schrodinger.application.matsci.yamlutils module

Utilities for working with yaml

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.yamlutils.yaml_tuple_constructor(obj, node)

Add the ability to parse tuples to a YAML Constructor object

Note - this function is for ruamel yaml with Python 3.11 and beyond

Parameters

• obj (yaml.SafeConstructor) – The constructor object

• node (yaml.nodes.SequenceNode) – The tuple node

Return type

tuple

Returns

The tuple derived from node

schrodinger.application.matsci.yamlutils.yaml_tuple_representer(obj, data)

Add the ability to write tuples to a YAML Representer object

Note - this function is for ruamel yaml with Python 3.11 and beyond

Parameters

• obj (yaml.Representer) – The constructor object

• data – The tuple to represent

Return type

str

Returns

A YAML representation of a tuple

schrodinger.application.matsci.yamlutils.get_safe_yaml_with_tuples()

Get a safe YAML loader that can handle tuples

Return type

yaml.YAML

Returns

A safe yaml loader that can handle tuples

class schrodinger.application.matsci.yamlutils.TupleSafeLoader(*args, **kwargs)

Bases: ruamel.yaml.loader.SafeLoader

Yaml Loader that recognizes tuple tags.

Note - this class is for ruamel yaml with Python < 3.11

__init__(*args, **kwargs)

Initialize the scanner.

DEFAULT_MAPPING_TAG = 'tag:yaml.org,2002:map'

DEFAULT_SCALAR_TAG = 'tag:yaml.org,2002:str'

DEFAULT_SEQUENCE_TAG = 'tag:yaml.org,2002:seq'

DEFAULT_TAGS = {'!': '!', '!!': 'tag:yaml.org,2002:'}

ESCAPE_CODES = {'U': 8, 'u': 4, 'x': 2}

ESCAPE_REPLACEMENTS = {'\t': '\t', ' ': ' ', '"': '"', '/': '/', '0': '\x00', 'L': '\u2028', 'N': '\x85', 'P': '\u2029', '\\': '\\', '_': '\xa0', 'a': '\x07', 'b': '\x08', 'e': '\x1b', 'f': '\x0c', 'n': '\n', 'r': '\r', 't': '\t', 'v': '\x0b'}

NON_PRINTABLE = <ruamel.yaml.util.LazyEval object>

classmethod add_constructor(tag: Any, constructor: Any) → None

classmethod add_implicit_resolver(tag: Any, regexp: Any, first: Any) → None

classmethod add_implicit_resolver_base(tag: Any, regexp: Any, first: Any) → None

add_indent(column: int) → bool

classmethod add_multi_constructor(tag_prefix: Any, multi_constructor: Any) → None

classmethod add_path_resolver(tag: Any, path: Any, kind: Any = None) → None

add_version_implicit_resolver(version: VersionType, tag: Any, regexp: Any, first: Any) → None

ascend_resolver() → None

bool_values = {'false': False, 'n': False, 'no': False, 'off': False, 'on': True, 'true': True, 'y': True, 'yes': True}

check_block_entry() → Any

check_data() → Any

check_directive() → Any

check_document_end() → Any

check_document_start() → Any

check_end_doc_comment(end_event: Any, node: Any) → None

check_event(*choices: Any) → bool

check_key() → Any

check_mapping_key(node: Any, key_node: Any, mapping: Any, key: Any, value: Any) → bool

return True if key is unique

check_node() → Any

check_plain() → Any

check_printable(data: Any) → None

check_resolver_prefix(depth: int, path: Text, kind: Any, current_node: Any, current_index: Any) → bool

check_set_key(node: Any, key_node: Any, setting: Any, key: Any) → None

check_token(*choices: Any) → bool

check_value() → Any

compose_document() → Any

compose_mapping_node(anchor: Any) → Any

compose_node(parent: Any, index: Any) → Any

compose_scalar_node(anchor: Any) → Any

compose_sequence_node(anchor: Any) → Any

property composer

construct_document(node: Any) → Any

construct_mapping(node: Any, deep: bool = False) → Any

deep is True when creating an object/mapping recursively, in that case want the underlying elements available during construction

construct_non_recursive_object(node: Any, tag: Optional[str] = None) → Any

construct_object(node: Any, deep: bool = False) → Any

deep is True when creating an object/mapping recursively, in that case want the underlying elements available during construction

construct_pairs(node: Any, deep: bool = False) → Any

construct_scalar(node: Any) → Any

construct_sequence(node: Any, deep: bool = False) → Any

deep is True when creating an object/mapping recursively, in that case want the underlying elements available during construction

construct_undefined(node: Any) → None

construct_yaml_binary(node: Any) → Any

construct_yaml_bool(node: Any) → bool

construct_yaml_float(node: Any) → float

construct_yaml_int(node: Any) → int

construct_yaml_map(node: Any) → Any

construct_yaml_null(node: Any) → Any

construct_yaml_object(node: Any, cls: Any) → Any

construct_yaml_omap(node: Any) → Any

construct_yaml_pairs(node: Any) → Any

construct_yaml_seq(node: Any) → Any

construct_yaml_set(node: Any) → Any

construct_yaml_str(node: Any) → Any

construct_yaml_timestamp(node: Any, values: Any = None) → Any

descend_resolver(current_node: Any, current_index: Any) → None

determine_encoding() → None

dispose() → None

fetch_alias() → None

fetch_anchor() → None

fetch_block_entry() → None

fetch_block_scalar(style: Any) → None

fetch_comment(comment: Any) → None

fetch_directive() → None

fetch_document_end() → None

fetch_document_indicator(TokenClass: Any) → None

fetch_document_start() → None

fetch_double() → None

fetch_flow_collection_end(TokenClass: Any) → None

fetch_flow_collection_start(TokenClass: Any, to_push: Text) → None

fetch_flow_entry() → None

fetch_flow_mapping_end() → None

fetch_flow_mapping_start() → None

fetch_flow_scalar(style: Any) → None

fetch_flow_sequence_end() → None

fetch_flow_sequence_start() → None

fetch_folded() → None

fetch_key() → None

fetch_literal() → None

fetch_more_tokens() → Any

fetch_plain() → None

fetch_single() → None

fetch_stream_end() → None

fetch_stream_start() → None

fetch_tag() → None

fetch_value() → None

flatten_mapping(node: Any) → Any

This implements the merge key feature http://yaml.org/type/merge.html by inserting keys from the merge dict/list of dicts if not yet available in this node

property flow_level

forward(length: int = 1) → None

forward_1_1(length: int = 1) → None

get_data() → Any

get_event() → Any

get_loader_version(version: Optional[VersionType]) → Any

get_mark() → Any

get_node() → Any

get_single_data() → Any

get_single_node() → Any

get_token() → Any

inf_value = inf

nan_value = nan

need_more_tokens() → bool

next_possible_simple_key() → Any

parse_block_mapping_first_key() → Any

parse_block_mapping_key() → Any

parse_block_mapping_value() → Any

parse_block_node() → Any

parse_block_node_or_indentless_sequence() → Any

parse_block_sequence_entry() → Any

parse_block_sequence_first_entry() → Any

parse_document_content() → Any

parse_document_end() → Any

parse_document_start() → Any

parse_flow_mapping_empty_value() → Any

parse_flow_mapping_first_key() → Any

parse_flow_mapping_key(first: Any = False) → Any

parse_flow_mapping_value() → Any

parse_flow_node() → Any

parse_flow_sequence_entry(first: bool = False) → Any

parse_flow_sequence_entry_mapping_end() → Any

parse_flow_sequence_entry_mapping_key() → Any

parse_flow_sequence_entry_mapping_value() → Any

parse_flow_sequence_first_entry() → Any

parse_implicit_document_start() → Any

parse_indentless_sequence_entry() → Any

parse_node(block: bool = False, indentless_sequence: bool = False) → Any

parse_stream_start() → Any

property parser

peek(index: int = 0) → Text

peek_event() → Any

peek_token() → Any

prefix(length: int = 1) → Any

process_directives() → Any

process_empty_scalar(mark: Any, comment: Any = None) → Any

property processing_version

property reader

remove_possible_simple_key() → None

reset_parser() → None

reset_reader() → None

reset_scanner() → None

resolve(kind: Any, value: Any, implicit: Any) → Any

property resolver

save_possible_simple_key() → None

scan_anchor(TokenClass: Any) → Any

scan_block_scalar(style: Any, rt: Optional[bool] = False) → Any

scan_block_scalar_breaks(indent: int) → Any

scan_block_scalar_ignored_line(start_mark: Any) → Any

scan_block_scalar_indentation() → Any

scan_block_scalar_indicators(start_mark: Any) → Any

scan_directive() → Any

scan_directive_ignored_line(start_mark: Any) → None

scan_directive_name(start_mark: Any) → Any

scan_flow_scalar(style: Any) → Any

scan_flow_scalar_breaks(double: Any, start_mark: Any) → Any

scan_flow_scalar_non_spaces(double: Any, start_mark: Any) → Any

scan_flow_scalar_spaces(double: Any, start_mark: Any) → Any

scan_line_break() → Any

scan_plain() → Any

scan_plain_spaces(indent: Any, start_mark: Any) → Any

scan_tag() → Any

scan_tag_directive_handle(start_mark: Any) → Any

scan_tag_directive_prefix(start_mark: Any) → Any

scan_tag_directive_value(start_mark: Any) → Any

scan_tag_handle(name: Any, start_mark: Any) → Any

scan_tag_uri(name: Any, start_mark: Any) → Any

scan_to_next_token() → Any

scan_uri_escapes(name: Any, start_mark: Any) → Any

scan_yaml_directive_number(start_mark: Any) → Any

scan_yaml_directive_value(start_mark: Any) → Any

property scanner

property scanner_processing_version

stale_possible_simple_keys() → None

property stream

timestamp_regexp = <ruamel.yaml.util.LazyEval object>

transform_tag(handle: Any, suffix: Any) → Any

unwind_indent(column: Any) → None

update(length: int) → None

update_raw(size: Optional[int] = None) → None

property versioned_resolver

select the resolver based on the version we are parsing

yaml_constructors: Dict[Any, Any] = {'tag:yaml.org,2002:null': <function SafeConstructor.construct_yaml_null>, 'tag:yaml.org,2002:bool': <function SafeConstructor.construct_yaml_bool>, 'tag:yaml.org,2002:int': <function SafeConstructor.construct_yaml_int>, 'tag:yaml.org,2002:float': <function SafeConstructor.construct_yaml_float>, 'tag:yaml.org,2002:binary': <function SafeConstructor.construct_yaml_binary>, 'tag:yaml.org,2002:timestamp': <function SafeConstructor.construct_yaml_timestamp>, 'tag:yaml.org,2002:omap': <function SafeConstructor.construct_yaml_omap>, 'tag:yaml.org,2002:pairs': <function SafeConstructor.construct_yaml_pairs>, 'tag:yaml.org,2002:set': <function SafeConstructor.construct_yaml_set>, 'tag:yaml.org,2002:str': <function SafeConstructor.construct_yaml_str>, 'tag:yaml.org,2002:seq': <function SafeConstructor.construct_yaml_seq>, 'tag:yaml.org,2002:map': <function SafeConstructor.construct_yaml_map>, None: <function SafeConstructor.construct_undefined>}

yaml_implicit_resolvers: Dict[Any, Any] = {}

yaml_multi_constructors: Dict[Any, Any] = {}

yaml_path_resolvers: Dict[Any, Any] = {}

schrodinger.application.matsci.yamlutils.read_safe_yaml_file(path)

Read a yaml file safely and properly interpret tuples

Parameters

path (str) – The path to the yaml file

Returns

The data from the yaml file

schrodinger.application.matsci.yamlutils.dump_yaml_file(path, data)

Write a yaml file safely and properly interpret tuples

Parameters

• path (str) – The path to the yaml file

• data – The data to write out

Returns

The data from the yaml file