diff --git a/.buildinfo b/.buildinfo index 6ae6fc4..45b76a8 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: 9457f6f4933d9502416d1db4035a8346 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 52a5008e41b72d28c57a6159c9ab24d0 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 869043c..0dff04b 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -4,8 +4,8 @@ - - Overview: module code - SingleCellExperiment 0.4.7 documentation + + Overview: module code - SingleCellExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation
@@ -287,8 +287,8 @@

All modules for which code is available

-
- +
+ diff --git a/_modules/singlecellexperiment/SingleCellExperiment.html b/_modules/singlecellexperiment/SingleCellExperiment.html index 3fd564f..1310ef9 100644 --- a/_modules/singlecellexperiment/SingleCellExperiment.html +++ b/_modules/singlecellexperiment/SingleCellExperiment.html @@ -4,8 +4,8 @@ - - singlecellexperiment.SingleCellExperiment - SingleCellExperiment 0.4.7 documentation + + singlecellexperiment.SingleCellExperiment - SingleCellExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -284,9 +284,7 @@

Source code for singlecellexperiment.SingleCellExperiment

def _validate_reduced_dims(reduced_dims, shape): if reduced_dims is None: - raise ValueError( - "'reduced_dims' cannot be `None`, must be assigned to an empty dictionary." - ) + raise ValueError("'reduced_dims' cannot be `None`, must be assigned to an empty dictionary.") if not isinstance(reduced_dims, dict): raise TypeError("'reduced_dims' is not a dictionary.") @@ -294,21 +292,16 @@

Source code for singlecellexperiment.SingleCellExperiment

for rdname, mat in reduced_dims.items(): if not hasattr(mat, "shape"): raise TypeError( - f"Reduced dimension: '{rdname}' must be a matrix-like object." - "Does not contain a `shape` property." + f"Reduced dimension: '{rdname}' must be a matrix-like object." "Does not contain a `shape` property." ) if shape[1] != mat.shape[0]: - raise ValueError( - f"Reduced dimension: '{rdname}' does not contain embeddings for all cells." - ) + raise ValueError(f"Reduced dimension: '{rdname}' does not contain embeddings for all cells.") def _validate_alternative_experiments(alternative_experiments, shape): if alternative_experiments is None: - raise ValueError( - "'alternative_experiments' cannot be `None`, must be assigned to an empty dictionary." - ) + raise ValueError("'alternative_experiments' cannot be `None`, must be assigned to an empty dictionary.") if not isinstance(alternative_experiments, dict): raise TypeError("'alternative_experiments' is not a dictionary.") @@ -321,10 +314,7 @@

Source code for singlecellexperiment.SingleCellExperiment

) if shape[1] != alternative_experiment.shape[1]: - raise ValueError( - f"Alternative experiment: '{alt_name}' does not contain same number of" - " cells." - ) + raise ValueError(f"Alternative experiment: '{alt_name}' does not contain same number of" " cells.") def _validate_pairs(pairs): @@ -462,18 +452,14 @@

Source code for singlecellexperiment.SingleCellExperiment

self._reduced_dims = reduced_dims if reduced_dims is not None else {} - self._alternative_experiments = ( - alternative_experiments if alternative_experiments is not None else {} - ) + self._alternative_experiments = alternative_experiments if alternative_experiments is not None else {} self._row_pairs = row_pairs if row_pairs is not None else {} self._column_pairs = column_pairs if column_pairs is not None else {} if validate: _validate_reduced_dims(self._reduced_dims, self._shape) - _validate_alternative_experiments( - self._alternative_experiments, self._shape - ) + _validate_alternative_experiments(self._alternative_experiments, self._shape) _validate_pairs(self._row_pairs) _validate_pairs(self._column_pairs)
@@ -579,14 +565,10 @@

Source code for singlecellexperiment.SingleCellExperiment

output += ", row_ranges=" + self._row_ranges.__repr__() if self._alternative_experiments is not None: - output += ", alternative_experiments=" + ut.print_truncated_list( - self.alternative_experiment_names - ) + output += ", alternative_experiments=" + ut.print_truncated_list(self.alternative_experiment_names) if self._reduced_dims is not None: - output += ", reduced_dims=" + ut.print_truncated_list( - self.reduced_dim_names - ) + output += ", reduced_dims=" + ut.print_truncated_list(self.reduced_dim_names) if self._main_experiment_name is not None: output += ", main_experiment_name=" + self._main_experiment_name @@ -615,10 +597,14 @@

Source code for singlecellexperiment.SingleCellExperiment

output += f"assays({len(self.assay_names)}): {ut.print_truncated_list(self.assay_names)}\n" - output += f"row_data columns({len(self._rows.column_names)}): {ut.print_truncated_list(self._rows.column_names)}\n" + output += ( + f"row_data columns({len(self._rows.column_names)}): {ut.print_truncated_list(self._rows.column_names)}\n" + ) output += f"row_names({0 if self._row_names is None else len(self._row_names)}): {' ' if self._row_names is None else ut.print_truncated_list(self._row_names)}\n" - output += f"column_data columns({len(self._cols.column_names)}): {ut.print_truncated_list(self._cols.column_names)}\n" + output += ( + f"column_data columns({len(self._cols.column_names)}): {ut.print_truncated_list(self._cols.column_names)}\n" + ) output += f"column_names({0 if self._column_names is None else len(self._column_names)}): {' ' if self._column_names is None else ut.print_truncated_list(self._column_names)}\n" output += f"main_experiment_name: {' ' if self._main_experiment_name is None else self._main_experiment_name}\n" @@ -649,9 +635,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_reduced_dims( - self, reduced_dims: Dict[str, Any], in_place: bool = False - ) -> "SingleCellExperiment": + def set_reduced_dims(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment": """Set new reduced dimensions. Args: @@ -703,9 +687,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_reduced_dim_names( - self, names: List[str], in_place: bool = False - ) -> "SingleCellExperiment": + def set_reduced_dim_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment": """Replace :py:attr:`~.reduced_dims`'s names. Args: @@ -721,9 +703,7 @@

Source code for singlecellexperiment.SingleCellExperiment

""" current_names = self.get_reduced_dim_names() if len(names) != len(current_names): - raise ValueError( - "Length of 'names' does not match the number of `reduced_dims`." - ) + raise ValueError("Length of 'names' does not match the number of `reduced_dims`.") new_reduced_dims = OrderedDict() for idx in range(len(names)): @@ -784,9 +764,7 @@

Source code for singlecellexperiment.SingleCellExperiment

return self._reduced_dims[dimension] - raise TypeError( - f"'dimension' must be a string or integer, provided '{type(dimension)}'." - )
+ raise TypeError(f"'dimension' must be a string or integer, provided '{type(dimension)}'.")
################################ @@ -806,9 +784,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_main_experiment_name( - self, name: Optional[str], in_place: bool = False - ) -> "SingleCellExperiment": + def set_main_experiment_name(self, name: Optional[str], in_place: bool = False) -> "SingleCellExperiment": """Set new experiment data (assays). Args: @@ -912,9 +888,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_alternative_experiment_names( - self, names: List[str], in_place: bool = False - ) -> "SingleCellExperiment": + def set_alternative_experiment_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment": """Replace :py:attr:`~.alternative_experiment`'s names. Args: @@ -930,15 +904,11 @@

Source code for singlecellexperiment.SingleCellExperiment

""" current_names = self.get_alternative_experiment_names() if len(names) != len(current_names): - raise ValueError( - "Length of 'names' does not match the number of `alternative_experiments`." - ) + raise ValueError("Length of 'names' does not match the number of `alternative_experiments`.") new_alt_expts = OrderedDict() for idx in range(len(names)): - new_alt_expts[names[idx]] = self._alternative_experiments.pop( - current_names[idx] - ) + new_alt_expts[names[idx]] = self._alternative_experiments.pop(current_names[idx]) output = self._define_output(in_place) output._alternative_experiments = new_alt_expts @@ -986,13 +956,9 @@

Source code for singlecellexperiment.SingleCellExperiment

raise IndexError("Index cannot be negative.") if name > len(self.alternative_experiment_names): - raise IndexError( - "Index greater than the number of alternative experiments." - ) + raise IndexError("Index greater than the number of alternative experiments.") - return self._alternative_experiments[ - self.alternative_experiment_names[name] - ] + return self._alternative_experiments[self.alternative_experiment_names[name]] elif isinstance(name, str): if name not in self._alternative_experiments: raise AttributeError(f"Alternative experiment: {name} does not exist.") @@ -1019,9 +985,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_row_pairs( - self, pairs: Dict[str, Any], in_place: bool = False - ) -> "SingleCellExperiment": + def set_row_pairs(self, pairs: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment": """Replace :py:attr:`~.row_pairs`'s names. Args: @@ -1073,9 +1037,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_row_pair_names( - self, names: List[str], in_place: bool = False - ) -> "SingleCellExperiment": + def set_row_pair_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment": """Replace :py:attr:`~.row_pair`'s names. Args: @@ -1091,9 +1053,7 @@

Source code for singlecellexperiment.SingleCellExperiment

""" current_names = self.get_row_pair_names() if len(names) != len(current_names): - raise ValueError( - "Length of 'names' does not match the number of `row_pairs`." - ) + raise ValueError("Length of 'names' does not match the number of `row_pairs`.") new_row_pairs = OrderedDict() for idx in range(len(names)): @@ -1135,9 +1095,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_column_pairs( - self, pairs: Dict[str, Any], in_place: bool = False - ) -> "SingleCellExperiment": + def set_column_pairs(self, pairs: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment": """Replace :py:attr:`~.column_pairs`'s names. Args: @@ -1189,9 +1147,7 @@

Source code for singlecellexperiment.SingleCellExperiment

[docs] - def set_column_pair_names( - self, names: List[str], in_place: bool = False - ) -> "SingleCellExperiment": + def set_column_pair_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment": """Replace :py:attr:`~.column_pair`'s names. Args: @@ -1207,9 +1163,7 @@

Source code for singlecellexperiment.SingleCellExperiment

""" current_names = self.get_column_pair_names() if len(names) != len(current_names): - raise ValueError( - "Length of 'names' does not match the number of `column_pairs`." - ) + raise ValueError("Length of 'names' does not match the number of `column_pairs`.") new_column_pairs = OrderedDict() for idx in range(len(names)): @@ -1607,9 +1561,7 @@

Source code for singlecellexperiment.SingleCellExperiment

_new_rdim = None try: - _new_rdim = relaxed_merge_numpy_generic( - x, by="row", attr="reduced_dims", names_attr="reduced_dim_names" - ) + _new_rdim = relaxed_merge_numpy_generic(x, by="row", attr="reduced_dims", names_attr="reduced_dim_names") except Exception as e: warn( f"Cannot combine 'reduced_dimensions' across experiments, {str(e)}", @@ -1618,9 +1570,7 @@

Source code for singlecellexperiment.SingleCellExperiment

_new_alt_expt = None try: - _new_alt_expt = relaxed_merge_generic( - x, by="column", attr="alternative_experiments" - ) + _new_alt_expt = relaxed_merge_generic(x, by="column", attr="alternative_experiments") except Exception as e: warn( f"Cannot combine 'alternative_experiments' across experiments, {str(e)}", @@ -1683,8 +1633,8 @@

Source code for singlecellexperiment.SingleCellExperiment

- +
+ diff --git a/_modules/singlecellexperiment/io/h5ad.html b/_modules/singlecellexperiment/io/h5ad.html index 64b5167..fa8380a 100644 --- a/_modules/singlecellexperiment/io/h5ad.html +++ b/_modules/singlecellexperiment/io/h5ad.html @@ -4,8 +4,8 @@ - - singlecellexperiment.io.h5ad - SingleCellExperiment 0.4.7 documentation + + singlecellexperiment.io.h5ad - SingleCellExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -308,8 +308,8 @@

Source code for singlecellexperiment.io.h5ad
-
- +
+ diff --git a/_modules/singlecellexperiment/io/tenx.html b/_modules/singlecellexperiment/io/tenx.html index fb7c927..e018466 100644 --- a/_modules/singlecellexperiment/io/tenx.html +++ b/_modules/singlecellexperiment/io/tenx.html @@ -4,8 +4,8 @@ - - singlecellexperiment.io.tenx - SingleCellExperiment 0.4.7 documentation + + singlecellexperiment.io.tenx - SingleCellExperiment 0.5.0 documentation @@ -166,7 +166,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -190,7 +190,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -334,9 +334,7 @@

Source code for singlecellexperiment.io.tenx

# read the matrix
     shape = tuple(h5["matrix"]["shape"][:])
 
-    counts = Hdf5CompressedSparseMatrix(
-        path=path, group_name="matrix", by_column=True, shape=shape
-    )
+    counts = Hdf5CompressedSparseMatrix(path=path, group_name="matrix", by_column=True, shape=shape)
 
     if realize_assays is True:
         counts = da.to_scipy_sparse_matrix(counts, "csr")
@@ -370,9 +368,7 @@ 
Source code for singlecellexperiment.io.tenx
h5.close()
 
-    return SingleCellExperiment(
-        assays={"counts": counts}, row_data=features, column_data=barcodes
-    )

+    return SingleCellExperiment(assays={"counts": counts}, row_data=features, column_data=barcodes)
@@ -406,8 +402,8 @@

Source code for singlecellexperiment.io.tenx
-
- +
+ diff --git a/_sources/changelog.md.txt b/_sources/changelog.md.txt index 5524118..04e1ab8 100644 --- a/_sources/changelog.md.txt +++ b/_sources/changelog.md.txt @@ -1,5 +1,10 @@ # Changelog +## Version 0.5.0 + +- chore: Remove Python 3.8 (EOL) +- precommit: Replace docformatter with ruff's formatter + ## Version 0.4.7 - Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82). 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/documentation_options.js b/_static/documentation_options.js index 6166180..240446d 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.4.7', + VERSION: '0.5.0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', 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/searchtools.js b/_static/searchtools.js index b08d58c..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) => { @@ -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 = []; @@ -337,6 +345,7 @@ const Search = { null, score + boost, filenames[file], + SearchResultKind.title, ]); } } @@ -354,6 +363,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.index, ]; if (isMain) { normalResults.push(result); @@ -475,6 +485,7 @@ const Search = { descr, score, filenames[match[0]], + SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -585,6 +596,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.text, ]); } return results; diff --git a/api/modules.html b/api/modules.html index fa2ebe4..2cc9ebd 100644 --- a/api/modules.html +++ b/api/modules.html @@ -5,8 +5,8 @@ - - singlecellexperiment - SingleCellExperiment 0.4.7 documentation + + singlecellexperiment - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -378,8 +378,8 @@

singlecellexperiment

-
- +
+ diff --git a/api/singlecellexperiment.html b/api/singlecellexperiment.html index ef82a61..4f9a8a5 100644 --- a/api/singlecellexperiment.html +++ b/api/singlecellexperiment.html @@ -5,8 +5,8 @@ - - singlecellexperiment package - SingleCellExperiment 0.4.7 documentation + + singlecellexperiment package - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -289,11 +289,11 @@

Submodules
class singlecellexperiment.SingleCellExperiment.SingleCellExperiment(assays=None, row_ranges=None, row_data=None, column_data=None, row_names=None, column_names=None, metadata=None, reduced_dims=None, main_experiment_name=None, alternative_experiments=None, row_pairs=None, column_pairs=None, validate=True)[source]¶
-

Bases: RangedSummarizedExperiment

+

Bases: RangedSummarizedExperiment

Container class for single-cell experiments, extending -RangedSummarizedExperiment to provide slots for +RangedSummarizedExperiment to provide slots for embeddings and alternative experiments that share the same cells.

-

In contrast to R, ndarray or scipy matrices are unnamed and do +

In contrast to R, ndarray or scipy matrices are unnamed and do not contain rownames and colnames. Hence, these matrices cannot be directly used as values in assays or alternative experiments. We strictly enforce type checks in these cases.

To relax these restrictions for alternative experiments, set @@ -329,50 +329,50 @@

Submodules
Parameters:
    -

  • assays (Optional[Dict[str, Any]]) –

    A dictionary containing matrices, with assay names as keys +

  • assays (Dict[str, Any]) –

    A dictionary containing matrices, with assay names as keys and 2-dimensional matrices represented as either -ndarray or spmatrix.

    +ndarray or spmatrix.

    Alternatively, you may use any 2-dimensional matrix that has the shape property and implements the slice operation using the __getitem__ dunder method.

    All matrices in assays must be 2-dimensional and have the same shape (number of rows, number of columns).

    • -

  • row_ranges (Union[GenomicRanges, GenomicRangesList, None]) – Genomic features, must be the same length as the number of rows of +

  • row_ranges (Union[GenomicRanges, GenomicRangesList, None]) – Genomic features, must be the same length as the number of rows of the matrices in assays.

    • -

  • row_data (Optional[BiocFrame]) –

    Features, must be the same length as the number of rows of +

  • row_data (Optional[BiocFrame]) –

    Features, must be the same length as the number of rows of the matrices in assays.

    Feature information is coerced to a -BiocFrame. Defaults to None.

    +BiocFrame. Defaults to None.

    • -

  • column_data (Optional[BiocFrame]) –

    Sample data, must be the same length as the number of +

  • column_data (Optional[BiocFrame]) –

    Sample data, must be the same length as the number of columns of the matrices in assays.

    Sample information is coerced to a -BiocFrame. Defaults to None.

    +BiocFrame. Defaults to None.

    • -

  • row_names (Optional[List[str]]) – A list of strings, same as the number of rows.Defaults to None.

    • -

  • column_names (Optional[List[str]]) – A list of string, same as the number of columns. Defaults to None.

    • -

  • metadata (Optional[dict]) – Additional experimental metadata describing the methods. +

  • row_names (Optional[List[str]]) – A list of strings, same as the number of rows.Defaults to None.

    • +

  • column_names (Optional[List[str]]) – A list of string, same as the number of columns. Defaults to None.

    • +

  • metadata (Optional[dict]) – Additional experimental metadata describing the methods. Defaults to None.

    • -

  • reduced_dims (Optional[Dict[str, Any]]) –

    Slot for low-dimensionality embeddings.

    +

  • reduced_dims (Optional[Dict[str, Any]]) –

    Slot for low-dimensionality embeddings.

    Usually a dictionary with the embedding method as keys (e.g., t-SNE, UMAP) and the dimensions as values.

    Embeddings may be represented as a matrix or a data frame, must contain a shape.

    • -

  • main_experiment_name (Optional[str]) – A string, specifying the main experiment name.

    • -

  • alternative_experiments (Optional[Dict[str, Any]]) –

    Used to manage multi-modal experiments performed on the same sample/cells.

    +

  • main_experiment_name (Optional[str]) – A string, specifying the main experiment name.

    • +

  • alternative_experiments (Optional[Dict[str, Any]]) –

    Used to manage multi-modal experiments performed on the same sample/cells.

    Alternative experiments must contain the same cells (rows) as the primary experiment. It’s a dictionary with keys as the names of the alternative experiments (e.g., sc-atac, crispr) and values as subclasses of -SummarizedExperiment.

    +SummarizedExperiment.

    • -

  • row_pairs (Optional[Any]) –

    Row pairings/relationships between features.

    +

  • row_pairs (Optional[Any]) –

    Row pairings/relationships between features.

    Defaults to None.

    • -

  • column_pairs (Optional[Any]) –

    Column pairings/relationships between cells.

    +

  • column_pairs (Optional[Any]) –

    Column pairings/relationships between cells.

    Defaults to None.

    • -

  • validate (bool) – Internal use only.

    • +

  • validate (bool) – Internal use only.

@@ -383,7 +383,7 @@

Submodules__repr__()[source]¶
Return type:
-

str

+

str

Returns:

A string representation.

@@ -397,16 +397,16 @@

Submodules
Parameters:
-

name (Union[str, int]) – Name or index position of the alternative experiment.

+

name (Union[str, int]) – Name or index position of the alternative experiment.

Raises:
    -

  • AttributeError – If the dimension name does not exist.

    • -

  • IndexError – If index is greater than the number of reduced dimensions.

    • +

  • AttributeError – If the dimension name does not exist.

    • +

  • IndexError – If index is greater than the number of reduced dimensions.

Return type:
-

Any

+

Any

Returns:

The alternative experiment.

@@ -416,25 +416,25 @@

Submodules
-property alternative_experiment_names: List[str]¶
+property alternative_experiment_names: List[str]¶

Alias for get_alternative_experiment_names().

-property alternative_experiments: Dict[str, Any]¶
+property alternative_experiments: Dict[str, Any]¶

Alias for get_alternative_experiments().

-property column_pair_names: List[str]¶
+property column_pair_names: List[str]¶

Alias for get_column_pair_names().

-property column_pairs: Dict[str, Any]¶
+property column_pairs: Dict[str, Any]¶

Alias for get_column_pairs().

@@ -475,7 +475,7 @@

Submodules
Return type:
-

List[str]

+

List[str]

Returns:

List of alternative experiment names.

@@ -489,7 +489,7 @@

Submodules
Return type:
-

Dict[str, Any]

+

Dict[str, Any]

Returns:

A dictionary with names of @@ -504,7 +504,7 @@

Submodules
Return type:
-

List[str]

+

List[str]

Returns:

List of column pair names.

@@ -518,7 +518,7 @@

Submodules
Return type:
-

Dict[str, Any]

+

Dict[str, Any]

Returns:

Access column pairs.

@@ -532,7 +532,7 @@

Submodules
Return type:
-

Optional[str]

+

Optional[str]

Returns:

Name if available, otherwise None.

@@ -546,7 +546,7 @@

Submodules
Return type:
-

List[str]

+

List[str]

Returns:

List of reduced dimensionality names.

@@ -560,7 +560,7 @@

Submodules
Return type:
-

Dict[str, Any]

+

Dict[str, Any]

Returns:

A dictionary with keys as names of embedding method and value @@ -575,7 +575,7 @@

Submodules
Return type:
-

List[str]

+

List[str]

Returns:

List of row pair names.

@@ -589,7 +589,7 @@

Submodules
Return type:
-

Dict[str, Any]

+

Dict[str, Any]

Returns:

Access row pairs.

@@ -610,7 +610,7 @@

Submodules
-property main_experiment_name: str | None¶
+property main_experiment_name: str | None¶

Alias for get_main_experiment_name().

@@ -620,16 +620,16 @@

Submodules
Parameters:
-

dimension (Union[str, int]) – Name or index position of the reduced dimension.

+

dimension (Union[str, int]) – Name or index position of the reduced dimension.

Raises:
    -

  • AttributeError – If the dimension name does not exist.

    • -

  • IndexError – If index is greater than the number of reduced dimensions.

    • +

  • AttributeError – If the dimension name does not exist.

    • +

  • IndexError – If index is greater than the number of reduced dimensions.

Return type:
-

Any

+

Any

Returns:

The embedding.

@@ -639,25 +639,25 @@

Submodules
-property reduced_dim_names: List[str]¶
+property reduced_dim_names: List[str]¶

Alias for get_reduced_dim_names().

-property reduced_dims: Dict[str, Any]¶
+property reduced_dims: Dict[str, Any]¶

Alias for get_reduced_dims().

-property row_pair_names: List[str]¶
+property row_pair_names: List[str]¶

Alias for get_row_pair_names().

-property row_pairs: Dict[str, Any]¶
+property row_pairs: Dict[str, Any]¶

Alias for get_row_pairs().

@@ -668,8 +668,8 @@

Submodules
Parameters:
    -

  • names (List[str]) – New alternative experiment names.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • names (List[str]) – New alternative experiment names.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -689,8 +689,8 @@

Submodules
Parameters:
    -

  • alternative_experiments (Dict[str, Any]) – New alternative experiments.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • alternative_experiments (Dict[str, Any]) – New alternative experiments.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -710,8 +710,8 @@

Submodules
Parameters:
    -

  • names (List[str]) – New names.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • names (List[str]) – New names.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -732,7 +732,7 @@

SubmodulesParameters:

  • names – New column pairs.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -752,8 +752,8 @@

Submodules
Parameters:
    -

  • name (Optional[str]) – New main experiment name.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • name (Optional[str]) – New main experiment name.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -773,8 +773,8 @@

Submodules
Parameters:
    -

  • names (List[str]) – New dimensionality names.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • names (List[str]) – New dimensionality names.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -794,8 +794,8 @@

Submodules
Parameters:
    -

  • reduced_dims (Dict[str, Any]) – New embeddings.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • reduced_dims (Dict[str, Any]) – New embeddings.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -815,8 +815,8 @@

Submodules
Parameters:
    -

  • names (List[str]) – New names.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • names (List[str]) – New names.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -837,7 +837,7 @@

SubmodulesParameters:

  • names – New row pairs.

    • -

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

    • +

  • in_place (bool) – Whether to modify the SingleCellExperiment in place.

Return type:
@@ -856,7 +856,7 @@

SubmodulesSingleCellExperiment-like into a AnnData representation.

Parameters:
-

include_alternative_experiments (bool) – Whether to transform alternative experiments.

+

include_alternative_experiments (bool) – Whether to transform alternative experiments.

Returns:

A tuple with AnnData main experiment and a list of alternative experiments.

@@ -937,7 +937,7 @@

Submodules
singlecellexperiment.SingleCellExperiment.relaxed_combine_rows(*x)[source]¶
-

A relaxed version of the combine_rows() method for +

A relaxed version of the combine_rows() method for SingleCellExperiment objects. Whereas combine_rows expects that all objects have the same columns, relaxed_combine_rows allows for different columns. Absent columns in any object are filled in with appropriate placeholder values before combining.

@@ -1081,8 +1081,8 @@

Submodules - +

+ diff --git a/api/singlecellexperiment.io.html b/api/singlecellexperiment.io.html index 7bbba90..b87879e 100644 --- a/api/singlecellexperiment.io.html +++ b/api/singlecellexperiment.io.html @@ -5,8 +5,8 @@ - - singlecellexperiment.io package - SingleCellExperiment 0.4.7 documentation + + singlecellexperiment.io package - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -271,7 +271,7 @@

SubmodulesSingleCellExperiment from a H5AD file.

Parameters:
-

path (str) – Path to a H5AD file.

+

path (str) – Path to a H5AD file.

Return type:

SingleCellExperiment

@@ -293,8 +293,8 @@

Submodules
Parameters:
    -

  • path (str) – Path to 10x H5 file.

    • -

  • realize_assays (bool) – Whether to realize assays into memory. +

  • path (str) – Path to 10x H5 file.

    • +

  • realize_assays (bool) – Whether to realize assays into memory. Defaults to False.

@@ -313,7 +313,7 @@

SubmodulesSingleCellExperiment.

Parameters:
-

path (str) –

Path to 10X MTX directory.

+

path (str) –

Path to 10X MTX directory.

Directory must contain matrix.mtx, and optionally a genes.tsv to represent featires and barcodes.tsv for cell annotations.

@@ -412,8 +412,8 @@

Submodules - +

+ diff --git a/authors.html b/authors.html index 99cc995..701ce29 100644 --- a/authors.html +++ b/authors.html @@ -5,8 +5,8 @@ - - Contributors - SingleCellExperiment 0.4.7 documentation + + Contributors - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -314,8 +314,8 @@

Contributors - +

+ diff --git a/changelog.html b/changelog.html index 95d8aed..205555f 100644 --- a/changelog.html +++ b/changelog.html @@ -5,8 +5,8 @@ - - Changelog - SingleCellExperiment 0.4.7 documentation + + Changelog - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -260,6 +260,13 @@

Changelog¶

+
+

Version 0.5.0¶

+
    +

  • chore: Remove Python 3.8 (EOL)

    • +

  • precommit: Replace docformatter with ruff’s formatter

    • +
+

Version 0.4.7¶

    @@ -351,6 +358,7 @@

    Version 0.1
    • Changelog
        +
      • Version 0.5.0
      • Version 0.4.7
      • Version 0.4.2 - 0.4.6
      • Version 0.4.0 to 0.4.1
        • @@ -367,8 +375,8 @@

        Version 0.1 - +

+ diff --git a/contributing.html b/contributing.html index 5b54ad8..4566903 100644 --- a/contributing.html +++ b/contributing.html @@ -5,8 +5,8 @@ - - Contributing - SingleCellExperiment 0.4.7 documentation + + Contributing - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
-
SingleCellExperiment 0.4.7 documentation
 +
SingleCellExperiment 0.5.0 documentation
@@ -191,7 +191,7 @@
- SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -483,6 +483,9 @@

Releases

  • Run tox -e publish -- --repository pypi and check that everything was uploaded to PyPI correctly.

    • + + +
    @@ -493,9 +496,6 @@

    Releases of environments, including private companies and proprietary code bases.

    - - -

    @@ -579,8 +579,8 @@

    Releases

    -
    - +
    + diff --git a/genindex.html b/genindex.html index 0826149..c020cad 100644 --- a/genindex.html +++ b/genindex.html @@ -4,7 +4,7 @@ - Index - SingleCellExperiment 0.4.7 documentation + Index - SingleCellExperiment 0.5.0 documentation @@ -165,7 +165,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -189,7 +189,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -515,8 +515,8 @@

    T

    -
    - +
    + diff --git a/index.html b/index.html index 1bdd0de..c45429f 100644 --- a/index.html +++ b/index.html @@ -5,8 +5,8 @@ - - SingleCellExperiment 0.4.7 documentation + + SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -300,6 +300,7 @@

    Contents
  • License
  • Authors
  • Changelog
      +
    • Version 0.5.0
    • Version 0.4.7
    • Version 0.4.2 - 0.4.6
    • Version 0.4.0 to 0.4.1
      • @@ -380,8 +381,8 @@

      Indices and tables - +

    • + diff --git a/license.html b/license.html index a0db966..bc29333 100644 --- a/license.html +++ b/license.html @@ -5,8 +5,8 @@ - - License - SingleCellExperiment 0.4.7 documentation + + License - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -334,8 +334,8 @@

    License¶

    -
    - +
    + diff --git a/objects.inv b/objects.inv index 9d2e868..63d0d16 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html index 41ef5e3..9b6c05a 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -4,7 +4,7 @@ - Python Module Index - SingleCellExperiment 0.4.7 documentation + Python Module Index - SingleCellExperiment 0.5.0 documentation @@ -165,7 +165,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -189,7 +189,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -326,8 +326,8 @@

    Python Module Index

    -
    - +
    + diff --git a/readme.html b/readme.html index dedd2a4..cce16c1 100644 --- a/readme.html +++ b/readme.html @@ -5,8 +5,8 @@ - - SingleCellExperiment - SingleCellExperiment 0.4.7 documentation + + SingleCellExperiment - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -373,8 +373,8 @@

    Note¶

    -
    - +
    + diff --git a/search.html b/search.html index 9f1aca6..97b0b16 100644 --- a/search.html +++ b/search.html @@ -5,9 +5,9 @@ - + -Search - SingleCellExperiment 0.4.7 documentation +Search - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -295,8 +295,8 @@
    -
    - +
    + diff --git a/searchindex.js b/searchindex.js index 411744b..40c3d9c 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Access a reduced dimension": [[9, "access-a-reduced-dimension"]], "Changelog": [[4, null]], "Clone the repository": [[5, "clone-the-repository"]], "Code Contributions": [[5, "code-contributions"]], "Combining experiments": [[9, "combining-experiments"]], "Construction": [[9, "construction"]], "Contents": [[6, "contents"]], "Contributing": [[5, "contributing"]], "Contributors": [[3, null]], "Create an environment": [[5, "create-an-environment"]], "Documentation Improvements": [[5, "documentation-improvements"]], "Export as AnnData or MuData": [[9, "export-as-anndata-or-mudata"]], "From 10X formats": [[9, "from-10x-formats"]], "Getters/Setters": [[9, "getters-setters"]], "Implement your changes": [[5, "implement-your-changes"]], "Indices and tables": [[6, "indices-and-tables"]], "Install": [[6, "install"], [8, "install"]], "Installation": [[9, "installation"]], "Interop with anndata": [[9, "interop-with-anndata"]], "Issue Reports": [[5, "issue-reports"]], "License": [[7, null]], "Maintainer tasks": [[5, "maintainer-tasks"]], "Module contents": [[1, "module-singlecellexperiment"], [2, "module-singlecellexperiment.io"]], "Note": [[8, "note"]], "Releases": [[5, "releases"]], "Represent single-cell experiments": [[9, null]], "SingleCellExperiment": [[6, null], [8, null]], "Submit an issue": [[5, "submit-an-issue"]], "Submit your contribution": [[5, "submit-your-contribution"]], "Submodules": [[1, "submodules"], [2, "submodules"]], "Subpackages": [[1, "subpackages"]], "Subset experiments": [[9, "subset-experiments"]], "Todo": [[5, null], [5, "id2"], [5, "id3"], [5, "id5"], [5, "id6"], [5, "id7"], [5, "id8"], [5, "id9"], [5, "id10"], [5, "id11"], [5, "id12"]], "Troubleshooting": [[5, "troubleshooting"]], "Usage": [[8, "usage"]], "Version 0.1": [[4, "version-0-1"]], "Version 0.3.0": [[4, "version-0-3-0"]], 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9, "from": 9, "getter": 9, "h5ad": 2, "implement": 5, "improv": 5, "indic": 6, "instal": [6, 8, 9], "interop": 9, "io": 2, "issu": 5, "licens": 7, "maintain": 5, "modul": [1, 2], "mudata": 9, "note": 8, "packag": [1, 2], "reduc": 9, "releas": 5, "report": 5, "repositori": 5, "repres": 9, "setter": 9, "singl": 9, "singlecellexperi": [0, 1, 2, 6, 8], "submit": 5, "submodul": [1, 2], "subpackag": 1, "subset": 9, "tabl": 6, "task": 5, "tenx": 2, "todo": 5, "troubleshoot": 5, "usag": 8, "version": 4, "your": 5}}) \ No newline at end of file diff --git a/tutorial.html b/tutorial.html index 2eb9a0d..b371a99 100644 --- a/tutorial.html +++ b/tutorial.html @@ -5,8 +5,8 @@ - - Represent single-cell experiments - SingleCellExperiment 0.4.7 documentation + + Represent single-cell experiments - SingleCellExperiment 0.5.0 documentation @@ -167,7 +167,7 @@
    -
    SingleCellExperiment 0.4.7 documentation
     +
    SingleCellExperiment 0.5.0 documentation
    @@ -191,7 +191,7 @@
    - SingleCellExperiment 0.4.7 documentation + SingleCellExperiment 0.5.0 documentation @@ -435,7 +435,7 @@

    Interop with an layers: 'X', None)

    -
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.9/site-packages/anndata/_core/anndata.py:121: ImplicitModificationWarning: Transforming to str index.
+
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
   warnings.warn("Transforming to str index.", ImplicitModificationWarning)
 
    
 
    
@@ -483,13 +483,13 @@ 
    Getters/Setters
-
    array([[0.65444999, 0.90601852, 0.87720018, 0.09727131],
-       [0.27040466, 0.05925716, 0.40215101, 0.35083125],
-       [0.3231138 , 0.73572795, 0.98296675, 0.92569003],
-       [0.33351471, 0.57698531, 0.26307458, 0.06270545],
-       [0.51755486, 0.74829941, 0.09911028, 0.50273699],
-       [0.76457642, 0.9932149 , 0.4097655 , 0.1936202 ]])
+
    array([[0.63429425, 0.70280906, 0.04205235, 0.25499416],
+       [0.88151426, 0.18453009, 0.18427869, 0.97357572],
+       [0.49993478, 0.2066993 , 0.34895639, 0.47023364],
+       [0.23130893, 0.12814801, 0.92515617, 0.70829496],
+       [0.92224612, 0.01619865, 0.05958199, 0.12084088],
+       [0.02229804, 0.79214854, 0.88744618, 0.44622431]])
 
    
 
    
 
    
@@ -664,7 +664,7 @@ 
    Combining experiments
    -
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.9/site-packages/singlecellexperiment/SingleCellExperiment.py:1092: UserWarning: 'row_pairs' and 'column_pairs' are currently ignored during this operation.
+
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/singlecellexperiment/SingleCellExperiment.py:1046: UserWarning: 'row_pairs' and 'column_pairs' are currently ignored during this operation.
   warn(
 
    
 
    
@@ -694,7 +694,7 @@ 
    Combining experiments
    -
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.9/site-packages/singlecellexperiment/SingleCellExperiment.py:1134: UserWarning: 'row_pairs' and 'column_pairs' are currently ignored during this operation.
+
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/singlecellexperiment/SingleCellExperiment.py:1088: UserWarning: 'row_pairs' and 'column_pairs' are currently ignored during this operation.
   warn(
 
    
 
    
@@ -728,7 +728,7 @@ 
    Combining experiments
    -
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.9/site-packages/singlecellexperiment/SingleCellExperiment.py:1244: UserWarning: 'row_pairs' and 'column_pairs' are currently ignored during this operation.
+
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/singlecellexperiment/SingleCellExperiment.py:1198: UserWarning: 'row_pairs' and 'column_pairs' are currently ignored during this operation.
   warn("'row_pairs' and 'column_pairs' are currently ignored during this operation.")
 
    
 
    
@@ -746,8 +746,12 @@ 
    Export as AnnDa
    -
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.9/site-packages/anndata/_core/anndata.py:121: ImplicitModificationWarning: Transforming to str index.
+
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
   warnings.warn("Transforming to str index.", ImplicitModificationWarning)
+/home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
+  self._update_attr("var", axis=0, join_common=join_common)
+/home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
+  self._update_attr("obs", axis=1, join_common=join_common)
 
    
 
    
 
    MuData object with n_obs × n_vars = 6 × 200
@@ -777,7 +781,7 @@ 
    Export as AnnDa
 alternative experiments:  None
    -
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.9/site-packages/anndata/_core/anndata.py:121: ImplicitModificationWarning: Transforming to str index.
+
    /home/runner/work/SingleCellExperiment/SingleCellExperiment/.tox/docs/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
   warnings.warn("Transforming to str index.", ImplicitModificationWarning)
 
    
 
    
@@ -834,8 +838,8 @@ 
    Export as AnnDa
    -
    - +
    +