Merge branch 'main' into refactor/arg_check

theislab · Jul 3, 2024 · 085eae9 · 085eae9
2 parents add9ca6 + b864111
commit 085eae9
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Showing 9 changed files with 8 additions and 67 deletions.
diff --git a/src/moscot/_types.py b/src/moscot/_types.py
@@ -36,10 +36,6 @@
     "pnorm_p",
     "sq_pnorm",
     "cosine",
-    "elastic_l1",
-    "elastic_l2",
-    "elastic_stvs",
-    "elastic_sqk_overlap",
     "geodesic",
 ]
 OttCostFnMap_t = Union[OttCostFn_t, Mapping[Literal["xy", "x", "y"], OttCostFn_t]]

diff --git a/src/moscot/backends/ott/__init__.py b/src/moscot/backends/ott/__init__.py
@@ -12,7 +12,3 @@
 register_cost("cosine", backend="ott")(costs.Cosine)
 register_cost("pnorm_p", backend="ott")(costs.PNormP)
 register_cost("sq_pnorm", backend="ott")(costs.SqPNorm)
-register_cost("elastic_l1", backend="ott")(costs.ElasticL1)
-register_cost("elastic_l2", backend="ott")(costs.ElasticL2)
-register_cost("elastic_stvs", backend="ott")(costs.ElasticSTVS)
-register_cost("elastic_sqk_overlap", backend="ott")(costs.ElasticSqKOverlap)
diff --git a/tests/backends/ott/test_backend.py b/tests/backends/ott/test_backend.py
@@ -68,9 +68,7 @@ def test_solver_rank(self, y: Geom_t, rank: Optional[int], initializer: str):
         np.testing.assert_allclose(solver._problem.geom.cost_matrix, problem.geom.cost_matrix, rtol=RTOL, atol=ATOL)
         np.testing.assert_allclose(gt.matrix, pred.transport_matrix, rtol=RTOL, atol=ATOL)
 
-    @pytest.mark.parametrize(
-        ("rank", "cost_fn"), [(2, costs.Euclidean()), (3, costs.SqPNorm(p=1.5)), (5, costs.ElasticL1(0.1))]
-    )
+    @pytest.mark.parametrize(("rank", "cost_fn"), [(2, costs.Euclidean()), (3, costs.SqPNorm(p=1.5))])
     def test_geometry_rank(self, x: Geom_t, rank: int, cost_fn: costs.CostFn):
         eps = 0.05
         geom = PointCloud(x, epsilon=eps, cost_fn=cost_fn).to_LRCGeometry(rank=rank)

diff --git a/tests/costs/test_utils.py b/tests/costs/test_utils.py
@@ -16,10 +16,6 @@ class TestCostUtils:
             "cosine",
             "pnorm_p",
             "sq_pnorm",
-            "elastic_l1",
-            "elastic_l2",
-            "elastic_stvs",
-            "elastic_sqk_overlap",
         ),
     }
 

diff --git a/tests/problems/generic/test_fgw_problem.py b/tests/problems/generic/test_fgw_problem.py
@@ -5,16 +5,7 @@
 import numpy as np
 import pandas as pd
 from ott.geometry import epsilon_scheduler
-from ott.geometry.costs import (
-    Cosine,
-    ElasticL1,
-    ElasticL2,
-    ElasticSTVS,
-    Euclidean,
-    PNormP,
-    SqEuclidean,
-    SqPNorm,
-)
+from ott.geometry.costs import Cosine, Euclidean, PNormP, SqEuclidean, SqPNorm
 from ott.solvers.linear import acceleration
 
 from anndata import AnnData
@@ -191,9 +182,6 @@ def test_set_xy(self, adata_time: AnnData, tag: Literal["cost_matrix", "kernel"]
             ("cosine", Cosine, {}),
             ("pnorm_p", PNormP, {"p": 3}),
             ("sq_pnorm", SqPNorm, {"xy": {"p": 5}, "x": {"p": 3}, "y": {"p": 4}}),
-            ("elastic_l1", ElasticL1, {"scaling_reg": 1.1}),
-            ("elastic_l2", ElasticL2, {"scaling_reg": 1.1}),
-            ("elastic_stvs", ElasticSTVS, {"scaling_reg": 1.2}),
         ],
     )
     def test_prepare_costs(self, adata_time: AnnData, cost_str: str, cost_inst: Any, cost_kwargs: CostKwargs_t):
@@ -233,9 +221,6 @@ def test_prepare_costs(self, adata_time: AnnData, cost_str: str, cost_inst: Any,
             ("cosine", Cosine, {}),
             ("pnorm_p", PNormP, {"p": 3}),
             ("sq_pnorm", SqPNorm, {"xy": {"p": 5}, "x": {"p": 3}, "y": {"p": 4}}),
-            ("elastic_l1", ElasticL1, {"scaling_reg": 1.1}),
-            ("elastic_l2", ElasticL2, {"scaling_reg": 1.1}),
-            ("elastic_stvs", ElasticSTVS, {"scaling_reg": 1.2}),
         ],
     )
     def test_prepare_costs_with_callback(

diff --git a/tests/problems/generic/test_gw_problem.py b/tests/problems/generic/test_gw_problem.py
@@ -5,16 +5,7 @@
 import numpy as np
 import pandas as pd
 from ott.geometry import epsilon_scheduler
-from ott.geometry.costs import (
-    Cosine,
-    ElasticL1,
-    ElasticL2,
-    ElasticSTVS,
-    Euclidean,
-    PNormP,
-    SqEuclidean,
-    SqPNorm,
-)
+from ott.geometry.costs import Cosine, Euclidean, PNormP, SqEuclidean, SqPNorm
 from ott.solvers.linear import acceleration
 
 from anndata import AnnData
@@ -165,9 +156,6 @@ def test_pass_arguments(self, adata_space_rotate: AnnData, args_to_check: Mappin
             ("cosine", Cosine, {}),
             ("pnorm_p", PNormP, {"p": 3}),
             ("sq_pnorm", SqPNorm, {"x": {"p": 3}, "y": {"p": 4}}),
-            ("elastic_l1", ElasticL1, {"x": {"scaling_reg": 3}, "y": {"scaling_reg": 4}}),
-            ("elastic_l2", ElasticL2, {"x": {"scaling_reg": 3}, "y": {"scaling_reg": 4}}),
-            ("elastic_stvs", ElasticSTVS, {"x": {"scaling_reg": 3}, "y": {"scaling_reg": 4}}),
         ],
     )
     def test_prepare_costs(self, adata_time: AnnData, cost_str: str, cost_inst: Any, cost_kwargs: CostKwargs_t):
@@ -206,9 +194,6 @@ def test_prepare_marginals(self, adata_time: AnnData, marginal_keys):
             ("cosine", Cosine, {}),
             ("pnorm_p", PNormP, {"p": 3}),
             ("sq_pnorm", SqPNorm, {"x": {"p": 3}, "y": {"p": 4}}),
-            ("elastic_l1", ElasticL1, {"x": {"scaling_reg": 3}, "y": {"scaling_reg": 4}}),
-            ("elastic_l2", ElasticL2, {"x": {"scaling_reg": 3}, "y": {"scaling_reg": 4}}),
-            ("elastic_stvs", ElasticSTVS, {"x": {"scaling_reg": 3}, "y": {"scaling_reg": 4}}),
         ],
     )
     def test_prepare_costs_with_callback(

diff --git a/tests/problems/generic/test_sinkhorn_problem.py b/tests/problems/generic/test_sinkhorn_problem.py
@@ -5,16 +5,7 @@
 import numpy as np
 import pandas as pd
 from ott.geometry import epsilon_scheduler
-from ott.geometry.costs import (
-    Cosine,
-    ElasticL1,
-    ElasticL2,
-    ElasticSTVS,
-    Euclidean,
-    PNormP,
-    SqEuclidean,
-    SqPNorm,
-)
+from ott.geometry.costs import Cosine, Euclidean, PNormP, SqEuclidean, SqPNorm
 from ott.solvers.linear import acceleration
 
 from anndata import AnnData
@@ -79,9 +70,6 @@ def test_solve_balanced(self, adata_time: AnnData, marginal_keys):
             ("cosine", Cosine, {}),
             ("pnorm_p", PNormP, {"p": 3}),
             ("sq_pnorm", SqPNorm, {"p": 3}),
-            ("elastic_l1", ElasticL1, {"scaling_reg": 1.1}),
-            ("elastic_l2", ElasticL2, {"scaling_reg": 1.1}),
-            ("elastic_stvs", ElasticSTVS, {"scaling_reg": 1.2}),
         ],
     )
     def test_prepare_costs(self, adata_time: AnnData, cost_str: str, cost_inst: Any, cost_kwargs: Mapping[str, int]):
@@ -104,9 +92,6 @@ def test_prepare_costs(self, adata_time: AnnData, cost_str: str, cost_inst: Any,
             ("cosine", Cosine, {}),
             ("pnorm_p", PNormP, {"p": 3}),
             ("sq_pnorm", SqPNorm, {"p": 3}),
-            ("elastic_l1", ElasticL1, {"scaling_reg": 1.1}),
-            ("elastic_l2", ElasticL2, {"scaling_reg": 1.1}),
-            ("elastic_stvs", ElasticSTVS, {"scaling_reg": 1.2}),
         ],
     )
     def test_prepare_costs_with_callback(

diff --git a/tests/problems/time/test_mixins.py b/tests/problems/time/test_mixins.py
@@ -1,3 +1,4 @@
+import sys
 from typing import Tuple
 
 import pytest
@@ -235,6 +236,7 @@ def test_compute_interpolated_distance_pipeline(self, gt_temporal_adata: AnnData
         assert isinstance(interpolation_result, float)
         assert interpolation_result > 0
 
+    @pytest.mark.skipif(sys.version_info < (3, 9), reason="requires python3.9 or higher")
     def test_compute_interpolated_distance_regression(self, gt_temporal_adata: AnnData):
         config = gt_temporal_adata.uns
         key = config["key"]
@@ -262,6 +264,7 @@ def test_compute_interpolated_distance_regression(self, gt_temporal_adata: AnnDa
             interpolation_result, gt_temporal_adata.uns["interpolated_distance_10_105_11"], rtol=1e-6, atol=1e-6
         )
 
+    @pytest.mark.skipif(sys.version_info < (3, 9), reason="requires python3.9 or higher")
     def test_compute_time_point_distances_regression(self, gt_temporal_adata: AnnData):
         config = gt_temporal_adata.uns
         key = config["key"]
@@ -313,6 +316,7 @@ def test_compute_batch_distances_regression(self, gt_temporal_adata: AnnData):
         assert isinstance(result, float)
         np.testing.assert_allclose(result, gt_temporal_adata.uns["batch_distances_10"], rtol=1e-5)
 
+    @pytest.mark.skipif(sys.version_info < (3, 9), reason="requires python3.9 or higher")
     def test_compute_random_distance_regression(self, gt_temporal_adata: AnnData):
         config = gt_temporal_adata.uns
         key = config["key"]

diff --git a/tests/utils/test_tagged_array.py b/tests/utils/test_tagged_array.py
@@ -16,10 +16,6 @@ class TestTaggedArray:
             ("cosine", {}),
             ("pnorm_p", {"p": 3}),
             ("sq_pnorm", {"p": 2}),
-            ("elastic_l1", {"scaling_reg": 1.3}),
-            ("elastic_l2", {}),
-            ("elastic_stvs", {}),
-            ("elastic_sqk_overlap", {"k": 1}),
         ],
     )
     def test_from_adata_ott_cost_from_pointcloud(self, adata_time, cost: str, cost_kwargs: Mapping[str, Any]):