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stepup.reprep.bibsane

Sanitize BibTeX files.

BibsaneConfig

The configuration object controling BibSane behavior.

Note that the settings default to the most permissive and least invasive ones. We recommend the opposite settings, but you have to switch knowingly in the config file.

Source code in stepup/reprep/bibsane.py 
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@attrs.define
class BibsaneConfig:
    """The configuration object controling BibSane behavior.

    Note that the settings default to the most permissive and least invasive ones.
    We recommend the opposite settings, but you have to switch knowingly in the config file.
    """

    root: Path = attrs.field()
    """The parent directory of the configuration file."""

    amend: bool = attrs.field(default=False)
    """Set to `True` to amend loaded bibtex files as inputs to the StepUp workflow."""

    drop_entry_types: list[str] = attrs.field(default=attrs.Factory(list))
    """The entry types to drop from the BibTeX database."""

    normalize_doi: bool = attrs.field(default=False)
    """Set to `True` to normalize the DOIs in the entries."""

    duplicate_id: DuplicatePolicy = attrs.field(default=DuplicatePolicy.IGNORE)
    """The policy for duplicate BibTeX IDs: fail, merge or ignore."""

    duplicate_doi: DuplicatePolicy = attrs.field(default=DuplicatePolicy.IGNORE)
    """The policy for duplicate DOIs: fail, merge or ignore."""

    preambles_allowed: bool = attrs.field(default=True)
    """Set to `False` to disallow @preamble entries in the BibTeX database."""

    normalize_whitespace: bool = attrs.field(default=False)
    """Set to `True` to normalize the whitespace in the field values."""

    normalize_names: bool = attrs.field(default=False)
    """Set to `True` to normalize the author and editor names.

    (This currently broken.)
    """

    fix_page_double_hyphen: bool = attrs.field(default=False)
    """Set to `True` to fix the page ranges for which no double hyphen is used."""

    abbreviate_journals: bool = attrs.field(default=True)

    custom_abbreviations: dict[str, str] = attrs.field(factory=dict)
    """Custom journal abbreviations.

    By default, pyiso4 is used to abbreviate journal names.
    The custom abbreviations can override those provided by pyiso4.
    """

    sort: bool = attrs.field(default=False)
    """Set to `True` to sort the entries by year and first author.

    The sort key is `{year}{first author lowercase last name}`.
    """

    citation_policies: dict[str, dict[str, FieldPolicy]] = attrs.field(default=attrs.Factory(dict))
    """The field policies (must or may) for each entry type."""

    @classmethod
    def from_file(cls, fn_yaml: str, amend: bool = False):
        """Instantiate a configuration from a YAML config file."""
        if fn_yaml is None:
            config = cls(os.getcwd(), amend)
        else:
            with open(fn_yaml) as f:
                data = yaml.safe_load(f)
                data.setdefault("root", os.path.dirname(fn_yaml))
                data.setdefault("amend", amend)
                config = cattrs.structure(data, cls)
        return config

amend = attrs.field(default=False) class-attribute instance-attribute

Set to True to amend loaded bibtex files as inputs to the StepUp workflow.

citation_policies = attrs.field(default=attrs.Factory(dict)) class-attribute instance-attribute

The field policies (must or may) for each entry type.

custom_abbreviations = attrs.field(factory=dict) class-attribute instance-attribute

Custom journal abbreviations.

By default, pyiso4 is used to abbreviate journal names. The custom abbreviations can override those provided by pyiso4.

drop_entry_types = attrs.field(default=attrs.Factory(list)) class-attribute instance-attribute

The entry types to drop from the BibTeX database.

duplicate_doi = attrs.field(default=DuplicatePolicy.IGNORE) class-attribute instance-attribute

The policy for duplicate DOIs: fail, merge or ignore.

duplicate_id = attrs.field(default=DuplicatePolicy.IGNORE) class-attribute instance-attribute

The policy for duplicate BibTeX IDs: fail, merge or ignore.

fix_page_double_hyphen = attrs.field(default=False) class-attribute instance-attribute

Set to True to fix the page ranges for which no double hyphen is used.

normalize_doi = attrs.field(default=False) class-attribute instance-attribute

Set to True to normalize the DOIs in the entries.

normalize_names = attrs.field(default=False) class-attribute instance-attribute

Set to True to normalize the author and editor names.

(This currently broken.)

normalize_whitespace = attrs.field(default=False) class-attribute instance-attribute

Set to True to normalize the whitespace in the field values.

preambles_allowed = attrs.field(default=True) class-attribute instance-attribute

Set to False to disallow @preamble entries in the BibTeX database.

root = attrs.field() class-attribute instance-attribute

The parent directory of the configuration file.

sort = attrs.field(default=False) class-attribute instance-attribute

Set to True to sort the entries by year and first author.

The sort key is {year}{first author lowercase last name}.

from_file(fn_yaml, amend=False) classmethod

Instantiate a configuration from a YAML config file.

Source code in stepup/reprep/bibsane.py 
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@classmethod
def from_file(cls, fn_yaml: str, amend: bool = False):
    """Instantiate a configuration from a YAML config file."""
    if fn_yaml is None:
        config = cls(os.getcwd(), amend)
    else:
        with open(fn_yaml) as f:
            data = yaml.safe_load(f)
            data.setdefault("root", os.path.dirname(fn_yaml))
            data.setdefault("amend", amend)
            config = cattrs.structure(data, cls)
    return config