diff --git a/.buildinfo b/.buildinfo index 39019b1..0402c76 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 -# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: e07c3107a8a25d17473060fb2e6124ca +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 900432164b9c866aa53e1a3da1beb1fa tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 617a694..5d151f2 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -4,11 +4,11 @@ - + Overview: module code - singler unknown documentation - - + + @@ -87,19 +87,6 @@ - - Auto light/dark mode - - - - - - - - - - Auto light/dark, in light mode - @@ -211,7 +198,7 @@
@@ -295,8 +282,8 @@

All modules for which code is available

- + - + \ No newline at end of file diff --git a/_modules/singler/annotate_integrated.html b/_modules/singler/annotate_integrated.html index befa506..c30aad2 100644 --- a/_modules/singler/annotate_integrated.html +++ b/_modules/singler/annotate_integrated.html @@ -4,11 +4,11 @@ - + singler.annotate_integrated - singler unknown documentation - - + + @@ -87,19 +87,6 @@ - - Auto light/dark mode - - - - - - - - - - Auto light/dark, in light mode - @@ -211,7 +198,7 @@
    -
  • Overview
    • +
  • Usage
  • Contributions & Help
  • License
  • Authors
    • @@ -257,34 +244,34 @@

    Source code for singler.annotate_integrated

     from typing import Any, Optional, Sequence, Tuple, Union
 
-from biocframe import BiocFrame
+import biocframe
+import warnings
 
-from ._utils import _clean_matrix
-from .annotate_single import _resolve_reference
-from .build_integrated_references import build_integrated_references
-from .build_single_reference import build_single_reference
-from .classify_integrated_references import classify_integrated_references
-from .classify_single_reference import classify_single_reference
+from ._utils import _clean_matrix, _restrict_features
+from .train_single import train_single
+from .train_integrated import train_integrated
+from .classify_single import classify_single
+from .classify_integrated import classify_integrated
 
 
 
    
 [docs]
 def annotate_integrated(
     test_data: Any,
-    ref_data_list: Sequence[Union[Any, str]],
-    test_features: Optional[Union[Sequence, str]] = None,
-    ref_labels_list: Optional[Union[Optional[str], Sequence[Union[Sequence, str]]]] = None,
-    ref_features_list: Optional[Union[Optional[str], Sequence[Union[Sequence, str]]]] = None,
+    ref_data: Sequence,
+    ref_labels: list[Sequence],
+    test_features: Optional[Sequence] = None,
+    ref_features: Optional[list[Optional[Sequence]]] = None,
     test_assay_type: Union[str, int] = 0,
-    test_check_missing: bool = True,
     ref_assay_type: Union[str, int] = "logcounts",
+    test_check_missing: bool = False,
     ref_check_missing: bool = True,
-    build_single_args: dict = {},
+    train_single_args: dict = {},
     classify_single_args: dict = {},
-    build_integrated_args: dict = {},
+    train_integrated_args: dict = {},
     classify_integrated_args: dict = {},
     num_threads: int = 1,
-) -> Tuple[list[BiocFrame], BiocFrame]:
+) -> Tuple[list[biocframe.BiocFrame], biocframe.BiocFrame]:
     """Annotate a single-cell expression dataset based on the correlation
     of each cell to profiles in multiple labelled references, where the
     annotation from each reference is then integrated across references.
@@ -292,65 +279,42 @@ 
    Source code for singler.annotate_integrated
         Args:
         test_data:
             A matrix-like object representing the test dataset, where rows are
-            features and columns are samples (usually cells). Entries should be expression
-            values; only the ranking within each column will be used.
+            features and columns are samples (usually cells). Entries should be
+            expression values; only the ranking within each column is used.
 
             Alternatively, a
             :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
             containing such a matrix in one of its assays.
 
-        test_features:
-            Sequence of length equal to the number of rows in
-            ``test_data``, containing the feature identifier for each row.
-
-            Alternatively, if ``test_data`` is a ``SummarizedExperiment``, ``test_features``
-            may be a string speciying the column name in `row_data` that contains the
-            features. It can also be set to `None`, to use the `row_names` of the
-            experiment as features.
-
-        ref_data_list:
+        ref_data:
             Sequence consisting of one or more of the following:
 
             - A matrix-like object representing the reference dataset, where rows
               are features and columns are samples. Entries should be expression values,
-              usually log-transformed (see comments for the ``ref`` argument in
-              :py:meth:`~singler.build_single_reference.build_single_reference`).
-            - A
-              :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
-              object containing such a matrix in its assays.
-            - A string that can be passed as ``name`` to
-              :py:meth:`~singler.fetch_reference.fetch_github_reference`.
-              This will use the specified dataset as the reference.
-
-        ref_labels_list:
-            Sequence of the same length as ``ref_data``, where the contents
-            depend on the type of value in the corresponding entry of ``ref_data``:
-
-            - If ``ref_data_list[i]`` is a matrix-like object, ``ref_labels_list[i]`` should be
-              a sequence of length equal to the number of columns of ``ref_data_list[i]``,
-              containing the label associated with each column.
-            - If ``ref_data_list[i]`` is a string, ``ref_labels_list[i]`` should be a string
-              specifying the label type to use, e.g., "main", "fine", "ont".
-              If a single string is supplied, it is recycled for all ``ref_data``.
-            - If ``ref_data_list[i]`` is a ``SummarizedExperiment``, ``ref_labels_list[i]``
-              may be a string speciying the column name in `column_data` that contains the
-              features. It can also be set to `None`, to use the `column_names`of the
-              experiment as features.
-
-        ref_features_list:
-            Sequence of the same length as ``ref_data_list``, where the contents
-            depend on the type of value in the corresponding entry of ``ref_data``:
-
-            - If ``ref_data_list[i]`` is a matrix-like object, ``ref_features_list[i]`` should be
-              a sequence of length equal to the number of rows of ``ref_data_list[i]``,
-              containing the feature identifier associated with each row.
-            - If ``ref_data_list[i]`` is a string, ``ref_features_list[i]`` should be a string
-              specifying the feature type to use, e.g., "ensembl", "symbol".
-              If a single string is supplied, it is recycled for all ``ref_data``.
-            - If ``ref_data_list[i]`` is a ``SummarizedExperiment``, ``ref_features_list[i]``
-              may be a string speciying the column name in `row_data` that contains the
-              features. It can also be set to `None`, to use the `row_names` of the
-              experiment as features.
+              usually log-transformed (see comments for the ``ref_data`` argument in
+              :py:func:`~singler.train_single.train_single`).
+            - A ``SummarizedExperiment`` object containing such a matrix in its assays.
+
+        ref_labels:
+            Sequence of the same length as ``ref_data``. The ``i``-th entry
+            should be a sequence of length equal to the number of columns of
+            ``ref_data[i]``, containing the label associated with each column.
+
+        test_features:
+            Sequence of length equal to the number of rows in ``test_data``,
+            containing the feature identifier for each row.  Alternatively
+            ``None``, to use the row names of the experiment as features.
+
+        ref_features:
+            Sequence of the same length as ``ref_data``. The ``i``-th entry
+            should be a sequence of length equal to the number of rows of
+            ``ref_data[i]``, containing the feature identifier associated with
+            each row. It can also be set to ``None`` to use the row names of
+            the experiment as features.
+
+            This can also be ``None`` to indicate that the row names should be
+            used for all references, assuming ``ref_data`` only contains
+            ``SummarizedExperiment`` objects.
 
         test_assay_type:
             Assay of ``test_data`` containing the expression matrix, if ``test_data`` is a
@@ -360,58 +324,50 @@ 
    Source code for singler.annotate_integrated
                 Whether to check for and remove missing (i.e., NaN) values from the test dataset.
 
         ref_assay_type:
-            Assay containing the expression matrix for any entry of ``ref_data_list`` that is a
+            Assay containing the expression matrix for any entry of ``ref_data`` that is a
             :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
 
         ref_check_missing:
             Whether to check for and remove missing (i.e., NaN) values from the reference datasets.
 
-        build_single_args:
+        train_single_args:
             Further arguments to pass to
-            :py:meth:`~singler.build_single_reference.build_single_reference`.
+            :py:func:`~singler.train_single.train_single`.
 
         classify_single_args:
             Further arguments to pass to
-            :py:meth:`~singler.classify_single_reference.classify_single_reference`.
+            :py:func:`~singler.classify_single.classify_single`.
 
-        build_integrated_args:
+        train_integrated_args:
             Further arguments to pass to
-            :py:meth:`~singler.build_integrated_references.build_integrated_references`.
+            :py:func:`~singler.train_integrated.train_integrated`.
 
         classify_integrated_args:
             Further arguments to pass to
-            :py:meth:`~singler.classify_integrated_references.classify_integrated_references`.
+            :py:func:`~singler.classify_integrated.classify_integrated`.
 
         num_threads:
             Number of threads to use for the various steps.
 
     Returns:
         Tuple where the first element contains per-reference results (i.e. a
-        list of BiocFrame outputs equivalent to running
-        :py:meth:`~singler.annotate_single.annotate_single` on each reference)
+        list of BiocFrame outputs, roughly equivalent to running
+        :py:func:`~singler.annotate_single.annotate_single` on each reference)
         and the second element contains integrated results across references
         (i.e., a BiocFrame from
-        :py:meth:`~singler.classify_integrated_references.classify_integrated_references`).
+        :py:func:`~singler.classify_integrated.classify_integrated`).
     """
-    nrefs = len(ref_data_list)
-
-    if isinstance(ref_labels_list, str):
-        ref_labels_list = [ref_labels_list] * nrefs
-    elif ref_labels_list is None:
-        ref_labels_list = [None] * nrefs
-
-    if nrefs != len(ref_labels_list):
-        raise ValueError("'ref_data_list' and 'ref_labels_list' must be the same length")
-
-    if isinstance(ref_features_list, str):
-        ref_features_list = [ref_features_list] * nrefs
-    elif ref_features_list is None:
-        ref_features_list = [None] * nrefs
-
-    if nrefs != len(ref_features_list):
-        raise ValueError("'ref_data_list' and 'ref_features_list' must be the same length")
-
-    test_ptr, test_features = _clean_matrix(
+    nrefs = len(ref_data)
+    if nrefs != len(ref_labels):
+        raise ValueError("'ref_data' and 'ref_labels' must be the same length")
+    if ref_features is None:
+        ref_features = [None] * nrefs
+    if nrefs != len(ref_features):
+        raise ValueError("'ref_data' and 'ref_features' must be the same length")
+    if nrefs != len(ref_labels):
+        raise ValueError("'ref_data' and 'ref_labels' must be the same length")
+
+    test_data, test_features = _clean_matrix(
         test_data,
         test_features,
         assay_type=test_assay_type,
@@ -422,66 +378,72 @@ 
    Source code for singler.annotate_integrated
         all_ref_data = []
     all_ref_labels = []
     all_ref_features = []
-    all_built = []
-    all_results = []
-    test_features_set = set(test_features)
-
     for r in range(nrefs):
-        curref_mat, curref_labels, curref_features = _resolve_reference(
-            ref_data=ref_data_list[r],
-            ref_labels=ref_labels_list[r],
-            ref_features=ref_features_list[r],
-            build_args=build_single_args,
-        )
+        curref_labels = ref_labels[r]
+        if isinstance(curref_labels, str):
+            warnings.warn(
+                "setting 'ref_labels' to a column name of the column data is deprecated",
+                category=DeprecationWarning
+            )
+            curref_labels = ref_data[r].get_column_data().column(curref_labels)
+        all_ref_labels.append(curref_labels)
 
-        curref_ptr, curref_features = _clean_matrix(
-            curref_mat,
-            curref_features,
+        curref_data, curref_features = _clean_matrix(
+            ref_data[r],
+            ref_features[r],
             assay_type=ref_assay_type,
             check_missing=ref_check_missing,
             num_threads=num_threads,
         )
 
-        curbuilt = build_single_reference(
-            ref_data=curref_ptr,
-            ref_labels=curref_labels,
-            ref_features=curref_features,
-            restrict_to=test_features_set,
-            **build_single_args,
+        all_ref_data.append(curref_data)
+        all_ref_features.append(curref_features)
+
+        # Pre-slicing the test dataset so that we force the downstream analysis
+        # to only consider genes that are present in all datasets (test and
+        # reference). This avoids the warning in classify_integrated().
+        test_data, test_features = _restrict_features(
+            test_data,
+            test_features,
+            curref_features
+        )
+
+    if test_data.shape[0] == 0:
+        raise ValueError("no genes in common across test and reference datasets")
+
+    all_built = []
+    all_results = []
+
+    for r in range(nrefs):
+        curbuilt = train_single(
+            ref_data=all_ref_data[r],
+            ref_labels=all_ref_labels[r],
+            ref_features=all_ref_features[r],
+            test_features=test_features,
+            **train_single_args,
+            check_missing=False,
             num_threads=num_threads,
         )
 
-        res = classify_single_reference(
+        res = classify_single(
             test_data,
-            test_features=test_features,
             ref_prebuilt=curbuilt,
             **classify_single_args,
             num_threads=num_threads,
         )
 
-        all_ref_data.append(curref_ptr)
-        all_ref_labels.append(curref_labels)
-        all_ref_features.append(curref_features)
         all_built.append(curbuilt)
         all_results.append(res)
 
-        res.metadata = {
-            "markers": curbuilt.markers,
-            "unique_markers": curbuilt.marker_subset(),
-        }
-
-    ibuilt = build_integrated_references(
+    ibuilt = train_integrated(
         test_features=test_features,
-        ref_data_list=all_ref_data,
-        ref_labels_list=all_ref_labels,
-        ref_features_list=all_ref_features,
-        ref_prebuilt_list=all_built,
-        **build_integrated_args,
+        ref_prebuilt=all_built,
+        **train_integrated_args,
         num_threads=num_threads,
     )
 
-    ires = classify_integrated_references(
-        test_data=test_ptr,
+    ires = classify_integrated(
+        test_data=test_data,
         results=all_results,
         integrated_prebuilt=ibuilt,
         **classify_integrated_args,
@@ -523,8 +485,8 @@ 
    Source code for singler.annotate_integrated
         
   
    
 
    
-    
+    
     
-    
+    
     
 
\ No newline at end of file
diff --git a/_modules/singler/annotate_single.html b/_modules/singler/annotate_single.html
index e649834..d6f4c2e 100644
--- a/_modules/singler/annotate_single.html
+++ b/_modules/singler/annotate_single.html
@@ -4,11 +4,11 @@
     
     
 
-    
+    
         singler.annotate_single - singler unknown documentation
       
-    
-    
+    
+    
     
     
 
@@ -87,19 +87,6 @@
       
     
   
-  
-    Auto light/dark mode
-    
-      
-      
-      
-      
-      
-      
-      
-    
-  
   
     Auto light/dark, in light mode
     
       
       
-      
     
   
   
@@ -211,7 +198,7 @@
 
 
    
   
      
-
    • Overview
      • 
+
    • Usage
      • 
 
    • Contributions & Help
      • 
 
    • License
      • 
 
    • Authors
      • 
@@ -258,45 +245,12 @@ 
      Source code for singler.annotate_single
       import warnings
 from typing import Any, Optional, Sequence, Union
 
-from biocframe import BiocFrame
-from summarizedexperiment import SummarizedExperiment
-
-from .build_single_reference import build_single_reference
-from .classify_single_reference import classify_single_reference
-
-
-def _resolve_reference(ref_data, ref_labels, ref_features, build_args):
-    if isinstance(ref_data, SummarizedExperiment) or issubclass(type(ref_data), SummarizedExperiment):
-        if ref_features is None:
-            ref_features = ref_data.get_row_names()
-        elif isinstance(ref_features, str):
-            ref_features = ref_data.get_row_data().column(ref_features)
-
-        ref_features = list(ref_features)
-
-        if ref_labels is None:
-            ref_labels = ref_data.get_column_names()
-        elif isinstance(ref_labels, str):
-            ref_labels = ref_data.get_column_data().column(ref_labels)
+import biocframe
+import summarizedexperiment
 
-        ref_labels = list(ref_labels)
-
-        try:
-            _default_asy = "logcounts"
-            if "assay_type" in build_args:
-                _default_asy = build_args["assay_type"]
-
-            ref_data = ref_data.assay(_default_asy)
-        except Exception as _:
-            raise ValueError(f"Reference dataset must contain log-normalized count ('{_default_asy}') assay.")
-
-    if ref_labels is None:
-        raise ValueError("'ref_labels' cannot be `None`.")
-
-    if ref_features is None:
-        raise ValueError("'ref_features' cannot be `None`.")
-
-    return ref_data, ref_labels, ref_features
+from .train_single import train_single 
+from .classify_single import classify_single
+from ._utils import _clean_matrix, _restrict_features
 
 
 
      
@@ -304,13 +258,17 @@ 
      Source code for singler.annotate_single
       def annotate_single(
     test_data: Any,
     ref_data: Any,
-    ref_labels: Optional[Union[Sequence, str]],
-    test_features: Optional[Union[Sequence, str]] = None,
-    ref_features: Optional[Union[Sequence, str]] = None,
-    build_args: dict = {},
+    ref_labels: Sequence,
+    test_features: Optional[Sequence] = None,
+    ref_features: Optional[Sequence] = None,
+    test_assay_type: Union[str, int] = 0,
+    ref_assay_type: Union[str, int] = 0,
+    test_check_missing: bool = False,
+    ref_check_missing: bool = True,
+    train_args: dict = {},
     classify_args: dict = {},
     num_threads: int = 1,
-) -> BiocFrame:
+) -> biocframe.BiocFrame:
     """Annotate a single-cell expression dataset based on the correlation
     of each cell to profiles in a labelled reference.
 
@@ -325,20 +283,11 @@ 
      Source code for singler.annotate_single
                   containing such a matrix in one of its assays. Non-default assay
             types can be specified in ``classify_args``.
 
-        test_features:
-            Sequence of length equal to the number of rows in
-            ``test_data``, containing the feature identifier for each row.
-
-            Alternatively, if ``test_data`` is a ``SummarizedExperiment``, ``test_features``
-            may be a string speciying the column name in `row_data` that contains the
-            features. It can also be set to `None`, to use the `row_names` of
-            the experiment as features.
-
         ref_data:
             A matrix-like object representing the reference dataset, where rows
             are features and columns are samples. Entries should be expression values,
             usually log-transformed (see comments for the ``ref`` argument in
-            :py:meth:`~singler.build_single_reference.build_single_reference`).
+            :py:func:`~singler.train_single.train_single`).
 
             Alternatively, a
             :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
@@ -346,89 +295,94 @@ 
      Source code for singler.annotate_single
                   types can be specified in ``classify_args``.
 
         ref_labels:
-            If ``ref_data`` is a matrix-like object, ``ref_labels`` should be
-            a sequence of length equal to the number of columns of ``ref_data``,
+            Sequence of length equal to the number of columns of ``ref_data``,
             containing the label associated with each column.
 
-            Alternatively, if ``ref_data`` is a ``SummarizedExperiment``, 
-            ``ref_labels`` may be a string specifying the label type to use,
-            e.g., "main", "fine", "ont". It can also be set to `None`, to use 
-            the `row_names` of the experiment as features.
+        test_features:
+            Sequence of length equal to the number of rows in ``test_data``,
+            containing the feature identifier for each row. Alternatively
+            ``None``, to use the row names of the experiment as features.
 
         ref_features:
-            If ``ref_data`` is a matrix-like object, ``ref_features`` should be
-            a sequence of length equal to the number of rows of ``ref_data``,
-            containing the feature identifier associated with each row.
+            Sequence of length equal to the number of rows of ``ref_data``,
+            containing the feature identifier for each row. Alternatively
+            ``None``, to use the row names of the experiment as features.
+
+        test_assay_type:
+            Assay containing the expression matrix, if ``test_data`` is a
+            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
+
+        ref_assay_type:
+            Assay containing the expression matrix, if ``ref_data`` is a
+            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
 
-            Alternatively, if ``ref_data`` is a ``SummarizedExperiment``, 
-            ``ref_features`` may be a string speciying the column name in `column_data`
-            that contains the features. It can also be set to `None`, to use the 
-            `row_names` of the experiment as features.
+        test_assay_type:
+            Whether to remove rows with missing values from the test dataset.
 
-        build_args:
+        ref_assay_type:
+            Whether to remove rows with missing values from the reference dataset.
+
+        train_args:
             Further arguments to pass to
-            :py:meth:`~singler.build_single_reference.build_single_reference`.
+            :py:func:`~singler.train_single.train_single`.
 
         classify_args:
             Further arguments to pass to
-            :py:meth:`~singler.classify_single_reference.classify_single_reference`.
+            :py:func:`~singler.classify_single.classify_single`.
 
         num_threads:
             Number of threads to use for the various steps.
 
     Returns:
-        A data frame containing the labelling results, see
-        :py:meth:`~singler.classify_single_reference.classify_single_reference`
-        for details. The metadata also contains a ``markers`` dictionary,
-        specifying the markers that were used for each pairwise comparison
-        between labels; and a list of ``unique_markers`` across all labels.
+        A :py:class:`~biocframe.BiocFrame.BiocFrame` of labelling results, see
+        :py:func:`~singler.classify_single.classify_single` for details.
     """
+    if isinstance(ref_labels, str):
+        warnings.warn(
+            "setting 'ref_labels' to a column name of the column data is deprecated",
+            category=DeprecationWarning
+        )
+        ref_labels = ref_data.get_column_data().column(ref_labels)
+
+    test_data, test_features = _clean_matrix(
+        test_data,
+        test_features,
+        assay_type=test_assay_type,
+        check_missing=test_check_missing,
+        num_threads=num_threads
+    )
 
-    if isinstance(test_data, SummarizedExperiment):
-        if test_features is None:
-            test_features = test_data.get_row_names()
-        elif isinstance(test_features, str):
-            test_features = test_data.get_row_data().column(test_features)
-
-    if test_features is None:
-        raise ValueError("'test_features' cannot be `None`.")
-
-    test_features_set = set(test_features)
-    if len(test_features_set) != len(test_features):
-        warnings.warn("'test_features' is not unique, subsetting test matrix...", UserWarning)
-        _idxs = [test_features.index(x) for x in test_features_set]
-        print("modifying test data")
-        test_data = test_data[_idxs,]
+    ref_data, ref_features = _clean_matrix(
+        ref_data,
+        ref_features,
+        assay_type=ref_assay_type,
+        check_missing=ref_check_missing,
+        num_threads=num_threads
+    )
 
-    ref_data, ref_labels, ref_features = _resolve_reference(
-        ref_data=ref_data,
-        ref_labels=ref_labels,
-        ref_features=ref_features,
-        build_args=build_args,
+    # Pre-slicing the test dataset for consistency with annotate_integrated.
+    test_data, test_features = _restrict_features(
+        test_data,
+        test_features,
+        ref_features
     )
 
-    built = build_single_reference(
+    built = train_single(
         ref_data=ref_data,
         ref_labels=ref_labels,
         ref_features=ref_features,
-        restrict_to=test_features_set,
-        **build_args,
+        test_features=test_features,
+        check_missing=False,
         num_threads=num_threads,
+        **train_args,
     )
 
-    output = classify_single_reference(
+    return classify_single(
         test_data,
-        test_features=test_features,
         ref_prebuilt=built,
         **classify_args,
         num_threads=num_threads,
-    )
-
-    output.metadata = {
-        "markers": built.markers,
-        "unique_markers": built.marker_subset(),
-    }
-    return output
      
+    )
      
 
 
      
         
@@ -463,8 +417,8 @@ 
      Source code for singler.annotate_single
           
   
      
 
      
-    
+    
     
-    
+    
     
 
\ No newline at end of file
diff --git a/_modules/singler/build_integrated_references.html b/_modules/singler/build_integrated_references.html
deleted file mode 100644
index ba18ab9..0000000
--- a/_modules/singler/build_integrated_references.html
+++ /dev/null
@@ -1,472 +0,0 @@
-
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-  
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-        singler.build_integrated_references - singler unknown documentation
-      
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-    
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      singler unknown documentation
      
-    
      
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-  
      
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-          Back to top
-        
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-          
-        
      
-        
      
-          
      Source code for singler.build_integrated_references
      -from typing import Sequence, Optional, Union
-from numpy import array, ndarray, int32, uintp
-
-import biocutils as ut
-
-from .build_single_reference import SinglePrebuiltReference
-from . import _cpphelpers as lib
-from ._utils import _stable_union, _factorize, _clean_matrix
-
-
-
      
-[docs]
-class IntegratedReferences:
-    """Object containing integrated references, typically constructed by
-    :py:meth:`~singler.build_integrated_references.build_integrated_references`."""
-
-    def __init__(self, ptr, ref_names, ref_labels, test_features):
-        self._ptr = ptr
-        self._names = ref_names
-        self._labels = ref_labels
-        self._features = test_features
-
-    def __del__(self):
-        lib.free_integrated_references(self._ptr)
-
-    @property
-    def reference_names(self) -> Union[Sequence[str], None]:
-        """Sequence containing the names of the references. Alternatively
-        None, if no names were supplied."""
-        return self._names
-
-    @property
-    def reference_labels(self) -> list:
-        """List of lists containing the names of the labels for each reference.
-
-        Each entry corresponds to a reference in :py:attr:`~reference_names`,
-        if ``reference_names`` is not None.
-        """
-        return self._labels
-
-    @property
-    def test_features(self) -> list[str]:
-        """Sequence containing the names of the test features."""
-        return self._features
      
-
-
-
-
      
-[docs]
-def build_integrated_references(
-    test_features: Sequence,
-    ref_data_list: dict,
-    ref_labels_list: list[Sequence],
-    ref_features_list: list[Sequence],
-    ref_prebuilt_list: list[SinglePrebuiltReference],
-    ref_names: Optional[Sequence[str]] = None,
-    assay_type: Union[str, int] = "logcounts",
-    check_missing: bool = True,
-    num_threads: int = 1,
-) -> IntegratedReferences:
-    """Build a set of integrated references for classification of a test dataset.
-
-    Arguments:
-        test_features:
-            Sequence of features for the test dataset.
-
-        ref_data_list:
-            List of reference datasets, where each entry is equivalent to ``ref_data`` in
-            :py:meth:`~singler.build_single_reference.build_single_reference`.
-
-        ref_labels_list:
-            List of reference labels, where each entry is equivalent to ``ref_labels`` in
-            :py:meth:`~singler.build_single_reference.build_single_reference`.
-
-        ref_features_list:
-            List of reference features, where each entry is equivalent to ``ref_features`` in
-            :py:meth:`~singler.build_single_reference.build_single_reference`.
-
-        ref_prebuilt_list:
-            List of prebuilt references, typically created by
-            calling :py:meth:`~singler.build_single_reference.build_single_reference` on the corresponding
-            elements of ``ref_data_list``, ``ref_labels_list`` and ``ref_features_list``.
-
-        ref_names:
-            Sequence of names for the references.
-            If None, these are automatically generated.
-
-        assasy_type:
-            Assay containing the expression matrix for any entry of ``ref_data_list`` that is a
-            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
-
-        check_missing:
-            Whether to check for and remove rows with missing (NaN) values
-            from each entry of ``ref_data_list``.
-
-        num_threads:
-            Number of threads.
-
-    Returns:
-        Integrated references for classification with
-        :py:meth:`~singler.classify_integrated_references.classify_integrated_references`.
-    """
-    nrefs = len(ref_data_list)
-    if nrefs != len(ref_features_list):
-        raise ValueError(
-            "'ref_features_list' and 'ref_data_list' should have the same length"
-        )
-
-    universe = _stable_union(test_features, *ref_features_list)
-    original_test_features = test_features
-    test_features = array(ut.match(test_features, universe), dtype=int32)
-
-    converted_ref_data = []
-    ref_data_ptrs = ndarray(nrefs, dtype=uintp)
-    converted_feature_data = []
-    ref_features_ptrs = ndarray(nrefs, dtype=uintp)
-
-    for i, x in enumerate(ref_data_list):
-        curptr, curfeatures = _clean_matrix(
-            x,
-            ref_features_list[i],
-            assay_type=assay_type,
-            check_missing=check_missing,
-            num_threads=num_threads,
-        )
-        converted_ref_data.append(curptr)
-        ref_data_ptrs[i] = curptr.ptr
-
-        ind = array(ut.match(curfeatures, universe), dtype=int32)
-        converted_feature_data.append(ind)
-        ref_features_ptrs[i] = ind.ctypes.data
-
-    if nrefs != len(ref_labels_list):
-        raise ValueError(
-            "'ref_labels_list' and 'ref_data_list' should have the same length"
-        )
-    converted_label_levels = []
-    converted_label_indices = []
-    ref_labels_ptrs = ndarray(nrefs, dtype=uintp)
-    for i, x in enumerate(ref_labels_list):
-        lev, ind = _factorize(x)
-        converted_label_levels.append(lev)
-        ind = array(ind, dtype=int32)
-        converted_label_indices.append(ind)
-        ref_labels_ptrs[i] = ind.ctypes.data
-
-    if nrefs != len(ref_prebuilt_list):
-        raise ValueError(
-            "'ref_prebuilt_list' and 'ref_data_list' should have the same length"
-        )
-    ref_prebuilt_ptrs = ndarray(nrefs, dtype=uintp)
-    for i, x in enumerate(ref_prebuilt_list):
-        ref_prebuilt_ptrs[i] = x._ptr
-
-    if ref_names is not None:
-        if nrefs != len(ref_names):
-            raise ValueError(
-                "'ref_names' and 'ref_data_list' should have the same length"
-            )
-        elif nrefs != len(set(ref_names)):
-            raise ValueError("'ref_names' should contain unique names")
-
-    output = lib.build_integrated_references(
-        len(test_features),
-        test_features,
-        nrefs,
-        ref_data_ptrs.ctypes.data,
-        ref_labels_ptrs.ctypes.data,
-        ref_features_ptrs.ctypes.data,
-        ref_prebuilt_ptrs.ctypes.data,
-        num_threads,
-    )
-
-    return IntegratedReferences(
-        output, ref_names, converted_label_levels, original_test_features
-    )
      
-
-
      
-        
      
-      
      
-      
      
-        
-        
      
-          
-          
-        
      
-        
      
-          
      
-            
      
-                Copyright © 2023, Aaron Lun
-            
      
-            Made with Sphinx and @pradyunsg's
-            
-            Furo
-            
-          
      
-          
      
-            
-          
      
-        
      
-        
-      
      
-    
      
-    
-  
      
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\ No newline at end of file
diff --git a/_modules/singler/build_single_reference.html b/_modules/singler/build_single_reference.html
deleted file mode 100644
index 9067903..0000000
--- a/_modules/singler/build_single_reference.html
+++ /dev/null
@@ -1,522 +0,0 @@
-
-
-  
-    
-    
-
-    
-        singler.build_single_reference - singler unknown documentation
-      
-    
-    
-    
-    
-
-
-
-  
-    
-    
-    
-
-
-  
-    Contents
-    
-      
-    
-  
-  
-    Menu
-    
-      
-      
-      
-    
-  
-  
-    Expand
-    
-      
-    
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-    Light mode
-    
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-    
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-  
      
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-      
      singler unknown documentation
      
-    
      
-    
      
-      
      
-        
-      
      
-      
-    
      
-  
      
-  
-  
      
-    
      
-      
      
-        
-          
-            
-          
-          Back to top
-        
-        
      
-          
      
-            
-          
      
-          
-        
      
-        
      
-          
      Source code for singler.build_single_reference
      -from typing import Any, Literal, Optional, Sequence, Union
-
-import biocutils as ut
-from numpy import array, int32, ndarray
-
-from . import _cpphelpers as lib
-from ._Markers import _Markers
-from ._utils import _clean_matrix, _factorize, _restrict_features
-from .get_classic_markers import _get_classic_markers_raw
-
-
-
      
-[docs]
-class SinglePrebuiltReference:
-    """A prebuilt reference object, typically created by
-    :py:meth:`~singler.build_single_reference.build_single_reference`. This is intended for advanced users only and
-    should not be serialized.
-    """
-
-    def __init__(
-        self,
-        ptr,
-        labels: Sequence,
-        features: Sequence,
-        markers: dict[Any, dict[Any, Sequence]],
-    ):
-        self._ptr = ptr
-        self._features = features
-        self._labels = labels
-        self._markers = markers
-
-    def __del__(self):
-        lib.free_single_reference(self._ptr)
-
-
      
-[docs]
-    def num_markers(self) -> int:
-        """
-        Returns:
-            Number of markers to be used for classification. This is the
-            same as the size of the array from :py:meth:`~marker_subset`.
-        """
-        return lib.get_nsubset_from_single_reference(self._ptr)
      
-
-
-
      
-[docs]
-    def num_labels(self) -> int:
-        """
-        Returns:
-            Number of unique labels in this reference.
-        """
-        return lib.get_nlabels_from_single_reference(self._ptr)
      
-
-
-    @property
-    def features(self) -> Sequence:
-        """
-        Returns:
-            The universe of features known to this reference, usually as strings.
-        """
-        return self._features
-
-    @property
-    def labels(self) -> Sequence:
-        """
-        Returns:
-            Unique labels in this reference.
-        """
-        return self._labels
-
-    @property
-    def markers(self) -> dict[Any, dict[Any, Sequence]]:
-        """
-        Returns:
-            Markers for every pairwise comparison between labels.
-        """
-        return self._markers
-
-
      
-[docs]
-    def marker_subset(self, indices_only: bool = False) -> Union[ndarray, list]:
-        """
-        Args:
-            indices_only:
-                Whether to return the markers as indices
-                into :py:attr:`~features`, or as a list of feature identifiers.
-
-        Returns:
-            If ``indices_only = False``, a list of feature identifiers for the markers.
-
-            If ``indices_only = True``, a NumPy array containing the integer indices of
-            features in ``features`` that were chosen as markers.
-        """
-        nmarkers = self.num_markers()
-        buffer = ndarray(nmarkers, dtype=int32)
-        lib.get_subset_from_single_reference(self._ptr, buffer)
-        if indices_only:
-            return buffer
-        else:
-            return [self._features[i] for i in buffer]
      
-
      
-
-
-
-
      
-[docs]
-def build_single_reference(
-    ref_data: Any,
-    ref_labels: Sequence,
-    ref_features: Sequence,
-    assay_type: Union[str, int] = "logcounts",
-    check_missing: bool = True,
-    restrict_to: Optional[Union[set, dict]] = None,
-    markers: Optional[dict[Any, dict[Any, Sequence]]] = None,
-    marker_method: Literal["classic"] = "classic",
-    marker_args: dict = {},
-    approximate: bool = True,
-    num_threads: int = 1,
-) -> SinglePrebuiltReference:
-    """Build a single reference dataset in preparation for classification.
-
-    Args:
-        ref_data:
-            A matrix-like object where rows are features, columns are
-            reference profiles, and each entry is the expression value.
-            If `markers` is not provided, expression should be normalized
-            and log-transformed in preparation for marker prioritization via
-            differential expression analyses. Otherwise, any expression values
-            are acceptable as only the ranking within each column is used.
-
-            Alternatively, a
-            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
-            containing such a matrix in one of its assays.
-
-        labels:
-            Sequence of labels for each reference profile,
-            i.e., column in ``ref``.
-
-        features:
-            Sequence of identifiers for each feature,
-            i.e., row in ``ref``.
-
-        assay_type:
-            Assay containing the expression matrix,
-            if `ref_data` is a
-            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
-
-        check_missing:
-            Whether to check for and remove rows with missing (NaN) values
-            from ``ref_data``.
-
-        restrict_to:
-            Subset of available features to restrict to. Only features in
-            ``restrict_to`` will be used in the reference building. If None,
-            no restriction is performed.
-
-        markers:
-            Upregulated markers for each pairwise comparison between labels.
-            Specifically, ``markers[a][b]`` should be a sequence of features
-            that are upregulated in ``a`` compared to ``b``. All such features
-            should be present in ``features``, and all labels in ``labels``
-            should have keys in the inner and outer dictionaries.
-
-        marker_method:
-            Method to identify markers from each pairwise comparisons between
-            labels in ``ref_data``.  If "classic", we call
-            :py:meth:`~singler.get_classic_markers.get_classic_markers`.
-            Only used if ``markers`` is not supplied.
-
-        marker_args:
-            Further arguments to pass to the chosen marker detection method.
-            Only used if ``markers`` is not supplied.
-
-        approximate:
-            Whether to use an approximate neighbor search to compute scores
-            during classification.
-
-        num_threads:
-            Number of threads to use for reference building.
-
-    Returns:
-        The pre-built reference, ready for use in downstream methods like
-        :py:meth:`~singler.classify_single_reference.classify_single_reference`.
-    """
-
-    ref_ptr, ref_features = _clean_matrix(
-        ref_data,
-        ref_features,
-        assay_type=assay_type,
-        check_missing=check_missing,
-        num_threads=num_threads,
-    )
-
-    ref_ptr, ref_features = _restrict_features(ref_ptr, ref_features, restrict_to)
-
-    if markers is None:
-        if marker_method == "classic":
-            mrk, lablev, ref_features = _get_classic_markers_raw(
-                ref_ptrs=[ref_ptr],
-                ref_labels=[ref_labels],
-                ref_features=[ref_features],
-                num_threads=num_threads,
-                **marker_args,
-            )
-            markers = mrk.to_dict(lablev, ref_features)
-            labind = array(ut.match(ref_labels, lablev), dtype=int32)
-        else:
-            raise NotImplementedError("other marker methods are not implemented, sorry")
-    else:
-        lablev, labind = _factorize(ref_labels)
-        labind = array(labind, dtype=int32)
-        mrk = _Markers.from_dict(markers, lablev, ref_features)
-
-    return SinglePrebuiltReference(
-        lib.build_single_reference(
-            ref_ptr.ptr,
-            labels=labind,
-            markers=mrk._ptr,
-            approximate=approximate,
-            nthreads=num_threads,
-        ),
-        labels=lablev,
-        features=ref_features,
-        markers=markers,
-    )
      
-
-
      
-        
      
-      
      
-      
      
-        
-        
      
-          
-          
-        
      
-        
      
-          
      
-            
      
-                Copyright © 2023, Aaron Lun
-            
      
-            Made with Sphinx and @pradyunsg's
-            
-            Furo
-            
-          
      
-          
      
-            
-          
      
-        
      
-        
-      
      
-    
      
-    
-  
      
-
      
-    
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diff --git a/_modules/singler/classify_integrated_references.html b/_modules/singler/classify_integrated.html
similarity index 56%
rename from _modules/singler/classify_integrated_references.html
rename to _modules/singler/classify_integrated.html
index b4f0cf8..870ba9f 100644
--- a/_modules/singler/classify_integrated_references.html
+++ b/_modules/singler/classify_integrated.html
@@ -4,11 +4,11 @@
     
     
 
-    
-        singler.classify_integrated_references - singler unknown documentation
+    
+        singler.classify_integrated - singler unknown documentation
       
-    
-    
+    
+    
     
     
 
@@ -87,19 +87,6 @@
       
     
   
-  
-    Auto light/dark mode
-    
-      
-      
-      
-      
-      
-      
-      
-    
-  
   
     Auto light/dark, in light mode
     
       
       
-      
     
   
   
@@ -211,7 +198,7 @@
 
 
      
   
      
         
      
-          
      Source code for singler.classify_integrated_references
      +          
      Source code for singler.classify_integrated
       from typing import Any, Sequence, Union
 
-import biocutils as ut
-from biocframe import BiocFrame
-from mattress import TatamiNumericPointer, tatamize
-from numpy import array, float64, int32, ndarray, uintp
-from summarizedexperiment import SummarizedExperiment
+import biocutils
+import biocframe 
+import mattress
+import summarizedexperiment
+import numpy
 
-from . import _cpphelpers as lib
-from .build_integrated_references import IntegratedReferences
+from . import lib_singler as lib
+from .train_integrated import TrainedIntegratedReferences
 
 
-
      
-[docs]
-def classify_integrated_references(
+
      
+[docs]
+def classify_integrated(
     test_data: Any,
-    results: list[Union[BiocFrame, Sequence]],
-    integrated_prebuilt: IntegratedReferences,
+    results: list[biocframe.BiocFrame],
+    integrated_prebuilt: TrainedIntegratedReferences,
     assay_type: Union[str, int] = 0,
     quantile: float = 0.8,
+    use_fine_tune: bool = True,
+    fine_tune_threshold: float = 0.05,
     num_threads: int = 1,
-) -> BiocFrame:
+) -> biocframe.BiocFrame:
     """Integrate classification results across multiple references for a single test dataset.
 
     Args:
@@ -292,17 +281,16 @@ 
      Source code for singler.classify_integrated_references
              results:
             List of classification results generated by running
-            :py:meth:`~singler.classify_single_reference.classify_single_reference`
-            on ``test_data`` with each reference. This may be either the full
-            data frame or just the ``"best"`` column. References should be ordered
-            as in ``integrated_prebuilt.reference_names``.
+            :py:func:`~singler.classify_single.classify_single` on
+            ``test_data`` with each reference. References should be in the
+            same order as that used to construct ``integrated_prebuilt``.
 
         integrated_prebuilt:
             Integrated reference object, constructed with
-            :py:meth:`~singler.build_integrated_references.build_integrated_references`.
+            :py:func:`~singler.train_integrated.train_integrated`.
 
-        assay_type: Assay containing the expression matrix,
-            if `test_data` is a
+        assay_type:
+            Assay containing the expression matrix, if ``test_data`` is a
             :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
 
         quantile:
@@ -310,96 +298,83 @@ 
      Source code for singler.classify_integrated_references
                  Larger values increase sensitivity of matches at the expense of
             similarity to the average behavior of each label.
 
+        use_fine_tune:
+            Whether fine-tuning should be performed. This improves accuracy for
+            distinguishing between references with similar best labels but
+            requires more computational work.
+
+        fine_tune_threshold:
+            Maximum difference from the maximum correlation to use in
+            fine-tuning. All references above this threshold are used for
+            another round of fine-tuning.
+
         num_threads:
             Number of threads to use during classification.
 
     Returns:
-        A data frame containing the ``best_label`` across all
-        references, defined as the assigned label in the best reference; the
-        identity of the ``best_reference``, either as a name string or an
-        integer index; the ``scores`` for each reference, as a nested
-        BiocFrame; and the ``delta`` from the best to the second-best
-        reference. Each row corresponds to a column of ``test``.
+        A :py:class:`~biocframe.BiocFrame.BiocFrame` containing the
+        ``best_label`` across all references, defined as the assigned label in
+        the best reference; the identity of the ``best_reference``, either as a
+        name string or an integer index; the ``scores`` for the best label in
+        each reference, as a nested ``BiocFrame``; and the ``delta`` from the
+        best to the second-best reference. Each row corresponds to a column of
+        ``test_data``.
     """
-    # Don't use _clean_matrix; the features are fixed so no filtering is possible at this point.
-    if not isinstance(test_data, TatamiNumericPointer):
-        if isinstance(test_data, SummarizedExperiment):
-            test_data = test_data.assay(assay_type)
-
-    test_ptr = tatamize(test_data)
-    if test_ptr.nrow() != len(integrated_prebuilt.test_features):
-        raise ValueError(
-            "number of rows in 'test_data' should equal number of features in 'integrated_prebuilt'"
-        )
-    nc = test_ptr.ncol()
-
-    all_labels = integrated_prebuilt.reference_labels
-    nrefs = len(all_labels)
-    coerced_labels = []
-
-    all_refs = integrated_prebuilt.reference_names
-    has_names = all_refs is not None
-    if not has_names:
-        all_refs = [str(i) for i in range(nrefs)]
-
-    scores = {}
-    score_ptrs = ndarray((nrefs,), dtype=uintp)
-    assign_ptrs = ndarray((nrefs,), dtype=uintp)
-
-    if len(all_refs) != len(results):
-        raise ValueError(
-            "length of 'results' should equal number of references in 'integrated_prebuilt'"
-        )
-
-    for i, r in enumerate(all_refs):
-        current = ndarray((nc,), dtype=float64)
-        scores[r] = current
-        score_ptrs[i] = current.ctypes.data
-
-        curlabs = results[i]
-        if isinstance(curlabs, BiocFrame):
-            curlabs = curlabs.column("best")
-        if len(curlabs) != nc:
-            raise ValueError(
-                "each entry of 'results' should have results for all cells in 'test_data'"
-            )
-
-        ind = array(ut.match(curlabs, all_labels[i]), dtype=int32)
-        coerced_labels.append(ind)
-        assign_ptrs[i] = ind.ctypes.data
-
-    best = ndarray((nc,), dtype=int32)
-    delta = ndarray((nc,), dtype=float64)
-    lib.classify_integrated_references(
+    if isinstance(test_data, summarizedexperiment.SummarizedExperiment):
+        test_data = test_data.assay(assay_type)
+
+    if test_data.shape[0] != integrated_prebuilt._test_num_features: # TODO: move to singlepp.
+        raise ValueError("number of rows in 'test_data' is not consistent with 'test_features=' used to create 'integrated_prebuilt'")
+
+    ref_labs = integrated_prebuilt.reference_labels
+    if len(results) != len(ref_labs):
+        raise ValueError("length of 'results' should equal the number of references")
+
+    collated = []
+    for i, curres in enumerate(results):
+        if test_data.shape[1] != curres.shape[0]:
+            raise ValueError("numbers of cells in 'results' are not identical")
+        available = set(ref_labs[i])
+        curbest = curres.column("best")
+        for l in curbest:
+            if l not in available:
+                raise ValueError("not all labels in 'results' are present in the corresponding reference")
+        collated.append(biocutils.match(curbest, ref_labs[i], dtype=numpy.uint32))
+
+    test_ptr = mattress.initialize(test_data)
+    best_ref, raw_scores, delta = lib.classify_integrated(
         test_ptr.ptr,
-        assign_ptrs.ctypes.data,
+        collated,
         integrated_prebuilt._ptr,
         quantile,
-        score_ptrs.ctypes.data,
-        best,
-        delta,
-        num_threads,
-    )
-
-    best_label = []
-    for i, b in enumerate(best):
-        if isinstance(results[b], BiocFrame):
-            best_label.append(results[b].column("best")[i])
-        else:
-            best_label.append(results[b][i])
-
-    if has_names:
-        best = [all_refs[b] for b in best]
-
-    scores_df = BiocFrame(scores, number_of_rows=nc)
-    return BiocFrame(
-        {
-            "best_label": best_label,
-            "best_reference": best,
-            "scores": scores_df,
-            "delta": delta,
-        }
-    )
      
+        use_fine_tune,
+        fine_tune_threshold,
+        num_threads
+    ) 
+
+    by_ref = {}
+    for i, b in enumerate(best_ref):
+        if b not in by_ref:
+            by_ref[b] = []
+        by_ref[b].append(i)
+    best_label = [None] * test_data.shape[1]
+    for ref, which in by_ref.items():
+        curbest = results[ref].column("best")
+        for i in which:
+            best_label[i] = curbest[i]
+
+    all_refs = [str(i) for i in range(len(raw_scores))]
+    scores = {}
+    for i, l in enumerate(all_refs):
+        scores[l] = biocframe.BiocFrame({ "label": results[i].column("best"), "score": raw_scores[i] })
+    scores_df = biocframe.BiocFrame(scores, number_of_rows=test_data.shape[1], column_names=all_refs)
+
+    return biocframe.BiocFrame({
+        "best_label": best_label,
+        "best_reference": best_ref,
+        "scores": scores_df,
+        "delta": delta,
+    })
      
 
 
      
         
      
@@ -434,8 +409,8 @@ 
      Source code for singler.classify_integrated_references
      
-    
+    
     
-    
+    
     
 
\ No newline at end of file
diff --git a/_modules/singler/classify_single_reference.html b/_modules/singler/classify_single.html
similarity index 62%
rename from _modules/singler/classify_single_reference.html
rename to _modules/singler/classify_single.html
index a277502..cce44d8 100644
--- a/_modules/singler/classify_single_reference.html
+++ b/_modules/singler/classify_single.html
@@ -4,11 +4,11 @@
     
     
 
-    
-        singler.classify_single_reference - singler unknown documentation
+    
+        singler.classify_single - singler unknown documentation
       
-    
-    
+    
+    
     
     
 
@@ -87,19 +87,6 @@
       
     
   
-  
-    Auto light/dark mode
-    
-      
-      
-      
-      
-      
-      
-      
-    
-  
   
     Auto light/dark, in light mode
     
       
       
-      
     
   
   
@@ -211,7 +198,7 @@
 
 
      
   
      
         
      
-          
      Source code for singler.classify_single_reference
      +          
      Source code for singler.classify_single
       from typing import Any, Sequence, Union
 
-from biocframe import BiocFrame
-from numpy import float64, int32, ndarray, uintp
+import biocframe
+import mattress
+import summarizedexperiment
 
-from . import _cpphelpers as lib
-from ._utils import _clean_matrix, _create_map
-from .build_single_reference import SinglePrebuiltReference
+from . import lib_singler as lib
+from .train_single import TrainedSingleReference 
 
 
-
      
-[docs]
-def classify_single_reference(
+
      
+[docs]
+def classify_single(
     test_data: Any,
-    test_features: Sequence,
-    ref_prebuilt: SinglePrebuiltReference,
+    ref_prebuilt: TrainedSingleReference,
     assay_type: Union[str, int] = 0,
-    check_missing: bool = True,
     quantile: float = 0.8,
     use_fine_tune: bool = True,
     fine_tune_threshold: float = 0.05,
     num_threads: int = 1,
-) -> BiocFrame:
+) -> biocframe.BiocFrame:
     """Classify a test dataset against a reference by assigning labels from the latter to each column of the former
     using the SingleR algorithm.
 
@@ -292,28 +277,14 @@ 
      Source code for singler.classify_single_reference
                  :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
             containing such a matrix in one of its assays.
 
-        test_features:
-            Sequence of identifiers for each feature in the test
-            dataset, i.e., row in ``test_data``.
-
-            If ``test_data`` is a ``SummarizedExperiment``, ``test_features`` 
-            may be a string speciying the column name in `row_data`that contains the
-            features. Alternatively can be set to `None`, to use the `row_names` of 
-            the experiment as used as features.
-
         ref_prebuilt:
             A pre-built reference created with
-            :py:meth:`~singler.build_single_reference.build_single_reference`.
+            :py:func:`~singler.train_single.train_single`.
 
         assay_type:
-            Assay containing the expression matrix,
-            if `test_data` is a
+            Assay containing the expression matrix, if ``test_data`` is a
             :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
 
-        check_missing:
-            Whether to check for and remove rows with missing (NaN) values
-            from ``test_data``.
-
         quantile:
             Quantile of the correlation distribution for computing the score for each label.
             Larger values increase sensitivity of matches at the expense of
@@ -331,60 +302,47 @@ 
      Source code for singler.classify_single_reference
                  Number of threads to use during classification.
 
     Returns:
-        A data frame containing the ``best`` label, the ``scores``
-        for each label (as a nested BiocFrame), and the ``delta`` from the best
-        to the second-best label.  Each row corresponds to a column of ``test``.
+        A :py:class:`~BiocFrame.BiocFrame.BiocFrame` containing the ``best``
+        label, the ``scores`` for each label as a nested ``BiocFrame``, and the
+        ``delta`` from the best to the second-best label. Each row corresponds
+        to a column of ``test``. The metadata contains ``markers``, a list of
+        the markers from each pairwise comparison between labels; and ``used``,
+        a list containing the union of markers from all comparisons.
     """
-    mat_ptr, test_features = _clean_matrix(
-        test_data,
-        test_features,
-        assay_type=assay_type,
-        check_missing=check_missing,
-        num_threads=num_threads,
-    )
+    if isinstance(test_data, summarizedexperiment.SummarizedExperiment):
+        test_data = test_data.assay(assay_type)
 
-    nl = ref_prebuilt.num_labels()
-    nc = mat_ptr.ncol()
+    if test_data.shape[0] != ref_prebuilt._test_num_features: # TODO: move to singlepp
+        raise ValueError("number of rows in 'test_data' is not consistent with 'test_features=' used to create 'ref_prebuilt'")
 
-    best = ndarray((nc,), dtype=int32)
-    delta = ndarray((nc,), dtype=float64)
+    test_ptr = mattress.initialize(test_data)
 
-    scores = {}
-    all_labels = ref_prebuilt.labels
-    score_ptrs = ndarray((nl,), dtype=uintp)
-    for i in range(nl):
-        current = ndarray((nc,), dtype=float64)
-        scores[all_labels[i]] = current
-        score_ptrs[i] = current.ctypes.data
-
-    mapping = _create_map(test_features)
-
-    ref_subset = ref_prebuilt.marker_subset(indices_only=True)
-    ref_features = ref_prebuilt.features
-    subset = ndarray((len(ref_subset),), dtype=int32)
-    for i, y in enumerate(ref_subset):
-        x = ref_features[y]
-        if x not in mapping:
-            raise KeyError("failed to find gene '" + str(x) + "' in the test dataset")
-        subset[i] = mapping[x]
-
-    lib.classify_single_reference(
-        mat_ptr.ptr,
-        subset,
+    best, raw_scores, delta = lib.classify_single(
+        test_ptr.ptr,
         ref_prebuilt._ptr,
-        quantile=quantile,
-        use_fine_tune=use_fine_tune,
-        fine_tune_threshold=fine_tune_threshold,
-        nthreads=num_threads,
-        scores=score_ptrs.ctypes.data,
-        best=best,
-        delta=delta,
+        quantile,
+        use_fine_tune,
+        fine_tune_threshold,
+        num_threads
     )
 
-    scores_df = BiocFrame(scores, number_of_rows=nc)
-    return BiocFrame(
-        {"best": [all_labels[b] for b in best], "scores": scores_df, "delta": delta}
-    )
      
+    all_labels = ref_prebuilt.labels
+    scores = {}
+    for i, l in enumerate(all_labels):
+        scores[l] = raw_scores[i]
+    scores_df = biocframe.BiocFrame(scores, number_of_rows=test_data.shape[1], column_names=all_labels)
+
+    output = biocframe.BiocFrame({
+        "best": [all_labels[b] for b in best], 
+        "scores": scores_df, 
+        "delta": delta
+    })
+    output = output.set_metadata({
+        "used": ref_prebuilt.marker_subset(),
+        "markers": ref_prebuilt.markers,
+    })
+
+    return output
      
 
 
      
         
      
@@ -419,8 +377,8 @@ 
      Source code for singler.classify_single_reference
      
   
      
 
      
-    
+    
     
-    
+    
     
 
\ No newline at end of file
diff --git a/_modules/singler/get_classic_markers.html b/_modules/singler/get_classic_markers.html
index 4a24dad..45e72b2 100644
--- a/_modules/singler/get_classic_markers.html
+++ b/_modules/singler/get_classic_markers.html
@@ -4,11 +4,11 @@
     
     
 
-    
+    
         singler.get_classic_markers - singler unknown documentation
       
-    
-    
+    
+    
     
     
 
@@ -87,19 +87,6 @@
       
     
         
-  
-    Auto light/dark mode
-    
-      
-      
-      
-      
-      
-      
-      
-    
-  
   
     Auto light/dark, in light mode
     
       
       
-      
     
   
   
@@ -211,7 +198,7 @@
 
 
      
   
        
-
      • Overview
        • 
+
      • Usage
        • 
 
      • Contributions & Help
        • 
 
      • License
        • 
 
      • Authors
        • 
@@ -258,23 +245,20 @@ 
        Source code for singler.get_classic_markers
         from typing import Any, Optional, Sequence, Union
 
 import delayedarray
-from mattress import tatamize
-from numpy import int32, ndarray, uintp
+import mattress
+import numpy
+import biocutils
 
-from . import _cpphelpers as lib
-from ._Markers import _Markers
+from . import lib_singler as lib
 from ._utils import (
     _clean_matrix,
     _create_map,
-    _restrict_features,
     _stable_intersect,
     _stable_union,
 )
 
 
-def _get_classic_markers_raw(
-    ref_ptrs, ref_labels, ref_features, num_de=None, num_threads=1
-):
+def _get_classic_markers_raw(ref_ptrs: list, ref_labels: list, ref_features: list, num_de=None, num_threads=1):
     nrefs = len(ref_ptrs)
 
     # We assume that ref_ptrs and ref_features contains the outputs of
@@ -289,15 +273,15 @@ 
        Source code for singler.get_classic_markers
             # Defining the intersection of features.
     common_features = _stable_intersect(*ref_features)
     if len(common_features) == 0:
-        for feat in ref_features:
-            if len(feat):
+        for r in ref_ptrs:
+            if r.nrow():
                 raise ValueError("no common feature names across 'features'")
 
     common_features_map = _create_map(common_features)
 
-    # Creating medians.
+    # Computing medians for each group within each median.
     ref2 = []
-    ref2_ptrs = ndarray((nrefs,), dtype=uintp)
+    ref2_ptrs = []
     tmp_labels = []
 
     for i, x in enumerate(ref_ptrs):
@@ -309,28 +293,26 @@ 
        Source code for singler.get_classic_markers
                         remap[common_features_map[f]] = len(survivors) - 1
 
         da = delayedarray.DelayedArray(x)[survivors, :]
-        ptr = tatamize(da)
+        ptr = mattress.initialize(da)
         med, lev = ptr.row_medians_by_group(ref_labels[i], num_threads=num_threads)
         tmp_labels.append(lev)
 
-        finalptr = tatamize(med[remap, :])
+        finalptr = mattress.initialize(med[remap, :])
         ref2.append(finalptr)
-        ref2_ptrs[i] = finalptr.ptr
+        ref2_ptrs.append(finalptr.ptr)
 
     ref_labels = tmp_labels
 
-    # Defining the union of labels.
+    # Defining the union of labels across all references.
     common_labels = _stable_union(*ref_labels)
     common_labels_map = _create_map(common_labels)
 
     labels2 = []
-    labels2_ptrs = ndarray((nrefs,), dtype=uintp)
     for i, lab in enumerate(ref_labels):
-        converted = ndarray(len(lab), dtype=int32)
+        converted = numpy.ndarray(len(lab), dtype=numpy.uint32)
         for j, x in enumerate(lab):
             converted[j] = common_labels_map[x]
         labels2.append(converted)
-        labels2_ptrs[i] = converted.ctypes.data
 
     # Finally getting around to calling markers.
     if num_de is None:
@@ -338,14 +320,13 @@ 
        Source code for singler.get_classic_markers
             elif num_de <= 0:
         raise ValueError("'num_de' should be positive")
 
-    raw_markers = _Markers(
-        lib.find_classic_markers(
-            nref=nrefs,
-            labels=labels2_ptrs.ctypes.data,
-            ref=ref2_ptrs.ctypes.data,
-            de_n=num_de,
-            nthreads=num_threads,
-        )
+    raw_markers = lib.find_classic_markers(
+        len(common_labels),
+        len(common_features),
+        ref2_ptrs,
+        labels2,
+        num_de,
+        num_threads
     )
 
     return raw_markers, common_labels, common_features
@@ -359,7 +340,6 @@ 
        Source code for singler.get_classic_markers
             ref_features: Union[Sequence, list[Sequence]],
     assay_type: Union[str, int] = "logcounts",
     check_missing: bool = True,
-    restrict_to: Optional[Union[set, dict]] = None,
     num_de: Optional[int] = None,
     num_threads: int = 1,
 ) -> dict[Any, dict[Any, list]]:
@@ -368,54 +348,59 @@ 
        Source code for singler.get_classic_markers
         
     Args:
         ref_data:
-            A matrix-like object containing the log-normalized expression values of a reference dataset.
-            Each column is a sample and each row is a feature.
+            A matrix-like object containing the log-normalized expression
+            values of a reference dataset.  Each column is a sample and each
+            row is a feature.
             
-            Alternatively, this can be a :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
+            Alternatively, this can be a
+            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
             containing a matrix-like object in one of its assays.
             
-            Alternatively, a list of such matrices or ``SummarizedExperiment`` objects,
-            typically for multiple batches of the same reference;
-            it is assumed that different batches exhibit at least some overlap in their ``features`` and ``labels``.
+            Alternatively, a list of such matrices or ``SummarizedExperiment``
+            objects, typically for multiple batches of the same reference; it
+            is assumed that different batches exhibit at least some overlap in
+            their ``ref_features`` and ``ref_labels``.
 
         ref_labels:
-            A sequence of length equal to the number of columns of ``ref``,
+            If ``ref_data`` is not a list, ``ref_labels`` should be a sequence
+            of length equal to the number of columns of ``ref_data``,
             containing a label (usually a string) for each column.
-            Alternatively, a list of such sequences of length equal to that of a list ``ref``;
-            each sequence should have length equal to the number of columns of the corresponding entry of ``ref``.
+
+            If ``ref_data`` is a list, ``ref_labels`` should also be a list of
+            the same length. Each entry should be a sequence of length equal to
+            the number of columns of the corresponding entry of ``ref_data``.
 
         ref_features:
-            A sequence of length equal to the number of rows of ``ref``,
+            If ``ref_data`` is not a list, ``ref_features`` should be a
+            sequence of length equal to the number of rows of ``ref_data``,
             containing the feature name (usually a string) for each row.
-            Alternatively, a list of such sequences of length equal to that of a list ``ref``;
-            each sequence should have length equal to the number of rows of the corresponding entry of ``ref``.
+
+            If ``ref_data`` is a list, ``ref_features`` should also be a list
+            of the same length. Each entry should be a sequence of length
+            equal to the number of rows of the corresponding entry of ``ref``.
 
         assay_type:
-            Name or index of the assay containing the assay of interest,
-            if ``ref`` is or contains
-            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment` objects.
+            Name or index of the assay of interest, if ``ref`` is or contains
+            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
+            objects.
 
         check_missing:
-            Whether to check for and remove rows with missing (NaN) values in the reference matrices.
-            This can be set to False if it is known that no NaN values exist.
-
-        restrict_to:
-            Subset of available features to restrict to. Only features in
-            ``restrict_to`` will be used in the reference building. If None,
-            no restriction is performed.
+            Whether to check for and remove rows with missing (NaN) values in
+            the reference matrices. This can be set to False if it is known
+            that no NaN values exist.
 
         num_de:
-            Number of differentially expressed genes to use as markers for each pairwise comparison between labels.
-            If None, an appropriate number of genes is automatically determined.
+            Number of differentially expressed genes to use as markers for each
+            pairwise comparison between labels. If ``None``, an appropriate
+            number of genes is automatically determined.
 
         num_threads:
             Number of threads to use for the calculations.
 
     Returns:
-        A dictionary of dictionary of lists
-        containing the markers for each pairwise comparison between labels,
-        i.e., ``markers[a][b]`` contains the upregulated markers for label
-        ``a`` over label ``b``.
+        A dictionary of dictionary of lists containing the markers for each
+        pairwise comparison between labels, i.e., ``markers[a][b]`` contains
+        the upregulated markers for label ``a`` over label ``b``.
     """
     if not isinstance(ref_data, list):
         ref_data = [ref_data]
@@ -429,7 +414,7 @@ 
        Source code for singler.get_classic_markers
                 raise ValueError("length of 'ref' and 'features' should be the same")
 
     ref_ptrs = []
-    tmp_features = []
+    cleaned_features = []
     for i in range(nrefs):
         r, f = _clean_matrix(
             ref_data[i],
@@ -438,31 +423,32 @@ 
        Source code for singler.get_classic_markers
                     check_missing=check_missing,
             num_threads=num_threads,
         )
-
-        r, f = _restrict_features(r, f, restrict_to)
-
-        ref_ptrs.append(r)
-        tmp_features.append(f)
-
-    ref_features = tmp_features
+        ref_ptrs.append(mattress.initialize(r))
+        cleaned_features.append(f)
 
     raw_markers, common_labels, common_features = _get_classic_markers_raw(
         ref_ptrs=ref_ptrs,
         ref_labels=ref_labels,
-        ref_features=ref_features,
+        ref_features=cleaned_features,
         num_de=num_de,
         num_threads=num_threads,
     )
 
-    return raw_markers.to_dict(common_labels, common_features)
        
+    markers = {}
+    for i, x in enumerate(common_labels):
+        current = {}
+        for j, y in enumerate(common_labels):
+            current[y] = biocutils.StringList(common_features[k] for k in raw_markers[i][j])
+        markers[x] = current
+    return markers
        
 
 
 
 
        
 [docs]
 def number_of_classic_markers(num_labels: int) -> int:
-    """Compute the number of markers to detect for a given number of labels, using the classic SingleR marker detection
-    algorithm.
+    """Compute the number of markers to detect for a given number of labels,
+    using the classic SingleR marker detection algorithm.
 
     Args:
         num_labels: Number of labels.
@@ -505,8 +491,8 @@ 
        Source code for singler.get_classic_markers
             
   
        
 
        
-    
+    
     
-    
+    
     
 
\ No newline at end of file
diff --git a/_modules/singler/train_integrated.html b/_modules/singler/train_integrated.html
new file mode 100644
index 0000000..5673ab7
--- /dev/null
+++ b/_modules/singler/train_integrated.html
@@ -0,0 +1,379 @@
+
+
+  
+    
+    
+
+    
+        singler.train_integrated - singler unknown documentation
+      
+    
+    
+    
+    
+
+
+
+  
+    
+    
+    
+
+
+  
+    Contents
+    
+      
+    
+  
+  
+    Menu
+    
+      
+      
+      
+    
+  
+  
+    Expand
+    
+      
+    
+  
+  
+    Light mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    Dark mode
+    
+      
+      
+    
+  
+  
+    Auto light/dark, in light mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    Auto light/dark, in dark mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    
+      
+      
+      
+      
+    
+  
+  
+    
+      
+      
+      
+      
+      
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
        
+  
        
+    
        
+      
+    
        
+    
        
+      
        singler unknown documentation
        
+    
        
+    
        
+      
        
+        
+      
        
+      
+    
        
+  
        
+  
+  
        
+    
        
+      
        
+        
+          
+            
+          
+          Back to top
+        
+        
        
+          
        
+            
+          
        
+          
+        
        
+        
        
+          
        Source code for singler.train_integrated
        +from typing import Sequence, Optional, Union
+
+import numpy 
+import biocutils
+import warnings
+import mattress
+
+from .train_single import TrainedSingleReference
+from . import lib_singler as lib
+from ._utils import _stable_union, _stable_intersect
+
+
+
        
+[docs]
+class TrainedIntegratedReferences:
+    """Object containing integrated references, typically constructed by
+    :py:meth:`~singler.train_integrated.train_integrated`."""
+
+    def __init__(self, ptr: int, ref_labels: list, test_num_features: int):
+        self._ptr = ptr
+        self._labels = ref_labels
+        self._test_num_features = test_num_features # TODO: move to singlepp.
+
+    @property
+    def reference_labels(self) -> list:
+        """List of lists containing the names of the labels for each reference.
+
+        Each entry corresponds to a reference in :py:attr:`~reference_names`,
+        if ``reference_names`` is not ``None``.
+        """
+        return self._labels
        
+
+
+
+
        
+[docs]
+def train_integrated(
+    test_features: Sequence,
+    ref_prebuilt: list[TrainedSingleReference],
+    warn_lost: bool = True,
+    num_threads: int = 1,
+) -> TrainedIntegratedReferences:
+    """Build a set of integrated references for classification of a test dataset.
+
+    Arguments:
+        test_features:
+            Sequence of features for the test dataset.
+
+        ref_prebuilt:
+            List of prebuilt references, typically created by calling
+            :py:meth:`~singler.train_single.train_single`.
+
+        warn_lost:
+            Whether to emit a warning if the markers for each reference are not
+            all present in all references.
+
+        num_threads:
+            Number of threads.
+
+    Returns:
+        Integrated references for classification with
+        :py:meth:`~singler.classify_integrated_references.classify_integrated`.
+    """
+    # Checking the genes.
+    if warn_lost:
+        all_refnames = [x.features for x in ref_prebuilt]
+        intersected = set(_stable_intersect(*all_refnames))
+        for trained in ref_prebuilt:
+            for g in trained.marker_subset():
+                if g not in intersected:
+                    warnings.warn("not all markers in 'ref_prebuilt' are available in each reference")
+
+    all_inter_test = []
+    all_inter_ref = []
+    for i, trained in enumerate(ref_prebuilt):
+        common = _stable_intersect(test_features, trained.features)
+        all_inter_test.append(biocutils.match(common, test_features, dtype=numpy.uint32))
+        all_inter_ref.append(biocutils.match(common, trained.features, dtype=numpy.uint32))
+
+    all_data = [mattress.initialize(x._full_data) for x in ref_prebuilt]
+
+    # Applying the integration.
+    ibuilt = lib.train_integrated(
+        all_inter_test,
+        [x.ptr for x in all_data],
+        all_inter_ref,
+        [x._full_label_codes for x in ref_prebuilt],
+        [x._ptr for x in ref_prebuilt],
+        num_threads
+    )
+
+    return TrainedIntegratedReferences(
+        ptr=ibuilt,
+        ref_labels=[x.labels for x in ref_prebuilt],
+        test_num_features = len(test_features),
+    )
        
+
+
        
+        
        
+      
        
+      
        
+        
+        
        
+          
+          
+        
        
+        
        
+          
        
+            
        
+                Copyright © 2023, Aaron Lun
+            
        
+            Made with Sphinx and @pradyunsg's
+            
+            Furo
+            
+          
        
+          
        
+            
+          
        
+        
        
+        
+      
        
+    
        
+    
+  
        
+
        
+    
+    
+    
+    
+
\ No newline at end of file
diff --git a/_modules/singler/train_single.html b/_modules/singler/train_single.html
new file mode 100644
index 0000000..5583610
--- /dev/null
+++ b/_modules/singler/train_single.html
@@ -0,0 +1,615 @@
+
+
+  
+    
+    
+
+    
+        singler.train_single - singler unknown documentation
+      
+    
+    
+    
+    
+
+
+
+  
+    
+    
+    
+
+
+  
+    Contents
+    
+      
+    
+  
+  
+    Menu
+    
+      
+      
+      
+    
+  
+  
+    Expand
+    
+      
+    
+  
+  
+    Light mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    Dark mode
+    
+      
+      
+    
+  
+  
+    Auto light/dark, in light mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    Auto light/dark, in dark mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    
+      
+      
+      
+      
+    
+  
+  
+    
+      
+      
+      
+      
+      
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
        
+  
        
+    
        
+      
+    
        
+    
        
+      
        singler unknown documentation
        
+    
        
+    
        
+      
        
+        
+      
        
+      
+    
        
+  
        
+  
+  
        
+    
        
+      
        
+        
+          
+            
+          
+          Back to top
+        
+        
        
+          
        
+            
+          
        
+          
+        
        
+        
        
+          
        Source code for singler.train_single
        +from typing import Any, Literal, Optional, Sequence, Union
+
+import biocutils
+import numpy
+import knncolle
+import mattress
+import delayedarray
+import warnings
+
+from . import lib_singler as lib
+from ._utils import _clean_matrix, _restrict_features, _stable_intersect
+from .get_classic_markers import get_classic_markers
+
+
+
        
+[docs]
+class TrainedSingleReference:
+    """A prebuilt reference object, typically created by
+    :py:meth:`~singler.train_single.train_single`. This is intended for
+    advanced users only and should not be serialized.
+    """
+
+    def __init__(
+        self,
+        ptr: int,
+        full_data: Any,
+        full_label_codes: numpy.ndarray,
+        labels: Sequence,
+        features: Sequence,
+        markers: dict[Any, dict[Any, Sequence]],
+        test_num_features: int,
+    ):
+        self._ptr = ptr
+        self._full_data = full_data
+        self._full_label_codes = full_label_codes
+        self._features = features
+        self._labels = labels
+        self._markers = markers
+        self._test_num_features = test_num_features # TODO: move to singlepp.
+
+
        
+[docs]
+    def num_markers(self) -> int:
+        """
+        Returns:
+            Number of markers to be used for classification. This is the
+            same as the size of the array from :py:meth:`~marker_subset`.
+        """
+        return lib.get_num_markers_from_single_reference(self._ptr)
        
+
+
+
        
+[docs]
+    def num_labels(self) -> int:
+        """
+        Returns:
+            Number of unique labels in this reference.
+        """
+        return lib.get_num_labels_from_single_reference(self._ptr)
        
+
+
+    @property
+    def features(self) -> list:
+        """The universe of features known to this reference."""
+        return self._features
+
+    @property
+    def labels(self) -> Sequence:
+        """Unique labels in this reference."""
+        return self._labels
+
+    @property
+    def markers(self) -> dict[Any, dict[Any, list]]:
+        """Markers for every pairwise comparison between labels."""
+        return self._markers
+
+
        
+[docs]
+    def marker_subset(self, indices_only: bool = False) -> Union[numpy.ndarray, list]:
+        """
+        Args:
+            indices_only:
+                Whether to return the markers as indices
+                into :py:attr:`~features`, or as a list of feature identifiers.
+
+        Returns:
+            If ``indices_only = False``, a list of feature identifiers for the markers.
+
+            If ``indices_only = True``, a NumPy array containing the integer indices of
+            features in ``features`` that were chosen as markers.
+        """
+        buffer = lib.get_markers_from_single_reference(self._ptr)
+        if indices_only:
+            return buffer
+        else:
+            return biocutils.StringList(self._features[i] for i in buffer)
        
+
        
+
+
+
+def _markers_from_dict(markers: dict[Any, dict[Any, Sequence]], labels: Sequence, available_features: Sequence):
+    fmapping = {}
+    for i, x in enumerate(available_features):
+        fmapping[x] = i
+    return outer_instance
+
+
+
        
+[docs]
+def train_single(
+    ref_data: Any,
+    ref_labels: Sequence,
+    ref_features: Sequence,
+    test_features: Optional[Sequence] = None,
+    assay_type: Union[str, int] = "logcounts",
+    restrict_to: Optional[Union[set, dict]] = None,
+    check_missing: bool = True,
+    markers: Optional[dict[Any, dict[Any, Sequence]]] = None,
+    marker_method: Literal["classic"] = "classic",
+    marker_args: dict = {},
+    nn_parameters: Optional[knncolle.Parameters] = knncolle.VptreeParameters(),
+    num_threads: int = 1,
+) -> TrainedSingleReference:
+    """Build a single reference dataset in preparation for classification.
+
+    Args:
+        ref_data:
+            A matrix-like object where rows are features, columns are
+            reference profiles, and each entry is the expression value.
+            If ``markers`` is not provided, expression should be normalized
+            and log-transformed in preparation for marker prioritization via
+            differential expression analyses. Otherwise, any expression values
+            are acceptable as only the ranking within each column is used.
+
+            Alternatively, a
+            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
+            containing such a matrix in one of its assays.
+
+        ref_labels:
+            Sequence of labels for each reference profile, i.e., column in ``ref_data``.
+
+        ref_features:
+            Sequence of identifiers for each feature, i.e., row in ``ref_data``.
+
+        test_features:
+            Sequence of identifiers for each feature in the test dataset.
+
+        assay_type:
+            Assay containing the expression matrix,
+            if ``ref_data`` is a
+            :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
+
+        check_missing:
+            Whether to check for and remove rows with missing (NaN) values
+            from ``ref_data``.
+
+        restrict_to:
+            Subset of available features to restrict to. Only features in
+            ``restrict_to`` will be used in the reference building. If
+            ``None``, no restriction is performed.
+
+        markers:
+            Upregulated markers for each pairwise comparison between labels.
+            Specifically, ``markers[a][b]`` should be a sequence of features
+            that are upregulated in ``a`` compared to ``b``. All such features
+            should be present in ``features``, and all labels in ``labels``
+            should have keys in the inner and outer dictionaries.
+
+        marker_method:
+            Method to identify markers from each pairwise comparisons between
+            labels in ``ref_data``.  If "classic", we call
+            :py:meth:`~singler.get_classic_markers.get_classic_markers`.
+            Only used if ``markers`` is not supplied.
+
+        marker_args:
+            Further arguments to pass to the chosen marker detection method.
+            Only used if ``markers`` is not supplied.
+
+        nn_parameters:
+            Algorithm for constructing the neighbor search index, used to
+            compute scores during classification.
+
+        num_threads:
+            Number of threads to use for reference building.
+
+    Returns:
+        The pre-built reference, ready for use in downstream methods like
+        :py:meth:`~singler.classify_single_reference.classify_single`.
+    """
+    if isinstance(ref_labels, str):
+        warnings.warn(
+            "setting 'ref_labels' to a column name of the column data is deprecated",
+            category=DeprecationWarning
+        )
+        ref_labels = ref_data.get_column_data().column(ref_labels)
+
+    ref_data, ref_features = _clean_matrix(
+        ref_data,
+        ref_features,
+        assay_type=assay_type,
+        check_missing=check_missing,
+        num_threads=num_threads,
+    )
+
+    if len(set(ref_features)) != len(ref_features):
+        encountered = set()
+        keep = []
+        for i, rg in enumerate(ref_features):
+            if rg not in encountered:
+                encountered.add(rg)
+                keep.append(i)
+        if len(keep) < len(ref_features):
+            ref_features = biocutils.subset_sequence(ref_features, keep)
+            ref_data = delayedarray.DelayedArray(ref_data)[keep,:]
+
+    if None in ref_labels:
+        keep = []
+        for i, f in enumerate(ref_labels):
+            if not f is None:
+                keep.append(i)
+        ref_data = delayedarray.DelayedArray(ref_data)[:,keep]
+        ref_labels = biocutils.subset_sequence(ref_labels, keep)
+    ref_labels = biocutils.Factor.from_sequence(ref_labels, sort_levels=True) # TODO: add a dtype= option.
+    unique_labels = ref_labels.levels
+    label_idx = ref_labels.codes.astype(dtype=numpy.uint32, copy=False)
+
+    markers = _identify_genes(
+        ref_data=ref_data, 
+        ref_features=ref_features,
+        ref_labels=ref_labels,
+        unique_labels=unique_labels,
+        markers=markers,
+        marker_method=marker_method,
+        test_features=test_features,
+        restrict_to=restrict_to,
+        marker_args=marker_args,
+        num_threads=num_threads
+    )
+    markers_idx = [None] * len(unique_labels)
+    for outer_i, outer_k in enumerate(unique_labels):
+        inner_instance = [None] * len(unique_labels)
+        for inner_i, inner_k in enumerate(unique_labels):
+            current = markers[outer_k][inner_k]
+            inner_instance[inner_i] = biocutils.match(current, ref_features, dtype=numpy.uint32)
+        markers_idx[outer_i] = inner_instance
+
+    if test_features is None:
+        test_features_idx = numpy.array(range(len(ref_features)), dtype=numpy.uint32)
+        ref_features_idx = numpy.array(range(len(ref_features)), dtype=numpy.uint32)
+        test_num_features = len(ref_features)
+    else:
+        common_features = _stable_intersect(test_features, ref_features)
+        test_features_idx = biocutils.match(common_features, test_features, dtype=numpy.uint32)
+        ref_features_idx = biocutils.match(common_features, ref_features, dtype=numpy.uint32)
+        test_num_features = len(test_features)
+
+    ref_ptr = mattress.initialize(ref_data)
+    builder, _ = knncolle.define_builder(nn_parameters)
+    return TrainedSingleReference(
+        lib.train_single(
+            test_features_idx,
+            ref_ptr.ptr,
+            ref_features_idx,
+            label_idx,
+            markers_idx,
+            builder.ptr,
+            num_threads,
+        ),
+        full_data = ref_data,
+        full_label_codes = label_idx,
+        labels = unique_labels,
+        features = ref_features,
+        markers = markers,
+        test_num_features = test_num_features,
+    )
        
+
+
+
+def _identify_genes(ref_data, ref_features, ref_labels, unique_labels, markers, marker_method, test_features, restrict_to, marker_args, num_threads):
+    ref_data, ref_features = _restrict_features(ref_data, ref_features, test_features)
+    ref_data, ref_features = _restrict_features(ref_data, ref_features, restrict_to)
+
+    # Deriving the markers from expression data.
+    if markers is None:
+        if marker_method == "classic":
+            markers = get_classic_markers(
+                ref_data=[ref_data],
+                ref_labels=[ref_labels],
+                ref_features=[ref_features],
+                num_threads=num_threads,
+                **marker_args,
+            )
+        else:
+            raise NotImplementedError("other marker methods are not yet implemented, sorry")
+        return markers
+
+    # Validating a user-supplied list of markers.
+    if not isinstance(markers, dict):
+        raise ValueError("'markers' should be a list where the labels are keys")
+    if len(unique_labels) != len(markers):
+        raise ValueError("'markers' should have length equal to the number of unique labels")
+
+    available_features = set(ref_features)
+    new_markers = {}
+    for x, y in markers.items():
+        if x not in unique_labels:
+            raise ValueError("unknown label '" + x + "' in 'markers'")
+
+        if isinstance(y, list):
+            collected = []
+            for g in y:
+                if g in available_features:
+                    collected.append(g)
+            output = {} 
+            for l in unique_labels:
+                output[l] = biocutils.StringList()
+            output[x] = collected
+        elif isinstance(y, dict):
+            if len(unique_labels) != len(y):
+                raise ValueError("each value of 'markers' should have length equal to the number of unique labels")
+            output = {} 
+            for x_inner, y_inner in y.items():
+                collected = biocutils.StringList()
+                for g in y_inner:
+                    if g in available_features:
+                        collected.append(g)
+                output[x_inner] = collected
+        else:
+            raise ValueError("values of 'markers' should be dictionaries")
+
+        new_markers[x] = output
+
+    return new_markers
+
        
+        
        
+      
        
+      
        
+        
+        
        
+          
+          
+        
        
+        
        
+          
        
+            
        
+                Copyright © 2023, Aaron Lun
+            
        
+            Made with Sphinx and @pradyunsg's
+            
+            Furo
+            
+          
        
+          
        
+            
+          
        
+        
        
+        
+      
        
+    
        
+    
+  
        
+
        
+    
+    
+    
+    
+
\ No newline at end of file
diff --git a/_sources/api/singler.rst.txt b/_sources/api/singler.rst.txt
index 11deee1..4cc52ca 100644
--- a/_sources/api/singler.rst.txt
+++ b/_sources/api/singler.rst.txt
@@ -1,6 +1,11 @@
 singler package
 ===============
 
+.. automodule:: singler
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -20,50 +25,42 @@ singler.annotate\_single module
    :undoc-members:
    :show-inheritance:
 
-singler.build\_integrated\_references module
---------------------------------------------
-
-.. automodule:: singler.build_integrated_references
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-singler.build\_single\_reference module
----------------------------------------
+singler.classify\_integrated module
+-----------------------------------
 
-.. automodule:: singler.build_single_reference
+.. automodule:: singler.classify_integrated
    :members:
    :undoc-members:
    :show-inheritance:
 
-singler.classify\_integrated\_references module
------------------------------------------------
+singler.classify\_single module
+-------------------------------
 
-.. automodule:: singler.classify_integrated_references
+.. automodule:: singler.classify_single
    :members:
    :undoc-members:
    :show-inheritance:
 
-singler.classify\_single\_reference module
-------------------------------------------
+singler.get\_classic\_markers module
+------------------------------------
 
-.. automodule:: singler.classify_single_reference
+.. automodule:: singler.get_classic_markers
    :members:
    :undoc-members:
    :show-inheritance:
 
-singler.get\_classic\_markers module
-------------------------------------
+singler.train\_integrated module
+--------------------------------
 
-.. automodule:: singler.get_classic_markers
+.. automodule:: singler.train_integrated
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+singler.train\_single module
+----------------------------
 
-.. automodule:: singler
+.. automodule:: singler.train_single
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/_sources/index.md.txt b/_sources/index.md.txt
index 8362299..8d88c79 100644
--- a/_sources/index.md.txt
+++ b/_sources/index.md.txt
@@ -1,25 +1,9 @@
-# singler
-
-Add a short description here!
-
-
-## Note
-
-> This is the main page of your project's [Sphinx] documentation. It is
-> formatted in [Markdown]. Add additional pages by creating md-files in
-> `docs` or rst-files (formatted in [reStructuredText]) and adding links to
-> them in the `Contents` section below.
->
-> Please check [Sphinx] and [MyST] for more information
-> about how to document your project and how to configure your preferences.
-
-
 ## Contents
 
 ```{toctree}
 :maxdepth: 2
 
-Overview 
+Usage 
 Contributions & Help 
 License 
 Authors 
diff --git a/_static/basic.css b/_static/basic.css
index f316efc..7ebbd6d 100644
--- a/_static/basic.css
+++ b/_static/basic.css
@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {
diff --git a/_static/doctools.js b/_static/doctools.js
index 4d67807..0398ebb 100644
--- a/_static/doctools.js
+++ b/_static/doctools.js
@@ -1,12 +1,5 @@
 /*
- * doctools.js
- * ~~~~~~~~~~~
- *
  * Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 
diff --git a/_static/language_data.js b/_static/language_data.js
index 367b8ed..c7fe6c6 100644
--- a/_static/language_data.js
+++ b/_static/language_data.js
@@ -1,13 +1,6 @@
 /*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
diff --git a/_static/scripts/furo.js b/_static/scripts/furo.js
index 0267c7e..0abb2af 100644
--- a/_static/scripts/furo.js
+++ b/_static/scripts/furo.js
@@ -1,3 +1,3 @@
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 //# sourceMappingURL=furo.js.map
\ No newline at end of file
diff --git a/_static/scripts/furo.js.map b/_static/scripts/furo.js.map
index c3b37aa..80ea12b 100644
--- a/_static/scripts/furo.js.map
+++ b/_static/scripts/furo.js.map
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contentClass: \"active\",\n\n      // Nested navigation\n      nested: 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      var bounds = elem.getBoundingClientRect();\n      var offset = getOffset(settings);\n      if (bottom) {\n        return (\n          parseInt(bounds.bottom, 10) <\n          (window.innerHeight || document.documentElement.clientHeight)\n        );\n      }\n      return parseInt(bounds.top, 10) <= offset;\n    };\n\n    /**\n     * Check if at the bottom of the viewport\n     * @return {Boolean} If true, page is at the bottom of the viewport\n     */\n    var isAtBottom = function () {\n      if (\n        Math.ceil(window.innerHeight + window.pageYOffset) >=\n        getDocumentHeight()\n      )\n        return true;\n      return false;\n    };\n\n    /**\n     * Check if the last item should be used (even if not at the top of the page)\n     * @param  {Object} item     The last item\n     * @param  {Object} settings The settings for this instantiation\n     * @return {Boolean}         If true, use the last item\n     */\n    var useLastItem = function (item, settings) {\n      if (isAtBottom() && isInView(item.content, settings, true)) return true;\n      return false;\n    };\n\n    /**\n     * Get the active content\n     * @param  {Array}  contents The 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          contents.push({\n            nav: item,\n            content: content,\n          });\n        });\n\n        // Sort contents by the order they appear in the DOM\n        sortContents(contents);\n      };\n\n      /**\n       * Detect which content is currently active\n       */\n      publicAPIs.detect = function () {\n        // Get the active content\n        var active = getActive(contents, settings);\n\n        // if there's no active content, deactivate and bail\n        if (!active) {\n          if (current) {\n            deactivate(current, settings);\n            current = null;\n          }\n          return;\n        }\n\n        // If the active content is the one currently active, do nothing\n        if (current && active.content === current.content) return;\n\n        // Deactivate the current content and activate the new content\n        deactivate(current, settings);\n        activate(active, settings);\n\n        // Update the currently active content\n        current = active;\n      };\n\n      /**\n       * Detect the active content on scroll\n       * Debounced for performance\n       */\n      var scrollHandler = function (event) {\n        // If there's a timer, cancel it\n        if (timeout) {\n          window.cancelAnimationFrame(timeout);\n        }\n\n        // Setup debounce callback\n        timeout = window.requestAnimationFrame(publicAPIs.detect);\n      };\n\n      /**\n       * Update content sorting on resize\n       * Debounced for 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 /**\n       * Initialize the 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 = 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contentClass: \"active\",\n\n      // Nested navigation\n      nested: 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      var bounds = elem.getBoundingClientRect();\n      var offset = getOffset(settings);\n      if (bottom) {\n        return (\n          parseInt(bounds.bottom, 10) <\n          (window.innerHeight || document.documentElement.clientHeight)\n        );\n      }\n      return parseInt(bounds.top, 10) <= offset;\n    };\n\n    /**\n     * Check if at the bottom of the viewport\n     * @return {Boolean} If true, page is at the bottom of the viewport\n     */\n    var isAtBottom = function () {\n      if (\n        Math.ceil(window.innerHeight + window.pageYOffset) >=\n        getDocumentHeight()\n      )\n        return true;\n      return false;\n    };\n\n    /**\n     * Check if the last item should be used (even if not at the top of the page)\n     * @param  {Object} item     The last item\n     * @param  {Object} settings The settings for this instantiation\n     * @return {Boolean}         If true, use the last item\n     */\n    var useLastItem = function (item, settings) {\n      if (isAtBottom() && isInView(item.content, settings, true)) return true;\n      return false;\n    };\n\n    /**\n     * Get the active content\n     * @param  {Array}  contents The 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          contents.push({\n            nav: item,\n            content: content,\n          });\n        });\n\n        // Sort contents by the order they appear in the DOM\n        sortContents(contents);\n      };\n\n      /**\n       * Detect which content is currently active\n       */\n      publicAPIs.detect = function () {\n        // Get the active content\n        var active = getActive(contents, settings);\n\n        // if there's no active content, deactivate and bail\n        if (!active) {\n          if (current) {\n            deactivate(current, settings);\n            current = null;\n          }\n          return;\n        }\n\n        // If the active content is the one currently active, do nothing\n        if (current && active.content === current.content) return;\n\n        // Deactivate the current content and activate the new content\n        deactivate(current, settings);\n        activate(active, settings);\n\n        // Update the currently active content\n        current = active;\n      };\n\n      /**\n       * Detect the active content on scroll\n       * Debounced for performance\n       */\n      var scrollHandler = function (event) {\n        // If there's a timer, cancel it\n        if (timeout) {\n          window.cancelAnimationFrame(timeout);\n        }\n\n        // Setup debounce callback\n        timeout = window.requestAnimationFrame(publicAPIs.detect);\n      };\n\n      /**\n       * Update content sorting on resize\n       * Debounced for performance\n       */\n      var resizeHandler = function (event) {\n        // If there's a timer, cancel it\n        if (timeout) {\n          window.cancelAnimationFrame(timeout);\n        }\n\n        // Setup debounce callback\n        timeout = window.requestAnimationFrame(function () {\n          sortContents(contents);\n          publicAPIs.detect();\n        });\n      };\n\n      /**\n       * Destroy the current instantiation\n       */\n      publicAPIs.destroy = function () {\n        // Undo DOM changes\n        if (current) {\n          deactivate(current, settings);\n        }\n\n        // Remove event listeners\n        window.removeEventListener(\"scroll\", scrollHandler, false);\n        if (settings.reflow) {\n          window.removeEventListener(\"resize\", resizeHandler, false);\n        }\n\n        // Reset variables\n        contents = null;\n        navItems = null;\n        current = null;\n        timeout = null;\n        settings = null;\n      };\n\n      /**\n       * Initialize the 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 = __webpack_module_cache__[moduleId] = {\n\t\t// no module.id needed\n\t\t// no module.loaded needed\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId].call(module.exports, module, module.exports, __webpack_require__);\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n","// getDefaultExport function for compatibility with non-harmony modules\n__webpack_require__.n = (module) => {\n\tvar getter = module && module.__esModule ?\n\t\t() => (module['default']) :\n\t\t() => (module);\n\t__webpack_require__.d(getter, { a: getter });\n\treturn getter;\n};","// define getter functions for harmony exports\n__webpack_require__.d = (exports, definition) => {\n\tfor(var key in definition) {\n\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n\t\t}\n\t}\n};","__webpack_require__.g = (function() {\n\tif (typeof 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  if (positionY < GO_TO_TOP_OFFSET) {\n    document.documentElement.classList.remove(\"show-back-to-top\");\n  } else {\n    if (positionY < lastScrollTop) {\n      document.documentElement.classList.add(\"show-back-to-top\");\n    } else if (positionY > lastScrollTop) {\n      document.documentElement.classList.remove(\"show-back-to-top\");\n    }\n  }\n  lastScrollTop = positionY;\n}\n\nfunction scrollHandlerForTOC(positionY) {\n  if (tocScroll === null) {\n    return;\n  }\n\n  // top of page.\n  if (positionY == 0) {\n    tocScroll.scrollTo(0, 0);\n  } else if (\n    // bottom of page.\n    Math.ceil(positionY) >=\n    Math.floor(document.documentElement.scrollHeight - window.innerHeight)\n  ) {\n    tocScroll.scrollTo(0, tocScroll.scrollHeight);\n  } else {\n    // somewhere in the middle.\n    const current = document.querySelector(\".scroll-current\");\n    if (current == null) {\n      return;\n    }\n\n    // https://github.com/pypa/pip/issues/9159 This breaks scroll behaviours.\n    // // scroll the currently \"active\" heading in toc, into view.\n    // const rect = current.getBoundingClientRect();\n    // if (0 > rect.top) {\n    //   current.scrollIntoView(true); // the argument is \"alignTop\"\n    // } else if (rect.bottom > window.innerHeight) {\n    //   current.scrollIntoView(false);\n    // }\n  }\n}\n\nfunction scrollHandler(positionY) {\n  scrollHandlerForHeader(positionY);\n  scrollHandlerForBackToTop(positionY);\n  scrollHandlerForTOC(positionY);\n}\n\n////////////////////////////////////////////////////////////////////////////////\n// Theme Toggle\n////////////////////////////////////////////////////////////////////////////////\nfunction setTheme(mode) {\n  if (mode !== \"light\" && mode !== \"dark\" && mode !== \"auto\") {\n    console.error(`Got invalid theme mode: ${mode}. Resetting to auto.`);\n    mode = \"auto\";\n  }\n\n  document.body.dataset.theme = mode;\n  localStorage.setItem(\"theme\", mode);\n  console.log(`Changed to ${mode} mode.`);\n}\n\nfunction cycleThemeOnce() {\n  const currentTheme = localStorage.getItem(\"theme\") || \"auto\";\n  const prefersDark = window.matchMedia(\"(prefers-color-scheme: dark)\").matches;\n\n  if (prefersDark) {\n    // Auto (dark) -> Light -> Dark\n    if (currentTheme === \"auto\") {\n      setTheme(\"light\");\n    } else if (currentTheme == \"light\") {\n      setTheme(\"dark\");\n    } else {\n      setTheme(\"auto\");\n    }\n  } else {\n    // Auto (light) -> Dark -> Light\n    if (currentTheme === \"auto\") {\n      setTheme(\"dark\");\n    } else if (currentTheme == \"dark\") {\n      setTheme(\"light\");\n    } else {\n      setTheme(\"auto\");\n    }\n  }\n}\n\n////////////////////////////////////////////////////////////////////////////////\n// Setup\n////////////////////////////////////////////////////////////////////////////////\nfunction setupScrollHandler() {\n  // Taken from https://developer.mozilla.org/en-US/docs/Web/API/Document/scroll_event\n  let last_known_scroll_position = 0;\n  let ticking = false;\n\n  window.addEventListener(\"scroll\", function (e) {\n    last_known_scroll_position = window.scrollY;\n\n    if (!ticking) {\n      window.requestAnimationFrame(function () {\n        scrollHandler(last_known_scroll_position);\n        ticking = false;\n      });\n\n      ticking = true;\n    }\n  });\n  window.scroll();\n}\n\nfunction setupScrollSpy() {\n  if (tocScroll === null) {\n    return;\n  }\n\n  // Scrollspy -- highlight table on contents, based on scroll\n  new Gumshoe(\".toc-tree a\", {\n    reflow: true,\n    recursive: true,\n    navClass: \"scroll-current\",\n    offset: () => {\n      let rem = parseFloat(getComputedStyle(document.documentElement).fontSize);\n      return header.getBoundingClientRect().height + 2.5 * rem + 1;\n    },\n  });\n}\n\nfunction setupTheme() {\n  // Attach event handlers for toggling themes\n  const buttons = document.getElementsByClassName(\"theme-toggle\");\n  Array.from(buttons).forEach((btn) => {\n    btn.addEventListener(\"click\", cycleThemeOnce);\n  });\n}\n\nfunction setup() {\n  setupTheme();\n  setupScrollHandler();\n  setupScrollSpy();\n}\n\n////////////////////////////////////////////////////////////////////////////////\n// Main entrypoint\n////////////////////////////////////////////////////////////////////////////////\nfunction main() {\n  document.body.parentNode.classList.remove(\"no-js\");\n\n  header = document.querySelector(\"header\");\n  tocScroll = document.querySelector(\".toc-scroll\");\n\n  setup();\n}\n\ndocument.addEventListener(\"DOMContentLoaded\", main);\n"],"names":["root","g","window","this","defaults","navClass","contentClass","nested","nestedClass","offset","reflow","events","emitEvent","type","elem","detail","settings","event","CustomEvent","bubbles","cancelable","dispatchEvent","getOffsetTop","location","offsetParent","offsetTop","sortContents","contents","sort","item1","item2","content","isInView","bottom","bounds","getBoundingClientRect","parseFloat","getOffset","parseInt","innerHeight","document","documentElement","clientHeight","top","isAtBottom","Math","ceil","pageYOffset","max","body","scrollHeight","offsetHeight","getActive","last","length","item","useLastItem","i","deactivateNested","nav","parentNode","li","closest","classList","remove","deactivate","items","link","activateNested","add","selector","options","navItems","current","timeout","publicAPIs","querySelectorAll","Array","prototype","forEach","call","getElementById","decodeURIComponent","hash","substr","push","active","activate","scrollHandler","cancelAnimationFrame","requestAnimationFrame","detect","resizeHandler","destroy","removeEventListener","merged","arguments","obj","key","hasOwnProperty","extend","setup","addEventListener","factory","__webpack_module_cache__","__webpack_require__","moduleId","cachedModule","undefined","exports","module","__webpack_modules__","n","getter","__esModule","d","a","definition","o","Object","defineProperty","enumerable","get","globalThis","Function","e","prop","tocScroll","header","lastScrollTop","scrollTop","GO_TO_TOP_OFFSET","cycleThemeOnce","currentTheme","localStorage","getItem","mode","matchMedia","matches","console","error","dataset","theme","setItem","log","buttons","getElementsByClassName","from","btn","setupTheme","last_known_scroll_position","ticking","scrollY","positionY","headerTop","floor","scrollHandlerForHeader","scrollHandlerForBackToTop","scrollTo","querySelector","scrollHandlerForTOC","scroll","setupScrollHandler","recursive","rem","getComputedStyle","fontSize","height"],"sourceRoot":""}
\ No newline at end of file
diff --git a/_static/searchtools.js b/_static/searchtools.js
index 92da3f8..2c774d1 100644
--- a/_static/searchtools.js
+++ b/_static/searchtools.js
@@ -1,12 +1,5 @@
 /*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
  * Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 
@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") {
     // and returns the new score.
     /*
     score: result => {
-      const [docname, title, anchor, descr, score, filename] = result
+      const [docname, title, anchor, descr, score, filename, kind] = result
       return score
     },
     */
@@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") {
   };
 }
 
+// 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);
 };
@@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
   const contentRoot = document.documentElement.dataset.content_root;
 
-  const [docName, title, anchor, descr, score, _filename] = item;
+  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") {
@@ -115,8 +120,10 @@ const _finishSearch = (resultCount) => {
       "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
     );
   else
-    Search.status.innerText = _(
-      "Search finished, found ${resultCount} page(s) matching the search query."
+    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 = (
@@ -138,7 +145,7 @@ const _displayNextItem = (
   else _finishSearch(resultCount);
 };
 // Helper function used by query() to order search results.
-// Each input is an array of [docname, title, anchor, descr, score, filename].
+// 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) => {
@@ -178,7 +185,7 @@ const Search = {
 
   htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
+    for (const removalQuery of [".headerlink", "script", "style"]) {
       htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
     }
     if (anchor) {
@@ -248,6 +255,7 @@ const Search = {
     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");
@@ -318,7 +326,7 @@ const Search = {
     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].
+    // Each is an array of [docname, title, anchor, descr, score, filename, kind].
     const normalResults = [];
     const nonMainIndexResults = [];
 
@@ -328,14 +336,16 @@ const Search = {
     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) {
-          let score = Math.round(100 * queryLower.length / title.length)
+          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,
+            score + boost,
             filenames[file],
+            SearchResultKind.title,
           ]);
         }
       }
@@ -353,6 +363,7 @@ const Search = {
             null,
             score,
             filenames[file],
+            SearchResultKind.index,
           ];
           if (isMain) {
             normalResults.push(result);
@@ -474,6 +485,7 @@ const Search = {
         descr,
         score,
         filenames[match[0]],
+        SearchResultKind.object,
       ]);
     };
     Object.keys(objects).forEach((prefix) =>
@@ -584,6 +596,7 @@ const Search = {
         null,
         score,
         filenames[file],
+        SearchResultKind.text,
       ]);
     }
     return results;
diff --git a/_static/styles/furo-extensions.css b/_static/styles/furo-extensions.css
index bc447f2..8229587 100644
--- a/_static/styles/furo-extensions.css
+++ b/_static/styles/furo-extensions.css
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diff --git a/_static/styles/furo-extensions.css.map b/_static/styles/furo-extensions.css.map
index 9ba5637..c26eac7 100644
--- a/_static/styles/furo-extensions.css.map
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diff --git a/_static/styles/furo.css b/_static/styles/furo.css
index e3d4e57..05a56b1 100644
--- a/_static/styles/furo.css
+++ b/_static/styles/furo.css
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Correct the color inheritance from `fieldset` elements in IE.\n * 3. Remove the padding so developers are not caught out when they zero out\n *    `fieldset` elements in all browsers.\n */\n\nlegend {\n  box-sizing: border-box; /* 1 */\n  color: inherit; /* 2 */\n  display: table; /* 1 */\n  max-width: 100%; /* 1 */\n  padding: 0; /* 3 */\n  white-space: normal; /* 1 */\n}\n\n/**\n * Add the correct vertical alignment in Chrome, Firefox, and Opera.\n */\n\nprogress {\n  vertical-align: baseline;\n}\n\n/**\n * Remove the default vertical scrollbar in IE 10+.\n */\n\ntextarea {\n  overflow: auto;\n}\n\n/**\n * 1. Add the correct box sizing in IE 10.\n * 2. Remove the padding in IE 10.\n */\n\n[type=\"checkbox\"],\n[type=\"radio\"] {\n  box-sizing: border-box; /* 1 */\n  padding: 0; /* 2 */\n}\n\n/**\n * Correct the cursor style of increment and decrement buttons in Chrome.\n */\n\n[type=\"number\"]::-webkit-inner-spin-button,\n[type=\"number\"]::-webkit-outer-spin-button {\n  height: auto;\n}\n\n/**\n * 1. Correct the odd appearance in Chrome and Safari.\n * 2. Correct the outline style in Safari.\n */\n\n[type=\"search\"] {\n  -webkit-appearance: textfield; /* 1 */\n  outline-offset: -2px; /* 2 */\n}\n\n/**\n * Remove the inner padding in Chrome and Safari on macOS.\n */\n\n[type=\"search\"]::-webkit-search-decoration {\n  -webkit-appearance: none;\n}\n\n/**\n * 1. Correct the inability to style clickable types in iOS and Safari.\n * 2. Change font properties to `inherit` in Safari.\n */\n\n::-webkit-file-upload-button {\n  -webkit-appearance: button; /* 1 */\n  font: inherit; /* 2 */\n}\n\n/* Interactive\n   ========================================================================== */\n\n/*\n * Add the correct display in Edge, IE 10+, and Firefox.\n */\n\ndetails {\n  display: block;\n}\n\n/*\n * Add the correct display in all browsers.\n */\n\nsummary {\n  display: list-item;\n}\n\n/* Misc\n   ========================================================================== */\n\n/**\n * Add the correct display in IE 10+.\n */\n\ntemplate {\n  display: none;\n}\n\n/**\n * Add the correct display in IE 10.\n */\n\n[hidden] {\n  display: none;\n}\n","// This file contains styles for managing print media.\n\n////////////////////////////////////////////////////////////////////////////////\n// Hide elements not relevant to print media.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n  // Hide icon container.\n  .content-icon-container\n    display: none !important\n\n  // Hide showing header links if hovering over when printing.\n  .headerlink\n    display: none !important\n\n  // Hide mobile header.\n  .mobile-header\n    display: none !important\n\n  // Hide navigation links.\n  .related-pages\n    display: none !important\n\n////////////////////////////////////////////////////////////////////////////////\n// Tweaks related to decolorization.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n  // Apply a border around code which no longer have a color background.\n  .highlight\n    border: 0.1pt solid var(--color-foreground-border)\n\n////////////////////////////////////////////////////////////////////////////////\n// Avoid page break in some relevant cases.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n  ul, ol, dl, a, table, pre, blockquote\n    page-break-inside: avoid\n\n  h1, h2, h3, h4, h5, h6, img, figure, caption\n    page-break-inside: avoid\n    page-break-after: avoid\n\n  ul, ol, dl\n    page-break-before: avoid\n",".visually-hidden\n  position: absolute !important\n  width: 1px !important\n  height: 1px !important\n  padding: 0 !important\n  margin: -1px !important\n  overflow: hidden !important\n  clip: rect(0,0,0,0) !important\n  white-space: nowrap !important\n  border: 0 !important\n  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\n$icon-size: 1.25rem\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  vertical-align: middle\n\n.theme-toggle\n  cursor: pointer\n  border: none\n  padding: 0\n  background: transparent\n\n.theme-toggle svg\n  vertical-align: middle\n  height: $icon-size\n  width: $icon-size\n  color: var(--color-foreground-primary)\n  display: none\n\n.theme-toggle-header\n  float: left\n  padding: 1rem 0.5rem\n\n////////////////////////////////////////////////////////////////////////////////\n// Toggles for elements\n////////////////////////////////////////////////////////////////////////////////\n.toc-overlay-icon, .nav-overlay-icon\n  display: none\n  cursor: pointer\n\n  .icon\n    color: var(--color-foreground-secondary)\n    height: $icon-size\n    width: $icon-size\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: $icon-size\n      width: $icon-size\n\n.sidebar-toggle\n  position: absolute\n  display: none\n// \n.sidebar-toggle[name=\"__toc\"]\n  left: 20px\n.sidebar-toggle:checked\n  left: 40px\n// \n\n.overlay\n  position: fixed\n  top: 0\n  width: 0\n  height: 0\n\n  transition: width 0ms, height 0ms, opacity 250ms ease-out\n\n  opacity: 0\n  background-color: rgba(0, 0, 0, 0.54)\n.sidebar-overlay\n  z-index: 20\n.toc-overlay\n  z-index: 40\n\n// Keep things on top and smooth.\n.sidebar-drawer\n  z-index: 30\n  transition: left 250ms ease-in-out\n.toc-drawer\n  z-index: 50\n  transition: right 250ms ease-in-out\n\n// Show the Sidebar\n#__navigation:checked\n  & ~ .sidebar-overlay\n    width: 100%\n    height: 100%\n    opacity: 1\n  & ~ .page\n    .sidebar-drawer\n      top: 0\n      left: 0\n      // Show the toc sidebar\n#__toc:checked\n  & ~ .toc-overlay\n    width: 100%\n    height: 100%\n    opacity: 1\n  & ~ .page\n    .toc-drawer\n      top: 0\n      right: 0\n\n////////////////////////////////////////////////////////////////////////////////\n// Back to top\n////////////////////////////////////////////////////////////////////////////////\n.back-to-top\n  text-decoration: none\n\n  display: none\n  position: fixed\n  left: 0\n  top: 1rem\n  padding: 0.5rem\n  padding-right: 0.75rem\n  border-radius: 1rem\n  font-size: 0.8125rem\n\n  background: var(--color-background-primary)\n  box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), #6b728080 0px 0px 1px 0px\n\n  z-index: 10\n\n  margin-left: 50%\n  transform: translateX(-50%)\n  svg\n    height: 1rem\n    width: 1rem\n    fill: currentColor\n    display: inline-block\n\n  span\n    margin-left: 0.25rem\n\n  .show-back-to-top &\n    display: flex\n    align-items: center\n\n////////////////////////////////////////////////////////////////////////////////\n// Responsive layouting\n////////////////////////////////////////////////////////////////////////////////\n// Make things a bit bigger on bigger screens.\n@media (min-width: $full-width + $sidebar-width)\n  html\n    font-size: 110%\n\n@media (max-width: $full-width)\n  // Collapse \"toc\" into the icon.\n  .toc-content-icon\n    display: flex\n  .toc-drawer\n    position: fixed\n    height: 100vh\n    top: 0\n    right: -$sidebar-width\n    border-left: 1px solid var(--color-background-muted)\n  .toc-tree\n    border-left: none\n    font-size: var(--toc-font-size--mobile)\n\n  // Accomodate for a changed content width.\n  .sidebar-drawer\n    width: calc((100% - #{$full-width - $sidebar-width}) / 2 + #{$sidebar-width})\n\n@media (max-width: $full-width - $sidebar-width)\n  // Collapse \"navigation\".\n  .nav-overlay-icon\n    display: flex\n  .sidebar-drawer\n    position: fixed\n    height: 100vh\n    width: $sidebar-width\n\n    top: 0\n    left: -$sidebar-width\n\n  // Swap which icon is visible.\n  .toc-header-icon\n    display: flex\n  .toc-content-icon, .theme-toggle-content\n    display: none\n  .theme-toggle-header\n    display: block\n\n  // Show the header.\n  .mobile-header\n    position: sticky\n    top: 0\n    display: flex\n    justify-content: space-between\n    align-items: center\n\n    .header-left,\n    .header-right\n      display: flex\n      height: var(--header-height)\n      padding: 0 var(--header-padding)\n      label\n        height: 100%\n        width: 100%\n        user-select: none\n\n  .nav-overlay-icon .icon,\n  .theme-toggle svg\n    height: $icon-size\n    width: $icon-size\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  // Center the page, and accommodate for the header.\n  .page\n    flex-direction: column\n    justify-content: center\n  .content\n    margin-left: auto\n    margin-right: auto\n\n@media (max-width: $content-width + 2* $content-padding)\n  // Content should respect window limits.\n  .content\n    width: 100%\n    overflow-x: auto\n\n@media (max-width: $content-width)\n  .content\n    padding: 0 $content-padding--small\n    // Don't float sidebars to the right.\n  article aside.sidebar\n    float: none\n    width: 100%\n    margin: 1rem 0\n","// Overall Layout Variables\n//\n// Because CSS variables can't be used in media queries. The fact that this\n// makes the layout non-user-configurable is a good thing.\n$content-padding: 3em;\n$content-padding--small: 1em;\n$content-width: 46em;\n$sidebar-width: 15em;\n$full-width: $content-width + 2 * ($content-padding + $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",".table-wrapper\n  width: 100%\n  overflow-x: auto\n  margin-top: 1rem\n  margin-bottom: 0.5rem\n  padding: 0.2rem 0.2rem 0.75rem\n\ntable.docutils\n  border-radius: 0.2rem\n  border-spacing: 0\n  border-collapse: collapse\n\n  box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), 0 0 0.0625rem rgba(0, 0, 0, 0.1)\n\n  th\n    background: var(--color-table-header-background)\n\n  td,\n  th\n    // Space things out properly\n    padding: 0 0.25rem\n\n    // Get the borders looking just-right.\n    border-left: 1px solid var(--color-table-border)\n    border-right: 1px solid var(--color-table-border)\n    border-bottom: 1px solid var(--color-table-border)\n\n    p\n      margin: 0.25rem\n\n    &:first-child\n      border-left: none\n    &:last-child\n      border-right: none\n\n    // MyST-parser tables set these classes for control of column alignment\n    &.text-left\n      text-align: left\n    &.text-right\n      text-align: right\n    &.text-center\n      text-align: center\n",":target\n  scroll-margin-top: 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 
      
 
-
    • singler.build_integrated_references module
      • 
 
    
@@ -343,21 +330,17 @@ 
    Calling low-level functionsannotate_single() function is a convenient wrapper around a number of lower-level functions in singler.
 Advanced users may prefer to build the reference and run the classification separately.
 This allows us to re-use the same reference for multiple datasets without repeating the build step.
    
-
    built = singler.build_single_reference(
-    ref_data=ref_data.assay("logcounts"),
-    ref_labels=ref_data.col_data.column("label.main"),
-    ref_features=ref_data.get_row_names(),
-    restrict_to=features,
+
    built = singler.train_single(
+    ref_data = ref_data.assay("logcounts"),
+    ref_labels = ref_data.get_column_data().column("label.main"),
+    ref_features = ref_data.get_row_names(),
+    test_features = features,
 )
 
    
 
    
 
    And finally, we apply the pre-built reference to the test dataset to obtain our label assignments.
-This can be repeated with different datasets that have the same features or a superset of features.
    
-
    output = singler.classify_single_reference(
-    mat,
-    test_features=features,
-    ref_prebuilt=built,
-)
+This can be repeated with different datasets that have the same features as test_features=.
    
+
    output = singler.classify_single(mat, ref_prebuilt=built)
 
    
 
    
 
    ## output
@@ -381,21 +364,25 @@ 
    Integrating labels across referencesimport celldex
 
 blueprint_ref = celldex.fetch_reference("blueprint_encode", "2024-02-26", realize_assays=True)
-
 immune_cell_ref = celldex.fetch_reference("dice", "2024-02-26", realize_assays=True)
 
 single_results, integrated = singler.annotate_integrated(
     mat,
     features,
-    ref_data_list = (blueprint_ref, immune_cell_ref),
-    ref_labels_list = "label.main",
+    ref_data = [
+        blueprint_ref,
+        immune_cell_ref
+    ],
+    ref_labels = [
+        blueprint_ref.get_column_data().column("label.main"),
+        immune_cell_ref.get_column_data().column("label.main")
+    ],
     num_threads = 6
 )
 
    
 
    
 
    This annotates the test dataset against each reference individually to obtain the best per-reference label,
-and then it compares across references to find the best label from all references.
-Both the single and integrated annotations are reported for diagnostics.
    
+and then it compares across references to find the best label from all references.
    
 
    integrated.column("best_label")
 ## ['Monocytes', 
 ##  'Monocytes',
@@ -409,34 +396,16 @@ 
    Integrating labels across references## ]
 
 integrated.column("best_reference")
-## ['Blueprint',
-## 'Blueprint',
-## 'Blueprint',
-## 'Blueprint',
-## 'Blueprint',
-## 'Blueprint',
-## 'Blueprint',
-## ...
-##]
-
    
-
    
-
-
    
-
    Developer notes
    
-
    Build the shared object file:
    
-
    python setup.py build_ext --inplace
-
    
-
    
-
    For quick testing:
    
-
    pytest
-
    
-
    
-
    For more complex testing:
    
-
    python setup.py build_ext --inplace && tox
-
    
-
    
-
    To rebuild the ctypes bindings with cpptypes:
    
-
    cpptypes src/singler/lib --py src/singler/_cpphelpers.py --cpp src/singler/lib/bindings.cpp --dll _core
+## [0,
+##  0, 
+##  0,
+##  0,
+##  0,
+##  0,
+##  0,
+##  0,
+##  ...
+## ]
 
    
 
    
 
    
@@ -502,7 +471,6 @@ 
    Developer notesQuick start
 
  • Calling low-level functions
    • 
 
  • Integrating labels across references
    • 
-
  • Developer notes
    •
@@ -515,8 +483,8 @@

Developer notes - + - + \ No newline at end of file diff --git a/search.html b/search.html index c106973..dd1b0e8 100644 --- a/search.html +++ b/search.html @@ -5,11 +5,11 @@ - + Search - singler unknown documentation - - + + @@ -88,19 +88,6 @@ - - Auto light/dark mode - - - - - - - - - - Auto light/dark, in light mode - @@ -212,7 +199,7 @@
- + - + diff --git a/searchindex.js b/searchindex.js index d6ebd0a..6f4f0d4 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Calling low-level functions": [[7, "calling-low-level-functions"]], "Changelog": [[3, "changelog"]], "Clone the repository": [[4, "clone-the-repository"]], "Code Contributions": [[4, "code-contributions"]], "Contents": [[5, "contents"]], "Contributing": [[4, "contributing"]], "Contributors": [[2, "contributors"]], "Create an environment": [[4, "create-an-environment"]], "Developer notes": [[7, "developer-notes"]], "Documentation Improvements": [[4, "documentation-improvements"]], "Implement your changes": [[4, "implement-your-changes"]], "Indices and tables": [[5, "indices-and-tables"]], "Integrating labels across references": [[7, "integrating-labels-across-references"]], "Issue Reports": [[4, "issue-reports"]], "License": [[6, "license"]], "Maintainer tasks": [[4, "maintainer-tasks"]], "Module contents": [[1, "module-singler"]], "Note": [[5, "note"]], "Overview": [[7, "overview"]], "Quick start": [[7, "quick-start"]], "Releases": [[4, "releases"]], "Submit an issue": [[4, "submit-an-issue"]], "Submit your contribution": [[4, "submit-your-contribution"]], "Submodules": [[1, "submodules"]], "Tinder for single-cell data": [[7, "tinder-for-single-cell-data"]], "Todo": [[4, "id1"], [4, "id2"], [4, "id3"], [4, "id5"], [4, "id6"], [4, "id7"], [4, "id8"], [4, "id9"], [4, "id10"], [4, "id11"], [4, "id12"]], "Troubleshooting": [[4, "troubleshooting"]], "Version 0.1.0": [[3, "version-0-1-0"]], "Version 0.1.1": [[3, "version-0-1-1"]], "Version 0.2.0": [[3, "version-0-2-0"]], "Version 0.3.0": [[3, "version-0-3-0"]], "singler": [[0, "singler"], [5, "singler"]], "singler package": [[1, "singler-package"]], "singler.annotate_integrated module": [[1, "module-singler.annotate_integrated"]], "singler.annotate_single module": [[1, "module-singler.annotate_single"]], "singler.build_integrated_references module": [[1, "module-singler.build_integrated_references"]], "singler.build_single_reference module": [[1, "module-singler.build_single_reference"]], "singler.classify_integrated_references module": [[1, "module-singler.classify_integrated_references"]], "singler.classify_single_reference module": [[1, "module-singler.classify_single_reference"]], "singler.get_classic_markers module": [[1, "module-singler.get_classic_markers"]]}, "docnames": ["api/modules", "api/singler", "authors", "changelog", "contributing", "index", "license", "readme"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api/modules.rst", "api/singler.rst", "authors.md", 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