refactor: Use scverse template

.cruft.json

@@ -0,0 +1,44 @@
+
+{
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+    "checkout": "v0.6.0",
+    "context": {
+        "cookiecutter": {
+            "project_name": "scvi-tools",
+            "package_name": "scvi-tools",
+            "project_description": "Deep probabilistic analysis of single-cell omics data.",
+            "author_full_name": "Ori Kronfeld",
+            "author_email": "ori.kronfeld@weizmann.ac.il",
+            "github_user": "scverse",
+            "github_repo": "scvi-tools",
+            "license": "BSD 3-Clause License",
+            "ide_integration": true,
+            "_copy_without_render": [
+                ".github/workflows/build.yaml",
+                ".github/workflows/test_linux.yaml",
+                "docs/_templates/autosummary/**.rst"
+            ],
+            "_exclude_on_template_update": [
+                "CHANGELOG.md",
+                "LICENSE",
+                "README.md",
+                "docs/api.md",
+                "docs/index.md",
+                "docs/notebooks/example.ipynb",
+                "docs/references.bib",
+                "docs/references.md",
+                "src/**",
+                "tests/**"
+            ],
+            "_render_devdocs": false,
+            "_jinja2_env_vars": {
+                "lstrip_blocks": true,
+                "trim_blocks": true
+            },
+            "_template": "https://github.com/scverse/cookiecutter-scverse",
+            "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
+        }
+    },
+    "directory": null
+}

.gitignore

@@ -25,7 +25,6 @@ __pycache__/
 
 # IDEs
 /.idea/
-/.vscode/
 
 # node
 /node_modules/

.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}

.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Docs",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": { "PYTEST_ADDOPTS": "--color=yes" },
+            "presentation": { "hidden": true },
+        },
+    ],
+}

.vscode/settings.json

@@ -0,0 +1,27 @@
+{
+    "[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.pytestEnabled": true,
+    "python.testing.pytestArgs": [
+        "--color=yes",
+        "-vv",
+        "--strict-warnings",
+        //"-nauto",
+    ],
+    "python.terminal.activateEnvironment": true,
+}

biome.jsonc

@@ -0,0 +1,18 @@
+{
+    "$schema": "https://biomejs.dev/schemas/2.1.1/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "includes": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}