diff --git a/.buildinfo b/.buildinfo new file mode 100644 index 0000000..42ae373 --- /dev/null +++ b/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 2ede4f641b32fd3f5de96bd9dfeb95d2 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/CHANGELOG.html b/CHANGELOG.html new file mode 100644 index 0000000..99758c3 --- /dev/null +++ b/CHANGELOG.html @@ -0,0 +1,579 @@ + + + + + + + + + Change Log - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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Medical natural language parsing and utility library 1.7.0 documentation
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Change Log#

+

All notable changes to this project will be documented in this file.

+

The format is based on Keep a Changelog +and this project adheres to Semantic Versioning.

+
+

[Unreleased]#

+
+
+

[1.7.0] - 2024-04-14#

+
+

Removed#

+
    +

  • Deprecated feature document parser mednlp_combine_medfirst_doc_parser from +resource library.

    • +
+
+
+

Changed#

+
    +

  • Renamed MeddicalFeatureDocumentParser to MedCatFeatureDocumentParser +since the parser only adds MedCAT CUIs.

    • +

  • Fixed the configured parser that adds both ScispaCy biomed entities and +MedCAT CUIs in mednlp_combine_biomed_doc_parser.

    • +

  • Separated combiner with non-combiner models in configuration space. The +non-combiners (biomed ScispaCy and MedCAT) are parses that are used in their +respective combiners. These are then used by a new composite parser that +uses both (mednlp_combine_biomed_doc_parser). Unit test case added for +all configured parsers.

    • +
+
+
+
+

[1.6.0] - 2024-02-27#

+
+

Added#

+
    +

  • Added a ScispaCy biomedical document parser, which is enabled by setting +mednlp_default:doc_parser = mednlp_combine_biomed_doc_parser. This uses +better linguistic features and detects more entity span(s).

    • +
+
+
+

Changed#

+
    +

  • Fixed normalize token and sentence/token indexes from being clobbered by +combined medical parsers.

    • +

  • Fixed numeric entity feature from the combined medical parser is non-zero +for medical entities.

    • +

  • Combined medical parser defines linguistic and medical features in the +document parser object instance.

    • +
+
+
+
+

[1.5.0] - 2023-12-05#

+
+

Changed#

+
    +

  • Upgrade libraries: numpy, lxml, scikitlearn, scipy, medcat.

    • +

  • Added scispacy dependency.

    • +
+
+
+

Added#

+
    +

  • Support for Python 3.11.

    • +
+
+
+

Removed#

+
    +

  • Support for Python 3.9.

    • +
+
+
+
+

[1.4.1] - 2023-09-08#

+
+

Changed#

+
    +

  • Fix unit tests using the model provided for the MedCAT tutorials.

    • +

  • Re-enable GitHub workflow unit tests CI.

    • +
+
+
+
+

[1.4.0] - 2023-08-16#

+

Downstream moderate risk update release.

+
+

Changed#

+
    +

  • Switch order of medical specific and general spaCy language parsing and +chunking. Now the medical parser is the source parser and the default spaCy +parser is the target in MappingCombinerFeatureDocumentParser. This was +done to get better sentence chunking as MedCAT (used in the medical parser) +does not sentence chunk well as it was not designed for it.

    • +

  • Upgrade to zensols.util 1.13.0

    • +

  • Fix cui2vec weight archive re-download on each access.

    • +

  • Mapping combiner default is to use token’s character absolute index.

    • +
+
+
+
+

[1.3.2] - 2023-06-29#

+
+

Added#

+
    +

  • Feature document parser shortcut from application factory.

    • +
+
+
+

Changed#

+
    +

  • Resource library configuration to clean up model resources after download.

    • +
+
+
+
+

[1.3.1] - 2023-06-27#

+
+

Changed#

+
    +

  • Updated to zensols.nlp to 1.7.2 and use its new feature to auto load any +missing spaCy base model(s).

    • +

  • Remove configuration file requirement from the CLI.

    • +

  • Fix spaCy dependency requirement to align with scipy and zensols.nlp.

    • +
+
+
+
+

[1.3.0] - 2023-06-20#

+
+

Changed#

+
    +

  • Fix contraction tokenization. This was done by swapping the target and +source parser in the lang.conf:mednlp_combine_doc_parser resource library +configuration.

    • +
+
+
+
+

[1.2.0] - 2023-06-09#

+
+

Changed#

+
    +

  • Upgrade to medcat 1.7.0.

    • +

  • Better UTS error handling with raised exceptions and messages.

    • +
+
+
+
+

[1.1.0] - 2023-04-05#

+
+

Changed#

+ +
+
+
+

[1.0.0] - 2023-02-02#

+
+

Changed#

+ +
+
+
+

[0.1.1] - 2022-10-02#

+
+

Removed#

+
    +

  • Make scispacy optional and remove the dependency. See the test cases in +test.

    • +
+
+
+
+

[0.1.0] - 2022-10-01#

+
+

Added#

+
    +

  • Unit test in GitHub CI.

    • +
+
+
+

Changed#

+
    +

  • Upgrade to spaCy 2.2, MedCAT 3.0, zensols.nlp 1.4.0.

    • +

  • Make cui2vec a standard word embedding with vectorizer and layer.

    • +

  • Replace entity splitter by not embedding named entities as default +configuration.

    • +
+
+
+

Removed#

+
    +

  • Support for Python 3.7, 3.8 from dropped support in zensols.util.

    • +
+
+
+
+

[0.0.2] - 2022-05-04#

+
+

Added#

+
    +

  • A CSV features dump example.

    • +
+
+
+

Changed#

+
    +

  • Use token instead of sentence level mapping in cases where MedCAT creates +unaligned sentence boundaries.

    • +

  • Make medical parser stand-alone and use delegate mapping combiner instead of +using a class hierarchy.

    • +

  • Entity linker is now a token decorator.

    • +

  • Protect against unk (unknown) keys in TUIs.

    • +
+
+
+
+

[0.0.1] - 2022-01-30#

+
+

Added#

+
    +

  • Initial version.

    • +
+

[Unreleased]: https://github.com/Paul Landes/mednlp/compare/v1.7.0…HEAD +[1.7.0]: https://github.com/Paul Landes/mednlp/compare/v1.6.0…v1.7.0 +[1.6.0]: https://github.com/Paul Landes/mednlp/compare/v1.5.0…v1.6.0 +[1.5.0]: https://github.com/Paul Landes/mednlp/compare/v1.4.1…v1.5.0 +[1.4.1]: https://github.com/Paul Landes/mednlp/compare/v1.4.0…v1.4.1 +[1.4.0]: https://github.com/Paul Landes/mednlp/compare/v1.3.2…v1.4.0 +[1.3.2]: https://github.com/Paul Landes/mednlp/compare/v1.3.1…v1.3.2 +[1.3.1]: https://github.com/Paul Landes/mednlp/compare/v1.3.0…v1.3.1 +[1.3.0]: https://github.com/Paul Landes/mednlp/compare/v1.2.0…v1.3.0 +[1.2.0]: https://github.com/Paul Landes/mednlp/compare/v1.1.0…v1.2.0 +[1.1.0]: https://github.com/Paul Landes/mednlp/compare/v1.0.0…v1.1.0 +[1.0.0]: https://github.com/Paul Landes/mednlp/compare/v0.1.1…v1.0.0 +[0.1.1]: https://github.com/Paul Landes/mednlp/compare/v0.1.0…v0.1.1 +[0.1.0]: https://github.com/Paul Landes/mednlp/compare/v0.0.2…v0.1.0 +[0.0.2]: https://github.com/Paul Landes/mednlp/compare/v0.0.1…v0.0.2 +[0.0.1]: https://github.com/Paul Landes/mednlp/compare/v0.0.0…v0.0.1

+
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+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
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+ + + + + + + \ No newline at end of file diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html new file mode 100644 index 0000000..039c5f8 --- /dev/null +++ b/CONTRIBUTING.html @@ -0,0 +1,314 @@ + + + + + + + + + Contributing - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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Contributing#

+

If you discover issues, have ideas for improvements or new features, please +report them to the issue tracker of the repository or submit a pull +request. Please, try to follow these guidelines when you do so.

+
+

Issue reporting#

+
    +

  • Check that the issue has not already been reported.

    • +

  • Check that the issue has not already been fixed in the latest code +(a.k.a. master).

    • +

  • Be clear, concise and precise in your description of the problem.

    • +

  • Open an issue with a descriptive title and a summary in grammatically correct, +complete sentences.

    • +

  • Mention your mednlp Python dependency version and operating +system.

    • +

  • Include any relevant code to the issue summary.

    • +
+
+

Reporting bugs#

+

Adding information like the backtrace and the REPL messages to the bug report +makes it easier to track down bugs. Some steps to reproduce a bug reliably +would also make a huge difference.

+
+
+
+

Pull requests#

+ +
+
+ +
+
+ +
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/LICENSE.html b/LICENSE.html new file mode 100644 index 0000000..27a7d0e --- /dev/null +++ b/LICENSE.html @@ -0,0 +1,257 @@ + + + + + + + + + <no title> - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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MIT License

+

Copyright (c) 2021 - 2023 Paul Landes

+

Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the “Software”), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions:

+

The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software.

+

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.

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+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
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Source code for zensols.mednlp

+

+[docs]
+def surpress_warnings():
+    """Supress future warnings generated by spaCy and ScispaCy models."""
+    import warnings
+    # spaCy 3.6 and medcat 1.7 - 1.9 warns with what appears to be an
+    # unserialized regular expression from the language model; ScispaCy also
+    # complains
+    warnings.filterwarnings(
+        'ignore',
+        message=r'^Possible set union at position',
+        category=FutureWarning)

+
+
+
+from .domain import *
+from .uts import UTSError, NoResultsError, AuthenticationError, UTSClient
+from .resource import *
+from .tok import *
+from .lib import *
+from .parser import *
+from .app import *
+from .cli import *
+
+
+surpress_warnings()
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/app.html b/_modules/zensols/mednlp/app.html new file mode 100644 index 0000000..b20f9c1 --- /dev/null +++ b/_modules/zensols/mednlp/app.html @@ -0,0 +1,475 @@ + + + + + + + + zensols.mednlp.app - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.app

+"""A natural language medical domain parsing library.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import Optional
+from dataclasses import dataclass, field
+from enum import Enum, auto
+import sys
+import logging
+from io import TextIOBase
+import re
+from pprint import pprint
+from pathlib import Path
+import pandas as pd
+from zensols.config import Dictable, ConfigFactory
+from zensols.cli import ApplicationError
+from zensols.nlp import FeatureDocumentParser, FeatureDocument
+from zensols.nlp.dataframe import FeatureDataFrameFactory
+from . import MedCatResource, MedicalLibrary
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+class GroupInfo(Enum):
+    """Used to group TUI information in :meth:`.Application.group`
+
+    """
+    csv = auto()
+    byname = auto()

+
+
+
+

+[docs]
+@dataclass
+class Application(Dictable):
+    """A natural language medical domain parsing library.
+
+    """
+    config_factory: ConfigFactory = field()
+    """Used to create a cTAKES stash."""
+
+    doc_parser: FeatureDocumentParser = field()
+    """Parses and NER tags medical terms."""
+
+    library: MedicalLibrary = field()
+    """Medical resource library that contains UMLS access, cui2vec etc.."""
+
+    def _get_text(self, text_or_file: str) -> str:
+        """Return the text from a file or the text passed based on if
+        ``text_or_file`` is a file on the file system.
+
+        """
+        path = Path(text_or_file)
+        if path.is_file():
+            with open(path) as f:
+                text_or_file = f.read()
+        return text_or_file
+
+    def _write_doc(self, doc: FeatureDocument, only_medical: bool,
+                   depth: int = 0, writer: TextIOBase = sys.stdout):
+        for sent in doc.sents:
+            if len(sent.text.strip()) == 0:
+                continue
+            self._write_line(sent.text, depth, writer)
+            for tok in sent:
+                if not only_medical or tok.is_ent:
+                    self._write_line(f'{tok.norm}:', depth + 1, writer)
+                    tok.write_attributes(
+                        depth + 2, writer,
+                        feature_ids=self.doc_parser.token_feature_ids
+                    )
+            self._write_line('entities:', depth, writer)
+            for ents in sent.entities:
+                self._write_line(
+                    ' '.join(map(lambda e: e.norm, ents)), depth + 1, writer)
+
+

+[docs]
+    def show(self, text_or_file: str, only_medical: bool = False):
+        """Parse and output medical entities.
+
+        :param text_or_file: natural language to be processed
+
+        :param only_medical: only provide medical linked tokens
+
+        """
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'parsing: <{text_or_file}>...')
+        text: str = self._get_text(text_or_file)
+        doc: FeatureDocument = self.doc_parser.parse(text)
+        self._write_doc(doc, only_medical)

+
+
+    def _output_dataframe(self, df: pd.DataFrame, out: Optional[Path] = None):
+        """Output the dataframe generated by other actions of the app.
+
+        :param df: the dataframe to output:
+
+        :param out: the output path, or ``None`` standard out
+        """
+        if out is None:
+            out = sys.stdout
+        df.to_csv(out, index=False)
+        row_s = 's' if len(df) != 1 else ''
+        if out != sys.stdout:
+            logger.info(f'wrote {len(df)} row{row_s} to {out}')
+
+

+[docs]
+    def features(self, text_or_file: str, out: Path = None, ids: str = None,
+                 only_medical: bool = False):
+        """Dump features as CSV output.
+
+        :param text_or_file: natural language to be processed
+
+        :param out: the path to output the CSV file or stdout if missing
+
+        :param ids: the comma separate feature IDs to output
+
+        :param only_medical: only provide medical linked tokens
+
+        """
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'parsing: <{text_or_file}>...')
+        params = {}
+        if ids is None:
+            ids = self.doc_parser.token_feature_ids
+        else:
+            ids = set(re.split(r'\W+', ids))
+        needs = 'norm cui_ is_concept'.split()
+        missing = set(filter(lambda i: i not in ids, needs))
+        ids |= missing
+        params['token_feature_ids'] = ids
+        params['priority_feature_ids'] = needs
+        df_fac = FeatureDataFrameFactory(**params)
+        self.doc_parser.token_feature_ids = ids
+        text: str = self._get_text(text_or_file)
+        doc: FeatureDocument = self.doc_parser.parse(text)
+        df: pd.DataFrame = df_fac(doc)
+        if only_medical:
+            df = df[df['is_concept']]
+        self._output_dataframe(df, out)

+
+
+

+[docs]
+    def search(self, term: str):
+        """Search the UMLS database using UTS and show results.
+
+        :param term: the term to search for (eg 'lung cancer')
+
+        """
+        pprint(self.library.uts_client.search_term(term))

+
+
+

+[docs]
+    def atom(self, cui: str):
+        """Search the UMLS database using UTS and show results.
+
+        :param cui: the concept ID to search for (eg 'C0242379')
+
+        """
+        pprint(self.library.uts_client.get_atoms(cui))

+
+
+

+[docs]
+    def define(self, cui: str):
+        """Look up an entity by CUI.  This takes a long time.
+
+        :param cui: the concept ID to search for (eg 'C0242379')
+
+        """
+        entity = self.library.get_linked_entity(cui)
+        print(entity)

+
+
+

+[docs]
+    def group(self, info: GroupInfo, query: str = None):
+        """Get TUI group information.
+
+        :param info: the type of information to return
+
+        :param query: comma delimited name list used to subset the output data
+
+        """
+        res: MedCatResource = self.library.medcat_resource
+        df: pd.DataFrame = res.groups
+        if info == GroupInfo.csv:
+            path = Path('tui-groups.csv')
+            df.to_csv(path)
+            logger.info(f'wrote TUI groups to {path}')
+        elif info == GroupInfo.byname:
+            if query is None:
+                raise ApplicationError('Missing query string for grouping')
+            reg = '.*(' + '|'.join(query.split(',')) + ')'
+            df = df[df['name'].str.match(reg)]
+            print(','.join(df['tui'].tolist()))
+        else:
+            raise ApplicationError(f'Unknown query info type: {info}')

+
+
+

+[docs]
+    def ctakes(self, text_or_file: str, only_medical: bool = False):
+        """Invoke cTAKES on a directory with text files.
+
+        :param text_or_file: natural language to be processed
+
+        :param only_medical: only provide medical linked tokens
+
+        """
+        from .ctakes import CTakesParserStash
+        text: str = self._get_text(text_or_file)
+        stash: CTakesParserStash = self.library.get_new_ctakes_parser_stash()
+        stash.set_documents([text])
+        print(stash['0'].to_string())

+
+
+

+[docs]
+    def similarity(self, term: str):
+        """Get the cosine similarity between two CUIs.
+
+        """
+        for sim in self.library.similarity_by_term(term):
+            print(sim.cui)
+            sim.write(1)

+

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/cli.html b/_modules/zensols/mednlp/cli.html new file mode 100644 index 0000000..6b7b735 --- /dev/null +++ b/_modules/zensols/mednlp/cli.html @@ -0,0 +1,276 @@ + + + + + + + + zensols.mednlp.cli - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.cli

+"""Command line entry point to the application.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import List, Any, Dict, Type
+import sys
+from zensols.cli import ApplicationFactory, ActionResult, CliHarness
+from zensols.nlp import FeatureDocumentParser
+
+
+

+[docs]
+class ApplicationFactory(ApplicationFactory):
+

+[docs]
+    def __init__(self, *args, **kwargs):
+        kwargs['package_resource'] = 'zensols.mednlp'
+        super().__init__(*args, **kwargs)

+
+
+

+[docs]
+    @classmethod
+    def get_doc_parser(cls: Type) -> FeatureDocumentParser:
+        """Get the default application's document parser."""
+        return cls.create_harness().get_application().doc_parser

+

+
+
+
+

+[docs]
+def main(args: List[str] = sys.argv, **kwargs: Dict[str, Any]) -> ActionResult:
+    harness: CliHarness = ApplicationFactory.create_harness(relocate=False)
+    harness.invoke(args, **kwargs)

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/ctakes.html b/_modules/zensols/mednlp/ctakes.html new file mode 100644 index 0000000..9b9b2cb --- /dev/null +++ b/_modules/zensols/mednlp/ctakes.html @@ -0,0 +1,395 @@ + + + + + + + + zensols.mednlp.ctakes - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.ctakes

+"""Parse and normalize discharge notes.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import Iterable
+from dataclasses import dataclass, field
+import logging
+import os
+from pathlib import Path
+import pandas as pd
+from zensols.config import Dictable
+from zensols.persist import Stash, DirectoryStash, ReadOnlyStash, Primeable
+from zensols.util.executor import Executor
+import ctakes_parser.ctakes_parser as ctparser
+from . import MedNLPError
+
+logger = logging.getLogger(__name__)
+ctakes_logger = logging.getLogger(__name__ + '.ctakes')
+
+
+@dataclass
+class _TextDirectoryStash(DirectoryStash):
+    pattern: str = field(default='{name}.txt')
+
+    def _load_file(self, path: Path) -> str:
+        with open(path, 'r') as f:
+            return f.read()
+
+    def _dump_file(self, inst: str, path: Path):
+        with open(path, 'w') as f:
+            f.write(inst)
+
+
+

+[docs]
+@dataclass
+class CTakesParserStash(ReadOnlyStash, Primeable, Dictable):
+    """Runs the cTAKES CUI entity linker on a directory of medical notes.  For
+    each medical text file, it generates an ``xmi`` file, which is then parsed
+    by the the :mod:`ctakes_parser` library.
+
+    This straightforward wrapper around the ``ctparser`` library automates the
+    file system orchestration that needs to happen.  Configure an instance of
+    this class as an application configuration and use a
+    :class:`~zensols.config.ImportConfigFactory` to create the objects.  See
+    the ``examples/ctakes`` directory for a quick start guide on how to use
+    this class.
+
+    """
+    entry_point_bin: Path = field()
+    """Entry point script in to the cTAKES parser."""
+
+    entry_point_cmd: str = field()
+    """Command line arguments passed to cTAKES."""
+
+    home: Path = field()
+    """The directory where cTAKES is installed."""
+
+    source_dir: Path = field()
+    """Contains a path to the source directory where the text documents live.
+
+    """
+    output_dir: Path = field(default=None)
+    """The directory where to output the xmi files."""
+
+    def __post_init__(self):
+        super().__post_init__()
+        self.strict = True
+        self._pattern: str = field(default='{name}.txt.xmi')
+        if self.output_dir is None:
+            self.output_dir = self.source_dir.parent / 'output'
+        for attr in 'entry_point_bin source_dir output_dir'.split():
+            setattr(self, attr, getattr(self, attr).absolute())
+        self._source_stash = _TextDirectoryStash(self.source_dir)
+        self._out_stash = _TextDirectoryStash(
+            path=self.output_dir,
+            pattern=self._source_stash.pattern + '.xmi')
+
+    @property
+    def source_stash(self) -> Stash:
+        """The stash that tracks the text documents that are to be parsed by
+        cTAKES.
+
+        """
+        return self._source_stash
+
+

+[docs]
+    def set_documents(self, docs: Iterable[str]):
+        """Set the document to be parsed by cTAKES.
+
+        :param docs: an iterable of string text documents to persist to the
+                     file system, and then be parsed by cTAKES.
+
+        """
+        self.clear()
+        for i, doc in enumerate(docs):
+            self._source_stash.dump(str(i), doc)

+
+
+    def _run(self):
+        """Run cTAKES (see class docs)."""
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'running ctakes parser on {self.source_dir}')
+        os.environ['CTAKES_HOME'] = str(self.home.absolute())
+        cmd = self.entry_point_cmd.format(**self.asdict())
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'executing {cmd}')
+        exc = Executor(ctakes_logger)
+        exc.run(cmd)
+
+

+[docs]
+    def prime(self):
+        super().prime()
+        if not self.source_dir.is_dir():
+            raise MedNLPError('cTAKES temporary path is not an existing ' +
+                              f'directory: {self.source_dir}')
+        if len(self._source_stash) == 0:
+            raise MedNLPError(
+                f'Source directory contains no data: {self.source_dir}')
+        if len(self._out_stash) == 0:
+            self.output_dir.mkdir(parents=True, exist_ok=True)
+            self._run()

+
+
+

+[docs]
+    def load(self, name: str) -> pd.DataFrame:
+        self.prime()
+        path: Path = self._out_stash.key_to_path(name)
+        return ctparser.parse_file(file_path=str(path))

+
+
+

+[docs]
+    def keys(self) -> Iterable[str]:
+        self.prime()
+        return self._out_stash.keys()

+
+
+

+[docs]
+    def exists(self, name: str) -> bool:
+        self.prime()
+        return self._out_stash.exists(name)

+
+
+

+[docs]
+    def clear(self):
+        self._out_stash.clear()
+        self._source_stash.clear()

+

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/cui2vec.html b/_modules/zensols/mednlp/cui2vec.html new file mode 100644 index 0000000..a1bfb8a --- /dev/null +++ b/_modules/zensols/mednlp/cui2vec.html @@ -0,0 +1,298 @@ + + + + + + + + zensols.mednlp.cui2vec - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.cui2vec

+"""This module contains the embedding subclass for cui2vec embeddings.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import Dict, List
+from dataclasses import dataclass, field
+import logging
+import csv
+from h5py import Dataset
+from zensols.deepnlp.embed import (
+    WordEmbedError, TextWordEmbedModel, TextWordModelMetadata
+)
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+@dataclass
+class Cui2VecEmbedModel(TextWordEmbedModel):
+    """This class uses the pretrained cui2vec embeddings.
+
+    """
+    dimension: str = field(default=500)
+    """The word vector dimension."""
+
+    vocab_size: int = field(default=109053)
+    """Vocabulary size."""
+
+    def _populate_vec_lines(self, words: List[str], word2idx: Dict[str, int],
+                            ds: Dataset):
+        idx = 0
+        lc = 0
+        meta = self.metadata
+        with open(meta.source_path) as csvfile:
+            csv_reader = csv.reader(csvfile)
+            next(csv_reader)
+            for rix, line in enumerate(csv_reader):
+                lc += 1
+                word = line[0]
+                words.append(word)
+                word2idx[word] = idx
+                idx += 1
+                try:
+                    ds[rix, :] = tuple(map(float, line[1:]))
+                except Exception as e:
+                    raise WordEmbedError(
+                        f'Could not parse line {lc} (word: {word}): ' +
+                        f'{e}; line: {line}') from e
+
+    def _get_metadata(self) -> TextWordModelMetadata:
+        name = 'cui2vec'
+        dim = self.dimension
+        path = self.path.parent / self.resource.check_path
+        return TextWordModelMetadata(
+            name, 'default', dim, self.vocab_size, path,
+            sub_directory='cui2vec-bin')

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/domain.html b/_modules/zensols/mednlp/domain.html new file mode 100644 index 0000000..b7b27eb --- /dev/null +++ b/_modules/zensols/mednlp/domain.html @@ -0,0 +1,285 @@ + + + + + + + + zensols.mednlp.domain - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.domain

+"""Contains the classes for the medical token type and others.
+
+"""
+__author__ = 'Paul Landes'
+from typing import Optional
+from dataclasses import dataclass, field
+import logging
+from spacy.tokens.span import Span
+from zensols.util import APIError
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+class MedNLPError(APIError):
+    """Raised by any medical NLP speicic reason in this library."""
+    pass

+
+
+
+@dataclass
+class _MedicalEntity(object):
+    """Container class for general and medical specific named entities.
+    Instances of this class have the NER from a vanilla spaCy model output and
+    the NER+L linked UMLS concepts.
+
+    """
+    concept_span: Optional[Span] = field(default=None)
+    """The UMLS concept medical domain entity."""
+
+    @property
+    def is_concept(self) -> bool:
+        return self.concept_span is not None
+
+    @property
+    def is_ent(self) -> bool:
+        return self.concept_span is not None
+
+    @property
+    def cui(self) -> str:
+        return int(self.cui_[1:])
+
+    @property
+    def cui_(self) -> str:
+        return self.concept_span._.cui
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/entlink.html b/_modules/zensols/mednlp/entlink.html new file mode 100644 index 0000000..ae795b9 --- /dev/null +++ b/_modules/zensols/mednlp/entlink.html @@ -0,0 +1,381 @@ + + + + + + + + zensols.mednlp.entlink - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.entlink

+"""Contains the classes for the medical token type and others.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import List, Dict, Any, ClassVar
+from dataclasses import dataclass, field, InitVar
+import logging
+from scispacy.linking import EntityLinker
+from scispacy.linking_utils import Entity as SciSpacyEntity
+from zensols.persist import persisted, PersistedWork
+from zensols.config import Dictable
+from zensols.nlp import FeatureToken, FeatureTokenDecorator
+from . import MedicalLibrary
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+@dataclass
+class Entity(Dictable):
+    """A convenience container class that Wraps a SciSpacy entity.
+
+    """
+    _DICTABLE_ATTRIBUTES: ClassVar[List[str]] = 'cui name definition'.split()
+
+    sci_spacy_entity: SciSpacyEntity = field(repr=False)
+    """The entity identified by :mod:`scispacy.linking_utils`."""
+
+    @property
+    def name(self) -> str:
+        """The canonical name of the entity."""
+        return self.sci_spacy_entity.canonical_name
+
+    @property
+    def definition(self) -> str:
+        """The human readable description of the entity."""
+        return self.sci_spacy_entity.definition
+
+    @property
+    def cui(self) -> str:
+        """The unique concept identifier."""
+        return self.sci_spacy_entity.concept_id
+
+    def __str__(self) -> str:
+        return f'{self.name} ({self.cui})'
+
+    def __repr__(self):
+        return self.cui

+
+
+
+

+[docs]
+@dataclass
+class EntitySimilarity(Entity):
+    """A similarity measure of a medical concept in cui2vec.
+
+    :see: :meth:`.MedCatFeatureDocumentParser.similarity_by_term`
+    """
+    similiarty: float = field()

+
+
+
+

+[docs]
+@dataclass
+class EntityLinkerResource(object):
+    """Provides a way resolve :class:`scispacy.linking_utils.Entity` instances
+    from CUIs.
+
+    :see: :meth:`.get_linked_entity`
+
+    """
+    params: Dict[str, Any] = field(
+        default_factory=lambda: {'resolve_abbreviations': True,
+                                 'linker_name': 'umls'})
+    """Parameters given to the scispaCy entity linker."""
+
+    cache_global: InitVar[bool] = field(default=True)
+    """Whether or not to globally cache resources, which saves load time.
+
+    """
+    def __post_init__(self, cache_global: bool):
+        self._linker = PersistedWork(
+            '_linker', self, cache_global=cache_global)
+
+    @property
+    @persisted('_linker')
+    def linker(self) -> EntityLinker:
+        """The ScispaCy entity linker."""
+        self._silence_scispacy_warn()
+        return EntityLinker(**self.params)
+
+    @staticmethod
+    def _silence_scispacy_warn():
+        """This warning has should have no bearing on this application as we're
+        simply doing a CUI looking.
+
+        """
+        import warnings
+        s = '.*Trying to unpickle estimator Tfidf(?:Transformer|Vectorizer) from version.*'
+        warnings.filterwarnings('ignore', message=s)
+
+

+[docs]
+    def get_linked_entity(self, cui: str) -> Entity:
+        """Get a scispaCy linked entity.
+
+        :param cui: the unique concept ID
+
+        """
+        linker: EntityLinker = self.linker
+        se: SciSpacyEntity = linker.kb.cui_to_entity.get(cui)
+        if se is not None:
+            return Entity(se)

+

+
+
+
+

+[docs]
+@dataclass
+class LinkFeatureTokenDecorator(FeatureTokenDecorator):
+    """Adds linked SciSpacy definitions to tokens using the
+    :class:`.MedicalLibrary`.
+
+    """
+    lib: MedicalLibrary = field(default=None)
+    """The medical library used for linking entities."""
+
+

+[docs]
+    def decorate(self, token: FeatureToken):
+        e: SciSpacyEntity = self.lib.get_linked_entity(token.cui_)
+        if logger.isEnabledFor(logging.DEBUG):
+            logger.debug(f'entity: {token.cui_} -> {e} ({id(token)})')
+        if e is not None:
+            token._definition = e.definition

+

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/lib.html b/_modules/zensols/mednlp/lib.html new file mode 100644 index 0000000..f9537ac --- /dev/null +++ b/_modules/zensols/mednlp/lib.html @@ -0,0 +1,368 @@ + + + + + + + + zensols.mednlp.lib - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
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+
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+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.lib

+"""Medical resource library that contains UMLS access, cui2vec etc..
+
+"""
+from __future__ import annotations
+__author__ = 'Paul Landes'
+from typing import Any, List, Dict, Tuple
+from dataclasses import dataclass, field
+from zensols.config import ConfigFactory
+from . import MedCatResource, UTSClient
+
+
+

+[docs]
+@dataclass
+class MedicalLibrary(object):
+    """A utility class that provides access to medical APIs.
+
+    """
+    config_factory: ConfigFactory = field(default=None)
+    """The configuration factory used to create cTAKES and cui2vec instances.
+
+    """
+    medcat_resource: MedCatResource = field(default=None)
+    """The MedCAT factory resource."""
+
+    entity_linker_resource: 'EntityLinkerResource' = field(default=None)
+    """The entity linker resource."""
+
+    uts_client: UTSClient = field(default=None)
+    """Queries UMLS data."""
+
+

+[docs]
+    def get_entities(self, text: str) -> Dict[str, Any]:
+        """Return the all concept entity data.
+
+        :return: concepts as a multi-tiered dict
+
+        """
+        return self.medcat_resource.cat.get_entities(text)

+
+
+

+[docs]
+    def get_linked_entity(self, cui: str) -> 'Entity':
+        """Get a scispaCy linked entity.
+
+        :param cui: the unique concept ID
+
+        """
+        from .entlink import Entity
+        ent: Entity = self.entity_linker_resource.get_linked_entity(cui)
+        return ent

+
+
+

+[docs]
+    def get_atom(self, cui: str) -> Dict[str, str]:
+        """Get the UMLS atoms of a CUI from UTS.
+
+        :param cui: the concept ID used to query
+
+        :param preferred: if ``True`` only return preferred atoms
+
+        :return: a list of atom entries in dictionary form
+
+        """
+        return self.uts_client.get_atoms(cui, preferred=True)

+
+
+

+[docs]
+    def get_relations(self, cui: str) -> List[Dict[str, Any]]:
+        """Get the UMLS related concepts connected to a concept by ID.
+
+        :param cui: the concept ID used to get related concepts
+
+        :return: a list of relation entries in dictionary form in the order
+                 returned by UTS
+
+        """
+        return self.uts_client.get_relations(cui)

+
+
+

+[docs]
+    def get_new_ctakes_parser_stash(self) -> 'CTakesParserStash':
+        """Return a new instance of a ctakes parser stash.
+
+        """
+        return self.config_factory.new_instance('ctakes_parser_stash')

+
+
+    @property
+    def cui2vec_embedding(self) -> 'Cui2VecEmbedModel':
+        """The cui2vec embedding model.
+
+        """
+        return self.config_factory('cui2vec_500_embedding')
+
+

+[docs]
+    def similarity_by_term(self, term: str, topn: int = 5) -> \
+            List['EntitySimilarity']:
+        """Return similaries of a medical term.
+
+        :param term: the medical term (i.e. ``heart disease``)
+
+        :param topn: the top N count similarities to return
+
+        """
+        from .entlink import Entity, EntitySimilarity
+        from .cui2vec import Cui2VecEmbedModel
+        from gensim.models.keyedvectors import KeyedVectors
+        embedding: Cui2VecEmbedModel = self.cui2vec_embedding
+        kv: KeyedVectors = embedding.keyed_vectors
+        res: List[Dict[str, str]] = self.uts_client.search_term(term)
+        cui: str = res[0]['ui']
+        sims_by_word: List[Tuple[str, float]] = kv.similar_by_word(cui, topn)
+        sims: List[EntitySimilarity] = []
+        for rel_cui, proba in sims_by_word:
+            entity: Entity = self.get_linked_entity(rel_cui)
+            # name: str = entity.canonical_name.lower()
+            # defn: str = entity.definition
+            sim: float = embedding.keyed_vectors.similarity(cui, rel_cui)
+            sims.append(EntitySimilarity(entity.sci_spacy_entity, sim))
+        return sims

+

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/parser.html b/_modules/zensols/mednlp/parser.html new file mode 100644 index 0000000..98eff39 --- /dev/null +++ b/_modules/zensols/mednlp/parser.html @@ -0,0 +1,314 @@ + + + + + + + + zensols.mednlp.parser - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
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+ +
+
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+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.parser

+"""Medical langauge parser.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import Type, Iterable, Dict, Set
+from dataclasses import dataclass, field
+import logging
+import collections
+import textwrap as tw
+from spacy.tokens.doc import Doc
+from spacy.language import Language
+from zensols.nlp import FeatureToken, FeatureDocumentParser
+from zensols.nlp.sparser import SpacyFeatureDocumentParser
+from . import MedNLPError, MedCatResource, MedicalFeatureToken
+from .domain import _MedicalEntity
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+@dataclass
+class MedCatFeatureDocumentParser(SpacyFeatureDocumentParser):
+    """A medical based language resources that parses concepts.
+
+    """
+    TOKEN_FEATURE_IDS = frozenset(FeatureDocumentParser.TOKEN_FEATURE_IDS |
+                                  MedicalFeatureToken.FEATURE_IDS)
+    """Default token feature ID set for the medical parser.
+
+    """
+    token_feature_ids: Set[str] = field(default=TOKEN_FEATURE_IDS)
+    """The features to keep from spaCy tokens.
+
+    :see: :obj:`TOKEN_FEATURE_IDS`
+
+    """
+    token_class: Type[FeatureToken] = field(default=MedicalFeatureToken)
+    """The class to use for instances created by :meth:`features`."""
+
+    medcat_resource: MedCatResource = field(default=None)
+    """The MedCAT factory resource."""
+
+    def __post_init__(self):
+        if self.medcat_resource is None:
+            raise MedNLPError('No medcat resource set')
+        super().__post_init__()
+
+    def _create_model_key(self) -> str:
+        return f'name-{self.name}'
+
+    def _create_model(self) -> Language:
+        return self.medcat_resource.cat.pipe.spacy_nlp
+
+    def _normalize_tokens(self, doc: Doc) -> Iterable[FeatureToken]:
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'parsing: {tw.shorten(str(doc), 60)}')
+
+        # load/create model resources
+        res: MedCatResource = self.medcat_resource
+        ix2ent: Dict[int, _MedicalEntity] = \
+            collections.defaultdict(_MedicalEntity)
+
+        # add entities
+        for ent in doc.ents:
+            for i in range(ent.start, ent.end):
+                tok = doc[i]
+                ix2ent[tok.idx].concept_span = ent
+
+        if logger.isEnabledFor(logging.DEBUG):
+            logger.debug(f'normalizing with: {self.token_normalizer}')
+
+        return super()._normalize_tokens(doc, res=res, ix2ent=ix2ent)

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/resource.html b/_modules/zensols/mednlp/resource.html new file mode 100644 index 0000000..a30468e --- /dev/null +++ b/_modules/zensols/mednlp/resource.html @@ -0,0 +1,504 @@ + + + + + + + + zensols.mednlp.resource - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
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+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.resource

+"""MedCAT wrapper.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import Tuple, Iterable, Dict, Any, Set
+from dataclasses import dataclass, field, InitVar
+import logging
+import warnings
+from pathlib import Path
+import re
+from frozendict import frozendict
+import pandas as pd
+import spacy.util
+from medcat.config import Config, MixingConfig
+from medcat.vocab import Vocab
+from medcat.cdb import CDB
+from medcat.cat import CAT
+from medcat.meta_cat import MetaCAT
+from zensols.util import APIError
+from zensols.install import Resource, Installer
+from zensols.persist import persisted, PersistedWork
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+@dataclass
+class MedCatResource(object):
+    """A factory class that creates MedCAT resources.
+
+    """
+    _MODEL_REGEX = re.compile(r'^([^@]+) @ .+$')
+    """A regular expression for a spaCy model dependency (http syntax)."""
+
+    installer: Installer = field()
+    """Installs and provides paths to the model files."""
+
+    vocab_resource: Resource = field()
+    """The path to the ``vocab.dat`` file."""
+
+    cdb_resource: Resource = field()
+    """The ``cdb-medmen-v1.dat`` file.
+
+    """
+    mc_status_resource: Resource = field()
+    """The the ``mc_status`` directory.
+
+    """
+    umls_tuis: Resource = field()
+    """The UMLS TUIs (types) mapping resource that maps from TUIs to
+    descriptions.
+
+    :see: `Semantic Types <https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/documentation/SemanticTypesAndGroups.html>`_
+
+    """
+    umls_groups: Resource = field()
+    """Like :obj:`umls_tuis` but groups TUIs in gropus."""
+
+    filter_tuis: Set[str] = field(default=None)
+    """Types used to filter linked CUIs (i.e. ``{'T047', 'T048'}``).
+
+    """
+    filter_groups: Set[str] = field(default=None)
+    """Just like :obj:`filter_tuis` but each element is treated as a group used
+    to generate a list of CUIs from those mapped from ``name`` to ``tui` in
+    :obj:`groups`.
+
+    """
+    spacy_enable_components: Set[str] = field(
+        default_factory=lambda: set('sentencizer parser'.split()))
+    """By default, MedCAT disables several pipeline components.  Some of these
+    are needed for sentence chunking and other downstream tasks.  Otherwise
+    sentence indexing won't work because sentence boundaries are missing.
+
+    :see: `MedCAT Config <https://github.com/CogStack/MedCAT/blob/master/medcat/config.py>`_
+
+    """
+    cat_config: Dict[str, Dict[str, Any]] = field(default=None)
+    """If provieded, set the CDB configuration.  Keys are ``general``,
+    ``preprocessing`` and all other attributes documented in the `MedCAT Config
+    <https://github.com/CogStack/MedCAT/blob/master/medcat/config.py>`_
+
+    """
+    cache_global: InitVar[bool] = field(default=True)
+    """Whether or not to globally cache resources, which saves load time.
+
+    """
+    requirements_dir: Path = field(default=None)
+    """The directory with the pip requirements files."""
+
+    auto_install_models: Tuple[str, ...] = field(default=())
+    """A list of spaCy models that will be installed if not already."""
+
+    def __post_init__(self, cache_global: bool):
+        self._tuis = PersistedWork('_tuis', self, cache_global=cache_global)
+        self._cat = PersistedWork('_cat', self, cache_global=cache_global)
+        self._installed = False
+
+    @staticmethod
+    def _filter_medcat_logger():
+        class NoCdbExportFilter(logging.Filter):
+            def filter(self, record):
+                s = 'The CDB was exported by an unknown version of MedCAT.'
+                return not record.getMessage() == s
+
+        logging.getLogger('medcat.cdb').addFilter(NoCdbExportFilter())
+
+    def _assert_installed(self):
+        if not self._installed:
+            self.installer()
+            self._installed = True
+
+    def _override_config(self, targ: Config, src: Dict[str, Dict[str, Any]]):
+        src_top: str
+        src_conf = Dict[str, Any]
+        for src_top, src_conf in src.items():
+            targ_any: Any = getattr(targ, src_top)
+            if logger.isEnabledFor(logging.DEBUG):
+                logger.debug(f"updating dict '{src_top}' ({type(targ_any)}): " +
+                             f"<{targ_any}> with <{src_conf}>")
+            if isinstance(targ_any, dict):
+                targ_any.update(src_conf)
+            elif isinstance(targ_any, MixingConfig):
+                targ_any.merge_config(src_conf)
+            else:
+                setattr(targ, src_top, src_conf)
+
+    def _add_filters(self, config: Config, cdb: CDB):
+        filter_tuis = set()
+        if self.filter_tuis is not None:
+            filter_tuis.update(self.filter_tuis)
+        if self.filter_groups is not None:
+            df: pd.DataFrame = self.groups
+            reg = '.*(' + '|'.join(self.filter_groups) + ')'
+            df = df[df['name'].str.match(reg)]
+            filter_tuis.update(df['tui'].tolist())
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'filtering on tuis: {", ".join(filter_tuis)}')
+        if len(filter_tuis) > 0:
+            cui_filters = set()
+            for tui in filter_tuis:
+                cui_filters.update(cdb.addl_info['type_id2cuis'][tui])
+            config.linking['filters']['cuis'] = cui_filters
+
+    @property
+    @persisted('_tuis')
+    def tuis(self) -> Dict[str, str]:
+        """A mapping of type identifiers (TUIs) to their descriptions."""
+        self._assert_installed()
+        path: Path = self.installer[self.umls_tuis]
+        df = pd.read_csv(path, delimiter='|', header=None)
+        df.columns = 'abbrev tui desc'.split()
+        df_tups = df[['tui', 'desc']].itertuples(name=None, index=False)
+        return frozendict(df_tups)
+
+    @property
+    @persisted('_groups')
+    def groups(self) -> pd.DataFrame:
+        """A dataframe of TUIs, their abbreviations, descriptions and a group
+        name associated with each.
+
+        """
+        self._assert_installed()
+        path: Path = self.installer[self.umls_groups]
+        df = pd.read_csv(path, delimiter='|', header=None)
+        df.columns = 'abbrev name tui desc'.split()
+        return df
+
+    @property
+    @persisted('_cat')
+    def cat(self) -> CAT:
+        """The MedCAT NER tagger instance.
+
+        When this property is accessed, all models are downloaded first, then
+        loaded, if not already.
+
+        """
+        self._assert_installed()
+        # Load the vocab model you downloaded
+        vocab = Vocab.load(self.installer[self.vocab_resource])
+        # Load the cdb model you downloaded
+        cdb = CDB.load(self.installer[self.cdb_resource])
+        # mc status model
+        mc_status = MetaCAT.load(self.installer[self.mc_status_resource])
+        # enable sentence boundary annotation
+        for name in self.spacy_enable_components:
+            cdb.config.general['spacy_disabled_components'].remove(name)
+        # override configuration
+        if self.cat_config is not None:
+            self._override_config(cdb.config, self.cat_config)
+        # add TUI filters (i.e. filter out non-medical terms)
+        self._add_filters(cdb.config, cdb)
+        # ensure models are installed
+        self._assert_spacy_models()
+        # create cat - each cdb comes with a config that was used to train it;
+        # you can change that config in any way you want, before or after
+        # creating cat
+        try:
+            cat = CAT(cdb=cdb, config=cdb.config, vocab=vocab,
+                      meta_cats=[mc_status])
+        except OSError as e:
+            msg: str = str(e)
+            if msg.find("Can't find model") == -1:
+                raise e
+            else:
+                logger.info('no scispacy model found--attempting to install')
+                self._install_model()
+                cat = CAT(cdb=cdb, config=cdb.config, vocab=vocab,
+                          meta_cats=[mc_status])
+        return cat
+
+    def _install_model(self):
+        if self.requirements_dir is None:
+            raise APIError('model not installed and no requirements found')
+        else:
+            from pip._internal import main as pipmain
+            req_file: Path
+            for req_file in self.requirements_dir.iterdir():
+                pipmain(['install', '--use-deprecated=legacy-resolver',
+                         '-r', str(req_file), '--no-deps'])
+
+    def _get_model_requirements(self) -> Iterable[Tuple[str, str]]:
+        path: Path
+        for path in self.requirements_dir.iterdir():
+            with open(path) as f:
+                line: str
+                for line in map(str.strip, f.readlines()):
+                    m: re.Match = self._MODEL_REGEX.match(line)
+                    if m is not None:
+                        yield (m.group(1), line)
+
+    def _install_dependency(self, dep: str):
+        from pip._internal import main as pipmain
+        pipmain(['install', '--use-deprecated=legacy-resolver',
+                 dep, '--no-deps'])
+
+    def _assert_spacy_models(self):
+        missing: Set[str] = set()
+        model_name: str
+        for model_name in self.auto_install_models:
+            if not spacy.util.is_package(model_name):
+                missing.add(model_name)
+        if len(missing) > 0:
+            if logger.isEnabledFor(logging.INFO):
+                logger.info(f'installing missing models: {missing}')
+            reqs: Dict[str, str] = dict(self._get_model_requirements())
+            for model_name in missing:
+                dep: str = reqs.get(model_name)
+                if dep is None:
+                    raise APIError(
+                        f'Resource needs unmapped model: {model_name}')
+                self._install_dependency(dep)
+
+

+[docs]
+    def clear(self):
+        self._tuis.clear()
+        self._cat.clear()

+

+
+
+
+MedCatResource._filter_medcat_logger()
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/tok.html b/_modules/zensols/mednlp/tok.html new file mode 100644 index 0000000..2c53556 --- /dev/null +++ b/_modules/zensols/mednlp/tok.html @@ -0,0 +1,387 @@ + + + + + + + + zensols.mednlp.tok - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
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+ +
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+
+
+ + + + + Back to top + +
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+ +
+ +
+
+

Source code for zensols.mednlp.tok

+"""Contains the classes for the medical token type.
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import Dict, Tuple, Optional, Union
+import logging
+from functools import reduce
+from frozendict import frozendict
+from spacy.tokens.token import Token
+from spacy.tokens.span import Span
+from medcat.cdb import CDB
+from zensols.nlp import FeatureToken, SpacyFeatureToken
+from . import MedCatResource
+from .domain import _MedicalEntity
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+class MedicalFeatureToken(SpacyFeatureToken):
+    """A set of token features that optionally contains a medical concept.
+
+    """
+    FEATURE_IDS_BY_TYPE = frozendict({
+        'str': frozenset(('cui_ pref_name_ detected_name_ tuis_ ' +
+                          'definition_ tui_descs_').split()),
+        'bool': frozenset('is_concept'.split()),
+        'float': frozenset('context_similarity'.split()),
+        'int': frozenset('cui'.split()),
+        'list': frozenset('tuis sub_names'.split())})
+    FEATURE_IDS = frozenset(
+        reduce(lambda res, x: res | x, FEATURE_IDS_BY_TYPE.values()))
+    WRITABLE_FEATURE_IDS = tuple(list(FeatureToken.WRITABLE_FEATURE_IDS) +
+                                 'cui_'.split())
+    _NONE_SET = frozenset()
+
+

+[docs]
+    def __init__(self, spacy_token: Union[Token, Span], norm: str,
+                 res: MedCatResource, ix2ent: Dict[int, _MedicalEntity]):
+        super().__init__(spacy_token, norm)
+        self._definition: str = self.NONE
+        self._cdb: CDB = res.cat.cdb
+        self._res = res
+        med_ent: Optional[_MedicalEntity] = ix2ent.get(self.idx)
+        if med_ent is None:
+            med_ent = _MedicalEntity()
+        self.med_ent = med_ent
+        self.is_ent = med_ent.is_ent

+
+
+    @property
+    def ent_(self) -> str:
+        # self.med_ent.concept_span.label_ just gives 'concept', which then
+        # clobbers other useful entities in the combiner parsers
+        return self.NONE
+
+    @property
+    def ent(self) -> int:
+        # self.med_ent.concept_span.label just gives 'concept', which then
+        # clobbers other useful entities in the combiner parsers
+        return 0
+
+    @property
+    def is_concept(self) -> bool:
+        """``True`` if this has a CUI and identifies a medical concept."""
+        return self.is_ent
+
+    @property
+    def cui_(self) -> str:
+        """The unique UMLS concept ID."""
+        return self.med_ent.cui_ if self.is_concept else self.NONE
+
+    @property
+    def cui(self) -> int:
+        """Returns the numeric part of the concept ID."""
+        return -1 if not self.is_concept else int(self.cui_[1:])
+
+    @property
+    def pref_name_(self) -> str:
+        """The preferred name of the concept."""
+        if self.is_concept:
+            return self._cdb.cui2preferred_name.get(self.cui_)
+        else:
+            return self.NONE
+
+    @property
+    def detected_name_(self) -> str:
+        """The detected name of the concept."""
+        if self.is_concept:
+            return self.med_ent.concept_span._.detected_name
+        else:
+            return self.NONE
+
+    @property
+    def sub_names(self) -> Tuple[str, ...]:
+        """Return other names for the concept."""
+        if self.is_concept:
+            return tuple(sorted(self._cdb.cui2names[self.cui_]))
+        else:
+            return []
+
+    @property
+    def context_similarity(self) -> float:
+        """The similiarity of the concept."""
+        if self.is_concept:
+            return self.med_ent.concept_span._.context_similarity
+        else:
+            return -1
+
+    @property
+    def definition_(self) -> str:
+        """The definition if the concept."""
+        return self._definition or FeatureToken.NONE
+
+    @property
+    def tuis(self) -> Tuple[str, ...]:
+        """The the CUI type of the concept."""
+        if self.is_concept:
+            cui: str = self.cui_
+            return tuple(sorted(self._cdb.cui2type_ids.get(cui)))
+        else:
+            return self._NONE_SET
+
+    @property
+    def tuis_(self) -> str:
+        """All CUI TUIs (types) of the concept sorted as a comma delimited list.
+
+        """
+        return ','.join(sorted(self.tuis))
+
+    @property
+    def tui_descs_(self) -> str:
+        """Descriptions of :obj:`tuis_`."""
+        def map_tui(k: str) -> str:
+            v = self._res.tuis.get(k)
+            if v is None:
+                v = f'? ({k})'
+            return v
+
+        return ', '.join(map(map_tui, sorted(self.tuis)))
+
+    def __str__(self):
+        cui_str = f' ({self.cui_})' if self.is_concept else ''
+        return self.norm + cui_str

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_modules/zensols/mednlp/uts.html b/_modules/zensols/mednlp/uts.html new file mode 100644 index 0000000..e9bf3d7 --- /dev/null +++ b/_modules/zensols/mednlp/uts.html @@ -0,0 +1,558 @@ + + + + + + + + zensols.mednlp.uts - Medical natural language parsing and utility library 1.7.0 documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
+
+
+ +
+
+
Medical natural language parsing and utility library 1.7.0 documentation
 +
+
+
+ +
+ +
+
+ +
+
+
+ + + + + Back to top + +
+
+ +
+ +
+
+

Source code for zensols.mednlp.uts

+"""Interface to the UTS (UMLS Terminology Services (UTS)) RESTful service,
+which was taken from the UTS example repo.
+
+:see `UTS GitHug repo <https://github.com/HHS/uts-rest-api/>`_
+
+"""
+__author__ = 'Paul Landes'
+
+from typing import List, Dict, Any, Tuple, Union
+from dataclasses import dataclass, field
+import logging
+import re
+import json
+from json.decoder import JSONDecodeError
+import requests
+from lxml.html import fromstring
+from lxml.etree import _Element as Element
+from zensols.persist import Stash
+from . import MedNLPError
+
+logger = logging.getLogger(__name__)
+
+
+

+[docs]
+class UTSError(MedNLPError):
+    """An error thrown by wrapper of the UTS system.
+
+    """
+    pass

+
+
+
+

+[docs]
+class NoResultsError(UTSError):
+    """Thrown when no results, usually for a CUI not found.
+
+    """
+    pass

+
+
+
+

+[docs]
+class AuthenticationError(UTSError):
+    """Thrown when authentication fails."""
+

+[docs]
+    def __init__(self, api_key: str):
+        super().__init__(f'Authentication error using key: {api_key}')
+        self.api_key = api_key

+

+
+
+
+

+[docs]
+@dataclass
+class Authentication(object):
+    """A utility class to manage the authentication with the UTS system.
+
+    """
+    SERVICE = 'http://umlsks.nlm.nih.gov'
+    """The service endpoint URL."""
+
+    AUTH_URI = 'https://utslogin.nlm.nih.gov'
+    """The authetication service endpoint URL."""
+
+    api_key: str = field()
+    """The API key used for the RESTful NIH service."""
+
+    auth_endpoint: str = field(default='/cas/v1/api-key')
+    """The path of the authentication service endpoint."""
+
+

+[docs]
+    def gettgt(self):
+        params = {'apikey': self.api_key}
+        h = {'Content-type': 'application/x-www-form-urlencoded',
+             'Accept': 'text/plain',
+             'User-Agent': 'python'}
+        r = requests.post(
+            self.AUTH_URI + self.auth_endpoint, data=params, headers=h)
+        if r.text[0] == '{':
+            try:
+                obj = json.loads(r.text)
+                if 'authentication_exceptions' in obj:
+                    raise AuthenticationError(self.api_key)
+            except JSONDecodeError as e:
+                logger.warning('looks like JSON, but not decodable: ' +
+                               f'<{r.text}>: {e}')
+        response: Element = fromstring(r.text)
+        if isinstance(response, Element):
+            err: str = None
+            if response.tag == 'p':
+                try:
+                    content: str = json.loads(response.text)
+                    if 'name' in content and 'message' in content:
+                        name: str = content['name']
+                        err = f"{name}: {content['message']}"
+                        if name == 'UnauthorizedError':
+                            raise AuthenticationError(err)
+                    else:
+                        raise UTSError(f'Unknown response: {content}')
+                except json.decoder.JSONDecodeError as e:
+                    err = f'Appears to be an error, but can not parse: {e}'
+                    raise UTSError(err) from e
+            if err is not None:
+                raise UTSError(err)
+        # extract the entire URL needed from the HTML form (action attribute)
+        # returned - looks similar to
+        # https://utslogin.nlm.nih.gov/cas/v1/tickets/TGT-36471-aYqNLN2rFIJPXKzxwdTNC5ZT7z3B3cTAKfSc5ndHQcUxeaDOLN-cas
+        # we make a POST call to this URL in the getst method
+        tgt = response.xpath('//form/@action')[0]
+        return tgt

+
+
+

+[docs]
+    def getst(self, tgt):
+        params = {'service': self.SERVICE}
+        h = {'Content-type': 'application/x-www-form-urlencoded',
+             'Accept': 'text/plain',
+             'User-Agent': 'python'}
+        r = requests.post(tgt, data=params, headers=h)
+        st = r.text
+        return st

+

+
+
+
+

+[docs]
+@dataclass
+class UTSClient(object):
+    URI = 'https://uts-ws.nlm.nih.gov'
+    """The service URL endpoint."""
+
+    REL_ID_REGEX = re.compile(r'.*CUI\/(.+)$')
+    """Used to parse related CUIs in :meth:`get_related_cuis`."""
+
+    NO_RESULTS_ERR = 'No results containing all your search terms were found.'
+    """Error message from UTS indicating a missing CUI."""
+
+    MISSING_VALUE = '<missing>'
+    """Value to store in the stash when there is a missing CUI."""
+
+    api_key: str = field()
+    """The API key used for the RESTful NIH service."""
+
+    version: str = field(default='2020AA')
+    """The version of the UML we want."""
+
+    request_stash: Stash = field(default=None)
+
+    def _get_ticket(self) -> str:
+        """Generate a new service ticket for each page if needed."""
+        if logger.isEnabledFor(logging.INFO):
+            logger.info(f'logging in to UTS with {self.api_key}')
+        auth_client = Authentication(self.api_key)
+        tgt = auth_client.gettgt()
+        return auth_client.getst(tgt)
+
+    def _parse_json(self, s: str) -> Union[Exception, Dict[str, Any]]:
+        try:
+            return json.loads(s)
+        except JSONDecodeError as e:
+            logger.debug(f'can not parse: <{s}>: {e}')
+            return e
+
+    def _request_remote(self, url: str, query: Dict[str, str],
+                        expect: bool) -> Any:
+        query['ticket'] = self._get_ticket()
+        r = requests.get(url, params=query)
+        r.encoding = 'utf-8'
+        items = self._parse_json(r.text)
+        if isinstance(items, Exception):
+            raise UTSError(f'Could not parse: <{r.text}>, ' +
+                           f'code: {r.status_code}') from items
+        err = items.get('error')
+        if err is not None and err == self.NO_RESULTS_ERR:
+            if not expect:
+                return None
+            raise NoResultsError(
+                f'Could not request {url}, query={query}: {err}')
+        if r.status_code != 200:
+            if err is None:
+                msg = f'response: <{r.text}>'
+            else:
+                msg = err
+            raise UTSError(f'Could not request {url}, query={query}: {msg}')
+        if err is not None:
+            raise UTSError(f'Could not request {url}, query={query}: {err}')
+        if 'result' not in items:
+            raise UTSError(f'Unknown resposne: <{r.text}>')
+        return items['result']
+
+    def _request_cache(self, url: str, query: Dict[str, str],
+                       expect: bool) -> Any:
+        q = '&'.join(map(lambda k: f'{k}={query[k]}', sorted(query.keys())))
+        key = url + '?' + q
+        if logger.isEnabledFor(logging.DEBUG):
+            logger.debug(f'key: {key}')
+        val = self.request_stash.load(key)
+        if val is None:
+            val = self._request_remote(url, query, expect)
+            if val is None:
+                val = self.MISSING_VALUE
+            self.request_stash.dump(key, val)
+        if val == self.MISSING_VALUE:
+            val = None
+        return val
+
+    def _request(self, url: str, query: Dict[str, str], expect: bool) -> Any:
+        if self.request_stash is None:
+            return self._request_remote(url, query, expect)
+        else:
+            return self._request_cache(url, query, expect)
+
+

+[docs]
+    def search_term(self, term: str, pages: int = 1) -> List[Dict[str, str]]:
+        """Search for a string term in UMLS.
+
+        :param term: the string term to match against
+
+        :return: a list (one for each page), each with a dictionary of matching
+                 terms that have the ``name`` of the term, the ``ui`` (CUI),
+                 the ``uri`` of the term and the ``rootSource`` of the
+                 orginitating system
+
+        """
+        url = '{uri}/rest/search/{version}'.format(
+            **{'uri': self.URI, 'version': self.version})
+        res = []
+        for page_n in range(pages):
+            if logger.isEnabledFor(logging.DEBUG):
+                logger.debug(f'fetching page {page_n}')
+            query = {'string': term,
+                     'page_n': page_n}
+            res.extend(self._request(url, query, False)['results'])
+        return res

+
+
+

+[docs]
+    def get_atoms(self, cui: str, preferred: bool = True,
+                  expect: bool = True) -> \
+            Union[Dict[str, str], List[Dict[str, str]]]:
+        """Get the UMLS atoms of a CUI from UTS.
+
+        :param cui: the concept ID used to query
+
+        :param preferred: if ``True`` only return preferred atoms
+
+        :return: a list of atom entries in dictionary form or a single dict if
+        `        ``preferred`` is ``True``
+
+        """
+        pat = '{uri}/rest/content/{version}/CUI/{cui}/atoms/'
+        if preferred:
+            pat += 'preferred/'
+        url = pat.format(
+            **{'uri': self.URI, 'version': self.version, 'cui': cui})
+        if logger.isEnabledFor(logging.DEBUG):
+            logger.debug(f'fetching atom {cui}')
+        return self._request(url, {}, expect)

+
+
+

+[docs]
+    def get_relations(self, cui: str, expect: bool = True) -> \
+            List[Dict[str, Any]]:
+        """Get the UMLS related concepts connected to a concept by ID.
+
+        :param cui: the concept ID used to get related concepts
+
+        :return: a list of relation entries in dictionary form in the order
+                 returned by UTS
+
+        """
+        url = '{uri}/rest/content/{version}/CUI/{cui}/relations/'.format(
+            **{'uri': self.URI, 'version': self.version, 'cui': cui})
+        try:
+            return self._request(url, {}, expect)
+        except NoResultsError as e:
+            if expect:
+                raise e

+
+
+
+

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2024, Paul Landes +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/_sources/CHANGELOG.md.txt b/_sources/CHANGELOG.md.txt new file mode 100644 index 0000000..8f4915b --- /dev/null +++ b/_sources/CHANGELOG.md.txt @@ -0,0 +1,176 @@ +# Change Log +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](http://keepachangelog.com/) +and this project adheres to [Semantic Versioning](http://semver.org/). + + +## [Unreleased] + + +## [1.7.0] - 2024-04-14 +### Removed +- Deprecated feature document parser `mednlp_combine_medfirst_doc_parser` from + resource library. + +### Changed +- Renamed `MeddicalFeatureDocumentParser` to `MedCatFeatureDocumentParser` + since the parser only adds MedCAT CUIs. +- Fixed the configured parser that adds both ScispaCy biomed entities and + MedCAT CUIs in `mednlp_combine_biomed_doc_parser`. +- Separated combiner with non-combiner models in configuration space. The + non-combiners (biomed ScispaCy and MedCAT) are parses that are used in their + respective combiners. These are then used by a new composite parser that + uses both (`mednlp_combine_biomed_doc_parser`). Unit test case added for + all configured parsers. + + +## [1.6.0] - 2024-02-27 +### Added +- Added a ScispaCy biomedical document parser, which is enabled by setting + `mednlp_default:doc_parser = mednlp_combine_biomed_doc_parser`. This uses + better linguistic features and detects more entity span(s). + +### Changed +- Fixed normalize token and sentence/token indexes from being clobbered by + combined medical parsers. +- Fixed numeric entity feature from the combined medical parser is non-zero + for medical entities. +- Combined medical parser defines linguistic and medical features in the + document parser object instance. + + +## [1.5.0] - 2023-12-05 +### Changed +- Upgrade libraries: `numpy`, `lxml`, `scikitlearn`, `scipy`, `medcat`. +- Added `scispacy` dependency. + +### Added +- Support for Python 3.11. + +### Removed +- Support for Python 3.9. + + +## [1.4.1] - 2023-09-08 +### Changed +- Fix unit tests using the model provided for the MedCAT tutorials. +- Re-enable GitHub workflow unit tests CI. + + +## [1.4.0] - 2023-08-16 +Downstream moderate risk update release. + +### Changed +- Switch order of medical specific and general spaCy language parsing and + chunking. Now the medical parser is the source parser and the default spaCy + parser is the target in `MappingCombinerFeatureDocumentParser`. This was + done to get better sentence chunking as MedCAT (used in the medical parser) + does not sentence chunk well as it was not designed for it. +- Upgrade to [zensols.util] 1.13.0 +- Fix `cui2vec` weight archive re-download on each access. +- Mapping combiner default is to use token's character absolute index. + + +## [1.3.2] - 2023-06-29 +### Added +- Feature document parser shortcut from application factory. + +### Changed +- Resource library configuration to clean up model resources after download. + + +## [1.3.1] - 2023-06-27 +### Changed +- Updated to [zensols.nlp] to 1.7.2 and use its new feature to auto load any + missing spaCy base model(s). +- Remove configuration file requirement from the CLI. +- Fix spaCy dependency requirement to align with `scipy` and [zensols.nlp]. + + +## [1.3.0] - 2023-06-20 +### Changed +- Fix contraction tokenization. This was done by swapping the target and + source parser in the `lang.conf:mednlp_combine_doc_parser` resource library + configuration. + + +## [1.2.0] - 2023-06-09 +### Changed +- Upgrade to [medcat] 1.7.0. +- Better UTS error handling with raised exceptions and messages. + + +## [1.1.0] - 2023-04-05 +### Changed +- Install missing models and packages on start up. +- Updated [zensols.install] to 0.2.1 +- Updated [zensols.nlp] to 1.6.0. + + +## [1.0.0] - 2023-02-02 +### Changed +- Updated [zensols.util] to 1.12.1. +- Updated [zensols.nlp] to 1.5.0. + + +## [0.1.1] - 2022-10-02 +### Removed +- Make scispacy optional and remove the dependency. See the test cases in + [test](test/entlink). + + +## [0.1.0] - 2022-10-01 +### Added +- Unit test in GitHub CI. + +### Changed +- Upgrade to spaCy 2.2, MedCAT 3.0, `zensols.nlp` 1.4.0. +- Make `cui2vec` a standard word embedding with vectorizer and layer. +- Replace entity splitter by not embedding named entities as default + configuration. + +### Removed +- Support for Python 3.7, 3.8 from dropped support in `zensols.util`. + + +## [0.0.2] - 2022-05-04 +### Added +- A CSV features dump example. + +### Changed +- Use token instead of sentence level mapping in cases where MedCAT creates + unaligned sentence boundaries. +- Make medical parser stand-alone and use delegate mapping combiner instead of + using a class hierarchy. +- Entity linker is now a token decorator. +- Protect against `unk` (unknown) keys in TUIs. + + +## [0.0.1] - 2022-01-30 +### Added +- Initial version. + + + +[Unreleased]: https://github.com/Paul Landes/mednlp/compare/v1.7.0...HEAD +[1.7.0]: https://github.com/Paul Landes/mednlp/compare/v1.6.0...v1.7.0 +[1.6.0]: https://github.com/Paul Landes/mednlp/compare/v1.5.0...v1.6.0 +[1.5.0]: https://github.com/Paul Landes/mednlp/compare/v1.4.1...v1.5.0 +[1.4.1]: https://github.com/Paul Landes/mednlp/compare/v1.4.0...v1.4.1 +[1.4.0]: https://github.com/Paul Landes/mednlp/compare/v1.3.2...v1.4.0 +[1.3.2]: https://github.com/Paul Landes/mednlp/compare/v1.3.1...v1.3.2 +[1.3.1]: https://github.com/Paul Landes/mednlp/compare/v1.3.0...v1.3.1 +[1.3.0]: https://github.com/Paul Landes/mednlp/compare/v1.2.0...v1.3.0 +[1.2.0]: https://github.com/Paul Landes/mednlp/compare/v1.1.0...v1.2.0 +[1.1.0]: https://github.com/Paul Landes/mednlp/compare/v1.0.0...v1.1.0 +[1.0.0]: https://github.com/Paul Landes/mednlp/compare/v0.1.1...v1.0.0 +[0.1.1]: https://github.com/Paul Landes/mednlp/compare/v0.1.0...v0.1.1 +[0.1.0]: https://github.com/Paul Landes/mednlp/compare/v0.0.2...v0.1.0 +[0.0.2]: https://github.com/Paul Landes/mednlp/compare/v0.0.1...v0.0.2 +[0.0.1]: https://github.com/Paul Landes/mednlp/compare/v0.0.0...v0.0.1 + +[zensols.util]: https://github.com/plandes/util +[zensols.nlp]: https://github.com/plandes/nlparse +[zensols.install]: https://github.com/plandes/install +[medcat]: https://github.com/CogStack/MedCAT diff --git a/_sources/CONTRIBUTING.md.txt b/_sources/CONTRIBUTING.md.txt new file mode 100644 index 0000000..89c8df6 --- /dev/null +++ b/_sources/CONTRIBUTING.md.txt @@ -0,0 +1,47 @@ +# Contributing + +If you discover issues, have ideas for improvements or new features, please +report them to the [issue tracker][1] of the repository or submit a pull +request. Please, try to follow these guidelines when you do so. + + +## Issue reporting + +* Check that the issue has not already been reported. +* Check that the issue has not already been fixed in the latest code + (a.k.a. `master`). +* Be clear, concise and precise in your description of the problem. +* Open an issue with a descriptive title and a summary in grammatically correct, + complete sentences. +* Mention your `mednlp` Python dependency version and operating + system. +* Include any relevant code to the issue summary. + + +### Reporting bugs + +Adding information like the backtrace and the REPL messages to the bug report +makes it easier to track down bugs. Some steps to reproduce a bug reliably +would also make a huge difference. + + +## Pull requests + +* Read [how to properly contribute to open source projects on Github][2]. +* Use a topic branch to easily amend a pull request later, if necessary. +* Use the same coding conventions as the rest of the project. +* Make sure that the unit tests are passing (`make test`). +* Write [good commit messages][3]. +* Mention related tickets in the commit messages (e.g. `[Fix #N] Add command ...`). +* Update the [changelog][6]. +* [Squash related commits together][5]. +* Open a [pull request][4] that relates to *only* one subject with a clear title + and description in grammatically correct, complete sentences. + + +[1]: https://github.com/plandes/mednlp/issues +[2]: http://gun.io/blog/how-to-github-fork-branch-and-pull-request +[3]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html +[4]: https://help.github.com/articles/using-pull-requests +[5]: http://gitready.com/advanced/2009/02/10/squashing-commits-with-rebase.html +[6]: https://github.com/plandes/mednlp/blob/master/CHANGELOG.md diff --git a/_sources/LICENSE.md.txt b/_sources/LICENSE.md.txt new file mode 100644 index 0000000..ca5a3bf --- /dev/null +++ b/_sources/LICENSE.md.txt @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2021 - 2023 Paul Landes + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/_sources/api.rst.txt b/_sources/api.rst.txt new file mode 100644 index 0000000..26d1e58 --- /dev/null +++ b/_sources/api.rst.txt @@ -0,0 +1,8 @@ +API Reference +============= + +.. toctree:: + :maxdepth: 2 + :glob: + + api/* diff --git a/_sources/api/zensols.mednlp.rst.txt b/_sources/api/zensols.mednlp.rst.txt new file mode 100644 index 0000000..504a105 --- /dev/null +++ b/_sources/api/zensols.mednlp.rst.txt @@ -0,0 +1,123 @@ +zensols.mednlp package +====================== + +Submodules +---------- + +zensols.mednlp.app +------------------ +.. inheritance-diagram:: zensols.mednlp.app + :parts: 1 + +.. automodule:: zensols.mednlp.app + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.cli +------------------ +.. inheritance-diagram:: zensols.mednlp.cli + :parts: 1 + +.. automodule:: zensols.mednlp.cli + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.ctakes +--------------------- +.. inheritance-diagram:: zensols.mednlp.ctakes + :parts: 1 + +.. automodule:: zensols.mednlp.ctakes + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.cui2vec +---------------------- +.. inheritance-diagram:: zensols.mednlp.cui2vec + :parts: 1 + +.. automodule:: zensols.mednlp.cui2vec + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.domain +--------------------- +.. inheritance-diagram:: zensols.mednlp.domain + :parts: 1 + +.. automodule:: zensols.mednlp.domain + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.entlink +---------------------- +.. inheritance-diagram:: zensols.mednlp.entlink + :parts: 1 + +.. automodule:: zensols.mednlp.entlink + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.lib +------------------ +.. inheritance-diagram:: zensols.mednlp.lib + :parts: 1 + +.. automodule:: zensols.mednlp.lib + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.parser +--------------------- +.. inheritance-diagram:: zensols.mednlp.parser + :parts: 1 + +.. automodule:: zensols.mednlp.parser + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.resource +----------------------- +.. inheritance-diagram:: zensols.mednlp.resource + :parts: 1 + +.. automodule:: zensols.mednlp.resource + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.tok +------------------ +.. inheritance-diagram:: zensols.mednlp.tok + :parts: 1 + +.. automodule:: zensols.mednlp.tok + :members: + :undoc-members: + :show-inheritance: + +zensols.mednlp.uts +------------------ +.. inheritance-diagram:: zensols.mednlp.uts + :parts: 1 + +.. automodule:: zensols.mednlp.uts + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: zensols.mednlp + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/doc/api-usage.md.txt b/_sources/doc/api-usage.md.txt new file mode 100644 index 0000000..198de61 --- /dev/null +++ b/_sources/doc/api-usage.md.txt @@ -0,0 +1,336 @@ +# Medical NLP and Utility API + +This API primarily wraps others with the [Zensols Framework] to provide easy +way and reproducible method of utilization and experimentation with medical and +clinical natural language text. It provides the following functionality: + +* [UMLS Access via UTS] +* [Medical Concept and Entity Linking] +* [Using CUI as Word Embeddings](#using-cui-as-word-embeddings) +* [Entity Linking with cTAKES](#entity-linking-with-ctakes) + +The rest of this document is structured as a cookbook style tutorial. Each +sub-section describes the examples in the [examples] directory. + +**Important**: many of the examples use [UMLS] UTS service, which requires a +key that is provided by NIH. If you do not have a key, request one and add it +to the [UTS key file]. + + +## Medical Concept and Entity Linking + +Concept linking with [CUIs] is provided using the same interface as the +[Zensols NLP parsing API]. The resource library provided with this package +creates a `mednlp_doc_parser` as shown in the [entity-example]. First we start +with the configuration with file name `features.conf`, which starts with +telling the [CLI] to import the [Zensols NLP package] and this +(`zensols.mednlp`) package: +```ini +[import] +sections = list: imp_conf + +[imp_conf] +type = importini +config_files = list: + resource(zensols.nlp): resources/obj.conf, + resource(zensols.nlp): resources/mapper.conf, + resource(zensols.mednlp): resources/lang.conf +``` + +Next configure the parser with specific features, since otherwise, the parser +will retain all medical and non-medical features: +```ini +[mednlp_doc_parser] +token_feature_ids = set: norm, is_ent, cui, cui_, pref_name_, detected_name_, is_concept, ent_, ent +``` + +Finally, declare the application, which is needed by the [CLI] glue code to +invoke the class we will write afterward: +```ini +[app] +class_name = ${program:name}.Application +doc_parser = instance: mednlp_doc_parser +``` + +Next comes the application class: +```python +@dataclass +class Application(object): + doc_parser: FeatureDocumentParser = field() + + def show(self, sent: str = None): + if sent is None: + sent = 'He was diagnosed with kidney failure in the United States.' + doc: FeatureDocument = self.doc_parser(sent) + print('first three tokens:') + for tok in it.islice(doc.token_iter(), 3): + print(tok.norm) + tok.write_attributes(1, include_type=False) +``` +This uses the document parser to create the feature document, which has both +the medical and linguistic features in tokens (provided by `token_iter()`) of the document. + +Use the [CLI] API in the entry point to use the configuration and application +class: +```python +if (__name__ == '__main__'): + CliHarness( + app_config_resource='uts.conf', + app_config_context=ProgramNameConfigurator( + None, default='uts').create_section(), + proto_args='', + ).run() +``` + +Running the program produces one such token data: +``` +... +diagnosed + cui=11900 + cui_=C0011900 + detected_name_=diagnosed + ent=13188083023294932426 + ent_=concept + i=2 + i_sent=2 + idx=7 + is_concept=True + is_ent=True + norm=diagnosed + pref_name_=Diagnosis +... +``` +See the full [entity example] for the full example code, which will also output +both linguistic and medical features as a [Pandas] data frame. + + +## UMLS Access via UTS + +NIH provides a very rough REST client using the `requests` library given as an +example. This API takes that example, adds some "rigor" and structure in a +an easy to use class called `UTSClient`. This is configured by first defining +paths for where fetched entities are cached: +```ini +[default] +# root directory given by the application, which is the parent directory +root_dir = ${appenv:root_dir}/.. +# the directory to hold the cached UMLS data +cache_dir = ${root_dir}/cache +``` + +Next, import the this package's resource library (`zensols.mednlp`). Note we +have to refer to sections that substitute the `default` section's data: +```ini +[import] +references = list: uts, default +sections = list: imp_uts_key, imp_conf + +[imp_conf] +type = importini +config_file = resource(zensols.mednlp): resources/uts.conf + +[imp_uts_key] +type = json +default_section = uts +config_file = ${default:root_dir}/uts-key.json +``` +The `imp_uts_key` points to a file where you put add your UTS key, which is +given by NIH. + +Now indicate where to cache the [UMLS] data and define our application we'll +write afterward: +```ini +# UTS (UMLS access) +[uts] +cache_file = ${default:cache_dir}/uts-request.dat +``` + +For brevity the [CLI] application code and configuration is omitted (see [UMLS +Access via UTS] for more detail). + +To use the API to first search a term, then print entity information, we can +use the `search_term` method with `get_atoms`: +```python +@dataclass +class Application(object): + ... + def lookup(self, term: str = 'heart'): + # terms are returned as a list of pages with dictionaries of data + pages: List[Dict[str, str]] = self.uts_client.search_term(term) + # get all term dictionaries from the first page + terms: Dict[str, str] = pages[0] + # get the concept unique identifier + cui: str = terms['ui'] + + # print atoms of this concept + print('atoms:') + pprint(self.uts_client.get_atoms(cui)) +``` +This yields the following output: +``` +atoms: +{'ancestors': None, + 'classType': 'Atom', + 'code': 'https://uts-ws.nlm.nih.gov/rest/content/2020AA/source/MTH/NOCODE', + 'concept': 'https://uts-ws.nlm.nih.gov/rest/content/2020AA/CUI/C0018787', + 'contentViewMemberships': [{'memberUri': 'https://uts-ws.nlm.nih.gov/rest/content-views/2020AA/CUI/C1700357/member/A0066369', + 'name': 'MetaMap NLP View', + 'uri': 'https://uts-ws.nlm.nih.gov/rest/content-views/2020AA/CUI/C1700357'}], + 'name': 'Heart', + 'obsolete': 'false', + 'rootSource': 'MTH', +... +} +``` + +See the full [UTS example] for the full example code. + + +## Using CUI as Word Embeddings + +[cui2vec] was trained and can be in the same way as [word2vec]. Such examples +is computing a similarity between [UMLS] [CUIs]. This API provides access to +the vectors directly along with all the functionality using [cui2vec] with the +[gensim] package. This example computes the similarity between two medical +concepts. For brevity the [CLI] application code and configuration is omitted +(see [UMLS Access via UTS] for more detail). + +Let's jump right to how we import everything we need for the [cui2vec] example, +which the `uts` and `cui2vec` resource libraries: +```ini +[imp_conf] +type = importini +config_files = list: + resource(zensols.mednlp): resources/uts.conf, + resource(zensols.mednlp): resources/cui2vec.conf +``` +The UTS configuration is given as in the [UMLS Access via UTS] section and the +parser is configured as in the [Medical Concept and Entity Linking] section. + +With the high level classes given the configuration is class looks similar to +what we've seen before, this time we define a `similarity` method/[CLI] action: +```python +@dataclass +class Application(object): + def similarity(self, term: str = 'heart disease', topn: int = 5): +``` + +Next, get the [gensim] `KeyedVectors` instance, which provides (among *many* +other useful methods) one to compute the similarity between two words, or in +our case, two medical [CUIs]: +```python + embedding: Cui2VecEmbedModel = self.cui2vec_embedding + kv: KeyedVectors = embedding.keyed_vectors +``` + +Next we use UTS to get the term we're searching on, use [gensim] to find +similarities, and output them: +```python + res: List[Dict[str, str]] = self.uts_client.search_term(term) + cui: str = res[0]['ui'] + sims_by_word: List[Tuple[str, float]] = kv.similar_by_word(cui, topn) + for rel_cui, proba in sims_by_word: + rel_atom: Dict[str, str] = self.uts_client.get_atoms(rel_cui) + rel_name = rel_atom.get('name', 'Unknown') + print(f'{rel_name} ({rel_cui}): {proba * 100:.2f}%') +``` + +The output contains the top (`topn`) 5 matches and their similarity to the +search term in the example `heart`: +``` +Heart failure (C0018801): 72.03% +Atrial Premature Complexes (C0033036): 71.53% +Chronic myocardial ischemia (C0264694): 69.68% +Right bundle branch block (C0085615): 69.34% +First degree atrioventricular block (C0085614): 69.09% +``` + +See the full [cui2vec example] for the full example code. + + +## Entity Linking with cTAKES + +This package provides an interface to [cTAKES], which primarily manages the +file system and invokes the Java program to produce results. It then uses the +[ctakes-parser] to create a data frame of features and linked entities from +tokens of the source text. + +The configuration is a bit more involved since you have to indicate where the +[cTAKES] program is installed, and provide your NIH key as detailed in the +[UMLS Access via UTS] section: +```ini +[import] +# refer to sections for which we need substitution in this file +references = list: default, ctakes, uts +sections = list: imp_env, imp_uts_key, imp_conf + +# expose the user HOME environment variable +[imp_env] +type = environment +section_name = env +includes = set: HOME + +# import the Zensols NLP UTS resource library +[imp_conf] +type = importini +config_files = list: + resource(zensols.mednlp): resources/uts.conf, + resource(zensols.mednlp): resources/ctakes.conf + +# indicate where Apache cTAKES is installed +[ctakes] +home = ${env:home}/opt/app/ctakes-4.0.0.1 +source_dir = ${default:cache_dir}/ctakes/source +``` +For brevity the [CLI] application code and configuration is omitted, and other +configuration given in previous sections (see [UMLS Access via UTS] for more +detail). See the full [cTAKES example] for the full example code. + +The pertinent snippet to get the [Pandas] data frame from the medical text is +very simple: +```python +@dataclass +class Application(object): + def entities(self, sent: str = None, output: Path = None): + if sent is None: + sent = 'He was diagnosed with kidney failure in the United States.' + self.ctakes_stash.set_documents([sent]) + df: pd.DataFrame = self.ctakes_stash['0'] + print(df) + if output is not None: + df.to_csv(output) + print(f'wrote: {output}') +``` +The `set_documents` expects a list of text, which is saved to disk. When +[cTAKES] is run, the directory where this list of text is saved (one file per +element in the list). The access to the [Stash] accesses the first document by +element ID. **Note**: the element ID has to be a string to follow the [Stash] +API. + + + +[UMLS Access via UTS]: #umls-access-via-uts +[Medical Concept and Entity Linking]: #medical-concept-and-entity-linking + +[UMLS]: https://www.nlm.nih.gov/research/umls/ +[CUIs]: https://www.nlm.nih.gov/research/umls/new_users/online_learning/Meta_005.html +[cui2vec]: https://arxiv.org/abs/1804.01486 +[word2vec]: https://arxiv.org/abs/1301.3781 + +[Pandas]: https://pandas.pydata.org +[gensim]: https://radimrehurek.com/gensim/ +[cTAKES]: https://ctakes.apache.org +[ctakes-parser]: https://pypi.org/project/ctakes-parser + +[Zensols Framework]: https://arxiv.org/abs/2109.03383 +[CLI]: https://plandes.github.io/util/doc/command-line.html +[Stash]: https://plandes.github.io/util/api/zensols.persist.html#zensols.persist.domain.Stash +[Zensols NLP package]: https://github.com/plandes/nlparse +[Zensols NLP parsing API]: https://plandes.github.io/nlparse/doc/feature-doc.html + +[examples]: https://github.com/plandes/mednlp/tree/master/example +[entity example]: https://github.com/plandes/mednlp/tree/master/example/features +[cTAKES example]: https://github.com/plandes/mednlp/tree/master/example/ctakes +[cui2vec example]: https://github.com/plandes/mednlp/tree/master/example/cui2vec +[UTS example]: https://github.com/plandes/mednlp/tree/master/example/uts +[UTS key file]: https://github.com/plandes/mednlp/tree/master/example/uts-key.json diff --git a/_sources/index.md.txt b/_sources/index.md.txt new file mode 100644 index 0000000..14d255c --- /dev/null +++ b/_sources/index.md.txt @@ -0,0 +1,166 @@ +# Medical natural language parsing and utility library + +[![PyPI][pypi-badge]][pypi-link] +[![Python 3.10][python310-badge]][python310-link] +[![Python 3.11][python311-badge]][python311-link] +[![Build Status][build-badge]][build-link] + +A natural language medical domain parsing library. This library: + +- Provides an interface to the [UTS] ([UMLS] Terminology Services) RESTful + service with data caching (NIH login needed). +- Wraps the [MedCAT] library by parsing medical and clinical text into first + class Python objects reflecting the structure of the natural language + complete with [UMLS] entity linking with [CUIs] and other domain specific + features. +- Combines non-medical (such as POS and NER tags) and medical features (such as + [CUIs]) in one API and resulting data structure and/or as a [Pandas] data + frame. +- Provides [cui2vec] as a [word embedding model] for either fast indexing and + access or to use directly as features in a [Zensols Deep NLP embedding layer] + model. +- Provides access to [cTAKES] using as a dictionary like [Stash] abstraction. +- Includes a command line program to access all of these features without + having to write any code. + + +## Documentation + +See the [full documentation](https://plandes.github.io/mednlp/index.html). +The [API reference](https://plandes.github.io/mednlp/api.html) is also +available. + + +## Obtaining + +The easiest way to install the command line program is via the `pip` installer. +```bash +pip3 install zensols.mednlp +``` + +Binaries are also available on [pypi]. + + +## Usage + +To parse text, create features, and extract clinical concept identifiers: +```python +>>> from zensols.mednlp import ApplicationFactory +>>> doc_parser = ApplicationFactory.get_doc_parser() +>>> doc = doc_parser('John was diagnosed with kidney failure') +>>> for tok in doc.tokens: print(tok.norm, tok.pos_, tok.tag_, tok.cui_, tok.detected_name_) +John PROPN NNP -- -- +was AUX VBD -- -- +diagnosed VERB VBN -- -- +with ADP IN -- -- +kidney NOUN NN C0035078 kidney~failure +failure NOUN NN C0035078 kidney~failure +>>> print(doc.entities) +(, ) +``` +See the [full example](example/features/simple.py), and for other +functionality, see the [examples](example). + + +## MedCAT Models + +By default, this library uses the small MedCAT model used for +[tutorials](https://github.com/CogStack/MedCATtutorials/pull/12), and is not +sufficient for any serious project. To get the UMLS trained model,the [MedCAT +UMLS request form] from be filled out (see the [MedCAT] repository). + +After you obtain access and download the new model, add the following to +`~/.mednlprc` with the following: + +```ini +[medcat_status_resource] +url = file:///location/to/the/downloaded/file/umls_sm_wstatus_2021_oct.zip' +``` + + +## Attribution + +This API utilizes the following frameworks: + +* [MedCAT]: used to extract information from Electronic Health Records (EHRs) + and link it to biomedical ontologies like SNOMED-CT and UMLS. +* [cTAKES]: a natural language processing system for extraction of information + from electronic medical record clinical free-text. +* [cui2vec]: a new set of (like word) embeddings for medical concepts learned + using an extremely large collection of multimodal medical data. +* [Zensols Deep NLP library]: a deep learning utility library for natural + language processing that aids in feature engineering and embedding layers. +* [ctakes-parser]: parses [cTAKES] output in to a [Pandas] data frame. + + +## Citation + +If you use this project in your research please use the following BibTeX entry: + +```bibtex +@inproceedings{landes-etal-2023-deepzensols, + title = "{D}eep{Z}ensols: A Deep Learning Natural Language Processing Framework for Experimentation and Reproducibility", + author = "Landes, Paul and + Di Eugenio, Barbara and + Caragea, Cornelia", + editor = "Tan, Liling and + Milajevs, Dmitrijs and + Chauhan, Geeticka and + Gwinnup, Jeremy and + Rippeth, Elijah", + booktitle = "Proceedings of the 3rd Workshop for Natural Language Processing Open Source Software (NLP-OSS 2023)", + month = dec, + year = "2023", + address = "Singapore, Singapore", + publisher = "Empirical Methods in Natural Language Processing", + url = "https://aclanthology.org/2023.nlposs-1.16", + pages = "141--146" +} +``` + + +## Community + +Please star the project and let me know how and where you use this API. +Contributions as pull requests, feedback and any input is welcome. + + +## Changelog + +An extensive changelog is available [here](CHANGELOG.md). + + +## License + +[MIT License](LICENSE.md) + +Copyright (c) 2021 - 2023 Paul Landes + + + +[pypi]: https://pypi.org/project/zensols.mednlp/ +[pypi-link]: https://pypi.python.org/pypi/zensols.mednlp +[pypi-badge]: https://img.shields.io/pypi/v/zensols.mednlp.svg +[python310-badge]: https://img.shields.io/badge/python-3.10-blue.svg +[python310-link]: https://www.python.org/downloads/release/python-3100 +[python311-badge]: https://img.shields.io/badge/python-3.11-blue.svg +[python311-link]: https://www.python.org/downloads/release/python-3110 +[build-badge]: https://github.com/plandes/mednlp/workflows/CI/badge.svg +[build-link]: https://github.com/plandes/mednlp/actions + +[MedCAT]: https://github.com/CogStack/MedCAT +[MedCAT UMLS request form]: https://uts.nlm.nih.gov/uts/login?service=https:%2F%2Fmedcat.rosalind.kcl.ac.uk%2Fauth-callback + +[Pandas]: https://pandas.pydata.org +[ctakes-parser]: https://pypi.org/project/ctakes-parser + +[UTS]: https://uts.nlm.nih.gov/uts/ +[UMLS]: https://www.nlm.nih.gov/research/umls/ +[CUIs]: https://www.nlm.nih.gov/research/umls/new_users/online_learning/Meta_005.html +[cui2vec]: https://arxiv.org/abs/1804.01486 +[cTAKES]: https://ctakes.apache.org +[word embedding model]: https://plandes.github.io/deepnlp/api/zensols.deepnlp.embed.html#zensols.deepnlp.embed.domain.WordEmbedModel +[Zensols NLP parsing API]: https://plandes.github.io/nlparse/doc/feature-doc.html +[Zensols Deep NLP library]: https://github.com/plandes/deepnlp +[Zensols Deep NLP embedding layer]: https://plandes.github.io/deepnlp/api/zensols.deepnlp.layer.html#zensols.deepnlp.layer.embed.EmbeddingNetworkModule +[Stash]: https://plandes.github.io/util/api/zensols.persist.html#zensols.persist.domain.Stash diff --git a/_sources/top.rst.txt b/_sources/top.rst.txt new file mode 100644 index 0000000..25ddaf3 --- /dev/null +++ b/_sources/top.rst.txt @@ -0,0 +1,20 @@ +Medical natural language parsing and utility library +==================================================== +A natural language medical domain parsing library. + +.. toctree:: + :maxdepth: 3 + :glob: + + Overview + doc/* + API Reference + Contributing + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; 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+ } +} \ No newline at end of file diff --git a/_static/check-solid.svg b/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/_static/clipboard.min.js b/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/_static/copybutton.css b/_static/copybutton.css new file mode 100644 index 0000000..f1916ec --- /dev/null +++ b/_static/copybutton.css @@ -0,0 +1,94 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/_static/copybutton.js b/_static/copybutton.js new file mode 100644 index 0000000..2ea7ff3 --- /dev/null +++ b/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/_static/copybutton_funcs.js b/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/_static/debug.css b/_static/debug.css new file mode 100644 index 0000000..74d4aec --- /dev/null +++ b/_static/debug.css @@ -0,0 +1,69 @@ +/* + This CSS file should be overridden by the theme authors. It's + meant for debugging and developing the skeleton that this theme provides. +*/ +body { + font-family: -apple-system, "Segoe UI", Roboto, Helvetica, Arial, sans-serif, + "Apple Color Emoji", "Segoe UI Emoji"; + background: lavender; +} +.sb-announcement { + background: rgb(131, 131, 131); +} +.sb-announcement__inner { + background: black; + color: white; +} +.sb-header { + background: lightskyblue; +} +.sb-header__inner { + background: royalblue; + color: white; +} +.sb-header-secondary { + background: lightcyan; +} +.sb-header-secondary__inner { + background: cornflowerblue; + color: white; +} +.sb-sidebar-primary { + background: lightgreen; +} +.sb-main { + background: blanchedalmond; +} +.sb-main__inner { + background: antiquewhite; +} +.sb-header-article { + background: lightsteelblue; +} +.sb-article-container { + background: snow; +} +.sb-article-main { + background: white; +} +.sb-footer-article { + background: lightpink; +} +.sb-sidebar-secondary { + background: lightgoldenrodyellow; +} +.sb-footer-content { + background: plum; +} +.sb-footer-content__inner { + background: palevioletred; +} +.sb-footer { + background: pink; +} +.sb-footer__inner { + background: salmon; +} +.sb-article { + background: white; +} diff --git a/_static/doctools.js b/_static/doctools.js new file mode 100644 index 0000000..d06a71d --- /dev/null +++ b/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000..fea8c69 --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '1.7.0', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/_static/file.png differ diff --git a/_static/graphviz.css b/_static/graphviz.css new file mode 100644 index 0000000..8d81c02 --- /dev/null +++ b/_static/graphviz.css @@ -0,0 +1,19 @@ +/* + * graphviz.css + * ~~~~~~~~~~~~ + * + * Sphinx stylesheet -- graphviz extension. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +img.graphviz { + border: 0; + max-width: 100%; +} + +object.graphviz { + max-width: 100%; +} diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 0000000..250f566 --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,199 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, is available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/_static/minus.png differ diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/_static/plus.png differ diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 0000000..ed1f4cf --- /dev/null +++ b/_static/pygments.css @@ -0,0 +1,249 @@ +.highlight pre { line-height: 125%; } +.highlight td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +.highlight span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +.highlight td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight span.linenos.special { color: #000000; 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false,\n nestedClass: \"active\",\n\n // Offset & reflow\n offset: 0,\n reflow: false,\n\n // Event support\n events: true,\n };\n\n //\n // Methods\n //\n\n /**\n * Merge two or more objects together.\n * @param {Object} objects The objects to merge together\n * @returns {Object} Merged values of defaults and options\n */\n var extend = function () {\n var merged = {};\n Array.prototype.forEach.call(arguments, function (obj) {\n for (var key in obj) {\n if (!obj.hasOwnProperty(key)) return;\n merged[key] = obj[key];\n }\n });\n return merged;\n };\n\n /**\n * Emit a custom event\n * @param {String} type The event type\n * @param {Node} elem The element to attach the event to\n * @param {Object} detail Any details to pass along with the event\n */\n var emitEvent = function (type, elem, detail) {\n // Make sure events are enabled\n if (!detail.settings.events) return;\n\n // Create a new event\n var event = new CustomEvent(type, {\n bubbles: true,\n cancelable: true,\n detail: detail,\n });\n\n // Dispatch the event\n elem.dispatchEvent(event);\n };\n\n /**\n * Get an element's distance from the top of the Document.\n * @param {Node} elem The element\n * @return {Number} Distance from the top in pixels\n */\n var getOffsetTop = function (elem) {\n var location = 0;\n if (elem.offsetParent) {\n while (elem) {\n location += elem.offsetTop;\n elem = elem.offsetParent;\n }\n }\n return location >= 0 ? location : 0;\n };\n\n /**\n * Sort content from first to last in the DOM\n * @param {Array} contents The content areas\n */\n var sortContents = function (contents) {\n if (contents) {\n contents.sort(function (item1, item2) {\n var offset1 = getOffsetTop(item1.content);\n var offset2 = getOffsetTop(item2.content);\n if (offset1 < offset2) return -1;\n return 1;\n });\n }\n };\n\n /**\n * Get the offset to use for calculating position\n * @param {Object} settings The settings for this instantiation\n * @return {Float} The number of pixels to offset the 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content areas\n * @param {Object} settings The settings for this instantiation\n * @return {Object} The content area and matching navigation link\n */\n var getActive = function (contents, settings) {\n var last = contents[contents.length - 1];\n if (useLastItem(last, settings)) return last;\n for (var i = contents.length - 1; i >= 0; i--) {\n if (isInView(contents[i].content, settings)) return contents[i];\n }\n };\n\n /**\n * Deactivate parent navs in a nested navigation\n * @param {Node} nav The starting navigation element\n * @param {Object} settings The settings for this instantiation\n */\n var deactivateNested = function (nav, settings) {\n // If nesting isn't activated, bail\n if (!settings.nested || !nav.parentNode) return;\n\n // Get the parent navigation\n var li = nav.parentNode.closest(\"li\");\n if (!li) return;\n\n // Remove the active class\n li.classList.remove(settings.nestedClass);\n\n // Apply recursively to any parent navigation elements\n deactivateNested(li, settings);\n };\n\n /**\n * Deactivate a nav and content area\n * @param {Object} items The nav item and content to deactivate\n * @param {Object} settings The settings for this instantiation\n */\n var deactivate = function (items, settings) {\n // Make sure there are items to deactivate\n if (!items) return;\n\n // Get the parent list item\n var li = items.nav.closest(\"li\");\n if (!li) return;\n\n // Remove the active class from the nav and content\n li.classList.remove(settings.navClass);\n items.content.classList.remove(settings.contentClass);\n\n // Deactivate any parent navs in a nested navigation\n deactivateNested(li, settings);\n\n // Emit a custom event\n emitEvent(\"gumshoeDeactivate\", li, {\n link: items.nav,\n content: items.content,\n settings: settings,\n });\n };\n\n /**\n * Activate parent navs in a nested navigation\n * @param {Node} nav The starting navigation element\n * @param {Object} settings The settings for this instantiation\n */\n var activateNested = function (nav, settings) {\n // If nesting isn't activated, bail\n if (!settings.nested) return;\n\n // Get the parent navigation\n var li = nav.parentNode.closest(\"li\");\n if (!li) return;\n\n // Add the active class\n li.classList.add(settings.nestedClass);\n\n // Apply recursively to any parent navigation elements\n activateNested(li, settings);\n };\n\n /**\n * Activate a nav and content area\n * @param {Object} items The nav item and content to activate\n * @param {Object} settings The settings for this instantiation\n */\n var activate = function (items, settings) {\n // Make sure there are items to activate\n if (!items) return;\n\n // Get the parent list item\n var li = items.nav.closest(\"li\");\n if (!li) return;\n\n // Add the active class to the nav and content\n li.classList.add(settings.navClass);\n items.content.classList.add(settings.contentClass);\n\n // Activate any parent navs in a nested navigation\n activateNested(li, settings);\n\n // Emit a custom event\n emitEvent(\"gumshoeActivate\", li, {\n link: items.nav,\n content: items.content,\n settings: settings,\n });\n };\n\n /**\n * Create the Constructor object\n * @param {String} selector The selector to use for navigation items\n * @param {Object} options User options and settings\n */\n var Constructor = function (selector, options) {\n //\n // Variables\n //\n\n var publicAPIs = {};\n var navItems, contents, current, timeout, settings;\n\n //\n // Methods\n //\n\n /**\n * Set variables from DOM elements\n */\n publicAPIs.setup = function () {\n // Get all nav items\n navItems = document.querySelectorAll(selector);\n\n // Create contents array\n contents = [];\n\n // Loop through each item, get it's matching content, and push to the array\n Array.prototype.forEach.call(navItems, function (item) {\n // Get the content for the nav item\n var content = document.getElementById(\n decodeURIComponent(item.hash.substr(1)),\n );\n if (!content) return;\n\n // Push to the contents array\n 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\ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 0000000..7918c3f --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/skeleton.css b/_static/skeleton.css new file mode 100644 index 0000000..467c878 --- /dev/null +++ b/_static/skeleton.css @@ -0,0 +1,296 @@ +/* Some sane resets. */ +html { + height: 100%; +} + +body { + margin: 0; + min-height: 100%; +} + +/* All the flexbox magic! */ +body, +.sb-announcement, +.sb-content, +.sb-main, +.sb-container, +.sb-container__inner, +.sb-article-container, +.sb-footer-content, +.sb-header, +.sb-header-secondary, +.sb-footer { + display: flex; +} + +/* These order things vertically */ +body, +.sb-main, +.sb-article-container { + flex-direction: column; +} + +/* Put elements in the center */ +.sb-header, +.sb-header-secondary, +.sb-container, +.sb-content, +.sb-footer, +.sb-footer-content { + justify-content: center; +} +/* Put elements at the ends */ +.sb-article-container { + justify-content: space-between; +} + +/* These elements grow. */ +.sb-main, +.sb-content, +.sb-container, +article { + flex-grow: 1; +} + +/* Because padding making this wider is not fun */ +article { + box-sizing: border-box; +} + +/* The announcements element should never be wider than the page. */ +.sb-announcement { + max-width: 100%; +} + +.sb-sidebar-primary, +.sb-sidebar-secondary { + flex-shrink: 0; + width: 17rem; +} + +.sb-announcement__inner { + justify-content: center; + + box-sizing: border-box; + height: 3rem; + + overflow-x: auto; + white-space: nowrap; +} + +/* Sidebars, with checkbox-based toggle */ +.sb-sidebar-primary, +.sb-sidebar-secondary { + position: fixed; + height: 100%; + top: 0; +} + +.sb-sidebar-primary { + left: -17rem; + transition: left 250ms ease-in-out; +} +.sb-sidebar-secondary { + right: -17rem; + transition: right 250ms ease-in-out; +} + +.sb-sidebar-toggle { + display: none; +} +.sb-sidebar-overlay { + position: fixed; + top: 0; + width: 0; + height: 0; + + transition: width 0ms ease 250ms, height 0ms ease 250ms, opacity 250ms ease; + + opacity: 0; + background-color: rgba(0, 0, 0, 0.54); +} + +#sb-sidebar-toggle--primary:checked + ~ .sb-sidebar-overlay[for="sb-sidebar-toggle--primary"], +#sb-sidebar-toggle--secondary:checked + ~ .sb-sidebar-overlay[for="sb-sidebar-toggle--secondary"] { + width: 100%; + height: 100%; + opacity: 1; + transition: width 0ms ease, height 0ms ease, opacity 250ms ease; +} + +#sb-sidebar-toggle--primary:checked ~ .sb-container .sb-sidebar-primary { + left: 0; +} +#sb-sidebar-toggle--secondary:checked ~ .sb-container .sb-sidebar-secondary { + right: 0; +} + +/* Full-width mode */ +.drop-secondary-sidebar-for-full-width-content + .hide-when-secondary-sidebar-shown { + display: none !important; +} +.drop-secondary-sidebar-for-full-width-content .sb-sidebar-secondary { + display: none !important; +} + +/* Mobile views */ +.sb-page-width { + width: 100%; +} + +.sb-article-container, +.sb-footer-content__inner, +.drop-secondary-sidebar-for-full-width-content .sb-article, +.drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 100vw; +} + +.sb-article, +.match-content-width { + padding: 0 1rem; + box-sizing: border-box; +} + +@media (min-width: 32rem) { + .sb-article, + .match-content-width { + padding: 0 2rem; + } +} + +/* Tablet views */ +@media (min-width: 42rem) { + .sb-article-container { + width: auto; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 42rem; + } + .sb-article, + .match-content-width { + width: 42rem; + } +} +@media (min-width: 46rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 46rem; + } + .sb-article, + .match-content-width { + width: 46rem; + } +} +@media (min-width: 50rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 50rem; + } + .sb-article, + .match-content-width { + width: 50rem; + } +} + +/* Tablet views */ +@media (min-width: 59rem) { + .sb-sidebar-secondary { + position: static; + } + .hide-when-secondary-sidebar-shown { + display: none !important; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 59rem; + } + .sb-article, + .match-content-width { + width: 42rem; + } +} +@media (min-width: 63rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 63rem; + } + .sb-article, + .match-content-width { + width: 46rem; + } +} +@media (min-width: 67rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 67rem; + } + .sb-article, + .match-content-width { + width: 50rem; + } +} + +/* Desktop views */ +@media (min-width: 76rem) { + .sb-sidebar-primary { + position: static; + } + .hide-when-primary-sidebar-shown { + display: none !important; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 59rem; + } + .sb-article, + .match-content-width { + width: 42rem; + } +} + +/* Full desktop views */ +@media (min-width: 80rem) { + .sb-article, + .match-content-width { + width: 46rem; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 63rem; + } +} + +@media (min-width: 84rem) { + .sb-article, + .match-content-width { + width: 50rem; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 67rem; + } +} + +@media (min-width: 88rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 67rem; + } + .sb-page-width { + width: 88rem; + } +} diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/styles/furo-extensions.css b/_static/styles/furo-extensions.css new file mode 100644 index 0000000..bc447f2 --- /dev/null +++ b/_static/styles/furo-extensions.css @@ -0,0 +1,2 @@ +#furo-sidebar-ad-placement{padding:var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)}#furo-sidebar-ad-placement .ethical-sidebar{background:var(--color-background-secondary);border:none;box-shadow:none}#furo-sidebar-ad-placement .ethical-sidebar:hover{background:var(--color-background-hover)}#furo-sidebar-ad-placement .ethical-sidebar a{color:var(--color-foreground-primary)}#furo-sidebar-ad-placement .ethical-callout 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Correct the color inheritance from `fieldset` elements in IE.\n * 3. Remove the padding so developers are not caught out when they zero out\n * `fieldset` elements in all browsers.\n */\n\nlegend {\n box-sizing: border-box; /* 1 */\n color: inherit; /* 2 */\n display: table; /* 1 */\n max-width: 100%; /* 1 */\n padding: 0; /* 3 */\n white-space: normal; /* 1 */\n}\n\n/**\n * Add the correct vertical alignment in Chrome, Firefox, and Opera.\n */\n\nprogress {\n vertical-align: baseline;\n}\n\n/**\n * Remove the default vertical scrollbar in IE 10+.\n */\n\ntextarea {\n overflow: auto;\n}\n\n/**\n * 1. Add the correct box sizing in IE 10.\n * 2. Remove the padding in IE 10.\n */\n\n[type=\"checkbox\"],\n[type=\"radio\"] {\n box-sizing: border-box; /* 1 */\n padding: 0; /* 2 */\n}\n\n/**\n * Correct the cursor style of increment and decrement buttons in Chrome.\n */\n\n[type=\"number\"]::-webkit-inner-spin-button,\n[type=\"number\"]::-webkit-outer-spin-button {\n height: auto;\n}\n\n/**\n * 1. Correct the odd appearance in Chrome and Safari.\n * 2. Correct the outline style in Safari.\n */\n\n[type=\"search\"] {\n -webkit-appearance: textfield; /* 1 */\n outline-offset: -2px; /* 2 */\n}\n\n/**\n * Remove the inner padding in Chrome and Safari on macOS.\n */\n\n[type=\"search\"]::-webkit-search-decoration {\n -webkit-appearance: none;\n}\n\n/**\n * 1. Correct the inability to style clickable types in iOS and Safari.\n * 2. Change font properties to `inherit` in Safari.\n */\n\n::-webkit-file-upload-button {\n -webkit-appearance: button; /* 1 */\n font: inherit; /* 2 */\n}\n\n/* Interactive\n ========================================================================== */\n\n/*\n * Add the correct display in Edge, IE 10+, and Firefox.\n */\n\ndetails {\n display: block;\n}\n\n/*\n * Add the correct display in all browsers.\n */\n\nsummary {\n display: list-item;\n}\n\n/* Misc\n ========================================================================== */\n\n/**\n * Add the correct display in IE 10+.\n */\n\ntemplate {\n display: none;\n}\n\n/**\n * Add the correct display in IE 10.\n */\n\n[hidden] {\n display: none;\n}\n","// This file contains styles for managing print media.\n\n////////////////////////////////////////////////////////////////////////////////\n// Hide elements not relevant to print media.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n // Hide icon container.\n .content-icon-container\n display: none !important\n\n // Hide showing header links if hovering over when printing.\n .headerlink\n display: none !important\n\n // Hide mobile header.\n .mobile-header\n display: none !important\n\n // Hide navigation links.\n .related-pages\n display: none !important\n\n////////////////////////////////////////////////////////////////////////////////\n// Tweaks related to decolorization.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n // Apply a border around code which no longer have a color background.\n .highlight\n border: 0.1pt solid var(--color-foreground-border)\n\n////////////////////////////////////////////////////////////////////////////////\n// Avoid page break in some relevant cases.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n ul, ol, dl, a, table, pre, blockquote\n page-break-inside: avoid\n\n h1, h2, h3, h4, h5, h6, img, figure, caption\n page-break-inside: avoid\n page-break-after: avoid\n\n ul, ol, dl\n page-break-before: avoid\n",".visually-hidden\n position: absolute !important\n width: 1px !important\n height: 1px !important\n padding: 0 !important\n margin: -1px !important\n overflow: hidden !important\n clip: rect(0,0,0,0) !important\n white-space: nowrap !important\n border: 0 !important\n\n:-moz-focusring\n outline: auto\n","// This file serves as the \"skeleton\" of the theming logic.\n//\n// This contains the bulk of the logic for handling dark mode, color scheme\n// toggling and the handling of color-scheme-specific hiding of elements.\n\nbody\n @include fonts\n @include spacing\n @include icons\n @include admonitions\n @include default-admonition(#651fff, \"abstract\")\n @include default-topic(#14B8A6, \"pencil\")\n\n @include colors\n\n.only-light\n display: block !important\nhtml body .only-dark\n display: none !important\n\n// Ignore dark-mode hints if print media.\n@media not print\n // Enable dark-mode, if requested.\n body[data-theme=\"dark\"]\n @include colors-dark\n\n html & .only-light\n display: none !important\n .only-dark\n display: block !important\n\n // Enable dark mode, unless explicitly told to avoid.\n @media (prefers-color-scheme: dark)\n body:not([data-theme=\"light\"])\n @include colors-dark\n\n html & .only-light\n display: none !important\n .only-dark\n display: block !important\n\n//\n// Theme toggle presentation\n//\nbody[data-theme=\"auto\"]\n .theme-toggle svg.theme-icon-when-auto\n display: block\n\nbody[data-theme=\"dark\"]\n .theme-toggle svg.theme-icon-when-dark\n display: block\n\nbody[data-theme=\"light\"]\n .theme-toggle svg.theme-icon-when-light\n display: block\n","// Fonts used by this theme.\n//\n// There are basically two things here -- using the system font stack and\n// defining sizes for various elements in %ages. We could have also used `em`\n// but %age is easier to reason about for me.\n\n@mixin fonts {\n // These are adapted from https://systemfontstack.com/\n --font-stack: -apple-system, BlinkMacSystemFont, Segoe UI, Helvetica, Arial,\n sans-serif, Apple Color Emoji, Segoe UI Emoji;\n --font-stack--monospace: \"SFMono-Regular\", Menlo, Consolas, Monaco,\n Liberation Mono, Lucida Console, monospace;\n\n --font-size--normal: 100%;\n --font-size--small: 87.5%;\n --font-size--small--2: 81.25%;\n --font-size--small--3: 75%;\n --font-size--small--4: 62.5%;\n\n // Sidebar\n --sidebar-caption-font-size: var(--font-size--small--2);\n --sidebar-item-font-size: var(--font-size--small);\n --sidebar-search-input-font-size: var(--font-size--small);\n\n // Table of Contents\n --toc-font-size: var(--font-size--small--3);\n --toc-font-size--mobile: var(--font-size--normal);\n --toc-title-font-size: var(--font-size--small--4);\n\n // Admonitions\n //\n // These aren't defined in terms of %ages, since nesting these is permitted.\n --admonition-font-size: 0.8125rem;\n --admonition-title-font-size: 0.8125rem;\n\n // Code\n --code-font-size: var(--font-size--small--2);\n\n // API\n --api-font-size: var(--font-size--small);\n}\n","// Spacing for various elements on the page\n//\n// If the user wants to tweak things in a certain way, they are permitted to.\n// They also have to deal with the consequences though!\n\n@mixin spacing {\n // Header!\n --header-height: calc(\n var(--sidebar-item-line-height) + 4 * #{var(--sidebar-item-spacing-vertical)}\n );\n --header-padding: 0.5rem;\n\n // Sidebar\n --sidebar-tree-space-above: 1.5rem;\n --sidebar-caption-space-above: 1rem;\n\n --sidebar-item-line-height: 1rem;\n --sidebar-item-spacing-vertical: 0.5rem;\n --sidebar-item-spacing-horizontal: 1rem;\n --sidebar-item-height: calc(\n var(--sidebar-item-line-height) + 2 *#{var(--sidebar-item-spacing-vertical)}\n );\n\n --sidebar-expander-width: var(--sidebar-item-height); // be square\n\n --sidebar-search-space-above: 0.5rem;\n --sidebar-search-input-spacing-vertical: 0.5rem;\n --sidebar-search-input-spacing-horizontal: 0.5rem;\n --sidebar-search-input-height: 1rem;\n --sidebar-search-icon-size: var(--sidebar-search-input-height);\n\n // Table of Contents\n --toc-title-padding: 0.25rem 0;\n --toc-spacing-vertical: 1.5rem;\n --toc-spacing-horizontal: 1.5rem;\n --toc-item-spacing-vertical: 0.4rem;\n --toc-item-spacing-horizontal: 1rem;\n}\n","// Expose theme icons as CSS variables.\n\n$icons: (\n // Adapted from tabler-icons\n // url: https://tablericons.com/\n \"search\":\n url('data:image/svg+xml;charset=utf-8,'),\n // Factored out from mkdocs-material on 24-Aug-2020.\n // url: https://squidfunk.github.io/mkdocs-material/reference/admonitions/\n \"pencil\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"abstract\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"info\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"flame\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"question\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"warning\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"failure\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"spark\":\n url('data:image/svg+xml;charset=utf-8,')\n);\n\n@mixin icons {\n @each $name, $glyph in $icons {\n --icon-#{$name}: #{$glyph};\n }\n}\n","// Admonitions\n\n// Structure of these is:\n// admonition-class: color \"icon-name\";\n//\n// The colors are translated into CSS variables below. The icons are\n// used directly in the main declarations to set the `mask-image` in\n// the title.\n\n// prettier-ignore\n$admonitions: (\n // Each of these has an reST directives for it.\n \"caution\": #ff9100 \"spark\",\n \"warning\": #ff9100 \"warning\",\n \"danger\": #ff5252 \"spark\",\n \"attention\": #ff5252 \"warning\",\n \"error\": #ff5252 \"failure\",\n \"hint\": #00c852 \"question\",\n \"tip\": #00c852 \"info\",\n \"important\": #00bfa5 \"flame\",\n \"note\": #00b0ff \"pencil\",\n \"seealso\": #448aff \"info\",\n \"admonition-todo\": #808080 \"pencil\"\n);\n\n@mixin default-admonition($color, $icon-name) {\n --color-admonition-title: #{$color};\n --color-admonition-title-background: #{rgba($color, 0.2)};\n\n --icon-admonition-default: var(--icon-#{$icon-name});\n}\n\n@mixin default-topic($color, $icon-name) {\n --color-topic-title: #{$color};\n --color-topic-title-background: #{rgba($color, 0.2)};\n\n --icon-topic-default: var(--icon-#{$icon-name});\n}\n\n@mixin admonitions {\n @each $name, $values in $admonitions {\n --color-admonition-title--#{$name}: #{nth($values, 1)};\n --color-admonition-title-background--#{$name}: #{rgba(\n nth($values, 1),\n 0.2\n )};\n }\n}\n","// Colors used throughout this theme.\n//\n// The aim is to give the user more control. Thus, instead of hard-coding colors\n// in various parts of the stylesheet, the approach taken is to define all\n// colors as CSS variables and reusing them in all the places.\n//\n// `colors-dark` depends on `colors` being included at a lower specificity.\n\n@mixin colors {\n --color-problematic: #b30000;\n\n // Base Colors\n --color-foreground-primary: black; // for main text and headings\n --color-foreground-secondary: #5a5c63; // for secondary text\n --color-foreground-muted: #646776; // for muted text\n --color-foreground-border: #878787; // for content borders\n\n --color-background-primary: white; // for content\n --color-background-secondary: #f8f9fb; // for navigation + ToC\n --color-background-hover: #efeff4ff; // for navigation-item hover\n --color-background-hover--transparent: #efeff400;\n --color-background-border: #eeebee; // for UI borders\n --color-background-item: #ccc; // for \"background\" items (eg: copybutton)\n\n // Announcements\n --color-announcement-background: #000000dd;\n --color-announcement-text: #eeebee;\n\n // Brand colors\n --color-brand-primary: #2962ff;\n --color-brand-content: #2a5adf;\n\n // API documentation\n --color-api-background: var(--color-background-hover--transparent);\n --color-api-background-hover: var(--color-background-hover);\n --color-api-overall: var(--color-foreground-secondary);\n --color-api-name: var(--color-problematic);\n --color-api-pre-name: var(--color-problematic);\n --color-api-paren: var(--color-foreground-secondary);\n --color-api-keyword: var(--color-foreground-primary);\n --color-highlight-on-target: #ffffcc;\n\n // Inline code background\n --color-inline-code-background: var(--color-background-secondary);\n\n // Highlighted text (search)\n --color-highlighted-background: #ddeeff;\n --color-highlighted-text: var(--color-foreground-primary);\n\n // GUI Labels\n --color-guilabel-background: #ddeeff80;\n --color-guilabel-border: #bedaf580;\n --color-guilabel-text: var(--color-foreground-primary);\n\n // Admonitions!\n --color-admonition-background: transparent;\n\n //////////////////////////////////////////////////////////////////////////////\n // Everything below this should be one of:\n // - var(...)\n // - *-gradient(...)\n // - special literal values (eg: transparent, none)\n //////////////////////////////////////////////////////////////////////////////\n\n // Tables\n --color-table-header-background: var(--color-background-secondary);\n --color-table-border: var(--color-background-border);\n\n // Cards\n --color-card-border: var(--color-background-secondary);\n --color-card-background: transparent;\n --color-card-marginals-background: var(--color-background-secondary);\n\n // Header\n --color-header-background: var(--color-background-primary);\n --color-header-border: var(--color-background-border);\n --color-header-text: var(--color-foreground-primary);\n\n // Sidebar (left)\n --color-sidebar-background: var(--color-background-secondary);\n --color-sidebar-background-border: var(--color-background-border);\n\n --color-sidebar-brand-text: var(--color-foreground-primary);\n --color-sidebar-caption-text: var(--color-foreground-muted);\n --color-sidebar-link-text: var(--color-foreground-secondary);\n --color-sidebar-link-text--top-level: var(--color-brand-primary);\n\n --color-sidebar-item-background: var(--color-sidebar-background);\n --color-sidebar-item-background--current: var(\n --color-sidebar-item-background\n );\n --color-sidebar-item-background--hover: linear-gradient(\n 90deg,\n var(--color-background-hover--transparent) 0%,\n var(--color-background-hover) var(--sidebar-item-spacing-horizontal),\n var(--color-background-hover) 100%\n );\n\n --color-sidebar-item-expander-background: transparent;\n --color-sidebar-item-expander-background--hover: var(\n --color-background-hover\n );\n\n --color-sidebar-search-text: var(--color-foreground-primary);\n --color-sidebar-search-background: var(--color-background-secondary);\n --color-sidebar-search-background--focus: var(--color-background-primary);\n --color-sidebar-search-border: var(--color-background-border);\n --color-sidebar-search-icon: var(--color-foreground-muted);\n\n // Table of Contents (right)\n --color-toc-background: var(--color-background-primary);\n --color-toc-title-text: var(--color-foreground-muted);\n --color-toc-item-text: var(--color-foreground-secondary);\n --color-toc-item-text--hover: var(--color-foreground-primary);\n --color-toc-item-text--active: var(--color-brand-primary);\n\n // Actual page contents\n --color-content-foreground: var(--color-foreground-primary);\n --color-content-background: transparent;\n\n // Links\n --color-link: var(--color-brand-content);\n --color-link--hover: var(--color-brand-content);\n --color-link-underline: var(--color-background-border);\n --color-link-underline--hover: var(--color-foreground-border);\n}\n\n@mixin colors-dark {\n --color-problematic: #ee5151;\n\n // Base Colors\n --color-foreground-primary: #ffffffcc; // for main text and headings\n --color-foreground-secondary: #9ca0a5; // for secondary text\n --color-foreground-muted: #81868d; // for muted text\n --color-foreground-border: #666666; // for content borders\n\n --color-background-primary: #131416; // for content\n --color-background-secondary: #1a1c1e; // for navigation + ToC\n --color-background-hover: #1e2124ff; // for navigation-item hover\n --color-background-hover--transparent: #1e212400;\n --color-background-border: #303335; // for UI borders\n --color-background-item: #444; // for \"background\" items (eg: copybutton)\n\n // Announcements\n --color-announcement-background: #000000dd;\n --color-announcement-text: #eeebee;\n\n // Brand colors\n --color-brand-primary: #2b8cee;\n --color-brand-content: #368ce2;\n\n // Highlighted text (search)\n --color-highlighted-background: #083563;\n\n // GUI Labels\n --color-guilabel-background: #08356380;\n --color-guilabel-border: #13395f80;\n\n // API documentation\n --color-api-keyword: var(--color-foreground-secondary);\n --color-highlight-on-target: #333300;\n\n // Admonitions\n --color-admonition-background: #18181a;\n\n // Cards\n --color-card-border: var(--color-background-secondary);\n --color-card-background: #18181a;\n --color-card-marginals-background: var(--color-background-hover);\n}\n","// This file contains the styling for making the content throughout the page,\n// including fonts, paragraphs, headings and spacing among these elements.\n\nbody\n font-family: var(--font-stack)\npre,\ncode,\nkbd,\nsamp\n font-family: var(--font-stack--monospace)\n\n// Make fonts look slightly nicer.\nbody\n -webkit-font-smoothing: antialiased\n -moz-osx-font-smoothing: grayscale\n\n// Line height from Bootstrap 4.1\narticle\n line-height: 1.5\n\n//\n// Headings\n//\nh1,\nh2,\nh3,\nh4,\nh5,\nh6\n line-height: 1.25\n font-weight: bold\n\n border-radius: 0.5rem\n margin-top: 0.5rem\n margin-bottom: 0.5rem\n margin-left: -0.5rem\n margin-right: -0.5rem\n padding-left: 0.5rem\n padding-right: 0.5rem\n\n + p\n margin-top: 0\n\nh1\n font-size: 2.5em\n margin-top: 1.75rem\n margin-bottom: 1rem\nh2\n font-size: 2em\n margin-top: 1.75rem\nh3\n font-size: 1.5em\nh4\n font-size: 1.25em\nh5\n font-size: 1.125em\nh6\n font-size: 1em\n\nsmall\n opacity: 75%\n font-size: 80%\n\n// Paragraph\np\n margin-top: 0.5rem\n margin-bottom: 0.75rem\n\n// Horizontal rules\nhr.docutils\n height: 1px\n padding: 0\n margin: 2rem 0\n background-color: var(--color-background-border)\n border: 0\n\n.centered\n text-align: center\n\n// Links\na\n text-decoration: underline\n\n color: var(--color-link)\n text-decoration-color: var(--color-link-underline)\n\n &:hover\n color: var(--color-link--hover)\n text-decoration-color: var(--color-link-underline--hover)\n &.muted-link\n color: inherit\n &:hover\n color: var(--color-link)\n text-decoration-color: var(--color-link-underline--hover)\n","// This file contains the styles for the overall layouting of the documentation\n// skeleton, including the responsive changes as well as sidebar toggles.\n//\n// This is implemented as a mobile-last design, which isn't ideal, but it is\n// reasonably good-enough and I got pretty tired by the time I'd finished this\n// to move the rules around to fix this. Shouldn't take more than 3-4 hours,\n// if you know what you're doing tho.\n\n// HACK: Not all browsers account for the scrollbar width in media queries.\n// This results in horizontal scrollbars in the breakpoint where we go\n// from displaying everything to hiding the ToC. We accomodate for this by\n// adding a bit of padding to the TOC drawer, disabling the horizontal\n// scrollbar and allowing the scrollbars to cover the padding.\n// https://www.456bereastreet.com/archive/201301/media_query_width_and_vertical_scrollbars/\n\n// HACK: Always having the scrollbar visible, prevents certain browsers from\n// causing the content to stutter horizontally between taller-than-viewport and\n// not-taller-than-viewport pages.\n\nhtml\n overflow-x: hidden\n overflow-y: scroll\n scroll-behavior: smooth\n\n.sidebar-scroll, .toc-scroll, article[role=main] *\n // Override Firefox scrollbar style\n scrollbar-width: thin\n scrollbar-color: var(--color-foreground-border) transparent\n\n // Override Chrome scrollbar styles\n &::-webkit-scrollbar\n width: 0.25rem\n height: 0.25rem\n &::-webkit-scrollbar-thumb\n background-color: var(--color-foreground-border)\n border-radius: 0.125rem\n\n//\n// Overalls\n//\nhtml,\nbody\n height: 100%\n color: var(--color-foreground-primary)\n background: var(--color-background-primary)\n\narticle\n color: var(--color-content-foreground)\n background: var(--color-content-background)\n overflow-wrap: break-word\n\n.page\n display: flex\n // fill the viewport for pages with little content.\n min-height: 100%\n\n.mobile-header\n width: 100%\n height: var(--header-height)\n background-color: var(--color-header-background)\n color: var(--color-header-text)\n border-bottom: 1px solid var(--color-header-border)\n\n // Looks like sub-script/super-script have this, and we need this to\n // be \"on top\" of those.\n z-index: 10\n\n // We don't show the header on large screens.\n display: none\n\n // Add shadow when scrolled\n &.scrolled\n border-bottom: none\n box-shadow: 0 0 0.2rem rgba(0, 0, 0, 0.1), 0 0.2rem 0.4rem rgba(0, 0, 0, 0.2)\n\n .header-center\n a\n color: var(--color-header-text)\n text-decoration: none\n\n.main\n display: flex\n flex: 1\n\n// Sidebar (left) also covers the entire left portion of screen.\n.sidebar-drawer\n box-sizing: border-box\n\n border-right: 1px solid var(--color-sidebar-background-border)\n background: var(--color-sidebar-background)\n\n display: flex\n justify-content: flex-end\n // These next two lines took me two days to figure out.\n width: calc((100% - #{$full-width}) / 2 + #{$sidebar-width})\n min-width: $sidebar-width\n\n// Scroll-along sidebars\n.sidebar-container,\n.toc-drawer\n box-sizing: border-box\n width: $sidebar-width\n\n.toc-drawer\n background: var(--color-toc-background)\n // See HACK described on top of this document\n padding-right: 1rem\n\n.sidebar-sticky,\n.toc-sticky\n position: sticky\n top: 0\n height: min(100%, 100vh)\n height: 100vh\n\n display: flex\n flex-direction: column\n\n.sidebar-scroll,\n.toc-scroll\n flex-grow: 1\n flex-shrink: 1\n\n overflow: auto\n scroll-behavior: smooth\n\n// Central items.\n.content\n padding: 0 $content-padding\n width: $content-width\n\n display: flex\n flex-direction: column\n justify-content: space-between\n\n.icon\n display: inline-block\n height: 1rem\n width: 1rem\n svg\n width: 100%\n height: 100%\n\n//\n// Accommodate announcement banner\n//\n.announcement\n background-color: var(--color-announcement-background)\n color: var(--color-announcement-text)\n\n height: var(--header-height)\n display: flex\n align-items: center\n overflow-x: auto\n & + .page\n min-height: calc(100% - var(--header-height))\n\n.announcement-content\n box-sizing: border-box\n padding: 0.5rem\n min-width: 100%\n white-space: nowrap\n text-align: center\n\n a\n color: var(--color-announcement-text)\n text-decoration-color: var(--color-announcement-text)\n\n &:hover\n color: var(--color-announcement-text)\n text-decoration-color: var(--color-link--hover)\n\n////////////////////////////////////////////////////////////////////////////////\n// Toggles for theme\n////////////////////////////////////////////////////////////////////////////////\n.no-js .theme-toggle-container // don't show theme toggle if there's no JS\n display: none\n\n.theme-toggle-container\n vertical-align: middle\n\n.theme-toggle\n cursor: pointer\n border: none\n padding: 0\n background: transparent\n\n.theme-toggle svg\n vertical-align: middle\n height: 1rem\n width: 1rem\n color: var(--color-foreground-primary)\n display: none\n\n.theme-toggle-header\n float: left\n padding: 1rem 0.5rem\n\n////////////////////////////////////////////////////////////////////////////////\n// Toggles for elements\n////////////////////////////////////////////////////////////////////////////////\n.toc-overlay-icon, .nav-overlay-icon\n display: none\n cursor: pointer\n\n .icon\n color: var(--color-foreground-secondary)\n height: 1rem\n width: 1rem\n\n.toc-header-icon, .nav-overlay-icon\n // for when we set display: flex\n justify-content: center\n align-items: center\n\n.toc-content-icon\n height: 1.5rem\n width: 1.5rem\n\n.content-icon-container\n float: right\n display: flex\n margin-top: 1.5rem\n margin-left: 1rem\n margin-bottom: 1rem\n gap: 0.5rem\n\n .edit-this-page svg\n color: inherit\n height: 1rem\n width: 1rem\n\n.sidebar-toggle\n position: absolute\n display: none\n// \n.sidebar-toggle[name=\"__toc\"]\n left: 20px\n.sidebar-toggle:checked\n left: 40px\n// \n\n.overlay\n position: fixed\n top: 0\n width: 0\n height: 0\n\n transition: width 0ms, height 0ms, opacity 250ms ease-out\n\n opacity: 0\n background-color: rgba(0, 0, 0, 0.54)\n.sidebar-overlay\n z-index: 20\n.toc-overlay\n z-index: 40\n\n// Keep things on top and smooth.\n.sidebar-drawer\n z-index: 30\n transition: left 250ms ease-in-out\n.toc-drawer\n z-index: 50\n transition: right 250ms ease-in-out\n\n// Show the Sidebar\n#__navigation:checked\n & ~ .sidebar-overlay\n width: 100%\n height: 100%\n opacity: 1\n & ~ .page\n .sidebar-drawer\n top: 0\n left: 0\n // Show the toc sidebar\n#__toc:checked\n & ~ .toc-overlay\n width: 100%\n height: 100%\n opacity: 1\n & ~ .page\n .toc-drawer\n top: 0\n right: 0\n\n////////////////////////////////////////////////////////////////////////////////\n// Back to top\n////////////////////////////////////////////////////////////////////////////////\n.back-to-top\n text-decoration: none\n\n display: none\n position: fixed\n left: 0\n top: 1rem\n padding: 0.5rem\n padding-right: 0.75rem\n border-radius: 1rem\n font-size: 0.8125rem\n\n background: var(--color-background-primary)\n box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), #6b728080 0px 0px 1px 0px\n\n z-index: 10\n\n margin-left: 50%\n transform: translateX(-50%)\n svg\n height: 1rem\n width: 1rem\n fill: currentColor\n display: inline-block\n\n span\n margin-left: 0.25rem\n\n .show-back-to-top &\n display: flex\n align-items: center\n\n////////////////////////////////////////////////////////////////////////////////\n// Responsive layouting\n////////////////////////////////////////////////////////////////////////////////\n// Make things a bit bigger on bigger screens.\n@media (min-width: $full-width + $sidebar-width)\n html\n font-size: 110%\n\n@media (max-width: $full-width)\n // Collapse \"toc\" into the icon.\n .toc-content-icon\n display: flex\n .toc-drawer\n position: fixed\n height: 100vh\n top: 0\n right: -$sidebar-width\n border-left: 1px solid var(--color-background-muted)\n .toc-tree\n border-left: none\n font-size: var(--toc-font-size--mobile)\n\n // Accomodate for a changed content width.\n .sidebar-drawer\n width: calc((100% - #{$full-width - $sidebar-width}) / 2 + #{$sidebar-width})\n\n@media (max-width: $full-width - $sidebar-width)\n // Collapse \"navigation\".\n .nav-overlay-icon\n display: flex\n .sidebar-drawer\n position: fixed\n height: 100vh\n width: $sidebar-width\n\n top: 0\n left: -$sidebar-width\n\n // Swap which icon is visible.\n .toc-header-icon\n display: flex\n .toc-content-icon, .theme-toggle-content\n display: none\n .theme-toggle-header\n display: block\n\n // Show the header.\n .mobile-header\n position: sticky\n top: 0\n display: flex\n justify-content: space-between\n align-items: center\n\n .header-left,\n .header-right\n display: flex\n height: var(--header-height)\n padding: 0 var(--header-padding)\n label\n height: 100%\n width: 100%\n user-select: none\n\n .nav-overlay-icon .icon,\n .theme-toggle svg\n height: 1.25rem\n width: 1.25rem\n\n // Add a scroll margin for the content\n :target\n scroll-margin-top: var(--header-height)\n\n // Show back-to-top below the header\n .back-to-top\n top: calc(var(--header-height) + 0.5rem)\n\n // Center the page, and accommodate for the header.\n .page\n flex-direction: column\n justify-content: center\n .content\n margin-left: auto\n margin-right: auto\n\n@media (max-width: $content-width + 2* $content-padding)\n // Content should respect window limits.\n .content\n width: 100%\n overflow-x: auto\n\n@media (max-width: $content-width)\n .content\n padding: 0 $content-padding--small\n // Don't float sidebars to the right.\n article aside.sidebar\n float: none\n width: 100%\n margin: 1rem 0\n","//\n// The design here is strongly inspired by mkdocs-material.\n.admonition, .topic\n margin: 1rem auto\n padding: 0 0.5rem 0.5rem 0.5rem\n\n background: var(--color-admonition-background)\n\n border-radius: 0.2rem\n box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), 0 0 0.0625rem rgba(0, 0, 0, 0.1)\n\n font-size: var(--admonition-font-size)\n\n overflow: hidden\n page-break-inside: avoid\n\n // First element should have no margin, since the title has it.\n > :nth-child(2)\n margin-top: 0\n\n // Last item should have no margin, since we'll control that w/ padding\n > :last-child\n margin-bottom: 0\n\n.admonition p.admonition-title,\np.topic-title\n position: relative\n margin: 0 -0.5rem 0.5rem\n padding-left: 2rem\n padding-right: .5rem\n padding-top: .4rem\n padding-bottom: .4rem\n\n font-weight: 500\n font-size: var(--admonition-title-font-size)\n line-height: 1.3\n\n // Our fancy icon\n &::before\n content: \"\"\n position: absolute\n left: 0.5rem\n width: 1rem\n height: 1rem\n\n// Default styles\np.admonition-title\n background-color: var(--color-admonition-title-background)\n &::before\n background-color: var(--color-admonition-title)\n mask-image: var(--icon-admonition-default)\n mask-repeat: no-repeat\n\np.topic-title\n background-color: var(--color-topic-title-background)\n &::before\n background-color: var(--color-topic-title)\n mask-image: var(--icon-topic-default)\n mask-repeat: no-repeat\n\n//\n// Variants\n//\n.admonition\n border-left: 0.2rem solid var(--color-admonition-title)\n\n @each $type, $value in $admonitions\n &.#{$type}\n border-left-color: var(--color-admonition-title--#{$type})\n > .admonition-title\n background-color: var(--color-admonition-title-background--#{$type})\n &::before\n background-color: var(--color-admonition-title--#{$type})\n mask-image: var(--icon-#{nth($value, 2)})\n\n.admonition-todo > .admonition-title\n text-transform: uppercase\n","// This file stylizes the API documentation (stuff generated by autodoc). It's\n// deeply nested due to how autodoc structures the HTML without enough classes\n// to select the relevant items.\n\n// API docs!\ndl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)\n // Tweak the spacing of all the things!\n dd\n margin-left: 2rem\n > :first-child\n margin-top: 0.125rem\n > :last-child\n margin-bottom: 0.75rem\n\n // This is used for the arguments\n .field-list\n margin-bottom: 0.75rem\n\n // \"Headings\" (like \"Parameters\" and \"Return\")\n > dt\n text-transform: uppercase\n font-size: var(--font-size--small)\n\n dd:empty\n margin-bottom: 0.5rem\n dd > ul\n margin-left: -1.2rem\n > li\n > p:nth-child(2)\n margin-top: 0\n // When the last-empty-paragraph follows a paragraph, it doesn't need\n // to augument the existing spacing.\n > p + p:last-child:empty\n margin-top: 0\n margin-bottom: 0\n\n // Colorize the elements\n > dt\n color: var(--color-api-overall)\n\n.sig:not(.sig-inline)\n font-weight: bold\n\n font-size: var(--api-font-size)\n font-family: var(--font-stack--monospace)\n\n margin-left: -0.25rem\n margin-right: -0.25rem\n padding-top: 0.25rem\n padding-bottom: 0.25rem\n padding-right: 0.5rem\n\n // These are intentionally em, to properly match the font size.\n padding-left: 3em\n text-indent: -2.5em\n\n border-radius: 0.25rem\n\n background: var(--color-api-background)\n transition: background 100ms ease-out\n\n &:hover\n background: var(--color-api-background-hover)\n\n // adjust the size of the [source] link on the right.\n a.reference\n .viewcode-link\n font-weight: normal\n width: 3.5rem\n\nem.property\n font-style: normal\n &:first-child\n color: var(--color-api-keyword)\n.sig-name\n color: var(--color-api-name)\n.sig-prename\n font-weight: normal\n color: var(--color-api-pre-name)\n.sig-paren\n color: var(--color-api-paren)\n.sig-param\n font-style: normal\n\n.versionmodified\n font-style: italic\ndiv.versionadded, div.versionchanged, div.deprecated\n p\n margin-top: 0.125rem\n margin-bottom: 0.125rem\n\n// Align the [docs] and [source] to the right.\n.viewcode-link, .viewcode-back\n float: right\n text-align: right\n",".line-block\n margin-top: 0.5rem\n margin-bottom: 0.75rem\n .line-block\n margin-top: 0rem\n margin-bottom: 0rem\n padding-left: 1rem\n","// Captions\narticle p.caption,\ntable > caption,\n.code-block-caption\n font-size: var(--font-size--small)\n text-align: center\n\n// Caption above a TOCTree\n.toctree-wrapper.compound\n .caption, :not(.caption) > .caption-text\n font-size: var(--font-size--small)\n text-transform: uppercase\n\n text-align: initial\n margin-bottom: 0\n\n > ul\n margin-top: 0\n margin-bottom: 0\n","// Inline code\ncode.literal, .sig-inline\n background: var(--color-inline-code-background)\n border-radius: 0.2em\n // Make the font smaller, and use padding to recover.\n font-size: var(--font-size--small--2)\n padding: 0.1em 0.2em\n\n pre.literal-block &\n font-size: inherit\n padding: 0\n\n p &\n border: 1px solid var(--color-background-border)\n\n.sig-inline\n font-family: var(--font-stack--monospace)\n\n// Code and Literal Blocks\n$code-spacing-vertical: 0.625rem\n$code-spacing-horizontal: 0.875rem\n\n// Wraps every literal block + line numbers.\ndiv[class*=\" highlight-\"],\ndiv[class^=\"highlight-\"]\n margin: 1em 0\n display: flex\n\n .table-wrapper\n margin: 0\n padding: 0\n\npre\n margin: 0\n padding: 0\n overflow: auto\n\n // Needed to have more specificity than pygments' \"pre\" selector. :(\n article[role=\"main\"] .highlight &\n line-height: 1.5\n\n &.literal-block,\n .highlight &\n font-size: var(--code-font-size)\n padding: $code-spacing-vertical $code-spacing-horizontal\n\n // Make it look like all the other blocks.\n &.literal-block\n margin-top: 1rem\n margin-bottom: 1rem\n\n border-radius: 0.2rem\n background-color: var(--color-code-background)\n color: var(--color-code-foreground)\n\n// All code is always contained in this.\n.highlight\n width: 100%\n border-radius: 0.2rem\n\n // Make line numbers and prompts un-selectable.\n .gp, span.linenos\n user-select: none\n pointer-events: none\n\n // Expand the line-highlighting.\n .hll\n display: block\n margin-left: -$code-spacing-horizontal\n margin-right: -$code-spacing-horizontal\n padding-left: $code-spacing-horizontal\n padding-right: $code-spacing-horizontal\n\n/* Make code block captions be nicely integrated */\n.code-block-caption\n display: flex\n padding: $code-spacing-vertical $code-spacing-horizontal\n\n border-radius: 0.25rem\n border-bottom-left-radius: 0\n border-bottom-right-radius: 0\n font-weight: 300\n border-bottom: 1px solid\n\n background-color: var(--color-code-background)\n color: var(--color-code-foreground)\n border-color: var(--color-background-border)\n\n + div[class]\n margin-top: 0\n pre\n border-top-left-radius: 0\n border-top-right-radius: 0\n\n// When `html_codeblock_linenos_style` is table.\n.highlighttable\n width: 100%\n display: block\n tbody\n display: block\n\n tr\n display: flex\n\n // Line numbers\n td.linenos\n background-color: var(--color-code-background)\n color: var(--color-code-foreground)\n padding: $code-spacing-vertical $code-spacing-horizontal\n padding-right: 0\n border-top-left-radius: 0.2rem\n border-bottom-left-radius: 0.2rem\n\n .linenodiv\n padding-right: $code-spacing-horizontal\n font-size: var(--code-font-size)\n box-shadow: -0.0625rem 0 var(--color-foreground-border) inset\n\n // Actual code\n td.code\n padding: 0\n display: block\n flex: 1\n overflow: hidden\n\n .highlight\n border-top-left-radius: 0\n border-bottom-left-radius: 0\n\n// When `html_codeblock_linenos_style` is inline.\n.highlight\n span.linenos\n display: inline-block\n padding-left: 0\n padding-right: $code-spacing-horizontal\n margin-right: $code-spacing-horizontal\n box-shadow: -0.0625rem 0 var(--color-foreground-border) inset\n","// Inline Footnote Reference\n.footnote-reference\n font-size: var(--font-size--small--4)\n vertical-align: super\n\n// Definition list, listing the content of each note.\n// docutils <= 0.17\ndl.footnote.brackets\n font-size: var(--font-size--small)\n color: var(--color-foreground-secondary)\n\n display: grid\n grid-template-columns: max-content auto\n dt\n margin: 0\n > .fn-backref\n margin-left: 0.25rem\n\n &:after\n content: \":\"\n\n .brackets\n &:before\n content: \"[\"\n &:after\n content: \"]\"\n\n dd\n margin: 0\n padding: 0 1rem\n\n// docutils >= 0.18\naside.footnote\n font-size: var(--font-size--small)\n color: var(--color-foreground-secondary)\n\naside.footnote > span,\ndiv.citation > span\n float: left\n font-weight: 500\n padding-right: 0.25rem\n\naside.footnote > p,\ndiv.citation > p\n margin-left: 2rem\n","//\n// Figures\n//\nimg\n box-sizing: border-box\n max-width: 100%\n height: auto\n\narticle\n figure, .figure\n border-radius: 0.2rem\n\n margin: 0\n :last-child\n margin-bottom: 0\n\n .align-left\n float: left\n clear: left\n margin: 0 1rem 1rem\n\n .align-right\n float: right\n clear: right\n margin: 0 1rem 1rem\n\n .align-default,\n .align-center\n display: block\n text-align: center\n margin-left: auto\n margin-right: auto\n\n // WELL, table needs to be stylised like a table.\n table.align-default\n display: table\n text-align: initial\n",".genindex-jumpbox, .domainindex-jumpbox\n border-top: 1px solid var(--color-background-border)\n border-bottom: 1px solid var(--color-background-border)\n padding: 0.25rem\n\n.genindex-section, .domainindex-section\n h2\n margin-top: 0.75rem\n margin-bottom: 0.5rem\n ul\n margin-top: 0\n margin-bottom: 0\n","ul,\nol\n padding-left: 1.2rem\n\n // Space lists out like paragraphs\n margin-top: 1rem\n margin-bottom: 1rem\n // reduce margins within li.\n li\n > p:first-child\n margin-top: 0.25rem\n margin-bottom: 0.25rem\n\n > p:last-child\n margin-top: 0.25rem\n\n > ul,\n > ol\n margin-top: 0.5rem\n margin-bottom: 0.5rem\n\nol\n &.arabic\n list-style: decimal\n &.loweralpha\n list-style: lower-alpha\n &.upperalpha\n list-style: upper-alpha\n &.lowerroman\n list-style: lower-roman\n &.upperroman\n list-style: upper-roman\n\n// Don't space lists out when they're \"simple\" or in a `.. toctree::`\n.simple,\n.toctree-wrapper\n li\n > ul,\n > ol\n margin-top: 0\n margin-bottom: 0\n\n// Definition Lists\n.field-list,\n.option-list,\ndl:not([class]),\ndl.simple,\ndl.footnote,\ndl.glossary\n dt\n font-weight: 500\n margin-top: 0.25rem\n + dt\n margin-top: 0\n\n .classifier::before\n content: \":\"\n margin-left: 0.2rem\n margin-right: 0.2rem\n\n dd\n > p:first-child,\n ul\n margin-top: 0.125rem\n\n ul\n margin-bottom: 0.125rem\n",".math-wrapper\n width: 100%\n overflow-x: auto\n\ndiv.math\n position: relative\n text-align: center\n\n .headerlink,\n &:focus .headerlink\n display: none\n\n &:hover .headerlink\n display: inline-block\n\n span.eqno\n position: absolute\n right: 0.5rem\n top: 50%\n transform: translate(0, -50%)\n z-index: 1\n","// Abbreviations\nabbr[title]\n cursor: help\n\n// \"Problematic\" content, as identified by Sphinx\n.problematic\n color: var(--color-problematic)\n\n// Keyboard / Mouse \"instructions\"\nkbd:not(.compound)\n margin: 0 0.2rem\n padding: 0 0.2rem\n border-radius: 0.2rem\n border: 1px solid var(--color-foreground-border)\n color: var(--color-foreground-primary)\n vertical-align: text-bottom\n\n font-size: var(--font-size--small--3)\n display: inline-block\n\n box-shadow: 0 0.0625rem 0 rgba(0, 0, 0, 0.2), inset 0 0 0 0.125rem var(--color-background-primary)\n\n background-color: var(--color-background-secondary)\n\n// Blockquote\nblockquote\n border-left: 4px solid var(--color-background-border)\n background: var(--color-background-secondary)\n\n margin-left: 0\n margin-right: 0\n padding: 0.5rem 1rem\n\n .attribution\n font-weight: 600\n text-align: right\n\n &.pull-quote,\n &.highlights\n font-size: 1.25em\n\n &.epigraph,\n &.pull-quote\n border-left-width: 0\n border-radius: 0.5rem\n\n &.highlights\n border-left-width: 0\n background: transparent\n\n// Center align embedded-in-text images\np .reference img\n vertical-align: middle\n","p.rubric\n line-height: 1.25\n font-weight: bold\n font-size: 1.125em\n\n // For Numpy-style documentation that's got rubrics within it.\n // https://github.com/pradyunsg/furo/discussions/505\n dd &\n line-height: inherit\n font-weight: inherit\n\n font-size: var(--font-size--small)\n text-transform: uppercase\n","article .sidebar\n float: right\n clear: right\n width: 30%\n\n margin-left: 1rem\n margin-right: 0\n\n border-radius: 0.2rem\n background-color: var(--color-background-secondary)\n border: var(--color-background-border) 1px solid\n\n > *\n padding-left: 1rem\n padding-right: 1rem\n\n > ul, > ol // lists need additional padding, because bullets.\n padding-left: 2.2rem\n\n .sidebar-title\n margin: 0\n padding: 0.5rem 1rem\n border-bottom: var(--color-background-border) 1px solid\n\n font-weight: 500\n\n// TODO: subtitle\n// TODO: dedicated variables?\n",".table-wrapper\n width: 100%\n overflow-x: auto\n margin-top: 1rem\n margin-bottom: 0.5rem\n padding: 0.2rem 0.2rem 0.75rem\n\ntable.docutils\n border-radius: 0.2rem\n border-spacing: 0\n border-collapse: collapse\n\n box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), 0 0 0.0625rem rgba(0, 0, 0, 0.1)\n\n th\n background: var(--color-table-header-background)\n\n td,\n th\n // Space things out properly\n padding: 0 0.25rem\n\n // Get the borders looking just-right.\n border-left: 1px solid var(--color-table-border)\n border-right: 1px solid var(--color-table-border)\n border-bottom: 1px solid var(--color-table-border)\n\n p\n margin: 0.25rem\n\n &:first-child\n border-left: none\n &:last-child\n border-right: none\n\n // MyST-parser tables set these classes for control of column alignment\n &.text-left\n text-align: left\n &.text-right\n text-align: right\n &.text-center\n text-align: center\n",":target\n scroll-margin-top: 0.5rem\n\n@media (max-width: $full-width - $sidebar-width)\n :target\n scroll-margin-top: calc(0.5rem + var(--header-height))\n\n // When a heading is selected\n section > span:target\n scroll-margin-top: calc(0.8rem + var(--header-height))\n\n// Permalinks\n.headerlink\n font-weight: 100\n user-select: none\n\nh1,\nh2,\nh3,\nh4,\nh5,\nh6,\ndl dt,\np.caption,\nfigcaption p,\ntable > caption,\n.code-block-caption\n > .headerlink\n margin-left: 0.5rem\n visibility: hidden\n &:hover > .headerlink\n visibility: visible\n\n // Don't change to link-like, if someone adds the contents directive.\n > .toc-backref\n color: inherit\n text-decoration-line: none\n\n// Figure and table captions are special.\nfigure:hover > figcaption > p > .headerlink,\ntable:hover > caption > .headerlink\n visibility: visible\n\n:target >, // Regular section[id] style anchors\nspan:target ~ // Non-regular span[id] style \"extra\" anchors\n h1,\n h2,\n h3,\n h4,\n h5,\n h6\n &:nth-of-type(1)\n background-color: var(--color-highlight-on-target)\n // .headerlink\n // visibility: visible\n code.literal\n background-color: transparent\n\ntable:target > caption,\nfigure:target\n background-color: var(--color-highlight-on-target)\n\n// Inline page contents\n.this-will-duplicate-information-and-it-is-still-useful-here li :target\n background-color: var(--color-highlight-on-target)\n\n// Code block permalinks\n.literal-block-wrapper:target .code-block-caption\n background-color: var(--color-highlight-on-target)\n\n// When a definition list item is selected\n//\n// There isn't really an alternative to !important here, due to the\n// high-specificity of API documentation's selector.\ndt:target\n background-color: var(--color-highlight-on-target) !important\n\n// When a footnote reference is selected\n.footnote > dt:target + dd,\n.footnote-reference:target\n background-color: var(--color-highlight-on-target)\n",".guilabel\n background-color: var(--color-guilabel-background)\n border: 1px solid var(--color-guilabel-border)\n color: var(--color-guilabel-text)\n\n padding: 0 0.3em\n border-radius: 0.5em\n font-size: 0.9em\n","// This file contains the styles used for stylizing the footer that's shown\n// below the content.\n\nfooter\n font-size: var(--font-size--small)\n display: flex\n flex-direction: column\n\n margin-top: 2rem\n\n// Bottom of page information\n.bottom-of-page\n display: flex\n align-items: center\n justify-content: space-between\n\n margin-top: 1rem\n padding-top: 1rem\n padding-bottom: 1rem\n\n color: var(--color-foreground-secondary)\n border-top: 1px solid var(--color-background-border)\n\n line-height: 1.5\n\n @media (max-width: $content-width)\n text-align: center\n flex-direction: column-reverse\n gap: 0.25rem\n\n .left-details\n font-size: var(--font-size--small)\n\n .right-details\n display: flex\n flex-direction: column\n gap: 0.25rem\n text-align: right\n\n .icons\n display: flex\n justify-content: flex-end\n gap: 0.25rem\n font-size: 1rem\n\n a\n text-decoration: none\n\n svg,\n img\n font-size: 1.125rem\n height: 1em\n width: 1em\n\n// Next/Prev page information\n.related-pages\n a\n display: flex\n align-items: center\n\n text-decoration: none\n &:hover .page-info .title\n text-decoration: underline\n color: var(--color-link)\n text-decoration-color: var(--color-link-underline)\n\n svg.furo-related-icon,\n svg.furo-related-icon > use\n flex-shrink: 0\n\n color: var(--color-foreground-border)\n\n width: 0.75rem\n height: 0.75rem\n margin: 0 0.5rem\n\n &.next-page\n max-width: 50%\n\n float: right\n clear: right\n text-align: right\n\n &.prev-page\n max-width: 50%\n\n float: left\n clear: left\n\n svg\n transform: rotate(180deg)\n\n.page-info\n display: flex\n flex-direction: column\n overflow-wrap: anywhere\n\n .next-page &\n align-items: flex-end\n\n .context\n display: flex\n align-items: center\n\n padding-bottom: 0.1rem\n\n color: var(--color-foreground-muted)\n font-size: var(--font-size--small)\n text-decoration: none\n","// This file contains the styles for the contents of the left sidebar, which\n// contains the navigation tree, logo, search etc.\n\n////////////////////////////////////////////////////////////////////////////////\n// Brand on top of the scrollable tree.\n////////////////////////////////////////////////////////////////////////////////\n.sidebar-brand\n display: flex\n flex-direction: column\n flex-shrink: 0\n\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)\n text-decoration: none\n\n.sidebar-brand-text\n color: var(--color-sidebar-brand-text)\n overflow-wrap: break-word\n margin: var(--sidebar-item-spacing-vertical) 0\n font-size: 1.5rem\n\n.sidebar-logo-container\n margin: var(--sidebar-item-spacing-vertical) 0\n\n.sidebar-logo\n margin: 0 auto\n display: block\n max-width: 100%\n\n////////////////////////////////////////////////////////////////////////////////\n// Search\n////////////////////////////////////////////////////////////////////////////////\n.sidebar-search-container\n display: flex\n align-items: center\n margin-top: var(--sidebar-search-space-above)\n\n position: relative\n\n background: var(--color-sidebar-search-background)\n &:hover,\n &:focus-within\n background: var(--color-sidebar-search-background--focus)\n\n &::before\n content: \"\"\n position: absolute\n left: var(--sidebar-item-spacing-horizontal)\n width: var(--sidebar-search-icon-size)\n height: var(--sidebar-search-icon-size)\n\n background-color: var(--color-sidebar-search-icon)\n mask-image: var(--icon-search)\n\n.sidebar-search\n box-sizing: border-box\n\n border: none\n border-top: 1px solid var(--color-sidebar-search-border)\n border-bottom: 1px solid var(--color-sidebar-search-border)\n\n padding-top: var(--sidebar-search-input-spacing-vertical)\n padding-bottom: var(--sidebar-search-input-spacing-vertical)\n padding-right: var(--sidebar-search-input-spacing-horizontal)\n padding-left: calc(var(--sidebar-item-spacing-horizontal) + var(--sidebar-search-input-spacing-horizontal) + var(--sidebar-search-icon-size))\n\n width: 100%\n\n color: var(--color-sidebar-search-foreground)\n background: transparent\n z-index: 10\n\n &:focus\n outline: none\n\n &::placeholder\n font-size: var(--sidebar-search-input-font-size)\n\n//\n// Hide Search Matches link\n//\n#searchbox .highlight-link\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal) 0\n margin: 0\n text-align: center\n\n a\n color: var(--color-sidebar-search-icon)\n font-size: var(--font-size--small--2)\n\n////////////////////////////////////////////////////////////////////////////////\n// Structure/Skeleton of the navigation tree (left)\n////////////////////////////////////////////////////////////////////////////////\n.sidebar-tree\n font-size: var(--sidebar-item-font-size)\n margin-top: var(--sidebar-tree-space-above)\n margin-bottom: var(--sidebar-item-spacing-vertical)\n\n ul\n padding: 0\n margin-top: 0\n margin-bottom: 0\n\n display: flex\n flex-direction: column\n\n list-style: none\n\n li\n position: relative\n margin: 0\n\n > ul\n margin-left: var(--sidebar-item-spacing-horizontal)\n\n .icon\n color: var(--color-sidebar-link-text)\n\n .reference\n box-sizing: border-box\n color: var(--color-sidebar-link-text)\n\n // Fill the parent.\n display: inline-block\n line-height: var(--sidebar-item-line-height)\n text-decoration: none\n\n // Don't allow long words to cause wrapping.\n overflow-wrap: anywhere\n\n height: 100%\n width: 100%\n\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)\n\n &:hover\n background: var(--color-sidebar-item-background--hover)\n\n // Add a nice little \"external-link\" arrow here.\n &.external::after\n content: url('data:image/svg+xml,')\n margin: 0 0.25rem\n vertical-align: middle\n color: var(--color-sidebar-link-text)\n\n // Make the current page reference bold.\n .current-page > .reference\n font-weight: bold\n\n label\n position: absolute\n top: 0\n right: 0\n height: var(--sidebar-item-height)\n width: var(--sidebar-expander-width)\n\n cursor: pointer\n user-select: none\n\n display: flex\n justify-content: center\n align-items: center\n\n .caption, :not(.caption) > .caption-text\n font-size: var(--sidebar-caption-font-size)\n color: var(--color-sidebar-caption-text)\n\n font-weight: bold\n text-transform: uppercase\n\n margin: var(--sidebar-caption-space-above) 0 0 0\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)\n\n // If it has children, add a bit more padding to wrap the content to avoid\n // overlapping with the