diff --git a/pkgs/development/python-modules/zarr/default.nix b/pkgs/development/python-modules/zarr/default.nix
index 755d64cc780d..b7f738c1d92c 100644
--- a/pkgs/development/python-modules/zarr/default.nix
+++ b/pkgs/development/python-modules/zarr/default.nix
@@ -1,7 +1,7 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGitHub,
 
   # build-system
   hatchling,
@@ -11,25 +11,61 @@
   donfig,
   numpy,
   numcodecs,
+  google-crc32c,
   packaging,
   typing-extensions,
 
-  # tests
-  hypothesis,
-  pytest-asyncio,
-  pytest-xdist,
+  # optional-dependencies
+  # remote
+  fsspec,
+  obstore ? null, # TODO: Package
+  # gpu
+  cupy,
+  # cli
+  typer,
+  # test
   pytestCheckHook,
+  pytest-asyncio,
+  pytest-cov,
+  pytest-accept ? null, # TODO: Package
+  rich,
+  mypy,
+  numpydoc,
+  hypothesis,
+  pytest-xdist,
   tomlkit,
+  uv,
+  # remote_tests
+  botocore,
+  s3fs,
+  moto,
+  requests,
+  # optional
+  universal-pathlib,
+  # docs
+  mkdocs-material,
+  mkdocs,
+  mkdocstrings,
+  mkdocstrings-python,
+  mike,
+  mkdocs-redirects,
+  markdown-exec ? null, # TODO: Package
+  griffe-inherited-docstrings ? null, # TODO: Package,
+  ruff,
+  towncrier,
+  astroid,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "zarr";
-  version = "3.1.1";
+  version = "3.1.5";
   pyproject = true;
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-F9ty838kiUUtITesiRxBM7j5dvkYnY79PnXzs63YTow=";
+  src = fetchFromGitHub {
+    owner = "zarr-developers";
+    repo = "zarr-python";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-1Kx8gN1JiaY4eHmwpdilvJ8+NdnzxhDvn7YZjphgtZw=";
   };
 
   build-system = [
@@ -40,35 +76,100 @@ buildPythonPackage rec {
   dependencies = [
     donfig
     numcodecs
+    google-crc32c
     numpy
     packaging
     typing-extensions
-  ]
-  ++ numcodecs.optional-dependencies.crc32c;
+  ];
+
+  passthru = {
+    optional-dependencies = {
+      remote = [
+        fsspec
+        obstore
+      ];
+      gpu = [
+        cupy
+      ];
+      cli = [
+        typer
+      ];
+      # Development extras
+      test = [
+        #pytest
+        pytest-asyncio
+        pytest-cov
+        pytest-accept
+        rich
+        mypy
+        numpydoc
+        hypothesis
+        # From some reason the existence of pytest-xdist makes the tests fail
+        # depending on $NIX_BUILD_CORES
+        #pytest-xdist
+        packaging
+        tomlkit
+        uv
+      ];
+      remote_tests = [
+        botocore
+        s3fs
+        moto
+        requests
+      ]
+      ++ moto.optional-dependencies.server
+      ++ moto.optional-dependencies.s3;
+      optional = [
+        rich
+        universal-pathlib
+      ];
+      docs = [
+        # Doc building
+        mkdocs-material
+        mkdocs
+        mkdocstrings
+        mkdocstrings-python
+        mike
+        mkdocs-redirects
+        markdown-exec
+        griffe-inherited-docstrings
+        ruff
+        towncrier # Changelog generation
+        # Optional dependencies to run examples
+        rich
+        s3fs
+        astroid
+        #pytest
+      ]
+      ++ mkdocs-material.optional-dependencies.imaging
+      ++ markdown-exec.optional-dependencies.ansi
+      ++ numcodecs.optional-dependencies.msgpack;
+    };
+  };
 
   nativeCheckInputs = [
-    hypothesis
-    pytest-asyncio
-    pytest-xdist
     pytestCheckHook
-    tomlkit
-  ];
+  ]
+  ++ finalAttrs.finalPackage.passthru.optional-dependencies.cli
+  # Not adding `passthru.optional-dependencies.remote{,_tests}` since the
+  # existence of these Python modules triggers tests that fail in the sandbox
+  # due to failed network requests.
+  ++ finalAttrs.finalPackage.passthru.optional-dependencies.test;
 
   disabledTestPaths = [
     # requires uv and then fails at setting up python envs
-    "tests/test_examples.py"
+    "tests/test_examples.py::test_scripts_can_run[script_path0]"
+    # Requires zarr==2.x to generate zarr stores for the tests
+    "tests/test_regression"
   ];
 
   pythonImportsCheck = [ "zarr" ];
 
-  # FIXME remove once zarr's reverse dependencies support v3
-  passthru.skipBulkUpdate = true;
-
   meta = {
     description = "Implementation of chunked, compressed, N-dimensional arrays for Python";
     homepage = "https://github.com/zarr-developers/zarr";
-    changelog = "https://github.com/zarr-developers/zarr-python/releases/tag/v${version}";
+    changelog = "https://github.com/zarr-developers/zarr-python/releases/tag/v${finalAttrs.version}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ doronbehar ];
   };
-}
+})