From 82027a8e2af9bdd4cb5fa7274a514b361fb433f8 Mon Sep 17 00:00:00 2001 From: Ryan Greer Date: Thu, 17 Apr 2025 12:47:17 -0600 Subject: [PATCH 1/2] table of contents in docs --- docs/API_Reference.rst | 7 + docs/Installation.rst | 2 + docs/Tutorials.rst | 3 + docs/_build/doctrees/API_Reference.doctree | Bin 0 -> 95076 bytes docs/_build/doctrees/Installation.doctree | Bin 0 -> 2432 bytes docs/_build/doctrees/Tutorials.doctree | Bin 0 -> 3184 bytes docs/_build/doctrees/environment.pickle | Bin 0 -> 72029 bytes docs/_build/doctrees/index.doctree | Bin 0 -> 5290 bytes docs/_build/html/.buildinfo | 4 + docs/_build/html/API_Reference.html | 525 ++++++++ docs/_build/html/Installation.html | 304 +++++ docs/_build/html/Tutorials.html | 305 +++++ docs/_build/html/_modules/index.html | 278 +++++ .../html/_modules/sbol2build/sbol2build.html | 1066 +++++++++++++++++ .../html/_sources/API_Reference.rst.txt | 7 + .../_build/html/_sources/Installation.rst.txt | 2 + docs/_build/html/_sources/Tutorials.rst.txt | 3 + docs/_build/html/_sources/index.rst.txt | 23 + docs/_build/html/_static/basic.css | 906 ++++++++++++++ docs/_build/html/_static/debug.css | 69 ++ docs/_build/html/_static/doctools.js | 149 +++ .../html/_static/documentation_options.js | 13 + docs/_build/html/_static/file.png | Bin 0 -> 286 bytes docs/_build/html/_static/language_data.js | 192 +++ docs/_build/html/_static/minus.png | Bin 0 -> 90 bytes docs/_build/html/_static/plus.png | Bin 0 -> 90 bytes docs/_build/html/_static/pygments.css | 258 ++++ .../html/_static/scripts/furo-extensions.js | 0 docs/_build/html/_static/scripts/furo.js | 3 + .../html/_static/scripts/furo.js.LICENSE.txt | 7 + docs/_build/html/_static/scripts/furo.js.map | 1 + docs/_build/html/_static/searchtools.js | 635 ++++++++++ docs/_build/html/_static/skeleton.css | 296 +++++ docs/_build/html/_static/sphinx_highlight.js | 154 +++ .../html/_static/styles/furo-extensions.css | 2 + .../_static/styles/furo-extensions.css.map | 1 + docs/_build/html/_static/styles/furo.css | 2 + docs/_build/html/_static/styles/furo.css.map | 1 + docs/_build/html/genindex.html | 408 +++++++ docs/_build/html/index.html | 316 +++++ docs/_build/html/objects.inv | Bin 0 -> 507 bytes docs/_build/html/py-modindex.html | 301 +++++ docs/_build/html/search.html | 291 +++++ docs/_build/html/searchindex.js | 1 + docs/conf.py | 7 + docs/index.rst | 10 +- src/sbol2build/sbol2build.py | 14 +- 47 files changed, 6555 insertions(+), 11 deletions(-) create mode 100644 docs/API_Reference.rst create mode 100644 docs/Installation.rst create mode 100644 docs/Tutorials.rst create mode 100644 docs/_build/doctrees/API_Reference.doctree create mode 100644 docs/_build/doctrees/Installation.doctree create mode 100644 docs/_build/doctrees/Tutorials.doctree create mode 100644 docs/_build/doctrees/environment.pickle create mode 100644 docs/_build/doctrees/index.doctree create mode 100644 docs/_build/html/.buildinfo create mode 100644 docs/_build/html/API_Reference.html create mode 100644 docs/_build/html/Installation.html create mode 100644 docs/_build/html/Tutorials.html create mode 100644 docs/_build/html/_modules/index.html create mode 100644 docs/_build/html/_modules/sbol2build/sbol2build.html create mode 100644 docs/_build/html/_sources/API_Reference.rst.txt create mode 100644 docs/_build/html/_sources/Installation.rst.txt create mode 100644 docs/_build/html/_sources/Tutorials.rst.txt create mode 100644 docs/_build/html/_sources/index.rst.txt create mode 100644 docs/_build/html/_static/basic.css create mode 100644 docs/_build/html/_static/debug.css create mode 100644 docs/_build/html/_static/doctools.js create mode 100644 docs/_build/html/_static/documentation_options.js create mode 100644 docs/_build/html/_static/file.png create mode 100644 docs/_build/html/_static/language_data.js create mode 100644 docs/_build/html/_static/minus.png create mode 100644 docs/_build/html/_static/plus.png create mode 100644 docs/_build/html/_static/pygments.css create mode 100644 docs/_build/html/_static/scripts/furo-extensions.js create mode 100644 docs/_build/html/_static/scripts/furo.js create mode 100644 docs/_build/html/_static/scripts/furo.js.LICENSE.txt create mode 100644 docs/_build/html/_static/scripts/furo.js.map create mode 100644 docs/_build/html/_static/searchtools.js create mode 100644 docs/_build/html/_static/skeleton.css create mode 100644 docs/_build/html/_static/sphinx_highlight.js create mode 100644 docs/_build/html/_static/styles/furo-extensions.css create mode 100644 docs/_build/html/_static/styles/furo-extensions.css.map create mode 100644 docs/_build/html/_static/styles/furo.css create mode 100644 docs/_build/html/_static/styles/furo.css.map create mode 100644 docs/_build/html/genindex.html create mode 100644 docs/_build/html/index.html create mode 100644 docs/_build/html/objects.inv create mode 100644 docs/_build/html/py-modindex.html create mode 100644 docs/_build/html/search.html create mode 100644 docs/_build/html/searchindex.js diff --git a/docs/API_Reference.rst b/docs/API_Reference.rst new file mode 100644 index 0000000..8dd46bd --- /dev/null +++ b/docs/API_Reference.rst @@ -0,0 +1,7 @@ +API Reference +============= + +.. automodule:: sbol2build.sbol2build + :members: + :undoc-members: + :show-inheritance: \ No newline at end of file diff --git a/docs/Installation.rst b/docs/Installation.rst new file mode 100644 index 0000000..dbc9b80 --- /dev/null +++ b/docs/Installation.rst @@ -0,0 +1,2 @@ +Installation +====================================== \ No newline at end of file diff --git a/docs/Tutorials.rst b/docs/Tutorials.rst new file mode 100644 index 0000000..8da6e92 --- /dev/null +++ b/docs/Tutorials.rst @@ -0,0 +1,3 @@ +Tutorials +====================================== +Let's get started with creating DNA assembly plans. 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zyOTcOfShy)AWAV3ws>dzvfIj77B!s3U*@=%c(NP$)R>Ykh)p*O<53{Rg*)q41_Q7% zvJAu)8R(}~mUS*(y8(Z0=|Q}p-b<$HFV$?ok2xN)`%HHQvx9I33PO+Dkwp5oE$t(V z65j#V+y!8A6gA1&Tp%h3=0mp)7H8==;$p}p{=$T-JoJy75x$f}ALqzw14o?>&*ftz zRZPpy<1WM;6Jw0Pm-z-S2Nz=Zex9LY_|HJ0g;Zq#{RR?|4uFBGE}Zg(!sPvhWnzTk z4rkFa8U5(JUjQ=bO$jo10t+|;fjx9*W31Yb7zPCyp-cO^8>~KAP3XX?9F#Tf&>dyz z(*ljft(DaT=?f&HIfrjDQAvx#$AyzH3dpi3w?Ga0t*_?p)SR^ZECDgJ4Vnkf#{Cx! z$XC6v{Jq1!=3nugYyJg)p1ZbxV<#C*^@IA?hdh7Azj&7ObN=xwjB=Vw{+$0Ncbl_8 z3~D!H0VsI8a8xPrxmvF)?VpvD>+o3xK_8(PHn<2&&nyU=)$KWr?fTTP>C~KllwEB> z=iS*wUDX?q2~?68BnxmstBIAAh&=9qUb6aTCI1}G__TP4tiZPj + + + + + + + + API Reference - SBOL2Build 0.0b1 documentation + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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API Reference

+
+
+sbol2build.sbol2build.append_extracts_to_doc(extract_tuples: List[Tuple[ComponentDefinition, Sequence]], doc: Document)[source]
+

Helper function for batch adding sbol2.ComponentDefinition and sbol2.Sequence to an sbol2.Document

+
+
Parameters:
+
    +

  • extract_tuples – list of tuples of sbol2.ComponentDefinition and sbol2.Sequence

    • +

  • doc – document which the content is to be added to

    • +
+
+
+
+ +
+
+sbol2build.sbol2build.backbone_digestion(reactant: ModuleDefinition, restriction_enzymes: List[ComponentDefinition], assembly_plan: ModuleDefinition, document: Document, **kwargs) → Tuple[List[Tuple[ComponentDefinition, Sequence]], ModuleDefinition][source]
+

Runs a simulated digestion on the top level sequence in the reactant ModuleDefinition with the given restriciton enzymes, creating an open backbone ComponentDefinition, a digestion Interaction, and converts existing scars to 5’ and 3’ overhangs. +The product ComponentDefinition is assumed the open backbone in this case.

+

Written for use with the SBOL2.3 output of https://sbolcanvas.org

+
+
Parameters:
+
    +

  • reactant – DNA to be digested as SBOL ModuleDefinition, usually a part_in_backbone.

    • +

  • restriction_enzymes – Restriction enzymes as sbol2.ComponentDefinition +(generate with rebase_restriction_enzyme()).

    • +

  • assembly_plan – SBOL ModuleDefinition to contain the functional components, interactions, and participations

    • +

  • document – original SBOL2 document to be used to extract referenced objects.

    • +
+
+
Returns:
+

A tuple of a list ComponentDefinitions and Sequences, and an assembly plan ModuleDefinition.

+
+
+
+ +
+
+sbol2build.sbol2build.dna_componentdefinition_with_sequence(identity: str, sequence: str, **kwargs) → Tuple[ComponentDefinition, Sequence][source]
+

Creates a DNA ComponentDefinition and its Sequence.

+
+
Parameters:
+
    +

  • identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.

    • +

  • sequence – The DNA sequence of the Component encoded in IUPAC.

    • +

  • kwargs – Keyword arguments of any other Component attribute.

    • +
+
+
Returns:
+

A tuple of ComponentDefinition and Sequence.

+
+
+
+ +
+
+class sbol2build.sbol2build.golden_gate_assembly_plan(name: str, parts_in_backbone: List[Document], plasmid_acceptor_backbone: Document, restriction_enzyme: str, document: Document)[source]
+

Bases: object

+

Creates an Assembly Plan.

+
+
Parameters:
+
    +

  • name – Name of the assembly plan ModuleDefinition.

    • +

  • parts_in_backbone – Parts in backbone to be assembled.

    • +

  • plasmid_acceptor_backbone – Backbone in which parts are inserted on the assembly.

    • +

  • restriction_enzyme – Restriction enzyme name used by PyDNA. Case sensitive, follow standard restriction enzyme nomenclature, i.e. ‘BsaI’

    • +

  • document – SBOL Document where the assembly plan will be created.

    • +
+
+
+
+
+run() → List[Tuple[ComponentDefinition, Sequence]][source]
+

Runs full assembly simulation.

+

document parameter of golden_gate_assembly_plan object is updated by reference to include assembly plan ModuleDefinition and all related information.

+

Runs part_digestion() for all parts_in_backbone and backbone_digestion() for plasmid_acceptor_backbone with restriction_enzyme. Then runs ligation() with these parts to form composites.

+
+
Returns:
+

List of all composites generated, in the form of tuples of ComponentDefinition and Sequence.

+
+
+
+ +
+ +
+
+sbol2build.sbol2build.is_circular(obj: ComponentDefinition) → bool[source]
+

Check if an SBOL Component or Feature is circular.

+
+
Parameters:
+

obj – design to be checked

+
+
Returns:
+

true if circular

+
+
+
+ +
+
+sbol2build.sbol2build.ligation(reactants: List[ComponentDefinition], assembly_plan: ModuleDefinition, document: Document, ligase: ComponentDefinition = None) → List[Tuple[ComponentDefinition, Sequence]][source]
+

Ligates Components using base complementarity and creates product Components and a ligation Interaction.

+
+
Parameters:
+
    +

  • reactants – DNA parts to be ligated as SBOL ModuleDefinition.

    • +

  • assembly_plan – SBOL ModuleDefinition to contain the functional components, interactions, and participants

    • +

  • document – SBOL2 document containing all reactant ComponentDefinitions.

    • +

  • ligase – as SBOL ComponentDefinition, optional (defaults to T4 ligase)

    • +
+
+
Returns:
+

List of all composites generated, in the form of tuples of ComponentDefinition and Sequence.

+
+
+
+ +
+
+sbol2build.sbol2build.number_to_suffix(n)[source]
+

Helper function for generating scar suffixes of the form: \(S=(A,B,C,…,Z,AA,AB,AC,…,AZ,BA,BB,…, S_n)\)

+
+
Parameters:
+

n – Number to convert to character suffix

+
+
Returns:
+

Character suffix corresponding to n

+
+
+
+ +
+
+sbol2build.sbol2build.part_digestion(reactant: ModuleDefinition, restriction_enzymes: List[ComponentDefinition], assembly_plan: ModuleDefinition, document: Document, **kwargs) → Tuple[List[Tuple[ComponentDefinition, Sequence]], ModuleDefinition][source]
+

Runs a simulated digestion on the top level sequence in the reactant ModuleDefinition with the given restriciton enzymes, creating a extracted part ComponentDefinition, a digestion Interaction, and converts existing scars to 5’ and 3’ overhangs. +The product ComponentDefinition is assumed the open backbone in this case.

+

Written for use with the SBOL2.3 output of https://sbolcanvas.org

+
+
Parameters:
+
    +

  • reactant – DNA to be digested as SBOL ModuleDefinition, usually a part_in_backbone.

    • +

  • restriction_enzymes – Restriction enzymes as sbol2.ComponentDefinition +(generate with rebase_restriction_enzyme()).

    • +

  • assembly_plan – SBOL ModuleDefinition to contain the functional components, interactions, and participations

    • +

  • document – original SBOL2 document to be used to extract referenced objects.

    • +
+
+
Returns:
+

A tuple of a list ComponentDefinitions and Sequences, and an assembly plan ModuleDefinition.

+
+
+
+ +
+
+sbol2build.sbol2build.part_in_backbone_from_sbol(identity: str | None, sbol_comp: ComponentDefinition, part_location: List[int], part_roles: List[str], fusion_site_length: int, document: Document, linear: bool = False, **kwargs) → Tuple[ComponentDefinition, Sequence][source]
+

Restructures a plasmid ComponentDefinition to follow the part-in-backbone pattern with scars following BP011. +It overwrites the SBOL2 ComponentDefinition provided. +A part inserted into a backbone is represented by a Component that includes both the part insert +as a feature that is a SubComponent and the backbone as another SubComponent. +For more information about BP011 visit https://github.com/SynBioDex/SBOL-examples/tree/main/SBOL/best-practices/BP011

+
+
Parameters:
+
    +

  • identity – The identity of the Component, is its a String it build a new SBOL Component, if None it adds on top of the input. The identity of Sequence is also identity with the suffix ‘_seq’.

    • +

  • sbol_comp – The SBOL2 Component that will be used to create the part in backbone Component and Sequence.

    • +

  • part_location – List of 2 integers that indicates the start and the end of the unitary part. Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science.

    • +

  • part_roles – List of strings that indicates the roles to add on the part.

    • +

  • fusion_site_length – Integer of the length of the fusion sites (eg. BsaI fusion site lenght is 4, SapI fusion site lenght is 3)

    • +

  • linear – Boolean than indicates if the backbone is linear, defaults to False (cicular topology).

    • +

  • kwargs – Keyword arguments of any other Component attribute.

    • +
+
+
Returns:
+

ModuleDefinition in the form that sbolcanvas would output

+
+
+
+ +
+
+sbol2build.sbol2build.rebase_restriction_enzyme(name: str, **kwargs) → ComponentDefinition[source]
+

Creates an ComponentDefinition Restriction Enzyme Component from rebase.

+
+
Parameters:
+
    +

  • name – Name of the SBOL ExternallyDefined, used by PyDNA. Case sensitive, follow standard restriction enzyme nomenclature, i.e. ‘BsaI’

    • +

  • kwargs – Keyword arguments of any other ComponentDefinition attribute.

    • +
+
+
Returns:
+

A ComponentDefinition object.

+
+
+
+ +
+ +
+
+ +
+ +
+
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/Installation.html b/docs/_build/html/Installation.html new file mode 100644 index 0000000..e786e15 --- /dev/null +++ b/docs/_build/html/Installation.html @@ -0,0 +1,304 @@ + + + + + + + + + Installation - SBOL2Build 0.0b1 documentation + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Installation

+
+ +
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+ +
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+ + + + + \ No newline at end of file diff --git a/docs/_build/html/Tutorials.html b/docs/_build/html/Tutorials.html new file mode 100644 index 0000000..3a98e38 --- /dev/null +++ b/docs/_build/html/Tutorials.html @@ -0,0 +1,305 @@ + + + + + + + + + Tutorials - SBOL2Build 0.0b1 documentation + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+
+

Tutorials

+

Let’s get started with creating DNA assembly plans. First we will demonstrate a workflow using plasmid files from SBOLCanvas:

+
+ +
+
+ +
+ +
+
+ + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html new file mode 100644 index 0000000..d772f58 --- /dev/null +++ b/docs/_build/html/_modules/index.html @@ -0,0 +1,278 @@ + + + + + + + + Overview: module code - SBOL2Build 0.0b1 documentation + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Copyright © 2025, Ryan Greer +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
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+ + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/sbol2build/sbol2build.html b/docs/_build/html/_modules/sbol2build/sbol2build.html new file mode 100644 index 0000000..a7bc425 --- /dev/null +++ b/docs/_build/html/_modules/sbol2build/sbol2build.html @@ -0,0 +1,1066 @@ + + + + + + + + sbol2build.sbol2build - SBOL2Build 0.0b1 documentation + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Source code for sbol2build.sbol2build

+#Put code here
+import sbol2
+from Bio import Restriction
+from Bio.Seq import Seq
+from pydna.dseqrecord import Dseqrecord
+from itertools import product
+from typing import List, Union, Tuple
+
+sbol2.Config.setHomespace('https://SBOL2Build.org')
+sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_COMPLIANT_URIS, True)
+sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, False)
+
+

+[docs]
+def rebase_restriction_enzyme(name:str, **kwargs) -> sbol2.ComponentDefinition:
+    """Creates an ComponentDefinition Restriction Enzyme Component from rebase.
+
+    :param name: Name of the SBOL ExternallyDefined, used by PyDNA. Case sensitive, follow standard restriction enzyme nomenclature, i.e. 'BsaI'
+    :param kwargs: Keyword arguments of any other ComponentDefinition attribute.
+    :return: A ComponentDefinition object.
+    """
+    check_enzyme = Restriction.__dict__[name]
+    definition=f'http://rebase.neb.com/rebase/enz/{name}.html' # TODO: replace with getting the URI from Enzyme when REBASE identifiers become available in biopython 1.8
+    cd = sbol2.ComponentDefinition(name)
+    cd.types = sbol2.BIOPAX_PROTEIN
+    cd.name = name
+    cd.roles = []
+    cd.wasDerivedFrom = definition
+    cd.description = f'Restriction enzyme {name} from REBASE.'
+    return cd

+
+
+

+[docs]
+def dna_componentdefinition_with_sequence(identity: str, sequence: str, **kwargs) -> Tuple[sbol2.ComponentDefinition, sbol2.Sequence]:
+    """Creates a DNA ComponentDefinition and its Sequence.
+
+    :param identity: The identity of the Component. The identity of Sequence is also identity with the suffix '_seq'.
+    :param sequence: The DNA sequence of the Component encoded in IUPAC.
+    :param kwargs: Keyword arguments of any other Component attribute.
+    :return: A tuple of ComponentDefinition and Sequence.
+    """
+    comp_seq = sbol2.Sequence(f'{identity}_seq', elements=sequence, encoding=sbol2.SBOL_ENCODING_IUPAC)
+    dna_comp = sbol2.ComponentDefinition(identity, sbol2.BIOPAX_DNA, **kwargs)
+    dna_comp.sequences = [comp_seq]
+
+    return dna_comp, comp_seq

+
+
+

+[docs]
+def part_in_backbone_from_sbol(identity: Union[str, None],  sbol_comp: sbol2.ComponentDefinition, part_location: List[int], part_roles:List[str], fusion_site_length:int, document: sbol2.Document, linear:bool=False, **kwargs) -> Tuple[sbol2.ComponentDefinition, sbol2.Sequence]:
+    """Restructures a plasmid ComponentDefinition to follow the part-in-backbone pattern with scars following BP011.
+    It overwrites the SBOL2 ComponentDefinition provided. 
+    A part inserted into a backbone is represented by a Component that includes both the part insert 
+    as a feature that is a SubComponent and the backbone as another SubComponent.
+    For more information about BP011 visit https://github.com/SynBioDex/SBOL-examples/tree/main/SBOL/best-practices/BP011 
+
+    :param identity: The identity of the Component, is its a String it build a new SBOL Component, if None it adds on top of the input. The identity of Sequence is also identity with the suffix '_seq'.
+    :param sbol_comp: The SBOL2 Component that will be used to create the part in backbone Component and Sequence.
+    :param part_location: List of 2 integers that indicates the start and the end of the unitary part. Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science.
+    :param part_roles: List of strings that indicates the roles to add on the part.
+    :param fusion_site_length: Integer of the length of the fusion sites (eg. BsaI fusion site lenght is 4, SapI fusion site lenght is 3)
+    :param linear: Boolean than indicates if the backbone is linear, defaults to False (cicular topology).    
+    :param kwargs: Keyword arguments of any other Component attribute.
+    :return: ModuleDefinition in the form that sbolcanvas would output
+    """
+    if len(part_location) != 2:
+        raise ValueError('The part_location only accepts 2 int values in a list.')
+    if len(sbol_comp.sequences)!=1:
+        raise ValueError(f'The reactant needs to have precisely one sequence. The input reactant has {len(sbol_comp.sequences)} sequences')
+    sequence = document.find(sbol_comp.sequences[0]).elements 
+    if identity == None:
+        part_in_backbone_component = sbol_comp 
+        part_in_backbone_seq =  document.find(sbol_comp.sequences[0]).elements
+        part_in_backbone_component.sequences = [part_in_backbone_seq]
+    else:
+        part_in_backbone_component, part_in_backbone_seq = dna_componentdefinition_with_sequence(identity, sequence, **kwargs)
+    # double stranded
+    part_in_backbone_component.addRole('http://identifiers.org/so/SO:0000985')
+    for part_role in part_roles:  
+        part_in_backbone_component.addRole(part_role)
+
+    # creating part annotation    
+    part_location_comp = sbol2.Range( start=part_location[0], end=part_location[1])
+    insertion_site_location1 = sbol2.Range( uri="insertloc1", start=part_location[0], end=part_location[0]+fusion_site_length) #order 1
+    insertion_site_location2 = sbol2.Range( uri="insertloc2", start=part_location[1]-fusion_site_length, end=part_location[1]) #order 3
+
+    part_sequence_annotation = sbol2.SequenceAnnotation('part_sequence_annotation')
+    part_sequence_annotation.roles = part_roles
+    part_sequence_annotation.locations.add(part_location_comp)
+
+    part_sequence_annotation.addRole('https://identifiers.org/SO:0000915') #engineered insert
+    insertion_sites_annotation = sbol2.SequenceAnnotation('insertion_sites_annotation')
+
+    insertion_sites_annotation.locations.add(insertion_site_location1)
+    insertion_sites_annotation.locations.add(insertion_site_location2)
+    
+    insertion_sites_annotation.roles = ['https://identifiers.org/so/SO:0000366'] #insertion site
+    if linear:
+        part_in_backbone_component.addRole('http://identifiers.org/so/SO:0000987') #linear
+        part_in_backbone_component.addRole('http://identifiers.org/so/SO:0000804') #engineered region
+        # creating backbone feature
+        open_backbone_location1 = sbol2.Range(start=1, end=part_location[0]+fusion_site_length-1) #order 1
+        open_backbone_location2 = sbol2.Range(start=part_location[1]-fusion_site_length, end=len(sequence)) #order 3
+        open_backbone_annotation = sbol2.SequenceAnnotation(locations=[open_backbone_location1, open_backbone_location2])
+    else: 
+        part_in_backbone_component.addRole('http://identifiers.org/so/SO:0000988') #circular
+        part_in_backbone_component.addRole('https://identifiers.org/so/SO:0000755') #plasmid vector
+        # creating backbone feature
+        open_backbone_location1 = sbol2.Range( uri="backboneloc1", start=1, end=part_location[0]+fusion_site_length-1 ) #order 2
+        open_backbone_location2 = sbol2.Range( uri="backboneloc2", start=part_location[1]-fusion_site_length, end=len(sequence)) #order 1
+        open_backbone_annotation = sbol2.SequenceAnnotation('open_backbone_annotation')
+        open_backbone_annotation.locations.add(open_backbone_location1)
+        open_backbone_annotation.locations.add(open_backbone_location2)
+        
+    part_in_backbone_component.sequenceAnnotations.add(part_sequence_annotation)
+    part_in_backbone_component.sequenceAnnotations.add(insertion_sites_annotation)
+    part_in_backbone_component.sequenceAnnotations.add(open_backbone_annotation) 
+    # use sequenceconstrait with precedes
+    # backbone_dropout_meets = sbol3.Constraint(restriction='http://sbols.org/v3#meets', subject=part_sequence_annotation, object=open_backbone_annotation) #????
+    backbone_dropout_meets = sbol2.sequenceconstraint.SequenceConstraint(uri='backbone_dropout_meets', restriction=sbol2.SBOL_RESTRICTION_PRECEDES) #might need to add uri as param 2
+    backbone_dropout_meets.subject = part_sequence_annotation
+    backbone_dropout_meets.object = open_backbone_annotation
+    
+    part_in_backbone_component.sequenceConstraints.add(backbone_dropout_meets)
+    #TODO: Add a branch to create a component without overwriting the WHOLE input component
+    #removing repeated types and roles
+    part_in_backbone_component.types = set(part_in_backbone_component.types)
+    part_in_backbone_component.roles = set(part_in_backbone_component.roles)
+    return part_in_backbone_component, part_in_backbone_seq

+
+
+# helper function
+

+[docs]
+def is_circular(obj: sbol2.ComponentDefinition) -> bool:
+    """Check if an SBOL Component or Feature is circular.
+
+    :param obj: design to be checked
+    :return: true if circular
+    """    
+    return any(n==sbol2.SO_CIRCULAR for n in obj.types)

+
+
+

+[docs]
+def part_digestion(reactant:sbol2.ModuleDefinition, restriction_enzymes:List[sbol2.ComponentDefinition], assembly_plan:sbol2.ModuleDefinition, document: sbol2.Document, **kwargs)-> Tuple[List[Tuple[sbol2.ComponentDefinition, sbol2.Sequence]], sbol2.ModuleDefinition]:
+    """Runs a simulated digestion on the top level sequence in the reactant ModuleDefinition with the given restriciton enzymes, creating a extracted part ComponentDefinition, a digestion Interaction, and converts existing scars to 5' and 3' overhangs.
+    The product ComponentDefinition is assumed the open backbone in this case.
+
+    Written for use with the SBOL2.3 output of https://sbolcanvas.org
+
+    :param reactant: DNA to be digested as SBOL ModuleDefinition, usually a part_in_backbone. 
+    :param restriction_enzymes: Restriction enzymes as :class:`sbol2.ComponentDefinition`
+                                (generate with :func:`rebase_restriction_enzyme`).
+    :param assembly_plan: SBOL ModuleDefinition to contain the functional components, interactions, and participations
+    :param document: original SBOL2 document to be used to extract referenced objects.
+    :return: A tuple of a list ComponentDefinitions and Sequences, and an assembly plan ModuleDefinition.
+    """
+    # extract component definition from module
+    reactant_displayId = reactant.functionalComponents[0].displayId
+    reactant_def_URI = reactant.functionalComponents[0].definition
+    reactant_component_definition = document.getComponentDefinition(reactant_def_URI)
+
+    if sbol2.BIOPAX_DNA not in reactant_component_definition.types:
+        raise TypeError(f'The reactant should has a DNA type. Types found {reactant.types}.')
+    if len(reactant_component_definition.sequences)!=1:
+        raise ValueError(f'The reactant needs to have precisely one sequence. The input reactant has {len(reactant.sequences)} sequences')
+    participations=[]
+    extracts_list=[]
+    restriction_enzymes_pydna=[] 
+    
+    for re in restriction_enzymes:
+        enzyme = Restriction.__dict__[re.name]
+        restriction_enzymes_pydna.append(enzyme)
+
+        enzyme_component = sbol2.FunctionalComponent(uri=f"{re.name}_enzyme")
+        enzyme_component.definition = re
+        enzyme_component.displayID = f"{re.name}_enzyme"
+        enzyme_in_module = False
+
+        for comp in assembly_plan.functionalComponents:
+            if (comp.displayId == enzyme_component.displayID): 
+                enzyme_component = comp
+                enzyme_in_module = True
+
+        if not enzyme_in_module:
+            assembly_plan.functionalComponents.add(enzyme_component)
+            
+        modifier_participation = sbol2.Participation(uri='restriction')
+        modifier_participation.participant = enzyme_component
+        modifier_participation.roles = ['http://identifiers.org/biomodels.sbo/SBO:0000019']
+        participations.append(modifier_participation)
+
+    # Inform topology to PyDNA, if not found assuming linear. 
+    if is_circular(reactant_component_definition):
+        circular=True
+        linear=False
+    else: 
+        circular=False
+        linear=True
+        
+    reactant_seq = reactant_component_definition.sequences[0]
+    reactant_seq = document.getSequence(reactant_seq).elements
+    # Dseqrecord is from PyDNA package with reactant sequence
+    ds_reactant = Dseqrecord(reactant_seq, circular=circular)
+    digested_reactant = ds_reactant.cut(restriction_enzymes_pydna) #TODO see if ds_reactant.cut is working, causing problems downstream
+
+
+    if len(digested_reactant)<2 or len(digested_reactant)>3: 
+        raise NotImplementedError(f'Not supported number of products. Found{len(digested_reactant)}')
+    #TODO select them based on content rather than size.
+    elif circular and len(digested_reactant)==2:
+        part_extract, backbone = sorted(digested_reactant, key=len)
+    elif linear and len(digested_reactant)==3:
+        prefix, part_extract, suffix = digested_reactant
+    else: raise NotImplementedError('The reactant has no valid topology type')
+
+    # Compute the length of single strand sticky ends or fusion sites
+    product_5_prime_ss_strand, product_5_prime_ss_end = part_extract.seq.five_prime_end()
+    product_3_prime_ss_strand, product_3_prime_ss_end = part_extract.seq.three_prime_end()
+    product_sequence = str(part_extract.seq)
+    prod_component_definition, prod_seq = dna_componentdefinition_with_sequence(identity=f'{reactant.functionalComponents[0].displayId}_extracted_part', sequence=product_sequence, **kwargs)
+    prod_component_definition.wasDerivedFrom = reactant_component_definition.identity
+    extracts_list.append((prod_component_definition, prod_seq))
+
+    # five prime overhang
+    five_prime_oh_definition = sbol2.ComponentDefinition(uri=f"{reactant_displayId}_five_prime_oh") # TODO: ensure circular type is preserved for sbh visualization
+    five_prime_oh_definition.addRole('http://identifiers.org/so/SO:0001932')
+    five_prime_oh_location = sbol2.Range(uri="five_prime_oh_location", start=1, end=len(product_5_prime_ss_end))
+    five_prime_oh_component = sbol2.Component(uri=f"{reactant_displayId}_five_prime_oh_component")
+    five_prime_oh_component.definition = five_prime_oh_definition
+    five_prime_overhang_annotation = sbol2.SequenceAnnotation(uri="five_prime_overhang")
+    five_prime_overhang_annotation.locations.add(five_prime_oh_location)
+
+    # extracted part => point straight to part from sbolcanvas
+    part_location = sbol2.Range(uri=f"{reactant_displayId}_part_location", start=len(product_5_prime_ss_end)+1, end=len(product_sequence)-len(product_3_prime_ss_end))
+    part_extract_annotation = sbol2.SequenceAnnotation(uri=f"{reactant_displayId}_part")
+    part_extract_annotation.locations.add(part_location)
+
+    # three prime overhang
+    three_prime_oh_definition = sbol2.ComponentDefinition(uri=f"{reactant_displayId}_three_prime_oh")
+    three_prime_oh_definition.addRole('http://identifiers.org/so/SO:0001933')
+    three_prime_oh_location = sbol2.Range(uri="three_prime_oh_location", start=len(product_sequence)-len(product_3_prime_ss_end)+1, end=len(product_sequence)) 
+    three_prime_oh_component = sbol2.Component(uri=f"{reactant_displayId}_three_prime_oh_component")
+    three_prime_oh_component.definition = three_prime_oh_definition
+    three_prime_overhang_annotation = sbol2.SequenceAnnotation(uri="three_prime_overhang")
+    three_prime_overhang_annotation.locations.add(three_prime_oh_location)
+
+    prod_component_definition.components = [five_prime_oh_component, three_prime_oh_component]
+    three_prime_overhang_annotation.component = three_prime_oh_component
+    five_prime_overhang_annotation.component = five_prime_oh_component
+
+    original_part_def_URI = ""
+
+    #enccode ontologies of overhangs
+    for definition in document.componentDefinitions:
+        for seqURI in definition.sequences:
+            seq = document.getSequence(seqURI)
+            if seq.elements.lower() == Seq(product_3_prime_ss_end).reverse_complement():
+                three_prime_oh_definition.wasDerivedFrom = definition.identity
+                three_prime_sequence = sbol2.Sequence(uri=f"{three_prime_oh_definition.displayId}_sequence", elements= seq.elements)
+                three_prime_sequence.wasDerivedFrom = seq.identity
+                three_prime_oh_definition.sequences = [three_prime_sequence]
+                three_prime_oh_definition.types.append("http://identifiers.org/so/SO:0000984") # single-stranded for overhangs
+                
+                extracts_list.append((three_prime_oh_definition, three_prime_sequence))
+                extracts_list.append((definition, seq)) #add scars to list
+
+            elif seq.elements.lower() == product_sequence[4:-4]: 
+                original_part_def_URI = definition.identity
+                extracts_list.append((definition, seq))
+
+            elif seq.elements.lower() == product_5_prime_ss_end:
+                five_prime_oh_definition.wasDerivedFrom = definition.identity
+                five_prime_sequence = sbol2.Sequence(uri=f"{five_prime_oh_definition.displayId}_sequence", elements= seq.elements)
+                five_prime_sequence.wasDerivedFrom = seq.identity
+                five_prime_oh_definition.sequences = [five_prime_sequence]
+                five_prime_oh_definition.types.append("http://identifiers.org/so/SO:0000984") # single-stranded for overhangs
+
+                extracts_list.append((five_prime_oh_definition, five_prime_sequence))
+                extracts_list.append((definition, seq))
+
+    #find + add original component to product def & annotation
+    for comp in reactant_component_definition.components:        
+        if comp.definition == original_part_def_URI:
+            prod_component_definition.components.add(comp)
+            part_extract_annotation.component = comp
+
+    prod_component_definition.sequenceAnnotations.add(three_prime_overhang_annotation)
+    prod_component_definition.sequenceAnnotations.add(five_prime_overhang_annotation)
+    prod_component_definition.sequenceAnnotations.add(part_extract_annotation)
+    prod_component_definition.addRole('https://identifiers.org/so/SO:0000915') #engineered insert
+    prod_component_definition.addType('http://identifiers.org/so/SO:0000987') #linear
+
+    #Add reference to part in backbone
+    reactant_component = sbol2.FunctionalComponent(uri=f"{reactant_displayId}_reactant")
+    reactant_component.definition = reactant_component_definition
+    assembly_plan.functionalComponents.add(reactant_component)
+
+    # Create reactant Participation.
+    reactant_participation = sbol2.Participation(uri=f"{reactant_displayId}_reactant")
+    reactant_participation.participant = reactant_component
+    reactant_participation.roles = [sbol2.SBO_REACTANT]
+    participations.append(reactant_participation)
+    
+    prod_component = sbol2.FunctionalComponent(uri=f"{reactant_displayId}_digestion_product")
+    prod_component.definition = prod_component_definition
+    assembly_plan.functionalComponents.add(prod_component)
+
+    product_participation = sbol2.Participation(uri=f"{reactant_displayId}_product")
+    product_participation.participant = prod_component
+    product_participation.roles = [sbol2.SBO_PRODUCT]
+    participations.append(product_participation)
+   
+    # Make Interaction
+    interaction = sbol2.Interaction(uri=f"{reactant_displayId}_digestion_interaction", interaction_type='http://identifiers.org/biomodels.sbo/SBO:0000178')
+    interaction.participations = participations
+    assembly_plan.interactions.add(interaction)
+                    
+    return extracts_list, assembly_plan

+
+
+

+[docs]
+def backbone_digestion(reactant:sbol2.ModuleDefinition, restriction_enzymes:List[sbol2.ComponentDefinition], assembly_plan:sbol2.ModuleDefinition, document: sbol2.Document, **kwargs)-> Tuple[List[Tuple[sbol2.ComponentDefinition, sbol2.Sequence]], sbol2.ModuleDefinition]:
+    """Runs a simulated digestion on the top level sequence in the reactant ModuleDefinition with the given restriciton enzymes, creating an open backbone ComponentDefinition, a digestion Interaction, and converts existing scars to 5' and 3' overhangs.
+    The product ComponentDefinition is assumed the open backbone in this case.
+
+    Written for use with the SBOL2.3 output of https://sbolcanvas.org
+
+    :param reactant: DNA to be digested as SBOL ModuleDefinition, usually a part_in_backbone. 
+    :param restriction_enzymes: Restriction enzymes as :class:`sbol2.ComponentDefinition`
+                                (generate with :func:`rebase_restriction_enzyme`).
+    :param assembly_plan: SBOL ModuleDefinition to contain the functional components, interactions, and participations
+    :param document: original SBOL2 document to be used to extract referenced objects.
+    :return: A tuple of a list ComponentDefinitions and Sequences, and an assembly plan ModuleDefinition.
+    """
+    # extract component definition from module
+    reactant_displayId = reactant.functionalComponents[0].displayId
+    reactant_def_URI = reactant.functionalComponents[0].definition
+    reactant_component_definition = document.getComponentDefinition(reactant_def_URI)
+
+    if sbol2.BIOPAX_DNA not in reactant_component_definition.types:
+        raise TypeError(f'The reactant should has a DNA type. Types founded {reactant.types}.')
+    if len(reactant_component_definition.sequences)!=1: # TODO review if true for MD, maybe for MD it will be 5
+        raise ValueError(f'The reactant needs to have precisely one sequence. The input reactant has {len(reactant.sequences)} sequences')
+    participations=[]
+    extracts_list=[]
+    restriction_enzymes_pydna=[] 
+    
+    for re in restriction_enzymes:
+        enzyme = Restriction.__dict__[re.name]
+        restriction_enzymes_pydna.append(enzyme)
+
+        enzyme_component = sbol2.FunctionalComponent(uri=f"{re.name}_enzyme")
+        enzyme_component.definition = re
+        enzyme_component.displayID = f"{re.name}_enzyme"
+        enzyme_in_module = False
+
+        for comp in assembly_plan.functionalComponents:
+            if (comp.displayId == enzyme_component.displayID):
+                enzyme_component = comp
+                enzyme_in_module = True
+
+        if not enzyme_in_module:
+            assembly_plan.functionalComponents.add(enzyme_component)
+            
+        modifier_participation = sbol2.Participation(uri='restriction')
+        modifier_participation.participant = enzyme_component
+        modifier_participation.roles = ['http://identifiers.org/biomodels.sbo/SBO:0000019'] # modifier
+        participations.append(modifier_participation)
+
+    # Inform topology to PyDNA, if not found assuming linear. 
+    if is_circular(reactant_component_definition):
+        circular=True
+        linear=False
+    else: 
+        circular=False
+        linear=True
+        
+    reactant_seq = reactant_component_definition.sequences[0]
+    reactant_seq = document.getSequence(reactant_seq).elements
+    # Dseqrecord is from PyDNA package with reactant sequence
+    ds_reactant = Dseqrecord(reactant_seq, circular=circular)
+    digested_reactant = ds_reactant.cut(restriction_enzymes_pydna) #TODO see if ds_reactant.cut is working, causing problems downstream
+
+
+    if len(digested_reactant)<2 or len(digested_reactant)>3: 
+        raise NotImplementedError(f'Not supported number of products. Found{len(digested_reactant)}')
+    #TODO select them based on content rather than size.
+    elif circular and len(digested_reactant)==2:
+        part_extract, backbone = sorted(digested_reactant, key=len)
+    elif linear and len(digested_reactant)==3:
+        prefix, part_extract, suffix = digested_reactant
+    else: raise NotImplementedError('The reactant has no valid topology type')
+
+    # Compute the length of single strand sticky ends or fusion sites
+    product_5_prime_ss_strand, product_5_prime_ss_end = backbone.seq.five_prime_end()
+    product_3_prime_ss_strand, product_3_prime_ss_end = backbone.seq.three_prime_end()
+    product_sequence = str(backbone.seq)
+    prod_backbone_definition, prod_seq = dna_componentdefinition_with_sequence(identity=f'{reactant_component_definition.displayId}_extracted_backbone', sequence=product_sequence, **kwargs)
+    prod_backbone_definition.wasDerivedFrom = reactant_component_definition.identity
+    extracts_list.append((prod_backbone_definition, prod_seq))
+
+    # five prime overhang
+    five_prime_oh_definition = sbol2.ComponentDefinition(uri=f"{reactant_displayId}_five_prime_oh") # TODO: ensure circular type is preserved for sbh visualization
+    five_prime_oh_definition.addRole('http://identifiers.org/so/SO:0001932') #overhang 5 prime
+    five_prime_oh_location = sbol2.Range(uri="five_prime_oh_location", start=1, end=len(product_5_prime_ss_end))
+    five_prime_oh_component = sbol2.Component(uri=f"{reactant_displayId}_five_prime_oh_component")
+    five_prime_oh_component.definition = five_prime_oh_definition
+    five_prime_overhang_annotation = sbol2.SequenceAnnotation(uri="five_prime_overhang")
+    five_prime_overhang_annotation.locations.add(five_prime_oh_location)
+
+    # extracted backbone => point straight to backbone from sbolcanvas
+    backbone_location = sbol2.Range(uri=f"{reactant_displayId}_backbone_location", start=len(product_5_prime_ss_end)+1, end=len(product_sequence)-len(product_3_prime_ss_end))
+    backbone_extract_annotation = sbol2.SequenceAnnotation(uri=f"{reactant_displayId}_backbone")
+    backbone_extract_annotation.locations.add(backbone_location)
+    
+    # three prime overhang
+    three_prime_oh_definition = sbol2.ComponentDefinition(uri=f"{reactant_displayId}_three_prime_oh")
+    three_prime_oh_definition.addRole('http://identifiers.org/so/SO:0001933') #overhang 3 prime
+    three_prime_oh_location = sbol2.Range(uri="three_prime_oh_location", start=len(product_sequence)-len(product_3_prime_ss_end)+1, end=len(product_sequence)) 
+    three_prime_oh_component = sbol2.Component(uri=f"{reactant_displayId}_three_prime_oh_component")
+    three_prime_oh_component.definition = three_prime_oh_definition
+    three_prime_overhang_annotation = sbol2.SequenceAnnotation(uri="three_prime_overhang")
+    three_prime_overhang_annotation.locations.add(three_prime_oh_location)
+
+    anno_component_dict = {}
+
+    prod_backbone_definition.components = [five_prime_oh_component, three_prime_oh_component]
+    three_prime_overhang_annotation.component = three_prime_oh_component
+    five_prime_overhang_annotation.component = five_prime_oh_component
+
+    # check these lines
+    original_backbone_def_URI = ""
+
+    #enccode ontologies of overhangs
+    for definition in document.componentDefinitions:
+        for seqURI in definition.sequences:
+            seq = document.getSequence(seqURI)
+            if seq.elements.lower() == Seq(product_3_prime_ss_end).reverse_complement():
+                three_prime_oh_definition.wasDerivedFrom = definition.identity
+                three_prime_sequence = sbol2.Sequence(uri=f"{three_prime_oh_definition.displayId}_sequence", elements= seq.elements)
+                three_prime_sequence.wasDerivedFrom = seq.identity
+                three_prime_oh_definition.sequences = [three_prime_sequence]
+                three_prime_oh_definition.types.append("http://identifiers.org/so/SO:0000984") # single-stranded for overhangs
+                
+                extracts_list.append((three_prime_oh_definition, three_prime_sequence))
+                extracts_list.append((definition, seq)) #add scars to list
+
+            elif seq.elements.lower() == product_sequence[4:-4]: 
+                original_backbone_def_URI = definition.identity
+                extracts_list.append((definition, seq))
+
+            elif seq.elements.lower() == product_5_prime_ss_end:
+                five_prime_oh_definition.wasDerivedFrom = definition.identity
+                five_prime_sequence = sbol2.Sequence(uri=f"{five_prime_oh_definition.displayId}_sequence", elements= seq.elements)
+                five_prime_sequence.wasDerivedFrom = seq.identity
+                five_prime_oh_definition.sequences = [five_prime_sequence]
+                five_prime_oh_definition.types.append("http://identifiers.org/so/SO:0000984") # single-stranded for overhangs
+
+                extracts_list.append((five_prime_oh_definition, five_prime_sequence))
+                extracts_list.append((definition, seq))
+
+    #find + add original component to product def & annotation
+    for comp in reactant_component_definition.components:        
+        if comp.definition == original_backbone_def_URI:
+            prod_backbone_definition.components.add(comp)
+            backbone_extract_annotation.component = comp
+
+    prod_backbone_definition.sequenceAnnotations.add(three_prime_overhang_annotation)
+    prod_backbone_definition.sequenceAnnotations.add(five_prime_overhang_annotation)
+    prod_backbone_definition.sequenceAnnotations.add(backbone_extract_annotation)
+    prod_backbone_definition.addRole('https://identifiers.org/so/SO:0000755') 
+
+    #Add reference to part in backbone
+    reactant_component = sbol2.FunctionalComponent(uri=f'{reactant_component_definition.displayId}_backbone_reactant')
+    reactant_component.definition = reactant_component_definition
+    assembly_plan.functionalComponents.add(reactant_component)
+
+    # Create reactant Participation.
+    reactant_participation = sbol2.Participation(uri=f'{reactant_component_definition.displayId}_backbone_reactant')
+    reactant_participation.participant = reactant_component
+    reactant_participation.roles = [sbol2.SBO_REACTANT]
+    participations.append(reactant_participation)
+    
+    prod_component = sbol2.FunctionalComponent(uri=f'{reactant_component_definition.displayId}_backbone_digestion_product')
+    prod_component.definition = prod_backbone_definition
+    assembly_plan.functionalComponents.add(prod_component)
+
+    product_participation = sbol2.Participation(uri=f'{reactant_component_definition.displayId}_backbone_product')
+    product_participation.participant = prod_component
+    product_participation.roles = [sbol2.SBO_PRODUCT]
+    participations.append(product_participation)
+   
+    # Make Interaction
+    interaction = sbol2.Interaction(uri=f"{reactant_component_definition.displayId}_digestion_interaction", interaction_type='http://identifiers.org/biomodels.sbo/SBO:0000178')
+    interaction.participations = participations
+    assembly_plan.interactions.add(interaction)
+                    
+    return extracts_list, assembly_plan

+
+
+

+[docs]
+def number_to_suffix(n):
+    """Helper function for generating scar suffixes of the form: :math:`S=(A,B,C,…,Z,AA,AB,AC,…,AZ,BA,BB,…, S_n)`
+
+    :param n: Number to convert to character suffix
+    :return: Character suffix corresponding to n
+    """
+    suffix = ""
+    while n > 0:
+        n -= 1 
+        remainder = n % 26 
+        suffix = chr(ord('A') + remainder) + suffix
+        n = n // 26 
+    return suffix

+
+
+

+[docs]
+def ligation(reactants:List[sbol2.ComponentDefinition], assembly_plan: sbol2.ModuleDefinition, document: sbol2.Document, ligase: sbol2.ComponentDefinition=None)->List[Tuple[sbol2.ComponentDefinition, sbol2.Sequence]]:
+    """Ligates Components using base complementarity and creates product Components and a ligation Interaction.
+
+    :param reactants: DNA parts to be ligated as SBOL ModuleDefinition. 
+    :param assembly_plan: SBOL ModuleDefinition to contain the functional components, interactions, and participants
+    :param document: SBOL2 document containing all reactant ComponentDefinitions.
+    :param ligase: as SBOL ComponentDefinition, optional (defaults to T4 ligase)
+    :return: List of all composites generated, in the form of tuples of ComponentDefinition and Sequence.
+    """
+    if ligase == None:
+        ligase = sbol2.ComponentDefinition(uri="T4_Ligase")
+        ligase.name = "T4_Ligase"
+        ligase.types = sbol2.BIOPAX_PROTEIN
+        document.add(ligase)
+
+    ligase_component = sbol2.FunctionalComponent(uri="T4_Ligase")
+    ligase_component.definition = ligase
+    assembly_plan.functionalComponents.add(ligase_component)
+
+    modifier_participation = sbol2.Participation(uri='ligation')
+    modifier_participation.participant = ligase_component
+    modifier_participation.roles = ['http://identifiers.org/biomodels.sbo/SBO:0000019'] # modifier
+
+    # Create a dictionary that maps each first and last 4 letters to a list of strings that have those letters.
+    reactant_parts = []
+    fusion_sites_set = set()
+    for reactant in reactants:
+        fusion_site_3prime_length = reactant.sequenceAnnotations[0].locations[0].end - reactant.sequenceAnnotations[0].locations[0].start
+        fusion_site_5prime_length = reactant.sequenceAnnotations[1].locations[0].end - reactant.sequenceAnnotations[1].locations[0].start
+        if fusion_site_3prime_length == fusion_site_5prime_length:
+            fusion_site_length = fusion_site_3prime_length + 1 # if the fusion site is 4 bp long, the start will be 1 and end 4, 4-1 = 3, so we add 1 to get 4.
+            fusion_sites_set.add(fusion_site_length)
+            if len(fusion_sites_set) > 1:
+                raise ValueError(f'Fusion sites of different length within different parts. Check {reactant.identity} ')
+        else:
+            raise ValueError(f'Fusion sites of different length within the same part. Check {reactant.identity}')
+        if 'https://identifiers.org/so/SO:0000755' in reactant.roles:
+            reactant_parts.append(reactant)
+        elif 'https://identifiers.org/so/SO:0000915' in reactant.roles:
+            reactant_parts.append(reactant)
+        else:
+            raise ValueError(f'Part {reactant.identity} does not have a valid role')
+        
+    # remove the backbones if any from the reactants, to create the composite
+    groups = {}
+    for reactant in reactant_parts:
+        reactant_seq = reactant.sequences[0]
+        first_four_letters = document.getSequence(reactant_seq).elements[:fusion_site_length].lower()
+        last_four_letters = document.getSequence(reactant_seq).elements[-fusion_site_length:].lower()
+        part_syntax = f'{first_four_letters}_{last_four_letters}'
+        if part_syntax not in groups:
+            groups[part_syntax] = []
+            groups[part_syntax].append(reactant)
+        else: groups[part_syntax].append(reactant)
+    # groups is a dictionary of lists of parts that have the same first and last 4 letters
+    # list_of_combinations_per_assembly is a list of tuples of parts that can be ligated together
+    list_of_parts_per_combination = list(product(*groups.values())) #cartesian product
+    # create list_of_composites_per_assembly from list_of_combinations_per_assembly
+    list_of_composites_per_assembly = []
+    for combination in list_of_parts_per_combination:
+        list_of_parts_per_composite = [combination[0]] 
+        insert_sequence_uri = combination[0].sequences[0]
+        insert_sequence = document.getSequence(insert_sequence_uri).elements
+        remaining_parts = list(combination[1:])
+        it = 1
+        while remaining_parts:   
+            remaining_parts_before = len(remaining_parts) 
+            for part in remaining_parts:
+                # match insert sequence 5' to part 3'
+                part_sequence_uri = part.sequences[0]
+                if document.getSequence(part_sequence_uri).elements[:fusion_site_length].lower() == insert_sequence[-fusion_site_length:].lower():
+                    insert_sequence = insert_sequence[:-fusion_site_length] + document.getSequence(part_sequence_uri).elements
+                    list_of_parts_per_composite.append(part) #add sequence annotation here, index based on insert_sequence
+                    remaining_parts.remove(part)
+                # match insert sequence 3' to part 5'
+                elif document.getSequence(part_sequence_uri).elements[-fusion_site_length:].lower() == insert_sequence[:fusion_site_length].lower():
+                    insert_sequence = document.getSequence(part_sequence_uri).elements + insert_sequence[fusion_site_length:]
+                    list_of_parts_per_composite.insert(0, part)
+                    remaining_parts.remove(part)
+                remaining_parts_after = len(remaining_parts)
+            
+            if remaining_parts_before == remaining_parts_after:
+                it += 1
+            if it > 5: #5 was chosen arbitrarily to avoid infinite loops
+                print(groups)
+                raise ValueError('No match found, check the parts and their fusion sites')
+        list_of_composites_per_assembly.append(list_of_parts_per_composite)
+
+    # transform list_of_parts_per_assembly into list of composites
+    products_list = []
+    participations = []
+    composite_number = 1
+    participations.append(modifier_participation)
+
+    # TODO: use componentinstances to append "subcomponents" to each definition that is a composite component. all composites share the "subcomponents"
+    for composite in list_of_composites_per_assembly: # a composite of the form [A,B,C]
+        # calculate sequence
+        composite_sequence_str = ""
+        composite_name = ""
+        prev_three_prime = composite[len(composite)-1].components[1].definition # componentdefinitionuri
+        prev_three_prime_definition = document.getComponentDefinition(prev_three_prime)
+        scar_index = 1
+        anno_list = []
+
+        part_extract_definitions = []
+        for part_extract in composite:
+            part_extract_sequence_uri = part_extract.sequences[0]
+            part_extract_sequence = document.getSequence(part_extract_sequence_uri).elements
+            temp_extract_components = []
+            reactant_component = sbol2.FunctionalComponent(uri=f"{part_extract.displayId}_reactant")
+            reactant_component.definition = part_extract # TODO do not make new components, instead derive product functionalcomponents from the assembly_plan moduledefinition to add to the ligation interaction/participation
+            for fc in assembly_plan.functionalComponents:
+                if fc.definition == reactant_component.definition:
+                   reactant_component = fc
+
+            reactant_participation = sbol2.Participation(uri=f'{part_extract.displayId}_ligation')
+            reactant_participation.participant = reactant_component
+            reactant_participation.roles = [sbol2.SBO_REACTANT]
+            participations.append(reactant_participation)
+
+            for comp in part_extract.components:
+                if  "http://identifiers.org/so/SO:0001932" in document.getComponentDefinition(comp.definition).roles: #five prime
+                    scar_definition = sbol2.ComponentDefinition(uri=f"Ligation_Scar_{number_to_suffix(scar_index)}")
+                    scar_sequence = sbol2.Sequence(uri=f"Ligation_Scar_{number_to_suffix(scar_index)}_sequence", elements=document.getSequence(prev_three_prime_definition.sequences[0]).elements)
+                    scar_definition.sequences = [scar_sequence]
+                    scar_definition.wasDerivedFrom = [comp.definition, prev_three_prime]
+                    scar_definition.roles = ["http://identifiers.org/so/SO:0001953"]
+                    temp_extract_components.append(scar_definition.identity)
+                    
+                    document.add(scar_definition)
+                    document.add(scar_sequence)
+
+                    scar_location = sbol2.Range(uri=f"Ligation_Scar_{number_to_suffix(scar_index)}_location", start= len(composite_sequence_str)+1, end=len(composite_sequence_str)+fusion_site_length)
+                    scar_anno = sbol2.SequenceAnnotation(uri=f"Ligation_Scar_{number_to_suffix(scar_index)}_annotation")
+                    scar_anno.locations.add(scar_location)
+                    anno_list.append(scar_anno)
+                    scar_index += 1
+                elif "http://identifiers.org/so/SO:0001933" in document.getComponentDefinition(comp.definition).roles: #three prime
+                    prev_three_prime = comp.definition
+                    prev_three_prime_definition = document.getComponentDefinition(prev_three_prime)
+                else:
+                    temp_extract_components.append(comp.definition)
+                    comp_location = sbol2.Range(uri=f"{comp.displayId}_location", start= len(composite_sequence_str)+fusion_site_length+1, end=len(composite_sequence_str)+len(part_extract_sequence[:-4])) #TODO check if seq len is correct
+                    comp_anno = sbol2.SequenceAnnotation(uri=f"{comp.displayId}_annotation")
+                    comp_anno.locations.add(comp_location)
+                    anno_list.append(comp_anno)
+
+            part_extract_definitions.extend(temp_extract_components)
+
+            composite_sequence_str = composite_sequence_str + part_extract_sequence[:-fusion_site_length] #needs a version for linear
+            
+
+        # create dna component and sequence
+        composite_component_definition, composite_seq = dna_componentdefinition_with_sequence(f'composite_{composite_number}', composite_sequence_str)
+        composite_component_definition.name = f'composite_{composite_number}'
+        composite_component_definition.addRole('http://identifiers.org/so/SO:0000804') #engineered region
+        composite_component_definition.addType('http://identifiers.org/so/SO:0000988')
+
+        part_extract_components = [] 
+        
+
+        for i, definition in enumerate(part_extract_definitions):
+            def_object = document.getComponentDefinition(definition)
+            comp = sbol2.Component(uri=def_object.displayId)
+            comp.definition = definition
+            composite_component_definition.components.add(comp)
+            
+            anno_list[i].component = comp           
+
+        composite_component_definition.sequenceAnnotations = anno_list
+
+        prod_functional_component = sbol2.FunctionalComponent(uri=f"{composite_component_definition.name}")
+        prod_functional_component.definition = composite_component_definition
+        assembly_plan.functionalComponents.add(prod_functional_component)
+
+        product_participation = sbol2.Participation(uri=f"{composite_component_definition.name}_product")
+        product_participation.participant = prod_functional_component
+        product_participation.roles = [sbol2.SBO_PRODUCT]
+        participations.append(product_participation)
+    
+        # Make Interaction
+        interaction = sbol2.Interaction(uri=f"{composite_component_definition.name}_ligation_interaction", interaction_type='http://identifiers.org/biomodels.sbo/SBO:0000695')
+        interaction.participations = participations
+        assembly_plan.interactions.add(interaction)
+
+        products_list.append([composite_component_definition, composite_seq])
+        composite_number += 1
+    return products_list

+
+
+

+[docs]
+def append_extracts_to_doc(extract_tuples: List[Tuple[sbol2.ComponentDefinition, sbol2.Sequence]], doc: sbol2.Document):
+    """Helper function for batch adding :class:`sbol2.ComponentDefinition` and :class:`sbol2.Sequence` to an :class:`sbol2.Document`
+
+    :param extract_tuples: list of tuples of :class:`sbol2.ComponentDefinition` and :class:`sbol2.Sequence`
+    :param doc: document which the content is to be added to
+    """
+    for extract, sequence in extract_tuples:
+        try:
+            print("adding: " + extract.displayId)
+            doc.add(extract)
+            doc.add(sequence)
+        except Exception as e: 
+            if '<SBOLErrorCode.SBOL_ERROR_URI_NOT_UNIQUE: 17>' in str(e):
+                pass
+            else:
+                raise e

+
+
+

+[docs]
+class golden_gate_assembly_plan():
+    """Creates an Assembly Plan.
+
+    :param name: Name of the assembly plan ModuleDefinition.
+    :param parts_in_backbone: Parts in backbone to be assembled. 
+    :param plasmid_acceptor_backbone:  Backbone in which parts are inserted on the assembly. 
+    :param restriction_enzyme: Restriction enzyme name used by PyDNA. Case sensitive, follow standard restriction enzyme nomenclature, i.e. 'BsaI'
+    :param document: SBOL Document where the assembly plan will be created.
+    """
+    def __init__(self, name: str, parts_in_backbone: List[sbol2.Document], plasmid_acceptor_backbone: sbol2.Document, restriction_enzyme: str, document: sbol2.Document):
+        self.name = name
+        self.parts_in_backbone = parts_in_backbone
+        self.backbone = plasmid_acceptor_backbone
+        self.restriction_enzyme = rebase_restriction_enzyme(restriction_enzyme)
+        self.extracted_parts = [] #list of tuples [ComponentDefinition, Sequence]
+        self.document = document
+
+        self.assembly_plan = sbol2.ModuleDefinition(name)
+        self.document.add(self.assembly_plan)
+        self.document.add(self.restriction_enzyme)
+        self.composites = []
+
+

+[docs]
+    def run(self) -> List[Tuple[sbol2.ComponentDefinition, sbol2.Sequence]]:
+        """Runs full assembly simulation.
+
+        `document` parameter of golden_gate_assembly_plan object is updated by reference to include assembly plan ModuleDefinition and all related information.
+        
+        Runs :func:`part_digestion` for all `parts_in_backbone` and :func:`backbone_digestion` for `plasmid_acceptor_backbone` with `restriction_enzyme`. Then runs :func:`ligation` with these parts to form composites. 
+
+        :return: List of all composites generated, in the form of tuples of ComponentDefinition and Sequence.
+        """
+        for part_doc in self.parts_in_backbone:
+            md = part_doc.getModuleDefinition('https://sbolcanvas.org/module1') #change to toplevel or some other index?
+            extracts_tuple_list, _ = part_digestion(md, [self.restriction_enzyme], self.assembly_plan, part_doc) #make sure assembly plan is pass-by-reference
+
+            append_extracts_to_doc(extracts_tuple_list, self.document)
+            self.extracted_parts.append(extracts_tuple_list[0][0])
+
+        md = self.backbone.getModuleDefinition('https://sbolcanvas.org/module1')
+        extracts_tuple_list, _ = backbone_digestion(md, [self.restriction_enzyme], self.assembly_plan, self.backbone)
+        
+        append_extracts_to_doc(extracts_tuple_list, self.document)
+        self.extracted_parts.append(extracts_tuple_list[0][0])
+
+        self.composites = ligation(self.extracted_parts, self.assembly_plan, self.document)
+
+        append_extracts_to_doc(self.composites, self.document)
+
+        return self.composites

+

+
+
+
+
+
+ +
+ + +
+
+
+
+ Copyright © 2025, Ryan Greer +
+ Made with Sphinx and @pradyunsg's + + Furo + +
+
+ +
+
+ +
+
+ +
+
+ + + + + \ No newline at end of file diff --git a/docs/_build/html/_sources/API_Reference.rst.txt b/docs/_build/html/_sources/API_Reference.rst.txt new file mode 100644 index 0000000..8dd46bd --- /dev/null +++ b/docs/_build/html/_sources/API_Reference.rst.txt @@ -0,0 +1,7 @@ +API Reference +============= + +.. automodule:: sbol2build.sbol2build + :members: + :undoc-members: + :show-inheritance: \ No newline at end of file diff --git a/docs/_build/html/_sources/Installation.rst.txt b/docs/_build/html/_sources/Installation.rst.txt new file mode 100644 index 0000000..dbc9b80 --- /dev/null +++ b/docs/_build/html/_sources/Installation.rst.txt @@ -0,0 +1,2 @@ +Installation +====================================== \ No newline at end of file diff --git a/docs/_build/html/_sources/Tutorials.rst.txt b/docs/_build/html/_sources/Tutorials.rst.txt new file mode 100644 index 0000000..8da6e92 --- /dev/null +++ b/docs/_build/html/_sources/Tutorials.rst.txt @@ -0,0 +1,3 @@ +Tutorials +====================================== +Let's get started with creating DNA assembly plans. First we will demonstrate a workflow using plasmid files from `SBOLCanvas `_: \ No newline at end of file diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt new file mode 100644 index 0000000..225bc38 --- /dev/null +++ b/docs/_build/html/_sources/index.rst.txt @@ -0,0 +1,23 @@ +.. SBOL2Build documentation master file, created by + sphinx-quickstart on Mon Apr 14 14:04:32 2025. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to SBOL2Build's documentation! +====================================== + +SBOL2Build is a Python library for assisting in the planning, documentation, and distribution of DNA assembly plans using the Synthetic Biology Open Language 2.3 data standard. + +It was developed to support build functionality and workflows in `SynBioSuite `_, based off the `SBOL Best Practices `_. + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + Installation + Tutorials + API_Reference + + + diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css new file mode 100644 index 0000000..4738b2e --- /dev/null +++ b/docs/_build/html/_static/basic.css @@ -0,0 +1,906 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin-top: 10px; +} + +ul.search li { + padding: 5px 0; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/docs/_build/html/_static/debug.css b/docs/_build/html/_static/debug.css new file mode 100644 index 0000000..74d4aec --- /dev/null +++ b/docs/_build/html/_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/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js new file mode 100644 index 0000000..0398ebb --- /dev/null +++ b/docs/_build/html/_static/doctools.js @@ -0,0 +1,149 @@ +/* + * Base JavaScript utilities for all Sphinx HTML documentation. + */ +"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/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js new file mode 100644 index 0000000..cd844a5 --- /dev/null +++ b/docs/_build/html/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '0.0b1', + 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/docs/_build/html/_static/file.png b/docs/_build/html/_static/file.png new file mode 100644 index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3 GIT binary patch literal 286 zcmV+(0pb3MP)s`hMrGg#P~ix$^RISR_I47Y|r1 z_CyJOe}D1){SET-^Amu_i71Lt6eYfZjRyw@I6OQAIXXHDfiX^GbOlHe=Ae4>0m)d(f|Me07*qoM6N<$f}vM^LjV8( literal 0 HcmV?d00001 diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js new file mode 100644 index 0000000..c7fe6c6 --- /dev/null +++ b/docs/_build/html/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +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, if 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 = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/docs/_build/html/_static/minus.png b/docs/_build/html/_static/minus.png new file mode 100644 index 0000000000000000000000000000000000000000..d96755fdaf8bb2214971e0db9c1fd3077d7c419d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu=nj kDsEF_5m^0CR;1wuP-*O&G^0G}KYk!hp00i_>zopr08q^qX#fBK literal 0 HcmV?d00001 diff --git a/docs/_build/html/_static/plus.png b/docs/_build/html/_static/plus.png new file mode 100644 index 0000000000000000000000000000000000000000..7107cec93a979b9a5f64843235a16651d563ce2d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu>-2 m3q%Vub%g%s<8sJhVPMczOq}xhg9DJoz~JfX=d#Wzp$Pyb1r*Kz literal 0 HcmV?d00001 diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css new file mode 100644 index 0000000..02b4b12 --- /dev/null +++ b/docs/_build/html/_static/pygments.css @@ -0,0 +1,258 @@ +.highlight pre { line-height: 125%; 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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 calculations\n */\n var getOffset = function (settings) {\n // if the offset is a function run it\n if (typeof settings.offset === \"function\") {\n return parseFloat(settings.offset());\n }\n\n // Otherwise, return it as-is\n return parseFloat(settings.offset);\n };\n\n /**\n * Get the document element's height\n * @private\n * @returns {Number}\n */\n var getDocumentHeight = function () {\n return Math.max(\n document.body.scrollHeight,\n document.documentElement.scrollHeight,\n document.body.offsetHeight,\n document.documentElement.offsetHeight,\n document.body.clientHeight,\n document.documentElement.clientHeight,\n );\n };\n\n /**\n * Determine if an element is in view\n * @param {Node} elem The element\n * @param {Object} settings The settings for this instantiation\n * @param {Boolean} bottom If true, check if element is above bottom of viewport instead\n * @return {Boolean} Returns true if element is in the viewport\n */\n var isInView = function (elem, settings, bottom) {\n 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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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current instantiation\n */\n var init = function () {\n // Merge user options into defaults\n settings = extend(defaults, options || {});\n\n // Setup variables based on the current DOM\n publicAPIs.setup();\n\n // Find the currently active content\n publicAPIs.detect();\n\n // Setup event listeners\n window.addEventListener(\"scroll\", scrollHandler, false);\n if (settings.reflow) {\n window.addEventListener(\"resize\", resizeHandler, false);\n }\n };\n\n //\n // Initialize and return the public APIs\n //\n\n init();\n return publicAPIs;\n };\n\n //\n // Return the Constructor\n //\n\n return Constructor;\n },\n);\n","// The module cache\nvar __webpack_module_cache__ = {};\n\n// The require function\nfunction __webpack_require__(moduleId) {\n\t// Check if module is in cache\n\tvar cachedModule = __webpack_module_cache__[moduleId];\n\tif (cachedModule !== undefined) {\n\t\treturn cachedModule.exports;\n\t}\n\t// Create a new module (and put it into the cache)\n\tvar module = 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globalThis === 'object') return globalThis;\n\ttry {\n\t\treturn this || new Function('return this')();\n\t} catch (e) {\n\t\tif (typeof window === 'object') return window;\n\t}\n})();","__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))","import Gumshoe from \"./gumshoe-patched.js\";\n\n////////////////////////////////////////////////////////////////////////////////\n// Scroll Handling\n////////////////////////////////////////////////////////////////////////////////\nvar tocScroll = null;\nvar header = null;\nvar lastScrollTop = document.documentElement.scrollTop;\nconst GO_TO_TOP_OFFSET = 64;\n\nfunction scrollHandlerForHeader(positionY) {\n const headerTop = Math.floor(header.getBoundingClientRect().top);\n\n console.log(`headerTop: ${headerTop}`);\n if (headerTop == 0 && positionY != headerTop) {\n header.classList.add(\"scrolled\");\n } else {\n header.classList.remove(\"scrolled\");\n }\n}\n\nfunction scrollHandlerForBackToTop(positionY) {\n 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + 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, anchor) + ); + // 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 = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +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); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (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; +}; + +/** + * 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, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. 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.setAttribute("role", "list"); + 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); + }, + + _parseQuery: (query) => { + // 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]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + 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; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // 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, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // 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; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // 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]], + SearchResultKind.object, + ]); + }; + 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 = []; + // find documents, if any, containing the query word in their text/title term indices + // use Object.hasOwnProperty to avoid mismatching against prototype properties + const arr = [ + { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term }, + { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], 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, new Map()); + const fileScores = scoreMap.get(file); + fileScores.set(word, record.score); + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(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).get(w))); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + 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, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + 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/docs/_build/html/_static/skeleton.css b/docs/_build/html/_static/skeleton.css new file mode 100644 index 0000000..467c878 --- /dev/null +++ b/docs/_build/html/_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/docs/_build/html/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/docs/_build/html/_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/docs/_build/html/_static/styles/furo-extensions.css b/docs/_build/html/_static/styles/furo-extensions.css new file mode 100644 index 0000000..8229587 --- /dev/null +++ b/docs/_build/html/_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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Remove the inheritance of text transform in Firefox.\n */\n\nbutton,\nselect { /* 1 */\n text-transform: none;\n}\n\n/**\n * Correct the inability to style clickable types in iOS and Safari.\n */\n\nbutton,\n[type=\"button\"],\n[type=\"reset\"],\n[type=\"submit\"] {\n -webkit-appearance: button;\n}\n\n/**\n * Remove the inner border and padding in Firefox.\n */\n\nbutton::-moz-focus-inner,\n[type=\"button\"]::-moz-focus-inner,\n[type=\"reset\"]::-moz-focus-inner,\n[type=\"submit\"]::-moz-focus-inner {\n border-style: none;\n padding: 0;\n}\n\n/**\n * Restore the focus styles unset by the previous rule.\n */\n\nbutton:-moz-focusring,\n[type=\"button\"]:-moz-focusring,\n[type=\"reset\"]:-moz-focusring,\n[type=\"submit\"]:-moz-focusring {\n outline: 1px dotted ButtonText;\n}\n\n/**\n * Correct the padding in Firefox.\n */\n\nfieldset {\n padding: 0.35em 0.75em 0.625em;\n}\n\n/**\n * 1. Correct the text wrapping in Edge and IE.\n * 2. 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, p\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 color: var(--color-foreground-primary)\n background: var(--color-background-primary)\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-light\n display: block\n\n @media (prefers-color-scheme: dark)\n .theme-toggle svg.theme-icon-when-auto-dark\n display: block\n .theme-toggle svg.theme-icon-when-auto-light\n display: none\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 --font-stack--headings: var(--font-stack);\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: #6b6f76; // 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: #0a4bff;\n --color-brand-content: #2757dd;\n --color-brand-visited: #872ee0;\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\n --color-api-added: #21632c;\n --color-api-added-border: #38a84d;\n --color-api-changed: #046172;\n --color-api-changed-border: #06a1bc;\n --color-api-deprecated: #605706;\n --color-api-deprecated-border: #f0d90f;\n --color-api-removed: #b30000;\n --color-api-removed-border: #ff5c5c;\n\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-underline: var(--color-background-border);\n --color-link--hover: var(--color-brand-content);\n --color-link-underline--hover: var(--color-foreground-border);\n\n --color-link--visited: var(--color-brand-visited);\n --color-link-underline--visited: var(--color-background-border);\n --color-link--visited--hover: var(--color-brand-visited);\n --color-link-underline--visited--hover: var(--color-foreground-border);\n}\n\n@mixin colors-dark {\n --color-problematic: #ee5151;\n\n // Base Colors\n --color-foreground-primary: #cfd0d0; // 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: #3d94ff;\n --color-brand-content: #5ca5ff;\n --color-brand-visited: #b27aeb;\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 --color-api-added: #3db854;\n --color-api-added-border: #267334;\n --color-api-changed: #09b0ce;\n --color-api-changed-border: #056d80;\n --color-api-deprecated: #b1a10b;\n --color-api-deprecated-border: #6e6407;\n --color-api-removed: #ff7575;\n --color-api-removed-border: #b03b3b;\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-family: var(--font-stack--headings)\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 &:visited\n color: var(--color-link--visited)\n text-decoration-color: var(--color-link-underline--visited)\n &:hover\n color: var(--color-link--visited--hover)\n text-decoration-color: var(--color-link-underline--visited--hover)\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--hover)\n text-decoration-color: var(--color-link-underline--hover)\n &:visited\n color: var(--color-link--visited--hover)\n text-decoration-color: var(--color-link-underline--visited--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\n.skip-to-content\n position: fixed\n padding: 1rem\n border-radius: 1rem\n left: 0.25rem\n top: 0.25rem\n z-index: 40\n background: var(--color-background-primary)\n color: var(--color-foreground-primary)\n\n transform: translateY(-200%)\n transition: transform 300ms ease-in-out\n\n &:focus-within\n transform: translateY(0%)\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 display: flex\n\n.theme-toggle\n display: flex\n cursor: pointer\n border: none\n padding: 0\n background: transparent\n\n.theme-toggle svg\n height: 1.25rem\n width: 1.25rem\n color: var(--color-foreground-primary)\n display: none\n\n.theme-toggle-header\n display: flex\n align-items: center\n justify-content: center\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: 1.5rem\n width: 1.5rem\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, .view-this-page\n svg\n color: inherit\n height: 1.25rem\n width: 1.25rem\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: $content-padded-width + $sidebar-width)\n // Center the page\n .content\n margin-left: auto\n margin-right: auto\n padding: 0 $content-padding--small\n\n@media (max-width: $content-padded-width--small + $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, .theme-toggle-header\n display: flex\n .toc-content-icon, .theme-toggle-content\n display: none\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: 1.5rem\n width: 1.5rem\n\n // Add a scroll margin for the content\n :target\n scroll-margin-top: calc(var(--header-height) + 2.5rem)\n\n // Show back-to-top below the header\n .back-to-top\n top: calc(var(--header-height) + 0.5rem)\n\n // Accommodate for the header.\n .page\n flex-direction: column\n justify-content: center\n\n@media (max-width: $content-width + 2* $content-padding--small)\n // Content should respect window limits.\n .content\n width: 100%\n overflow-x: auto\n\n@media (max-width: $content-width)\n article[role=main] aside.sidebar\n float: none\n width: 100%\n margin: 1rem 0\n","// Overall Layout Variables\n//\n// Because CSS variables can't be used in media queries. The fact that this\n// makes the layout non-user-configurable is a good thing.\n$content-padding: 3em;\n$content-padding--small: 1em;\n$content-width: 46em;\n$sidebar-width: 15em;\n$content-padded-width: $content-width + 2 * $content-padding;\n$content-padded-width--small: $content-width + 2 * $content-padding--small;\n$full-width: $content-padded-width + 2 * $sidebar-width;\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: 4.25rem\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\ndiv.versionadded,\ndiv.versionchanged,\ndiv.deprecated,\ndiv.versionremoved\n border-left: 0.1875rem solid\n border-radius: 0.125rem\n\n padding-left: 0.75rem\n\n p\n margin-top: 0.125rem\n margin-bottom: 0.125rem\n\ndiv.versionadded\n border-color: var(--color-api-added-border)\n .versionmodified\n color: var(--color-api-added)\n\ndiv.versionchanged\n border-color: var(--color-api-changed-border)\n .versionmodified\n color: var(--color-api-changed)\n\ndiv.deprecated\n border-color: var(--color-api-deprecated-border)\n .versionmodified\n color: var(--color-api-deprecated)\n\ndiv.versionremoved\n border-color: var(--color-api-removed-border)\n .versionmodified\n color: var(--color-api-removed)\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 > *:not(span),\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","[role=main] .table-wrapper.container\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: 2.5rem\n\n@media (max-width: $full-width - $sidebar-width)\n :target\n scroll-margin-top: calc(2.5rem + var(--header-height))\n\n // When a heading is selected\n section > span:target\n scroll-margin-top: calc(2.8rem + 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 color: var(--color-sidebar-link-text)\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