more readable PCA computation and info retrieval

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
     -   id: autopep8
         args: [-i]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/yesqa

scib/_package_tools.py

@@ -16,6 +16,7 @@ def wrapper(*args, **kwargs):
             f"Mixed case function naming is deprecated for '{name}'. "
             f"Please use '{func.__name__}' instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
         return func(*args, **kwargs)
 

scib/metrics/lisi.py

@@ -172,7 +172,7 @@ def clisi_graph(
 
     """
     if batch_key is not None:
-        warnings.warn("'batch_key' is deprecated and will be ignore")
+        warnings.warn("'batch_key' is deprecated and will be ignore", stacklevel=1)
 
     check_adata(adata)
     check_batch(label_key, adata.obs)

scib/metrics/pcr.py

@@ -194,17 +194,14 @@ def pc_regression(
 
         if verbose:
             print("compute PCA")
-        pca = sc.tl.pca(
+        X_pca, _, _, pca_var = sc.tl.pca(
             matrix,
             n_comps=n_comps,
             use_highly_variable=False,
             return_info=True,
             svd_solver=svd_solver,
             copy=True,
         )
-        X_pca = pca[0].copy()
-        pca_var = pca[3].copy()
-        del pca
     else:
         X_pca = matrix
         n_comps = matrix.shape[1]

setup.cfg

@@ -17,15 +17,15 @@ author = Malte D. Luecken, Maren Buettner, Daniel C. Strobl, Michaela F. Mueller
 author_email = malte.luecken@helmholtz-muenchen.de, michaela.mueller@helmholtz-muenchen.de
 license = MIT
 url = https://github.com/theislab/scib
-project_urls = 
+project_urls =
 	Pipeline = https://github.com/theislab/scib-pipeline
 	Reproducibility = https://theislab.github.io/scib-reproducibility
 	Bug Tracker = https://github.com/theislab/scib/issues
-keywords = 
+keywords =
 	benchmarking
 	single cell
 	data integration
-classifiers = 
+classifiers =
 	Development Status :: 3 - Alpha
 	Intended Audience :: Developers
 	Intended Audience :: Science/Research
@@ -40,13 +40,13 @@ classifiers =
 build_number = 1
 
 [options]
-packages = 
+packages =
 	scib
 	scib.metrics
 python_requires = >=3.7
-install_requires = 
+install_requires =
 	numpy
-	pandas
+	pandas<2
 	seaborn
 	matplotlib
 	numba
@@ -65,7 +65,7 @@ install_requires =
 zip_safe = False
 
 [options.package_data]
-scib = 
+scib =
 	resources/*.txt
 	knn_graph/*
 
@@ -95,7 +95,7 @@ skip_glob = docs/*
 line-length = 120
 target-version = py38
 include = \.pyi?$
-exclude = 
+exclude =
 	.eggs
 	.git
 	.venv
@@ -104,7 +104,7 @@ exclude =
 
 [flake8]
 max-line-length = 88
-ignore = 
+ignore =
 	W503
 	W504
 	E501
@@ -126,7 +126,7 @@ ignore =
 	RST304
 	C408
 exclude = .git,__pycache__,build,docs/_build,dist
-per-file-ignores = 
+per-file-ignores =
 	scib/*: D
 	tests/*: D
 	*/__init__.py: F401