation(self, new_citation: List[Union[Citation, UIDProxy]]) -> None:
    """
    set the Citation sub-object

    Parameters
    ----------
    new_citation : List[Citation]
        new list of Citation sub-objects

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, citation=new_citation)
    self._update_json_attrs_if_valid(new_attrs)

notes(new_notes)

set notes for Software_configuration

Parameters:

Name Type Description Default
new_notes str

new notes in plain text or JSON

 required

Returns:

Type Description
None
Source code in src/cript/nodes/subobjects/software_configuration.py 
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@notes.setter
@beartype
def notes(self, new_notes: str) -> None:
    """
    set notes for Software_configuration

    Parameters
    ----------
    new_notes : str
        new notes in plain text or JSON

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, notes=new_notes)
    self._update_json_attrs_if_valid(new_attrs)

software(new_software)

set the Software used

Parameters:

Name Type Description Default
new_software Union[Software, None]

new Software node

 required

Returns:

Type Description
None
Source code in src/cript/nodes/subobjects/software_configuration.py 
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@software.setter
@beartype
def software(self, new_software: Union[Software, None, UIDProxy]) -> None:
    """
    set the Software used

    Parameters
    ----------
    new_software : Union[Software, None]
        new Software node

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, software=new_software)
    self._update_json_attrs_if_valid(new_attrs)