update biome

.github/workflows/test-gpu.yml

@@ -39,22 +39,30 @@ jobs:
       - name: Nvidia SMI sanity check
         run: nvidia-smi
 
-      - uses: mamba-org/setup-micromamba@v2
+      - name: Install Python
+        uses: actions/setup-python@v5
         with:
-          environment-file: ci/environment.yml
-          init-shell: >-
-            bash
-          cache-environment: true
-          post-cleanup: 'all'
+          python-version: "3.12"
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+
+      - name: Set UV Timeout
+        env:
+          UV_HTTP_TIMEOUT: 120
+        run: echo "UV_HTTP_TIMEOUT is set to $UV_HTTP_TIMEOUT"
 
       - name: Install rapids-singlecell
-        run: pip install -e .[test]
+        run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com --index-strategy=unsafe-best-match
 
       - name: Pip list
         run: pip list
 
       - name: Run test
-        run: pytest
+        run: pytest --setup-show -vv -s
 
       - name: Remove 'run-gpu-ci' Label
         if: always()

.gitignore

@@ -4,7 +4,6 @@ __pycache__/
 /*cache/
 .ipynb_checkpoints/
 /data/
-.vscode/
 
 # Distribution / packaging
 /dist/

.vscode/settings.json

@@ -0,0 +1,22 @@
+{
+	"[python][toml][json][jsonc]": {
+		"editor.formatOnSave": true,
+		"editor.codeActionsOnSave": {
+			"source.organizeImports": "explicit",
+			"source.fixAll": "explicit",
+		},
+	},
+	"[python]": {
+		"editor.defaultFormatter": "charliermarsh.ruff",
+	},
+	"[toml]": {
+		"editor.defaultFormatter": "tamasfe.even-better-toml",
+	},
+	"[json][jsonc]": {
+		"editor.defaultFormatter": "biomejs.biome",
+	},
+	"python.analysis.typeCheckingMode": "basic",
+	"python.testing.pytestArgs": ["-vv", "--color=yes"],
+	"python.testing.pytestEnabled": true,
+	"python.terminal.activateEnvironment": true,
+}

biome.jsonc

@@ -0,0 +1,18 @@
+{
+	"$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+	"formatter": { "useEditorconfig": true },
+	"overrides": [
+		{
+			"include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+			"json": {
+				"formatter": {
+					"trailingCommas": "all",
+				},
+				"parser": {
+					"allowComments": true,
+					"allowTrailingCommas": true,
+				},
+			},
+		},
+	],
+}