Merge pull request #213 from lilab-bcb/compat

Updated for latest anndata. Updated pre-commit

Author: joshua-gould

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       # - id: double-quote-string-fixer  # for single quotes: uncomment and add black config “skip-string-normalization”
       - id: trailing-whitespace
@@ -11,19 +11,19 @@ repos:
       - id: docformatter
         args: ["--in-place", "--wrap-summaries=100", "--wrap-descriptions=100", "--config=./pyproject.toml"]
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.8.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/csachs/pyproject-flake8
-    rev: v6.1.0
+    rev: v7.0.0
     hooks:
       - id: pyproject-flake8
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         types_or: [css, javascript]

cirrocumulus/abstract_backed_dataset.py

@@ -3,10 +3,10 @@
 import pandas as pd
 import scipy.sparse
 from anndata import AnnData
+from anndata._core.sparse_dataset import sparse_dataset
 
 from cirrocumulus.abstract_dataset import AbstractDataset
 from cirrocumulus.anndata_util import ADATA_LAYERS_UNS_KEY, ADATA_MODULE_UNS_KEY
-from cirrocumulus.sparse_dataset import SparseDataset
 
 
 # string_dtype = h5py.check_string_dtype(dataset.dtype)
@@ -73,8 +73,8 @@ def get_X(self, var_ids, keys, node):
             get_item = var_ids.get_indexer_for(keys)
 
         if self.is_group(node):
-            sparse_dataset = SparseDataset(node)  # sparse
-            X = sparse_dataset[:, get_item]
+            ds = sparse_dataset(node)  # sparse
+            X = ds[:, get_item]
         else:  # dense
             X = self.slice_dense_array(node, get_item)
         var = pd.DataFrame(index=keys)

cirrocumulus/concat.py

@@ -148,9 +148,11 @@ def concat_spatial(paths: list[str], output_path: str, ncols: int = 2):
 
 def create_parser(description=False):
     parser = argparse.ArgumentParser(
-        description="Concatenate datasets in a grid layout. If all the datasets are spatial datasets, then tissue images are concatenated."
-        if description
-        else None
+        description=(
+            "Concatenate datasets in a grid layout. If all the datasets are spatial datasets, then tissue images are concatenated."
+            if description
+            else None
+        )
     )
     parser.add_argument(
         "dataset",

cirrocumulus/diff_exp.py

@@ -137,11 +137,15 @@ def __init__(
                 scores=scores,
                 pvals=pvals,
                 logfoldchanges=foldchanges,
-                frac_expressed1=frac_expressed_df.loc[group_one].values
-                if frac_expressed_df is not None
-                else None,
-                frac_expressed2=frac_expressed_df.loc[group_two].values
-                if frac_expressed_df is not None
-                else None,
+                frac_expressed1=(
+                    frac_expressed_df.loc[group_one].values
+                    if frac_expressed_df is not None
+                    else None
+                ),
+                frac_expressed2=(
+                    frac_expressed_df.loc[group_two].values
+                    if frac_expressed_df is not None
+                    else None
+                ),
             )
         self.pair2results = pair2results

cirrocumulus/local_db_api.py

@@ -50,8 +50,10 @@ def __init__(self, paths: list[str]):
                 if url.lower().endswith(".json.gz") or url.lower().endswith(".json"):
                     import gzip
 
-                    with gzip.open(fs.open(url)) if url.lower().endswith(".json.gz") else fs.open(
-                        url
+                    with (
+                        gzip.open(fs.open(url))
+                        if url.lower().endswith(".json.gz")
+                        else fs.open(url)
                     ) as f:
                         d = json.load(f)
                         if "id" in d: