Rename TransportMapKernel -> RealTimeKernel (#1080)

* Rename `TransportMapKernel` -> `RealTimeKernel`

* Enable testing on 3.11

* Update submodule

.github/workflows/test.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ['3.8', '3.10']  # , '3.11']
+        python: ['3.8', '3.10', '3.11']
         slepc: [noslepc]
         include:
         - os: macos-latest

docs/about/version2.rst

@@ -28,9 +28,9 @@ Important changes in version 2
 * Removal of the `external API`: anyone wishing to contribute to CellRank can do this now directly via :mod:`~cellrank.kernels` and
   :mod:`~cellrank.estimators`. We welcome any contribution to CellRank, see our :doc:`contribution guide <../contributing>`, and feel free to
   get in touch via an `issue <https://github.com/theislab/cellrank/issues/new/choose>`_ or `email <mailto:info@cellrank.org>`_.
-* Replacement of the old `WOTKernel` with a new :class:`~cellrank.kernels.TransportMapKernel`: this is CellRank's interface
+* Replacement of the old `WOTKernel` with a new :class:`~cellrank.kernels.RealTimeKernel`: this is CellRank's interface
   with `moscot <https://moscot-tools.org>`_, enabling us to analyze large-scale time-course studies with additional spatial or lineage readout :cite:`klein:23,lange:23`. In addition,
-  the :class:`~cellrank.kernels.TransportMapKernel` interfaces with `Waddington-OT <https://broadinstitute.github.io/wot/>`_ :cite:`schiebinger:19`.
+  the :class:`~cellrank.kernels.RealTimeKernel` interfaces with `Waddington-OT <https://broadinstitute.github.io/wot/>`_ :cite:`schiebinger:19`.
 
 There are many more changes and improvements in CellRank 2. For example, the computation of fate probabilities is 30x faster compared
 to version 1, we fixed many bugs, and improved and extended our documentation and :doc:`tutorials <../notebooks/tutorials/index>`.

docs/api/kernels.rst

@@ -19,5 +19,5 @@ takes in multi-view single-cell data and outputs a cell-cell transition matrix.
     kernels.ConnectivityKernel
     kernels.PseudotimeKernel
     kernels.CytoTRACEKernel
-    kernels.TransportMapKernel
+    kernels.RealTimeKernel
     kernels.PrecomputedKernel

src/cellrank/kernels/__init__.py

@@ -5,7 +5,7 @@
 from cellrank.kernels._experimental_time_kernel import ExperimentalTimeKernel
 from cellrank.kernels._precomputed_kernel import PrecomputedKernel
 from cellrank.kernels._pseudotime_kernel import PseudotimeKernel
-from cellrank.kernels._transport_map_kernel import TransportMapKernel
+from cellrank.kernels._real_time_kernel import RealTimeKernel
 from cellrank.kernels._velocity_kernel import VelocityKernel
 
 __all__ = [
@@ -16,6 +16,6 @@
     "ExperimentalTimeKernel",
     "PrecomputedKernel",
     "PseudotimeKernel",
-    "TransportMapKernel",
+    "RealTimeKernel",
     "VelocityKernel",
 ]

src/cellrank/kernels/_transport_map_kernel.py → src/cellrank/kernels/_real_time_kernel.py

@@ -32,7 +32,7 @@
 from cellrank.kernels._base_kernel import UnidirectionalKernel
 from cellrank.settings import settings
 
-__all__ = ["TransportMapKernel"]
+__all__ = ["RealTimeKernel"]
 
 if TYPE_CHECKING:
     from moscot.problems.spatiotemporal import SpatioTemporalProblem
@@ -53,7 +53,7 @@ class SelfTransitions(ModeEnum):
 
 # TODO(michalk8): subclass the `ExperimentalTimeKernel`
 @d.dedent
-class TransportMapKernel(UnidirectionalKernel):
+class RealTimeKernel(UnidirectionalKernel):
     """Kernel which computes transition matrix using optimal transport couplings.
 
     This class should be constructed using either:
@@ -146,7 +146,7 @@ def compute_transition_matrix(
         conn_weight: Optional[float] = None,
         conn_kwargs: Mapping[str, Any] = types.MappingProxyType({}),
         **kwargs: Any,
-    ) -> "TransportMapKernel":
+    ) -> "RealTimeKernel":
         """Compute transition matrix from optimal transport couplings.
 
         Parameters
@@ -224,7 +224,7 @@ def from_moscot(
         sparsify_kwargs: Mapping[str, Any] = types.MappingProxyType({}),
         copy: bool = False,
         **kwargs: Any,
-    ) -> "TransportMapKernel":
+    ) -> "RealTimeKernel":
         """Construct the kernel from :mod:`moscot` :cite:`klein:23`.
 
         Parameters
@@ -240,7 +240,7 @@ def from_moscot(
         copy
             Whether to copy the underlying arrays. Note that :class:`jax arrays <jax.Array>` are always copied.
         kwargs
-            Keyword arguments for :class:`~cellrank.kernels.TransportMapKernel`.
+            Keyword arguments for :class:`~cellrank.kernels.RealTimeKernel`.
 
         Returns
         -------
@@ -259,8 +259,8 @@ def from_moscot(
             problem = mt.problems.TemporalProblem(adata)
             problem = problem.prepare(time_key="day").solve()
 
-            tmk = cr.kernels.TransportMapKernel.from_moscot(problem)
-            tmk = tmk.compute_transition_matrix()
+            rtk = cr.kernels.RealTimeKernel.from_moscot(problem)
+            rtk = rtk.compute_transition_matrix()
         """
         from moscot.utils.subset_policy import SequentialPolicy, TriangularPolicy
 
@@ -305,7 +305,7 @@ def from_wot(
         path: Union[str, pathlib.Path],
         time_key: str,
         **kwargs: Any,
-    ) -> "TransportMapKernel":
+    ) -> "RealTimeKernel":
         """Construct the kernel from Waddington-OT :cite:`schiebinger:19`.
 
         Parameters
@@ -317,7 +317,7 @@ def from_wot(
         time_key
             Key in :attr:`~anndata.AnnData.obs` containing the experimental time.
         kwargs
-            Keyword arguments for :class:`~cellrank.kernels.TransportMapKernel`.
+            Keyword arguments for :class:`~cellrank.kernels.RealTimeKernel`.
 
         Returns
         -------
@@ -336,8 +336,8 @@ def from_wot(
             ot_model = wot.ot.OTModel(adata, day_field="day")
             ot_model.compute_all_transport_maps(tmap_out="tmaps/")
 
-            tmk = cr.kernels.TransportMapKernel.from_wot(adata, path="tmaps/", time_key="day")
-            tmk = tmk.compute_transition_matrix()
+            rtk = cr.kernels.RealTimeKernel.from_wot(adata, path="tmaps/", time_key="day")
+            rtk = rtk.compute_transition_matrix()
         """
         path = pathlib.Path(path)
         dtype = type(adata.obs[time_key].iloc[0])

tests/test_kernels.py

@@ -30,7 +30,7 @@
     CytoTRACEKernel,
     PrecomputedKernel,
     PseudotimeKernel,
-    TransportMapKernel,
+    RealTimeKernel,
     VelocityKernel,
 )
 from cellrank.kernels._base_kernel import (
@@ -1124,14 +1124,14 @@ def test_inversion_bwd(self, adata: AnnData):
         np.testing.assert_array_equal(np.max(pt) - pt, k.pseudotime)
 
 
-class TestTransportMapKernel:
+class TestRealTimeKernel:
     @pytest.mark.parametrize("policy", ["sequential", "triu"])
     @pytest.mark.parametrize("n", [5, 7])
     def test_default_initialization(self, adata: AnnData, n: int, policy: str):
         adata.obs["exp_time"] = pd.cut(adata.obs["dpt_pseudotime"], n)
         cats = adata.obs["exp_time"].cat.categories
 
-        tmk = TransportMapKernel(adata, time_key="exp_time", policy=policy)
+        tmk = RealTimeKernel(adata, time_key="exp_time", policy=policy)
 
         if policy == "sequential":
             assert tmk.couplings == {key: None for key in zip(cats[:-1], cats[1:])}
@@ -1155,7 +1155,7 @@ def test_explicit_initialization(self, adata: AnnData, correct_shape: bool):
                 val.var_names = adata.obs_names[col == tgt]
             couplings[src, tgt] = val
 
-        tmk = TransportMapKernel(adata, couplings=couplings, time_key="exp_time")
+        tmk = RealTimeKernel(adata, couplings=couplings, time_key="exp_time")
         assert tmk.couplings == couplings
 
         if correct_shape:
@@ -1180,7 +1180,7 @@ def test_explicit_shuffle(self, adata_large: AnnData):
         rng.shuffle(ixs)
         adata_large = adata_large[ixs].copy()
 
-        tmk = TransportMapKernel(adata_large, time_key="time", couplings=expected)
+        tmk = RealTimeKernel(adata_large, time_key="time", couplings=expected)
         tmk = tmk.compute_transition_matrix()
         tmat = tmk.transition_matrix
 
@@ -1220,7 +1220,7 @@ def test_from_moscot(
 
         problem = problem.prepare(policy=policy, time_key="exp_time", xy_callback_kwargs={"n_comps": 5}).solve()
 
-        tmk = TransportMapKernel.from_moscot(
+        tmk = RealTimeKernel.from_moscot(
             problem,
             sparse_mode=sparse_mode,
         )
@@ -1245,7 +1245,7 @@ def test_from_wot(self, adata: AnnData, tmpdir):
         ot_model = wot.ot.OTModel(adata, day_field="exp_time", growth_iters=gr_iters)
         ot_model.compute_all_transport_maps(tmap_out=f"{tmpdir}/")
 
-        tmk = TransportMapKernel.from_wot(adata, path=tmpdir, time_key="exp_time")
+        tmk = RealTimeKernel.from_wot(adata, path=tmpdir, time_key="exp_time")
         obs = pd.read_csv(tmpdir / "tmaps_g.txt", index_col=0, sep="\t")
         tmk = tmk.compute_transition_matrix()
 
@@ -1271,7 +1271,7 @@ def test_from_moscot_set_solution(self, adata_large: AnnData):
             expected[src, tgt] = tmp = tmp / np.sum(tmp, axis=-1, keepdims=True)
             subprob.set_solution(tmp)
 
-        tmk = TransportMapKernel.from_moscot(problem)
+        tmk = RealTimeKernel.from_moscot(problem)
         for (src, tgt), actual in tmk.couplings.items():
             np.testing.assert_allclose(actual.X, expected[src, tgt], rtol=1e-6, atol=1e-6)