Deploying to gh-pages from @ 0e145e7 🚀

.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: c2816a1d94bae1060883498f48c5259b
+config: c8acf869f0515f592e67571142b76a30
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

@@ -5,9 +5,10 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" />
 
     <!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>Overview: module code - cellarr 0.0.1 documentation</title>
+        <title>Overview: module code - cellarr 0.0.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=387cc868" />
+    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
 
 
@@ -178,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">cellarr 0.0.1 documentation</div></a>
+      <a href="../index.html"><div class="brand">cellarr 0.0.2 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">cellarr 0.0.1 documentation</span>
+  <span class="sidebar-brand-text">cellarr 0.0.2 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -211,7 +212,7 @@
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
-<li class="toctree-l1"><a class="reference internal" href="../readme.html">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributions &amp; Help</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../authors.html">Authors</a></li>
@@ -255,7 +256,11 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>All modules for which code is available</h1>
-<ul><li><a href="cellarr/skeleton.html">cellarr.skeleton</a></li>
+<ul><li><a href="cellarr/CellArrDataset.html">cellarr.CellArrDataset</a></li>
+<li><a href="cellarr/build_cellarrdataset.html">cellarr.build_cellarrdataset</a></li>
+<li><a href="cellarr/utils_anndata.html">cellarr.utils_anndata</a></li>
+<li><a href="cellarr/utils_tiledb_array.html">cellarr.utils_tiledb_array</a></li>
+<li><a href="cellarr/utils_tiledb_frame.html">cellarr.utils_tiledb_frame</a></li>
 </ul>
         </article>
       </div>
@@ -288,7 +293,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=d45e8c67"></script>
+</div><script src="../_static/documentation_options.js?v=e3a6060d"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=4e2eecee"></script>

_sources/api/cellarr.rst.txt

@@ -4,10 +4,50 @@ cellarr package
 Submodules
 ----------
 
-cellarr.skeleton module
------------------------
+cellarr.CellArrDataset module
+-----------------------------
 
-.. automodule:: cellarr.skeleton
+.. automodule:: cellarr.CellArrDataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cellarr.build\_cellarrdataset module
+------------------------------------
+
+.. automodule:: cellarr.build_cellarrdataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cellarr.dataloader module
+-------------------------
+
+.. automodule:: cellarr.dataloader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cellarr.utils\_anndata module
+-----------------------------
+
+.. automodule:: cellarr.utils_anndata
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cellarr.utils\_tiledb\_array module
+-----------------------------------
+
+.. automodule:: cellarr.utils_tiledb_array
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cellarr.utils\_tiledb\_frame module
+-----------------------------------
+
+.. automodule:: cellarr.utils_tiledb_frame
    :members:
    :undoc-members:
    :show-inheritance:

_sources/index.md.txt

@@ -1,25 +1,21 @@
 # cellarr
 
-Add a short description here!
+Cell Arrays is a Python package that provides a TileDB-backed store for large collections of genomic experimental data, such as millions of cells across multiple single-cell experiment objects.
 
+## Install
 
-## 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.
+To get started, install the package from [PyPI](https://pypi.org/project/cellarr/)
 
+```bash
+pip install cellarr
+```
 
 ## Contents
 
 ```{toctree}
 :maxdepth: 2
 
-Overview <readme>
+Overview <tutorial>
 Contributions & Help <contributing>
 License <license>
 Authors <authors>

_sources/tutorial.md.txt

@@ -0,0 +1,58 @@
+---
+file_format: mystnb
+kernelspec:
+  name: python
+---
+
+# Cell Arrays
+
+Cell Arrays is a Python package that provides a TileDB-backed store for large collections of genomic experimental data, such as millions of cells across multiple single-cell experiment objects.
+
+## Usage
+
+### Create the `CellArrDataset`
+
+Creating a CellArrDataset generates three TileDB files in the specified output directory:
+
+- `gene_metadata`: Contains feature annotations.
+- `cell_metadata`: Contains cell or sample metadata.
+- `matrix`: A TileDB-backed sparse array containing expression vectors.
+
+***Note: Currently only supports either paths to H5AD or `AnnData` objects***
+
+To build a `CellArrDataset` from a collection of `H5AD` or `AnnData` objects:
+
+```python
+import anndata
+import numpy as np
+import tempfile
+from cellarr import build_cellarrdataset, CellArrDataset
+
+# Create a temporary directory
+tempdir = tempfile.mkdtemp()
+
+# Read AnnData objects
+adata1 = anndata.read_h5ad("path/to/object1.h5ad")
+# or just provide the path
+adata2 = "path/to/object2.h5ad"
+
+# Build CellArrDataset
+dataset = build_cellarrdataset(
+     output_path=tempdir,
+     h5ad_or_adata=[adata1, adata2],
+     matrix_dim_dtype=np.float32
+)
+```
+----
+
+#### TODO: This following section does not work yet.
+
+Users have the option to reuse the `dataset` object retuned when building the dataset or by creating a `CellArrDataset` object by initializng it to the path where the files were created.
+
+```python
+# Create a CellArrDataset object from the existing dataset
+dataset = CellArrDataset(dataset_path=tempdir)
+
+# Query data from the dataset
+expression_data = dataset[10, ["gene1", "gene10", "gene500"]]
+```

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.0.1',
+    VERSION: '0.0.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',