Updated for latest anndata. Updated pre-commit

.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/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:

cirrocumulus/sparse_dataset.py

@@ -13,6 +13,7 @@
 
 import numpy as np
 import scipy.sparse as ss
+from anndata._core.index import _subset
 from scipy.sparse import _sparsetools
 
 
@@ -22,9 +23,6 @@
 except ImportError:
     _cs_matrix = ss.spmatrix
 
-from anndata._core.index import _subset
-
-
 Index1D = Union[slice, int, str, np.int64, np.ndarray]
 Index = Union[Index1D, Tuple[Index1D, Index1D], ss.spmatrix]
 

docs/release_notes.rst

@@ -1,6 +1,10 @@
 Release Notes
 -------------
 
+- 1.1.58 `September 17, 2024`
+    * Sort categories using natural sort order
+    * Compatibility with anndata 0.10.9
+
 - 1.1.57 `September 29, 2023`
     * Ensure group order is persisted when performing differential expression between two groups
     * Fixed drop-down arrow click for gene sets

src/AutocompleteVirtualized.js

@@ -262,8 +262,8 @@ export default function AutocompleteVirtualized(props) {
           result.text != null
             ? result.text
             : result.id != null
-            ? result.id
-            : result;
+              ? result.id
+              : result;
         textToOption.delete(text.toLowerCase());
       });
       tokens.forEach((token) => {

src/actions/index.js

@@ -2425,8 +2425,8 @@ function getNewEmbeddingData(state, features) {
       embedding.spatial != null
         ? embedding.spatial.type
         : embedding.type
-        ? embedding.type
-        : TRACE_TYPE_SCATTER;
+          ? embedding.type
+          : TRACE_TYPE_SCATTER;
     let coordinates =
       traceType !== TRACE_TYPE_META_IMAGE ? cachedData[embeddingKey] : null;
     if (coordinates == null && embedding.mode != null) {

src/util.js

@@ -680,10 +680,10 @@ export function rankdata(values) {
     return a.value < b.value
       ? -1
       : a.value === b.value
-      ? a.position < b.position
-        ? -1
-        : 1
-      : 1;
+        ? a.position < b.position
+          ? -1
+          : 1
+        : 1;
   });
 
   // Walk the sorted array, filling output array using sorted positions,
@@ -722,20 +722,20 @@ function indexSortPairs(ranks, ascending) {
       return a.value < b.value
         ? -1
         : a.value === b.value
-        ? a.position < b.position
-          ? -1
-          : 1
-        : 1;
+          ? a.position < b.position
+            ? -1
+            : 1
+          : 1;
     });
   } else {
     ranks.sort(function (a, b) {
       return a.value < b.value
         ? 1
         : a.value === b.value
-        ? a.position < b.position
-          ? 1
-          : -1
-        : -1;
+          ? a.position < b.position
+            ? 1
+            : -1
+          : -1;
     });
   }