[pre-commit.ci] pre-commit autoupdate (#747)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 24.8.0 → 24.10.0](psf/black@24.8.0...24.10.0)
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0)
- [github.com/asottile/pyupgrade: v3.17.0 → v3.18.0](asottile/pyupgrade@v3.17.0...v3.18.0)
- [github.com/asottile/blacken-docs: 1.18.0 → 1.19.0](adamchainz/blacken-docs@1.18.0...1.19.0)
- [github.com/astral-sh/ruff-pre-commit: v0.6.4 → v0.6.9](astral-sh/ruff-pre-commit@v0.6.4...v0.6.9)

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

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

* test examples fix?

* fix, pin version

* fix graph?

---------

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

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 3.0.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
@@ -13,7 +13,7 @@ repos:
         additional_dependencies: [numpy>=1.25.0]
         files: ^src
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -29,7 +29,7 @@ repos:
         additional_dependencies: [toml]
         args: [--order-by-type]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-merge-conflict
       - id: check-ast
@@ -42,12 +42,12 @@ repos:
       - id: check-yaml
       - id: check-toml
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py38-plus, --keep-runtime-typing]
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.0
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.1.0]
@@ -63,7 +63,7 @@ repos:
       - id: doc8
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.4
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

pyproject.toml

@@ -47,7 +47,7 @@ dependencies = [
     "numpy>=1.20.0",
     "scipy>=1.7.0",
     "pandas>=2.0.1",
-    "networkx>=2.6.3",
+    "networkx>=3.2",
     # https://github.com/scverse/scanpy/issues/2411
     "matplotlib>=3.5.0",
     "anndata>=0.9.1",

src/moscot/backends/ott/solver.py

@@ -533,7 +533,7 @@ def _prepare(  # type: ignore[override]
     ) -> Tuple[MultiLoader, MultiLoader]:
         train_loaders = []
         validate_loaders = []
-        seed = kwargs.get("seed", None)
+        seed = kwargs.get("seed")
         is_aligned = kwargs.get("is_aligned", False)
         if train_size == 1.0:
             for sample_pair in sample_pairs:

src/moscot/datasets.py

@@ -565,7 +565,9 @@ def _get_random_trees(
             assert len(leaf_names[i]) == n_leaves
     trees = []
     for tree_idx in range(n_trees):
-        G = nx.random_tree(n_initial_nodes, seed=seed, create_using=nx.DiGraph)
+        tempG = nx.random_labeled_tree(n_initial_nodes, seed=seed)
+        G = nx.DiGraph()
+        G.add_edges_from(tempG.edges)
         leaves = [x for x in G.nodes() if G.out_degree(x) == 0 and G.in_degree(x) == 1]
         inner_nodes = list(set(G.nodes()) - set(leaves))
         leaves_updated = leaves.copy()