refactor: updates to backend files to match scverse template cookiecutter

.cruft.json

@@ -0,0 +1,33 @@
+
+{
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+    "checkout": "v0.6.0",
+    "context": {
+        "cookiecutter": {
+            "project_name": "scvi-tutorials",
+            "package_name": "scvi-tutorials",
+            "project_description": "This repository contains the source notebooks for the tutorials on the scvi-tools site",
+            "author_full_name": "Ori Kronfeld",
+            "author_email": "[email protected]",
+            "github_user": "scverse",
+            "github_repo": "scvi-tutorials",
+            "license": "BSD 3-Clause License",
+            "ide_integration": true,
+            "_copy_without_render": [
+            ],
+            "_exclude_on_template_update": [
+                "LICENSE",
+                "README.md"
+            ],
+            "_render_devdocs": false,
+            "_jinja2_env_vars": {
+                "lstrip_blocks": true,
+                "trim_blocks": true
+            },
+            "_template": "https://github.com/scverse/cookiecutter-scverse",
+            "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
+        }
+    },
+    "directory": null
+}

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,71 @@
+name: Bug report
+description: Report something that is broken or incorrect
+#title: ...
+type: Bug
+labels:
+  - Triage 🩺
+#assignees: []
+body:
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Please make sure these conditions are met
+      # description: ...
+      options:
+        - label: I have checked that this issue has not already been reported.
+          required: true
+        - label: I have confirmed this bug exists on the latest version of scvi-tutorials and scvi-tools..
+          required: true
+        - label: (optional) I have confirmed this bug exists on the main branch of scvi-tutorials and scvi-tools.
+          required: false
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide][] detailing how to provide the necessary information for us to reproduce your bug.
+
+        [this guide]: https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports
+  - type: textarea
+    id: Report
+    attributes:
+      label: Report
+      description: |
+        Describe the bug you encountered, and what you were trying to do. Please use [github markdown][] features for readability.
+
+        [github markdown]: https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax
+      value: |
+        Code:
+
+        ```python
+
+        ```
+
+        Traceback:
+
+        ```pytb
+
+        ```
+    validations:
+      required: true
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of scvi-tutorials, scvi-tools and other related software you used.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button,
+        then paste the results into the text box below.
+
+        ```python
+        In[1]: import scvi, session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,5 @@
+blank_issues_enabled: false
 contact_links:
-  - name: Usage question
-    url: https://discourse.scvi-tools.org/
-    about: Please ask and answer non-development questions at https://discourse.scvi-tools.org/.
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for scvi-tutorials and scvi-tools
+type: Enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.gitignore

@@ -25,7 +25,6 @@ __pycache__/
 
 # IDEs
 /.idea/
-/.vscode/
 
 # Jupyter
 .ipynb_checkpoints/

.pre-commit-config.yaml

@@ -6,6 +6,16 @@ default_stages:
   - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.3.5
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.11.1
+    hooks:
+      - id: pyproject-fmt
+
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:
@@ -52,6 +62,13 @@ repos:
         args: [--fix=lf]
       - id: trailing-whitespace
       - id: check-case-conflict
+      - id: check-added-large-files
+      - id: check-toml
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: detect-private-key
+      - id: no-commit-to-branch
+        args: ["--branch=main"]
 
   - repo: local
     hooks:

.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,
+				},
+			},
+		},
+	],
+}