Update dependencies (#396)

* pin pandas 2 and adapt breaking code

* update scanorama

* set minimum python version to 3.8

.github/workflows/deployment.yml

@@ -15,10 +15,10 @@ jobs:
             with:
                 fetch-depth: 0
 
-        -   name: Set up Python 3.9
+        -   name: Set up Python 3.10
             uses: actions/setup-python@v2
             with:
-                python-version: 3.9
+                python-version: '3.10'
         -   name: Install pip dependencies
             run: |
                 python -m pip install --upgrade pip

.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
         -   name: Set up Python
             uses: actions/setup-python@v4
             with:
-                python-version: 3.9
+                python-version: '3.10'
 
         -   uses: actions/cache@v3
             with:
@@ -32,7 +32,7 @@ jobs:
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
-                python: [3.7, 3.9]
+                python: ['3.8', '3.10']
                 os: [ubuntu-latest, macos-latest]
 
         steps:
@@ -74,7 +74,7 @@ jobs:
         strategy:
             matrix:
                 r: [4.2]
-                python: [3.9]
+                python: ['3.10']
                 os: [ubuntu-latest]
         steps:
         -   uses: actions/checkout@v3
@@ -112,7 +112,7 @@ jobs:
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
-                python: [3.7, 3.9]
+                python: ['3.8', '3.10']
                 os: [ubuntu-latest]
 
         steps:

scib/metrics/cell_cycle.py

@@ -122,8 +122,12 @@ def cell_cycle(
 
     if agg_func is None:
         return pd.DataFrame(
-            [batches, scores_before, scores_after, scores_final],
-            columns=["batch", "before", "after", "score"],
+            {
+                "batch": pd.Series(batches, dtype=str),
+                "before": pd.Series(scores_before, dtype=float),
+                "after": pd.Series(scores_after, dtype=float),
+                "score": pd.Series(scores_final, dtype=float),
+            }
         )
     else:
         return agg_func(scores_final)

scib/metrics/trajectory.py

@@ -121,7 +121,7 @@ def get_root(adata_pre, adata_post, ct_key, pseudotime_key="dpt_pseudotime", dpt
         csgraph=adata_post.obsp["connectivities"], directed=False, return_labels=True
     )
 
-    start_clust = adata_pre.obs.groupby([ct_key]).mean()[pseudotime_key].idxmin()
+    start_clust = adata_pre.obs.groupby(ct_key)[pseudotime_key].mean().idxmin()
     min_dpt = adata_pre.obs[adata_pre.obs[ct_key] == start_clust].index
     which_max_neigh = (
         adata_post.obs["neighborhood"]

setup.cfg

@@ -17,36 +17,36 @@ author = Malte D. Luecken, Maren Buettner, Daniel C. Strobl, Michaela F. Mueller
 author_email = [email protected], [email protected]
 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
 	Topic :: Software Development :: Build Tools
 	License :: OSI Approved :: MIT License
 	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3.7
 	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
 
 [bdist_wheel]
 build_number = 1
 
 [options]
-packages = 
+packages =
 	scib
 	scib.metrics
-python_requires = >=3.7
-install_requires = 
+python_requires = >=3.8
+install_requires =
 	numpy
-	pandas<2
+	pandas>=2
 	seaborn
 	matplotlib
 	numba
@@ -65,7 +65,7 @@ install_requires =
 zip_safe = False
 
 [options.package_data]
-scib = 
+scib =
 	resources/*.txt
 	knn_graph/*
 
@@ -76,10 +76,10 @@ dev = build; twine; isort; bump2version; pre-commit
 docs = sphinx; sphinx_rtd_theme; myst_parser; sphinx-automodapi
 louvain = python-igraph; louvain>=0.8
 bbknn = bbknn ==1.3.9
-scanorama = scanorama ==1.7.0
+scanorama = scanorama >=1.7.4
 mnn = mnnpy ==0.1.9.5
 scgen = scgen  >=2.1.0
-scvi = scvi-tools  >=0.16.1
+scvi = scvi-tools  >=0.16
 trvae = trvae  ==1.1.2
 trvaep = trvaep  ==0.1.0
 desc = desc  ==2.0.3
@@ -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

tests/conftest.py

@@ -44,8 +44,8 @@ def adata_pbmc_template():
     adata_concat = adata_ref.concatenate(adata, batch_categories=["ref", "new"])
     adata_concat.obs.louvain = adata_concat.obs.louvain.astype("category")
     # fix category ordering
-    adata_concat.obs.louvain.cat.reorder_categories(
-        adata_ref.obs.louvain.cat.categories, inplace=True
+    adata_concat.obs["louvain"] = adata_concat.obs["louvain"].cat.set_categories(
+        adata_ref.obs["louvain"].cat.categories
     )
     adata_concat.obs["celltype"] = adata_concat.obs["louvain"]