Merge pull request #222 from lilab-bcb/anndata-0.12.2-fix

fix for anndata 0.12.2

Author: joshua-gould

.pre-commit-config.yaml

@@ -1,21 +1,21 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       # - id: double-quote-string-fixer  # for single quotes: uncomment and add black config “skip-string-normalization”
       - id: trailing-whitespace
       - id: end-of-file-fixer
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    rev: v1.7.7
     hooks:
       - id: docformatter
         args: ["--in-place", "--wrap-summaries=100", "--wrap-descriptions=100", "--config=./pyproject.toml"]
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 25.1.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
   - repo: https://github.com/csachs/pyproject-flake8

cirrocumulus/anndata_dataset.py

@@ -233,11 +233,9 @@ def read_dataset(self, filesystem, path, keys=None, dataset=None):
             for key in basis_keys:
                 embedding_data = adata.obsm[key]
                 obsm[key] = embedding_data
-            if X is None:  # anndata requires empty X
-                X = scipy.sparse.coo_matrix(([], ([], [])), shape=(embedding_data.shape[0], 0))
+
         if X is None and obs is None and len(obsm.keys()) == 0:
             obs = pd.DataFrame(index=pd.RangeIndex(adata.shape[0]).astype(str))
-
         adata = AnnData(X=X, obs=obs, var=var, obsm=obsm)
         if adata_modules is not None:
             adata.uns[ADATA_MODULE_UNS_KEY] = adata_modules

docs/release_notes.rst

@@ -1,6 +1,9 @@
 Release Notes
 -------------
 
+- 1.1.59 `August 21, 2025`
+    * Compatibility with anndata 0.12.2
+
 - 1.1.58 `September 17, 2024`
     * Sort categories using natural sort order
     * Compatibility with anndata 0.10.9

package.json

@@ -1,6 +1,6 @@
 {
   "name": "cirrocumulus",
-  "version": "1.1.57",
+  "version": "1.1.58",
   "private": true,
   "homepage": ".",
   "proxy": "http://127.0.0.1:5000",

requirements.txt

@@ -1,15 +1,14 @@
-anndata==0.9.2
-CacheControl==0.13.1
-flask==2.3.3
-flask-compress==1.14
-fsspec==2023.9.2
-gunicorn==21.2.0
-h5py==3.9.0
+anndata==0.12.2
+CacheControl==0.14.3
+Flask==3.1.2
+Flask-Compress==1.18
+fsspec==2025.7.0
+gunicorn==23.0.0
+h5py==3.14.0
 loompy==3.0.7
-numpy==1.26.0
-pandas==2.1.1
-pyarrow==13.0.0
-pymongo==4.5.0
-requests==2.31.0
-scipy==1.11.3
-zarr==2.16.1
+numpy==2.3.2
+pandas==2.3.2
+pymongo==4.14.1
+requests==2.32.5
+scipy==1.16.1
+zarr==3.1.1