[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

exploratory/notebooks/clustering_issues.ipynb

@@ -243,9 +243,10 @@
    ],
    "source": [
     "# Visualise the embeddings\n",
-    "from mmcontext.pl import plot_umap\n",
     "from mmcontext.pp.utils import consolidate_low_frequency_categories\n",
     "\n",
+    "from mmcontext.pl import plot_umap\n",
+    "\n",
     "adata_cut = consolidate_low_frequency_categories(adata, [\"cell_type\"], threshold=10)\n",
     "label_key = \"cell_type\"\n",
     "emb_key = \"mmcontext_emb\"\n",
@@ -364,9 +365,10 @@
    ],
    "source": [
     "# Visualise the embeddings\n",
-    "from mmcontext.pl import plot_umap\n",
     "from mmcontext.pp.utils import consolidate_low_frequency_categories\n",
     "\n",
+    "from mmcontext.pl import plot_umap\n",
+    "\n",
     "label_key = \"tissue\"\n",
     "adata_cut = consolidate_low_frequency_categories(adata, [\"tissue\"], threshold=0)\n",
     "emb_key = \"mmcontext_emb\"\n",
@@ -417,9 +419,10 @@
    ],
    "source": [
     "# Does maybe the original text embedding cluster after tissues?\n",
-    "from mmcontext.pl import plot_umap\n",
     "from mmcontext.pp.utils import consolidate_low_frequency_categories\n",
     "\n",
+    "from mmcontext.pl import plot_umap\n",
+    "\n",
     "label_key = \"tissue\"\n",
     "adata_cut = consolidate_low_frequency_categories(adata, [label_key], threshold=15)\n",
     "emb_key = \"og_text_emb\"\n",

exploratory/notebooks/mmcontext_train_old.ipynb

@@ -1767,9 +1767,10 @@
    ],
    "source": [
     "# Visualise the embeddings\n",
-    "from mmcontext.pl import plot_umap\n",
     "from mmcontext.pp.utils import consolidate_low_frequency_categories\n",
     "\n",
+    "from mmcontext.pl import plot_umap\n",
+    "\n",
     "label_key = \"_scvi_batch\"\n",
     "adata_cut = consolidate_low_frequency_categories(adata, [\"cell_type\"], threshold=5, remove=True)\n",
     "plot_umap(adata_cut, color_key=label_key, embedding_key=\"mmcontext_emb\")"

exploratory/notebooks/text_batches.ipynb

@@ -186,9 +186,10 @@
    ],
    "source": [
     "# Visualise the embeddings\n",
-    "from mmcontext.pl import plot_umap\n",
     "from mmcontext.pp.utils import consolidate_low_frequency_categories\n",
     "\n",
+    "from mmcontext.pl import plot_umap\n",
+    "\n",
     "adata_cut = consolidate_low_frequency_categories(adata, [\"cell_type\"], threshold=10)\n",
     "label_key = \"_scvi_batch\"\n",
     "plot_umap(adata_cut, color_key=label_key, embedding_key=\"X_text\")"

pyproject.toml

@@ -91,6 +91,9 @@ include = [ "mmcontext*" ]
 [tool.setuptools.package-data]
 #"mmcontext.conf" = [ "*.json" ]
 
+[tool.uv.sources]
+#sentence-transformers = { git = "https://github.com/mengerj/sentence-transformers.git", rev = "master" }
+
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
@@ -163,6 +166,3 @@ skip = [
   "docs/references.md",
   "docs/notebooks/example.ipynb",
 ]
-
-[tool.uv.sources]
-#sentence-transformers = { git = "https://github.com/mengerj/sentence-transformers.git", rev = "master" }