scib-metrics 0.5.6__tar.gz → 0.5.7__tar.gz

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/build.yaml

@@ -15,10 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
       - name: Install build dependencies

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/test_linux.yaml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ["3.10", "3.11", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
 
     name: Integration
 

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/test_linux_cuda.yaml

@@ -30,8 +30,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.11"]
-        cuda: ["11"]
+        python: ["3.12"]
+        cuda: ["12"]
 
     container:
       image: scverse/scvi-tools:py${{ matrix.python }}-cu${{ matrix.cuda }}-base

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/test_linux_pre.yaml

@@ -31,7 +31,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ["3.10", "3.11", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
 
     name: Integration (Prereleases)
 

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/test_macos.yaml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest]
-        python: ["3.10", "3.11", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
 
     name: Integration
 

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/test_macos_m1.yaml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-14]
-        python: ["3.10", "3.11", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
 
     name: Integration
 

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.github/workflows/test_windows.yaml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest]
-        python: ["3.10", "3.11", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
 
     name: Integration
 

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.12.12
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -19,7 +19,7 @@ repos:
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.10"
+    python: "3.11"
 sphinx:
   configuration: docs/conf.py
   # disable this for more lenient docs builds

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scib-metrics
-Version: 0.5.6
+Version: 0.5.7
 Summary: Accelerated and Python-only scIB metrics
 Project-URL: Documentation, https://scib-metrics.readthedocs.io/
 Project-URL: Source, https://github.com/yoseflab/scib-metrics
@@ -37,7 +37,7 @@ License: BSD 3-Clause License
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Requires-Dist: anndata
 Requires-Dist: chex
 Requires-Dist: igraph>0.9.0

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/pyproject.toml

@@ -5,10 +5,10 @@ requires = ["hatchling"]
 
 [project]
 name = "scib-metrics"
-version = "0.5.6"
+version = "0.5.7"
 description = "Accelerated and Python-only scIB metrics"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { file = "LICENSE" }
 authors = [{ name = "Adam Gayoso" }]
 maintainers = [{ name = "Adam Gayoso", email = "adamgayoso@berkeley.edu" }]

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/src/scib_metrics/benchmark/_core.py

@@ -1,3 +1,4 @@
+import gc
 import os
 import warnings
 from collections.abc import Callable
@@ -120,6 +121,8 @@ class Benchmarker:
     progress_bar
         Whether to show a progress bar for :meth:`~scib_metrics.benchmark.Benchmarker.prepare` and
         :meth:`~scib_metrics.benchmark.Benchmarker.benchmark`.
+    solver
+        SVD solver to use during PCA. can help stability issues. Choose from: "arpack", "randomized" or "auto"
 
     Notes
     -----
@@ -142,6 +145,7 @@ class Benchmarker:
         pre_integrated_embedding_obsm_key: str | None = None,
         n_jobs: int = 1,
         progress_bar: bool = True,
+        solver: str = "arpack",
     ):
         self._adata = adata
         self._embedding_obsm_keys = embedding_obsm_keys
@@ -158,6 +162,7 @@ class Benchmarker:
         self._n_jobs = n_jobs
         self._progress_bar = progress_bar
         self._compute_neighbors = True
+        self._solver = solver
 
         if self._bio_conservation_metrics is None and self._batch_correction_metrics is None:
             raise ValueError("Either batch or bio metrics must be defined.")
@@ -179,11 +184,13 @@ class Benchmarker:
             the data and the number of neighbors to compute and return a :class:`~scib_metrics.utils.nearest_neighbors.NeighborsResults`
             object.
         """
+        gc.collect()
+
         # Compute PCA
         if self._pre_integrated_embedding_obsm_key is None:
             # This is how scib does it
             # https://github.com/theislab/scib/blob/896f689e5fe8c57502cb012af06bed1a9b2b61d2/scib/metrics/pcr.py#L197
-            sc.tl.pca(self._adata, use_highly_variable=False)
+            sc.tl.pca(self._adata, svd_solver=self._solver, use_highly_variable=False)
             self._pre_integrated_embedding_obsm_key = "X_pca"
 
         for emb_key in self._embedding_obsm_keys:
@@ -240,6 +247,7 @@ class Benchmarker:
                 pbar = tqdm(total=num_metrics, desc="Metrics", position=1, leave=False, colour="blue")
             for metric_type, metric_collection in self._metric_collection_dict.items():
                 for metric_name, use_metric_or_kwargs in asdict(metric_collection).items():
+                    gc.collect()
                     if use_metric_or_kwargs:
                         pbar.set_postfix_str(f"{metric_type}: {metric_name}") if pbar is not None else None
                         metric_fn = getattr(scib_metrics, metric_name)

{scib_metrics-0.5.6 → scib_metrics-0.5.7}/tests/test_benchmarker.py

@@ -1,4 +1,5 @@
 import pandas as pd
+import pytest
 
 from scib_metrics.benchmark import BatchCorrection, Benchmarker, BioConservation
 from scib_metrics.nearest_neighbors import jax_approx_min_k
@@ -52,6 +53,7 @@ def test_benchmarker_custom_metric_booleans():
     assert "kbet_per_label" not in results.columns
     assert "graph_connectivity" not in results.columns
     assert "ilisi_knn" in results.columns
+    assert "bras" in results.columns
 
 
 def test_benchmarker_custom_metric_callable():
@@ -80,3 +82,13 @@ def test_benchmarker_custom_near_neighs():
     results = bm.get_results()
     assert isinstance(results, pd.DataFrame)
     bm.plot_results_table()
+
+
+@pytest.mark.parametrize("solver", ["arpack", "randomized"])
+def test_benchmarker_different_solvers(solver):
+    ad, emb_keys, batch_key, labels_key = dummy_benchmarker_adata()
+    bm = Benchmarker(ad, batch_key, labels_key, emb_keys, solver=solver)
+    bm.benchmark()
+    results = bm.get_results()
+    assert isinstance(results, pd.DataFrame)
+    bm.plot_results_table()