moscot 0.4.2__tar.gz → 0.4.3__tar.gz

{moscot-0.4.2 → moscot-0.4.3}/.pre-commit-config.yaml

@@ -63,7 +63,7 @@ repos:
       - id: doc8
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.10
+    rev: v0.11.7
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{moscot-0.4.2 → moscot-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moscot
-Version: 0.4.2
+Version: 0.4.3
 Summary: Multi-omic single-cell optimal transport tools
 Author: Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange
 Maintainer-email: Dominik Klein <dominik.klein@helmholtz-muenchen.de>, Giovanni Palla <giovanni.palla@helmholtz-muenchen.de>, Michal Klein <michal.klein@helmholtz-muenchen.de>
@@ -65,18 +65,18 @@ Requires-Dist: anndata>=0.9.1
 Requires-Dist: scanpy>=1.9.3
 Requires-Dist: wrapt>=1.13.2
 Requires-Dist: docrep>=0.3.2
+Requires-Dist: jax>=0.6.1
 Requires-Dist: ott-jax>=0.5.0
 Requires-Dist: cloudpickle>=2.2.0
 Requires-Dist: rich>=13.5
 Requires-Dist: docstring_inheritance>=2.0.0
 Requires-Dist: mudata>=0.2.2
+Requires-Dist: optax
+Requires-Dist: flax
+Requires-Dist: diffrax
+Requires-Dist: ott-jax[neural]>=0.5.0
 Provides-Extra: spatial
 Requires-Dist: squidpy>=1.2.3; extra == "spatial"
-Provides-Extra: neural
-Requires-Dist: optax; extra == "neural"
-Requires-Dist: flax; extra == "neural"
-Requires-Dist: diffrax; extra == "neural"
-Requires-Dist: ott-jax[neural]>=0.5.0; extra == "neural"
 Provides-Extra: dev
 Requires-Dist: pre-commit>=3.0.0; extra == "dev"
 Requires-Dist: tox>=4; extra == "dev"

{moscot-0.4.2 → moscot-0.4.3}/pyproject.toml

@@ -54,11 +54,16 @@ dependencies = [
     "scanpy>=1.9.3",
     "wrapt>=1.13.2",
     "docrep>=0.3.2",
+    "jax>=0.6.1",
     "ott-jax>=0.5.0",
     "cloudpickle>=2.2.0",
     "rich>=13.5",
     "docstring_inheritance>=2.0.0",
-    "mudata>=0.2.2"
+    "mudata>=0.2.2",
+    "optax",
+    "flax",
+    "diffrax",
+    "ott-jax[neural]>=0.5.0"
 ]
 
 [project.optional-dependencies]
@@ -66,13 +71,6 @@ spatial = [
     "squidpy>=1.2.3"
 ]
 
-neural = [
-    "optax",
-    "flax",
-    "diffrax",
-    "ott-jax[neural]>=0.5.0",
-
-]
 dev = [
     "pre-commit>=3.0.0",
     "tox>=4",

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/backends/ott/output.py

@@ -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 @@ class OTTOutput(BaseDiscreteSolverOutput):
         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 @@ class NeuralOutput(BaseNeuralOutput):
         # 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 @@ class GraphOTTOutput(OTTOutput):
         else:
             idx = 0
 
-        if not isinstance(device, xla_ext.Device):
+        if not isinstance(device, jax.Device):
             try:
                 device = jax.devices(device)[idx]
             except IndexError:

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/base/problems/_mixins.py

@@ -394,7 +394,7 @@ class AnalysisMixin(Generic[K, B], AbstractPushPullAdata, AbstractSolutionsProbl
 
     def _interpolate_transport(
         self,
-        # TODO(@giovp): rename this to 'explicit_steps', pass to policy.plan() and reintroduce (source_key, target_key)
+        # TODO(@giovp): rename this to 'explicit_steps'; pass to policy.plan() and reintroduce (source_key, target_key)
         path: Sequence[tuple[K, K]],
         scale_by_marginals: bool = True,
         **_: Any,

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/base/problems/birth_death.py

@@ -188,7 +188,7 @@ class BirthDeathProblem(BirthDeathMixin, OTProblem):
 
         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

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/costs/_costs.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

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/datasets.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
     ----------

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/problems/spatiotemporal/_spatio_temporal.py

@@ -67,7 +67,7 @@ class SpatioTemporalProblem(  # type: ignore[misc]
         .. 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

{moscot-0.4.2 → moscot-0.4.3}/src/moscot/utils/subset_policy.py

@@ -348,6 +348,13 @@ class StarPolicy(OrderedPolicy[K]):
             node = (node, self.reference)
         return super().remove_node(node)  # type: ignore[return-value]
 
+    def _plan(self, start: Optional[K] = None, end: Optional[K] = None, **_: Any) -> Sequence[Tuple[K, K]]:
+        if start is None and end is None:
+            return list(self._graph)
+        if start is not None and end is not None:
+            return [(start, end)]
+        raise ValueError("For `StarPolicy`, the start and end node must both be `None` or both must be specified.")
+
     @property
     def reference(self) -> K:
         """Central node."""

{moscot-0.4.2 → moscot-0.4.3}/src/moscot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moscot
-Version: 0.4.2
+Version: 0.4.3
 Summary: Multi-omic single-cell optimal transport tools
 Author: Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange
 Maintainer-email: Dominik Klein <dominik.klein@helmholtz-muenchen.de>, Giovanni Palla <giovanni.palla@helmholtz-muenchen.de>, Michal Klein <michal.klein@helmholtz-muenchen.de>
@@ -65,18 +65,18 @@ Requires-Dist: anndata>=0.9.1
 Requires-Dist: scanpy>=1.9.3
 Requires-Dist: wrapt>=1.13.2
 Requires-Dist: docrep>=0.3.2
+Requires-Dist: jax>=0.6.1
 Requires-Dist: ott-jax>=0.5.0
 Requires-Dist: cloudpickle>=2.2.0
 Requires-Dist: rich>=13.5
 Requires-Dist: docstring_inheritance>=2.0.0
 Requires-Dist: mudata>=0.2.2
+Requires-Dist: optax
+Requires-Dist: flax
+Requires-Dist: diffrax
+Requires-Dist: ott-jax[neural]>=0.5.0
 Provides-Extra: spatial
 Requires-Dist: squidpy>=1.2.3; extra == "spatial"
-Provides-Extra: neural
-Requires-Dist: optax; extra == "neural"
-Requires-Dist: flax; extra == "neural"
-Requires-Dist: diffrax; extra == "neural"
-Requires-Dist: ott-jax[neural]>=0.5.0; extra == "neural"
 Provides-Extra: dev
 Requires-Dist: pre-commit>=3.0.0; extra == "dev"
 Requires-Dist: tox>=4; extra == "dev"

{moscot-0.4.2 → moscot-0.4.3}/src/moscot.egg-info/requires.txt

@@ -7,11 +7,16 @@ anndata>=0.9.1
 scanpy>=1.9.3
 wrapt>=1.13.2
 docrep>=0.3.2
+jax>=0.6.1
 ott-jax>=0.5.0
 cloudpickle>=2.2.0
 rich>=13.5
 docstring_inheritance>=2.0.0
 mudata>=0.2.2
+optax
+flax
+diffrax
+ott-jax[neural]>=0.5.0
 
 [dev]
 pre-commit>=3.0.0
@@ -29,12 +34,6 @@ myst-nb>=0.17.1
 ipython>=7.20.0
 sphinx_design>=0.3.0
 
-[neural]
-optax
-flax
-diffrax
-ott-jax[neural]>=0.5.0
-
 [spatial]
 squidpy>=1.2.3