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

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

Author: pre-commit-ci[bot]

.cruft.json

@@ -1,23 +1,23 @@
 {
-  "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
-  "checkout": "main",
-  "context": {
-    "cookiecutter": {
-      "project_name": "sobolev_alignment",
-      "package_name": "sobolev_alignment",
-      "project_description": "Sobolev alignment of deep probabilistic models for comparing single cell profiles",
-      "author_full_name": "Soufiane Mourragui",
-      "author_email": "soufiane.mourragui@gmail.com",
-      "github_user": "saroudant",
-      "project_repo": "https://github.com/saroudant/sobolev_alignment",
-      "license": "MIT License",
-      "_copy_without_render": [
-        ".github/workflows/**.yaml",
-        "docs/_templates/autosummary/**.rst"
-      ],
-      "_template": "https://github.com/scverse/cookiecutter-scverse"
-    }
-  },
-  "directory": null
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
+    "checkout": "main",
+    "context": {
+        "cookiecutter": {
+            "project_name": "sobolev_alignment",
+            "package_name": "sobolev_alignment",
+            "project_description": "Sobolev alignment of deep probabilistic models for comparing single cell profiles",
+            "author_full_name": "Soufiane Mourragui",
+            "author_email": "soufiane.mourragui@gmail.com",
+            "github_user": "saroudant",
+            "project_repo": "https://github.com/saroudant/sobolev_alignment",
+            "license": "MIT License",
+            "_copy_without_render": [
+                ".github/workflows/**.yaml",
+                "docs/_templates/autosummary/**.rst"
+            ],
+            "_template": "https://github.com/scverse/cookiecutter-scverse"
+        }
+    },
+    "directory": null
 }

docs/conf.py.rej

@@ -1,8 +1,8 @@
 diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
 @@ -16,12 +16,15 @@ sys.path.insert(0, str(HERE / "extensions"))
- 
+
  # -- Project information -----------------------------------------------------
- 
+
 +# NOTE: If you installed your project in editable mode, this might be stale.
 +#       If this is the case, reinstall it to refresh the metadata
  info = metadata("sobolev_alignment")
@@ -13,7 +13,7 @@ diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
 -repository_url = f"https://github.com/saroudant/{project_name}"
 +urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
 +repository_url = urls["Source"]
- 
+
  # The full version, including alpha/beta/rc tags
  release = info["Version"]
 @@ -109,6 +113,7 @@ html_title = project_name
@@ -22,5 +22,5 @@ diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
      "use_repository_button": True,
 +    "path_to_docs": "docs/",
  }
- 
+
  pygments_style = "default"

pyproject.toml.rej

@@ -2,7 +2,7 @@ diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
 @@ -2,7 +2,6 @@
  build-backend = "hatchling.build"
  requires = ["hatchling"]
- 
+
 -
  [project]
  name = "sobolev_alignment"

sobolev_alignment/sobolev_alignment.py

@@ -526,7 +526,7 @@ def _generate_artificial_samples(
             Number of artificial samples to produce for source and for target.
 
         Returns
-        ----------
+        -------
         artificial_data: dict
             Dictionary containing the generated data for both source and target
         """
@@ -831,7 +831,7 @@ def compute_consensus_features(self, X_input: dict, n_similar_pv: int, fit: bool
             By default, return a DataFrame.
 
         Returns
-        ----------
+        -------
         interpolated_proj_df: pd.DataFrame or sc.AnnData
             DataFrame or AnnData of concatenated source and target samples after projection on consensus features.
         """
@@ -951,7 +951,7 @@ def scvi_model_selection(
             Proportion of samples (cells) to be taken inside the test data.
 
         Returns
-        ----------
+        -------
             SobolevAlignment instance.
         """
         data = {"source": X_source, "target": X_target}
@@ -1004,7 +1004,7 @@ def krr_model_selection(
             source or target models are aligned to themselves.
 
         Returns
-        ----------
+        -------
             SobolevAlignment instance.
         """
         # Log input if required

tests/test_basic.py

@@ -1,5 +1,4 @@
 import pytest
-
 import sobolev_alignment
 
 

tests/test_krr_approx.py

@@ -2,7 +2,6 @@
 import pytest
 import scipy
 import torch
-
 from sobolev_alignment import KRRApprox
 
 n_samples = 2000

tests/test_sobolev_alignment.py

@@ -2,7 +2,6 @@
 import pandas as pd
 import pytest
 from anndata import AnnData
-
 from sobolev_alignment import SobolevAlignment
 
 n_samples = 500