diff --git a/.cruft.json b/.cruft.json
new file mode 100644
index 0000000000..b462f35c1a
--- /dev/null
+++ b/.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
+}
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
deleted file mode 100644
index 1a9d7af2c1..0000000000
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ /dev/null
@@ -1,31 +0,0 @@
----
-name: Bug report
-about: Create a report to help us improve
-title: ""
-labels: bug
-assignees: ""
----
-
-<!-- Describe the bug -->
-
-[TEXT HERE]
-
-<!-- To reproduce -->
-
-```python
-# Your code here
-```
-
-<!-- Put your Error output in this code block (if applicable, else delete the block): -->
-
-```pytb
-[Paste the error output produced by the above code here]
-```
-
-#### Versions:
-
-<!-- Output of scvi.__version__ -->
-
-> VERSION
-
-<!-- Relevant screenshots -->
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 0000000000..b226a16dc8
--- /dev/null
+++ b/.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-tools.
+          required: true
+        - label: (optional) I have confirmed this bug exists on the main branch of 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-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
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
index b7628704a7..5b62547f9a 100644
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ b/.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.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
deleted file mode 100644
index fcd76a381a..0000000000
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ /dev/null
@@ -1,13 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for this project
-title: ""
-labels: enhancement
-assignees: ""
----
-
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
-
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 0000000000..3cde65b1ef
--- /dev/null
+++ b/.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
diff --git a/.gitignore b/.gitignore
index 6fd834b0b3..73d793fc37 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,7 +25,6 @@ __pycache__/
 
 # IDEs
 /.idea/
-/.vscode/
 
 # node
 /node_modules/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a13076ef43..8681798675 100644
--- a/.pre-commit-config.yaml
+++ b/.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/asottile/blacken-docs
     rev: 1.20.0
     hooks:
@@ -57,6 +67,13 @@ 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:
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index acedf0a788..be5e49ad73 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,8 +1,8 @@
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.13"
 sphinx:
   configuration: docs/conf.py
 python:
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000000..caaeb4f732
--- /dev/null
+++ b/.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",
+    ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 0000000000..5c5e982155
--- /dev/null
+++ b/.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 },
+        },
+    ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000000..7024abf5f2
--- /dev/null
+++ b/.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,
+}
diff --git a/biome.jsonc b/biome.jsonc
new file mode 100644
index 0000000000..3c34a20713
--- /dev/null
+++ b/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,
+                },
+            },
+        },
+    ],
+}
diff --git a/docs/_static/css/override.css b/docs/_static/css/override.css
index f31d6ec81a..4651d9d7fe 100644
--- a/docs/_static/css/override.css
+++ b/docs/_static/css/override.css
@@ -21,7 +21,9 @@
 .filter-btn:hover {
     color: var(--pst-color-table-row-hover);
     border-color: var(--pst-color-table-row-hover);
-    background-color: var(--pst-color-hover-background); /* Add hover background */
+    background-color: var(
+        --pst-color-hover-background
+    ); /* Add hover background */
     box-shadow: 0 4px 8px rgba(0, 0, 0, 0.15); /* Enhance shadow on hover */
 }
 
@@ -52,7 +54,7 @@
 
 .card a {
     text-decoration: none;
-    }
+}
 
 .card {
     border-radius: 1rem; /* Uniform border radius */
@@ -112,7 +114,9 @@
 }
 
 .tab:hover {
-    background-color: var(--pst-color-hover-background); /* Add hover background */
+    background-color: var(
+        --pst-color-hover-background
+    ); /* Add hover background */
     color: var(--pst-color-table-row-hover);
     box-shadow: 0 4px 8px rgba(0, 0, 0, 0.15); /* Enhance shadow on hover */
 }
diff --git a/docs/_static/js/custom.js b/docs/_static/js/custom.js
index 7646bcb2b5..d6fa636043 100644
--- a/docs/_static/js/custom.js
+++ b/docs/_static/js/custom.js
@@ -2,12 +2,14 @@
 function getUniqueTags() {
     let tagSet = new Set();
 
-    $(".card-container").each(function() {
-        let tags = $(this).attr('data-tags').split(",")
-        .map(tag => tag.trim()) // Get rid of whitespace
-        .filter(tag => tag !== ""); // Make sure there are no empty tags
+    $(".card-container").each(function () {
+        let tags = $(this)
+            .attr("data-tags")
+            .split(",")
+            .map((tag) => tag.trim()) // Get rid of whitespace
+            .filter((tag) => tag !== ""); // Make sure there are no empty tags
 
-        tags.forEach(tag => tagSet.add(tag)); // Add tag to the set
+        tags.forEach((tag) => tagSet.add(tag)); // Add tag to the set
     });
 
     let uniqueTags = Array.from(tagSet);
@@ -19,14 +21,14 @@ function getUniqueTags() {
 function getUniqueGroups() {
     let groupSet = new Set();
 
-    $(".card-container").each(function() {
-        let group = $(this).attr('data-group')
+    $(".card-container").each(function () {
+        let group = $(this).attr("data-group");
 
         if (group && group.trim() !== "") {
             groupSet.add(group.trim());
         }
 
-        groupSet.add(group)
+        groupSet.add(group);
     });
 
     let uniqueGroups = Array.from(groupSet);
@@ -37,10 +39,15 @@ function getUniqueGroups() {
 function createMenu() {
     let tags = getUniqueTags();
 
-    tags.forEach(item => {
+    tags.forEach((item) => {
         let displayName = item.replace(/-/g, " "); // Replace underscores with spaces
-        $(".filter-menu")
-        .append("<div class='filter filter-btn' data-tag='" + item + "'>" + displayName + "</div>")
+        $(".filter-menu").append(
+            "<div class='filter filter-btn' data-tag='" +
+                item +
+                "'>" +
+                displayName +
+                "</div>",
+        );
     });
 }
 
@@ -48,13 +55,14 @@ function createMenu() {
 function populateTabs() {
     let groups = getUniqueGroups();
 
-    groups.forEach(item => {
-        $(".tab-menu")
-        .append("<div class='tab' data-group='" + item + "'>" + item + "</div>")
+    groups.forEach((item) => {
+        $(".tab-menu").append(
+            "<div class='tab' data-group='" + item + "'>" + item + "</div>",
+        );
     });
 }
 
-$(document).ready(function() {
+$(document).ready(function () {
     createMenu();
     populateTabs();
 });
@@ -96,11 +104,14 @@ $(document).on("click", ".filter-btn", function () {
 function filterCards() {
     $(".card-container").each(function () {
         let tagsData = $(this).attr("data-tags") || "";
-        let cardTags = tagsData.split(",").map(tag => tag.trim());
+        let cardTags = tagsData.split(",").map((tag) => tag.trim());
         let groupName = $(this).attr("data-group");
 
-        let matchesTags = selectedTagSet.size === 0 || [...selectedTagSet].every(tag => cardTags.includes(tag));
-        let matchesGroup = selectedGroup === "all" || groupName === selectedGroup;
+        let matchesTags =
+            selectedTagSet.size === 0 ||
+            [...selectedTagSet].every((tag) => cardTags.includes(tag));
+        let matchesGroup =
+            selectedGroup === "all" || groupName === selectedGroup;
 
         $(this).toggleClass("hidden", !(matchesTags && matchesGroup));
 
@@ -115,7 +126,7 @@ function filterCards() {
 }
 
 // Add similar filtering functionality to the model group tabs (but only single select)
-let selectedGroup = "all"
+let selectedGroup = "all";
 
 // Handle tab selection and filtering
 $(document).on("click", ".tab", function () {
@@ -124,7 +135,7 @@ $(document).on("click", ".tab", function () {
     if (group !== selectedGroup) {
         $(".tab").removeClass("tab-selected"); // deselect current tab
         $(this).addClass("tab-selected");
-        selectedGroup = group
+        selectedGroup = group;
     }
 
     filterCards(); // Trigger filtering immediately
diff --git a/pyproject.toml b/pyproject.toml
index 0115d61c3c..ce7c915453 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,241 +1,233 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling"]
+requires = [ "hatchling" ]
 
 [project]
 name = "scvi-tools"
 version = "1.4.1"
 description = "Deep probabilistic analysis of single-cell omics data."
 readme = "README.md"
-requires-python = ">=3.11"
-license = {file = "LICENSE"}
-authors = [
-    {name = "The scvi-tools development team"},
-]
+license = { file = "LICENSE" }
 maintainers = [
-    {name = "The scvi-tools development team", email = "ori.kronfeld@weizmann.ac.il"},
+  { name = "The scvi-tools development team", email = "ori.kronfeld@weizmann.ac.il" },
 ]
 
-urls.Documentation = "https://scvi-tools.org"
-urls.Source = "https://github.com/scverse/scvi-tools"
-urls.Home-page = "https://scvi-tools.org"
+authors = [
+  { name = "The scvi-tools development team" },
+]
+requires-python = ">=3.11"
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
   "Natural Language :: English",
-  "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
-  "Programming Language :: Python :: 3.13",
   "Operating System :: MacOS :: MacOS X",
   "Operating System :: Microsoft :: Windows",
   "Operating System :: POSIX :: Linux",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [
-    "anndata>=0.11",
-    "docrep>=0.3.2",
-    "lightning>=2.0",
-    "ml-collections",
-    "mudata",
-    "numba>=0.60.0",
-    "numpy",
-    "pandas",
-    "pyro-ppl",
-    "rich",
-    "scanpy[skmisc]>=1.10",
-    "scikit-learn",
-    "scipy",
-    "sparse>=0.14.0",
-    "tensorboard",
-    "torch",
-    "torchmetrics",
-    "tqdm",
-    "xarray",
+  "anndata>=0.11",
+  "docrep>=0.3.2",
+  "lightning>=2",
+  "ml-collections",
+  "mudata",
+  "numba>=0.60",
+  "numpy",
+  "pandas",
+  "pyro-ppl",
+  "rich",
+  "scanpy[skmisc]>=1.10",
+  "scikit-learn",
+  "scipy",
+  "sparse>=0.14",
+  "tensorboard",
+  "torch",
+  "torchmetrics",
+  "tqdm",
+  "xarray",
 ]
 
-[project.optional-dependencies]
-tests = ["pytest", "pytest-pretty", "coverage", "scvi-tools[optional]"]
-editing = ["jupyter", "pre-commit"]
-dev = ["scvi-tools[editing,tests]"]
-test = ["scvi-tools[tests]"]
-cuda = ["torchvision", "torchaudio", "jax[cuda12]"]
-metal = ["torchvision", "torchaudio", "jax-metal"]
-
-docs = [
-    "docutils>=0.8,!=0.18.*,!=0.19.*", # see https://github.com/scverse/cookiecutter-scverse/pull/205
-    "sphinx",
-    "ipython",
-    "sphinx-book-theme>=1.0.1",
-    "sphinx_copybutton",
-    "sphinx-design",
-    "sphinxext-opengraph",
-    "sphinx-hoverxref",
-    "sphinxcontrib-bibtex",
-    "myst-parser",
-    "myst-nb",
-    "sphinx-autodoc-typehints",
-]
-docsbuild = ["scvi-tools[docs,autotune,hub,jax]"]
-
+optional-dependencies.all = [ "scvi-tools[dev,docs,tutorials]" ]
 # scvi.autotune
-autotune = ["hyperopt>=0.2", "ray[tune]", "scib-metrics", "muon"]
-# scvi.hub dependencies
-hub = ["huggingface_hub", "dvc[s3]", "boto3"]
-# scvi.data.add_dna_sequence
-regseq = ["biopython>=1.81", "genomepy"]
+optional-dependencies.autotune = [ "hyperopt>=0.2", "muon", "ray[tune]", "scib-metrics" ]
+optional-dependencies.cuda = [ "jax[cuda12]", "torchaudio", "torchvision" ]
+# for custom dataloders
+optional-dependencies.dataloaders = [
+  "cellxgene-census",
+  "lamindb>=1.12.1",
+  "tiledbsoma",
+  "tiledbsoma-ml",
+  "torchdata",
+]
+optional-dependencies.dev = [ "scvi-tools[editing,tests]" ]
+optional-dependencies.docs = [
+  "docutils>=0.8,!=0.18.*,!=0.19.*", # see https://github.com/scverse/cookiecutter-scverse/pull/205
+  "ipython",
+  "myst-nb",
+  "myst-parser",
+  "sphinx",
+  "sphinx-autodoc-typehints",
+  "sphinx-book-theme>=1.0.1",
+  "sphinx-copybutton",
+  "sphinx-design",
+  "sphinx-hoverxref",
+  "sphinxcontrib-bibtex",
+  "sphinxext-opengraph",
+]
+optional-dependencies.docsbuild = [ "scvi-tools[autotune,docs,hub,jax]" ]
+optional-dependencies.editing = [ "jupyter", "pre-commit" ]
 # for files sharing or handling
-file_sharing = ["pooch","gdown","readfcs","fcswrite"]
-# for parallelization engine
-parallel = ["dask[array]", "zarr"]
+optional-dependencies.file_sharing = [ "fcswrite", "gdown", "pooch", "readfcs" ]
+# scvi.hub dependencies
+optional-dependencies.hub = [ "boto3", "dvc[s3]", "huggingface-hub" ]
 # for models interpretability
-interpretability = ["captum", "shap", "decoupler"]
+optional-dependencies.interpretability = [ "captum", "decoupler", "shap" ]
 # for jax support
-jax = ["jax", "jaxlib", "optax", "numpyro", "flax"]
-# for custom dataloders
-dataloaders = ["lamindb>=1.12.1", "cellxgene-census", "tiledbsoma", "tiledbsoma_ml", "torchdata"]
+optional-dependencies.jax = [ "flax", "jax", "jaxlib", "numpyro", "optax" ]
+optional-dependencies.metal = [ "jax-metal", "torchaudio", "torchvision" ]
 # for mlflow
-mlflow = ["mlflow","psutil","GPUtil"]
-
-optional = [
-    "scvi-tools[autotune,mlflow,hub,jax,file_sharing,regseq,parallel,interpretability]",
-    "igraph","leidenalg","pynndescent",
+optional-dependencies.mlflow = [ "gputil", "mlflow", "psutil" ]
+optional-dependencies.optional = [
+  "igraph",
+  "leidenalg",
+  "pynndescent",
+  "scvi-tools[autotune,file_sharing,hub,interpretability,jax,mlflow,parallel,regseq]",
 ]
-tutorials = [
-    "biomart",
-    "cell2location",
-    "dataloaders",
-    "jupyter",
-    "seaborn",
-    "matplotlib",
-    "plotnine",
-    "scrublet",
-    "scvi-tools[optional]",
-    "squidpy>=1.6.0",
-    "umap-learn>=0.5.0",
+# for parallelization engine
+optional-dependencies.parallel = [ "dask[array]", "zarr" ]
+# scvi.data.add_dna_sequence
+optional-dependencies.regseq = [ "biopython>=1.81", "genomepy" ]
+optional-dependencies.test = [ "scvi-tools[tests]" ]
+optional-dependencies.tests = [ "coverage", "pytest", "pytest-pretty", "scvi-tools[optional]" ]
+optional-dependencies.tutorials = [
+  "biomart",
+  "cell2location",
+  "dataloaders",
+  "jupyter",
+  "matplotlib",
+  "plotnine",
+  "scrublet",
+  "scvi-tools[optional]",
+  "seaborn",
+  "squidpy>=1.6",
+  "umap-learn>=0.5",
 ]
-
-all = ["scvi-tools[dev,docs,tutorials]"]
+urls.Documentation = "https://scvi-tools.org"
+urls.Home-page = "https://scvi-tools.org"
+urls.Source = "https://github.com/scverse/scvi-tools"
 
 [tool.hatch.build.targets.wheel]
-packages = ['src/scvi']
-
-[tool.coverage.run]
-source = ["scvi"]
-omit = [
-    "**/test_*.py",
-]
-
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-xfail_strict = true
-markers = [
-    "internet: mark tests that requires internet access",
-    "optional: mark optional tests, usually take more time",
-    "private: mark tests that uses private keys, like HF",
-    "multigpu: mark tests that are used to check multi GPU performance",
-    "autotune: mark tests that are used to check ray autotune capabilities",
-    "custom dataloaders: mark tests that are used to check different custom data loaders",
-]
+packages = [ 'src/scvi' ]
 
 [tool.ruff]
-src = ["src"]
-line-length = 99
-indent-width = 4
 target-version = "py312"
 
+line-length = 99
+indent-width = 4
+src = [ "src" ]
 # Exclude a variety of commonly ignored directories.
 exclude = [
-    ".bzr",
-    ".direnv",
-    ".eggs",
-    ".git",
-    ".git-rewrite",
-    ".hg",
-    ".mypy_cache",
-    ".nox",
-    ".pants.d",
-    ".pytype",
-    ".ruff_cache",
-    ".svn",
-    ".tox",
-    ".venv",
-    "__pypackages__",
-    "_build",
-    "buck-out",
-    "build",
-    "dist",
-    "node_modules",
-    "venv",
+  ".bzr",
+  ".direnv",
+  ".eggs",
+  ".git",
+  ".git-rewrite",
+  ".hg",
+  ".mypy_cache",
+  ".nox",
+  ".pants.d",
+  ".pytype",
+  ".ruff_cache",
+  ".svn",
+  ".tox",
+  ".venv",
+  "__pypackages__",
+  "_build",
+  "buck-out",
+  "build",
+  "dist",
+  "node_modules",
+  "venv",
 ]
 
-[tool.ruff.lint]
-select = [
-    "F",  # Errors detected by Pyflakes
-    "E",  # Error detected by Pycodestyle
-    "W",  # Warning detected by Pycodestyle
-    "I",  # isort
-    "D",  # pydocstyle
-    "B",  # flake8-bugbear
-    "TID",  # flake8-tidy-imports
-    "C4",  # flake8-comprehensions
-    "BLE",  # flake8-blind-except
-    "UP",  # pyupgrade
-    "RUF100",  # Report unused noqa directives
-    "PT", # pytest style
-    "NPY", # numpy formatting
-    "TCH", # flake8-type-checking
-    "FA", # flake8-future-annotations
+# Like Black, indent with spaces, rather than tabs.
+format.indent-style = "space"
+# Like Black, use double quotes for strings.
+format.quote-style = "double"
+# Like Black, automatically detect the appropriate line ending.
+format.line-ending = "auto"
+# Like Black, respect magic trailing commas.
+format.skip-magic-trailing-comma = false
+format.docstring-code-format = true
+lint.select = [
+  "B",      # flake8-bugbear
+  "BLE",    # flake8-blind-except
+  "C4",     # flake8-comprehensions
+  "D",      # pydocstyle
+  "E",      # Error detected by Pycodestyle
+  "F",      # Errors detected by Pyflakes
+  "FA",     # flake8-future-annotations
+  "I",      # isort
+  "NPY",    # numpy formatting
+  "PT",     # pytest style
+  "RUF100", # Report unused noqa directives
+  "TCH",    # flake8-type-checking
+  "TID",    # flake8-tidy-imports
+  "UP",     # pyupgrade
+  "W",      # Warning detected by Pycodestyle
 ]
-ignore = [
-    # allow I, O, l as variable names -> I is the identity matrix
-    "E741",
-    # Missing docstring in the public package
-    "D104",
-    # Missing docstring in the public module
-    "D100",
-    # Missing docstring in __init__
-    "D107",
-    # Errors from function calls in argument defaults. These are fine when the result is immutable.
-    "B008",
-    # the first line should end with a period [Bug: doesn't work with single-line docstrings]
-    "D400",
-    # The first line should be in an imperative mood; try rephrasing
-    "D401",
-    # We want docstrings to start immediately after the opening triple quote
-    "D213",
-    # Raising ValueError is enough in tests.
-    "PT011",
-    # We support np.random functions.
-    "NPY002"
+lint.ignore = [
+  # Errors from function calls in argument defaults. These are fine when the result is immutable.
+  "B008",
+  # Missing docstring in the public module
+  "D100",
+  # Missing docstring in the public package
+  "D104",
+  # Missing docstring in __init__
+  "D107",
+  # We want docstrings to start immediately after the opening triple quote
+  "D213",
+  # the first line should end with a period [Bug: doesn't work with single-line docstrings]
+  "D400",
+  # The first line should be in an imperative mood; try rephrasing
+  "D401",
+  # allow I, O, l as variable names -> I is the identity matrix
+  "E741",
+  # We support np.random functions.
+  "NPY002",
+  # Raising ValueError is enough in tests.
+  "PT011",
 ]
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "BLE001", "I" ]
+lint.per-file-ignores."src/scvi/__init__.py" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.flake8-type-checking.exempt-modules = [  ]
+lint.flake8-type-checking.strict = true
+lint.pydocstyle.convention = "numpy"
 
-[tool.ruff.lint.pydocstyle]
-convention = "numpy"
-
-[tool.ruff.lint.per-file-ignores]
-"docs/*" = ["I", "BLE001"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
-"src/scvi/__init__.py" = ["I"]
-
-[tool.ruff.format]
-docstring-code-format = true
-# Like Black, use double quotes for strings.
-quote-style = "double"
-
-# Like Black, indent with spaces, rather than tabs.
-indent-style = "space"
-
-# Like Black, respect magic trailing commas.
-skip-magic-trailing-comma = false
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+markers = [
+  "internet: mark tests that requires internet access",
+  "optional: mark optional tests, usually take more time",
+  "private: mark tests that uses private keys, like HF",
+  "multigpu: mark tests that are used to check multi GPU performance",
+  "autotune: mark tests that are used to check ray autotune capabilities",
+  "custom dataloaders: mark tests that are used to check different custom data loaders",
+]
 
-# Like Black, automatically detect the appropriate line ending.
-line-ending = "auto"
+[tool.coverage.run]
+source = [ "scvi" ]
+omit = [
+  "**/test_*.py",
+]
 
 [tool.jupytext]
 formats = "ipynb,md"
-
-[tool.ruff.lint.flake8-type-checking]
-exempt-modules = []
-strict = true