Update notebook version (#824)

* Update notebook version

* fix references

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fixes and module update

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: LeonStadelmann

docs/notebooks

@@ -237,6 +237,17 @@ @article{Li-spatial:22
   year    = {2022},
 }
 
+@article{scperturb:24,
+  title={scPerturb: harmonized single-cell perturbation data},
+  author={Peidli, Stefan and Green, Tessa D and Shen, Ciyue and Gross, Torsten and Min, Joseph and Garda, Samuele and Yuan, Bo and Schumacher, Linus J and Taylor-King, Jake P and Marks, Debora S and others},
+  journal={Nature Methods},
+  volume={21},
+  number={3},
+  pages={531--540},
+  year={2024},
+  publisher={Nature Publishing Group US New York}
+}
+
 @article{Jones-spatial:22,
   author    = {Jones, Andrew and Townes, F. William and Li, Didong and Engelhardt, Barbara E.},
   publisher = {Cold Spring Harbor Laboratory},

docs/references.bib

@@ -1,7 +1,5 @@
 from typing import Any, Callable, List, Optional, Tuple, Union
 
-import jaxlib.xla_extension as xla_ext
-
 import jax
 import jax.numpy as jnp
 import numpy as np
@@ -209,7 +207,7 @@ def to(self, device: Optional[Device_t] = None) -> "OTTOutput":  # noqa: D102
         else:
             idx = 0
 
-        if not isinstance(device, xla_ext.Device):
+        if not isinstance(device, jax.Device):
             try:
                 device = jax.devices(device)[idx]
             except IndexError:
@@ -441,7 +439,7 @@ def to(
         # else:
         #     idx = 0
 
-        # if not isinstance(device, xla_ext.Device):
+        # if not isinstance(device, jax.Device):
         #     try:
         #         device = jax.devices(device)[idx]
         #     except IndexError as err:
@@ -509,7 +507,7 @@ def to(self, device: Optional[Device_t] = None) -> "GraphOTTOutput":  # noqa: D1
         else:
             idx = 0
 
-        if not isinstance(device, xla_ext.Device):
+        if not isinstance(device, jax.Device):
             try:
                 device = jax.devices(device)[idx]
             except IndexError:

src/moscot/backends/ott/output.py

@@ -188,7 +188,7 @@ def estimate_marginals(
 
         Examples
         --------
-        - See :doc:`../../notebooks/examples/problems/800_score_genes_for_marginals`
+        - See :doc:`../../notebooks/examples/problems/TemporalProblem/800_score_genes_for_marginals`
             on examples how to use :meth:`~moscot.problems.time.TemporalProblem.score_genes_for_marginals`.
 
         """  # noqa: D205

src/moscot/base/problems/birth_death.py

@@ -18,8 +18,8 @@ class BarcodeDistance(BaseCost):
     """Scaled `Hamming distance <https://en.wikipedia.org/wiki/Hamming_distance>`_ between barcodes.
 
     .. seealso::
-        - See :doc:`../../notebooks/examples/problems/700_barcode_distance` on how to use this cost
-          in the :class:`~moscot.problems.time.LineageProblem`.
+        - See :doc:`../../notebooks/examples/problems/LineageProblem/700_barcode_distance` on
+          how to use this cost in the :class:`~moscot.problems.time.LineageProblem`.
 
     Parameters
     ----------
@@ -68,7 +68,7 @@ class LeafDistance(BaseCost):
             This class ignores `attr` which is always set to `uns`.
 
     .. seealso::
-        - See :doc:`../../notebooks/examples/problems/600_leaf_distance` on how to use this cost
+        - See :doc:`../../notebooks/examples/problems/LineageProblem/600_leaf_distance` on how to use this cost
           in the :class:`~moscot.problems.time.LineageProblem`.
 
     Parameters

src/moscot/costs/_costs.py

@@ -369,7 +369,7 @@ def sciplex(
     """Perturbation dataset published in :cite:`srivatsan:20`.
 
     Transcriptomes of A549, K562, and mCF7 cells exposed to 188 compounds.
-    Data obtained from http://projects.sanderlab.org/scperturb/.
+    Data obtained from :cite:`scperturb:24`.
 
     Parameters
     ----------

src/moscot/datasets.py

@@ -67,7 +67,7 @@ def prepare(
         .. seealso::
             - See :doc:`../../notebooks/tutorials/500_spatiotemporal` on how to
               prepare and solve the :class:`~moscot.problems.spatiotemporal.SpatioTemporalProblem`.
-            - See :doc:`../../notebooks/examples/problems/800_score_genes_for_marginals` on how to
+            - See :doc:`../../notebooks/examples/problems/TemporalProblem/800_score_genes_for_marginals` on how to
               :meth:`score genes for proliferation and apoptosis <score_genes_for_marginals>`.
 
         Parameters