[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 3.0.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.20.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.25.0]
         files: ^src
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.3.1
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -23,13 +23,13 @@ repos:
       - id: prettier
         language_version: system
   - repo: https://github.com/PyCQA/isort
-    rev: 6.0.1
+    rev: 8.0.1
     hooks:
       - id: isort
         additional_dependencies: [toml]
         args: [--order-by-type]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-merge-conflict
       - id: check-ast
@@ -42,28 +42,28 @@ repos:
       - id: check-yaml
       - id: check-toml
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py38-plus, --keep-runtime-typing]
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.1.0]
   - repo: https://github.com/rstcheck/rstcheck
-    rev: v6.2.4
+    rev: v6.2.5
     hooks:
       - id: rstcheck
         additional_dependencies: [toml, sphinx]
         args: [--config=pyproject.toml]
   - repo: https://github.com/PyCQA/doc8
-    rev: v1.1.2
+    rev: v2.0.0
     hooks:
       - id: doc8
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.7
+    rev: v0.15.11
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

src/moscot/base/problems/_utils.py

@@ -695,7 +695,7 @@ def wrapper(*args, **kwargs):
             ixs = [np.arange(i * step, min((i + 1) * step, collection.shape[0])) for i in range(n_split)]  # type: ignore  # noqa: E501
             ixs[-1] = np.append(ixs[-1], np.arange(ixs[-1][-1] + 1, collection.shape[0]))  # type: ignore
 
-            collections = [collection[ix, :] for ix in filter(len, ixs)]  # type:ignore[call-overload]
+            collections = [collection[ix, :] for ix in filter(len, ixs)]  # type: ignore[call-overload]
     else:
         collections = list(filter(len, np.array_split(collection, n_split)))
 

src/moscot/base/problems/problem.py

@@ -181,7 +181,7 @@ def _split_mass(arr: ArrayLike) -> ArrayLike:
                     else np.ones((adata.n_obs,), dtype=float)
                 )
             else:
-                sset = subset if isinstance(subset, list) else [subset]  # type:ignore[list-item]
+                sset = subset if isinstance(subset, list) else [subset]  # type: ignore[list-item]
                 data = np.asarray(adata.obs[data].isin(sset), dtype=float)
         else:
             data = np.asarray(data, dtype=float)

src/moscot/problems/_utils.py

@@ -53,7 +53,7 @@ def _handle_mapping_joint_attr(
         }
         return xy, xy_callback, xy_callback_kwargs  # type: ignore[return-value]
 
-    if joint_attr.get("tag", None) == "cost_matrix" and (len(joint_attr) == 2 or joint_attr.get("attr") == "obsp"):
+    if joint_attr.get("tag") == "cost_matrix" and (len(joint_attr) == 2 or joint_attr.get("attr") == "obsp"):
         joint_attr.setdefault("cost", "custom")
         joint_attr.setdefault("attr", "obsp")
         xy_callback = "cost-matrix"
@@ -100,9 +100,9 @@ def handle_cost(
         "y": (y or y_callback) and "cost" not in y,
     }
     if isinstance(cost, Mapping):
-        cost_candidates = {k: cost[k] for k, v in cost_candidates.items() if v}  # type:ignore[index,misc]
+        cost_candidates = {k: cost[k] for k, v in cost_candidates.items() if v}  # type: ignore[index,misc]
     elif isinstance(cost, str):
-        cost_candidates = {k: cost for k, v in cost_candidates.items() if v}  # type:ignore[misc]
+        cost_candidates = {k: cost for k, v in cost_candidates.items() if v}  # type: ignore[misc]
     else:
         raise TypeError(f"Expected `cost` to be either `str` or `dict`, found `{type(cost)}`.")
 
@@ -120,9 +120,9 @@ def handle_cost(
             for k, v in items:
                 xy[f"x_{k}"] = xy[f"y_{k}"] = v
         if "x" in cost_candidates:
-            x.update(cost_kwargs.get("x", cost_kwargs))  # type:ignore[call-overload]
+            x.update(cost_kwargs.get("x", cost_kwargs))  # type: ignore[call-overload]
         if "y" in cost_candidates:
-            y.update(cost_kwargs.get("y", cost_kwargs))  # type:ignore[call-overload]
+            y.update(cost_kwargs.get("y", cost_kwargs))  # type: ignore[call-overload]
     return xy, x, y
 
 
@@ -199,5 +199,5 @@ def handle_cost_tmp(
         for k, v in items:
             xy[f"xy_{k}"] = xy[f"xy_{k}"] = v
     if xx and cost_kwargs:  # extract cost_kwargs explicit to x-term if possible
-        xx.update(cost_kwargs.get("xx", cost_kwargs))  # type:ignore[call-overload]
+        xx.update(cost_kwargs.get("xx", cost_kwargs))  # type: ignore[call-overload]
     return xy, xx

src/moscot/problems/time/_lineage.py

@@ -252,7 +252,7 @@ def solve(
         """
         if self.problem_kind == "linear":
             kwargs["lse_mode"] = lse_mode
-        return super().solve(  # type:ignore[return-value]
+        return super().solve(  # type: ignore[return-value]
             epsilon=epsilon,
             tau_a=tau_a,
             tau_b=tau_b,