diff --git a/apax/train/checkpoints.py b/apax/train/checkpoints.py
index 1b2bc7ae..1edf3255 100644
--- a/apax/train/checkpoints.py
+++ b/apax/train/checkpoints.py
@@ -69,12 +69,13 @@ def create_params(model, rng_key, sample_input: tuple, n_models: int):
 
 
 def load_state(state, ckpt_dir):
+    ckpt_dir = Path(ckpt_dir)
     start_epoch = 0
     target = {"model": state, "epoch": 0}
-    checkpoints_exist = Path(ckpt_dir).is_dir()
+    checkpoints_exist = ckpt_dir.is_dir()
     if checkpoints_exist:
         log.info("Loading checkpoint")
-        raw_restored = checkpoints.restore_checkpoint(ckpt_dir, target=target, step=None)
+        raw_restored = checkpoints.restore_checkpoint(ckpt_dir.resolve(), target=target, step=None)
         state = raw_restored["model"]
         start_epoch = raw_restored["epoch"] + 1
         log.info("Successfully restored checkpoint from epoch %d", raw_restored["epoch"])
diff --git a/poetry.lock b/poetry.lock
index 03e2cfa6..8e258938 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "absl-py"
@@ -35,87 +35,87 @@ files = [
 
 [[package]]
 name = "aiohttp"
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+version = "3.11.10"
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 optional = true
 python-versions = ">=3.9"
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 ]
 
 [package.dependencies]
@@ -147,13 +147,13 @@ aiohttp = "*"
 
 [[package]]
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-version = "1.3.1"
+version = "1.3.2"
 description = "aiosignal: a list of registered asynchronous callbacks"
 optional = true
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -334,18 +334,18 @@ files = [
 
 [[package]]
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-version = "2.18.0"
+version = "2.19.0"
 description = "AsyncSSH: Asynchronous SSHv2 client and server library"
 optional = true
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
 cryptography = ">=39.0"
-typing-extensions = ">=4.0.0"
+typing_extensions = ">=4.0.0"
 
 [package.extras]
 bcrypt = ["bcrypt (>=3.1.3)"]
@@ -755,13 +755,13 @@ files = [
 
 [[package]]
 name = "chex"
-version = "0.1.87"
+version = "0.1.88"
 description = "Chex: Testing made fun, in JAX!"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -771,7 +771,7 @@ jaxlib = ">=0.4.27"
 numpy = ">=1.24.1"
 setuptools = {version = "*", markers = "python_version >= \"3.12\""}
 toolz = ">=0.9.0"
-typing-extensions = ">=4.2.0"
+typing_extensions = ">=4.2.0"
 
 [[package]]
 name = "click"
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@@ -1119,13 +1117,13 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "databricks-sdk"
-version = "0.38.0"
+version = "0.39.0"
 description = "Databricks SDK for Python (Beta)"
 optional = true
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1139,37 +1137,37 @@ openai = ["httpx", "langchain-openai", "openai"]
 
 [[package]]
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+version = "1.8.11"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [[package]]
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@@ -1691,11 +1682,9 @@ files = [
 ]
 
 [package.dependencies]
-absl-py = {version = "*", optional = true, markers = "extra == \"etqdm\""}
 fsspec = {version = "*", optional = true, markers = "extra == \"epath\""}
 importlib_resources = {version = "*", optional = true, markers = "extra == \"epath\""}
 numpy = {version = "*", optional = true, markers = "extra == \"enp\""}
-tqdm = {version = "*", optional = true, markers = "extra == \"etqdm\""}
 typing_extensions = {version = "*", optional = true, markers = "extra == \"epath\" or extra == \"epy\""}
 zipp = {version = "*", optional = true, markers = "extra == \"epath\""}
 
@@ -1840,22 +1829,21 @@ six = ">=1.12,<2.0"
 
 [[package]]
 name = "flax"
-version = "0.8.4"
+version = "0.10.2"
 description = "Flax: A neural network library for JAX designed for flexibility"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 files = [
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 ]
 
 [package.dependencies]
-jax = ">=0.4.19"
+jax = ">=0.4.27"
 msgpack = "*"
 numpy = [
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     {version = ">=1.23.2", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
-    {version = ">=1.22", markers = "python_version < \"3.11\""},
+    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
 ]
 optax = "*"
 orbax-checkpoint = "*"
@@ -1866,7 +1854,9 @@ typing-extensions = ">=4.2"
 
 [package.extras]
 all = ["matplotlib"]
-testing = ["black[jupyter] (==23.7.0)", "clu", "clu (<=0.0.9)", "einops", "gymnasium[accept-rom-license,atari]", "jaxlib", "jraph (>=0.0.6dev0)", "ml-collections", "mypy", "nbstripout", "opencv-python", "penzai", "pytest", "pytest-cov", "pytest-custom-exit-code", "pytest-xdist", "pytype", "sentencepiece", "tensorflow", "tensorflow-datasets", "tensorflow-text (>=2.11.0)", "torch"]
+dev = ["pre-commit (>=3.8.0)"]
+docs = ["Pygments (>=2.6.1)", "dm-haiku", "docutils (==0.16)", "einops", "ipykernel", "ipython-genutils", "ipywidgets (>=8.1.5)", "jupytext (==1.13.8)", "kagglehub (>=0.3.3)", "matplotlib", "ml-collections", "myst-nb", "nbstripout", "recommonmark", "scikit-learn", "sphinx (>=3.3.1)", "sphinx-book-theme", "sphinx-design"]
+testing = ["cloudpickle (>=3.0.0)", "clu", "clu (<=0.0.9)", "einops", "gymnasium[accept-rom-license,atari]", "jaxlib", "jaxtyping", "jraph (>=0.0.6dev0)", "ml-collections", "mypy", "opencv-python", "pytest", "pytest-cov", "pytest-custom-exit-code", "pytest-xdist", "pytype", "sentencepiece", "tensorflow (>=2.12.0)", "tensorflow-datasets", "tensorflow-text (>=2.11.0)", "torch", "treescope (>=0.1.1)"]
 
 [[package]]
 name = "flufl-lock"
@@ -1885,61 +1875,61 @@ psutil = "*"
 
 [[package]]
 name = "fonttools"
-version = "4.55.1"
+version = "4.55.3"
 description = "Tools to manipulate font files"
 optional = false
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 [package.extras]
@@ -2173,13 +2163,13 @@ test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit",
 
 [[package]]
 name = "google-auth"
-version = "2.36.0"
+version = "2.37.0"
 description = "Google Authentication Library"
 optional = true
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -2190,6 +2180,7 @@ rsa = ">=3.1.4,<5"
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0.dev0)", "requests (>=2.20.0,<3.0.0.dev0)"]
 enterprise-cert = ["cryptography", "pyopenssl"]
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 pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
@@ -2751,73 +2742,73 @@ files = [
 
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+version = "0.4.37"
 description = "Differentiate, compile, and transform Numpy code."
 optional = false
 python-versions = ">=3.10"
 files = [
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 [package.dependencies]
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-ml-dtypes = ">=0.4.0"
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 numpy = [
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     {version = ">=1.24", markers = "python_version < \"3.12\""},
+    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
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+opt_einsum = "*"
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     {version = ">=1.10", markers = "python_version < \"3.12\""},
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 [package.extras]
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-cuda = ["jax-cuda12-plugin[with-cuda] (>=0.4.34,<=0.4.35)", "jaxlib (==0.4.34)"]
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-cuda12-pip = ["jax-cuda12-plugin[with-cuda] (>=0.4.34,<=0.4.35)", "jaxlib (==0.4.34)"]
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 name = "jaxlib"
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 [package.dependencies]
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 numpy = ">=1.24"
 scipy = [
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     {version = ">=1.10", markers = "python_version < \"3.12\""},
+    {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
 ]
 
 [[package]]
@@ -3169,7 +3160,6 @@ description = "Clang Python Bindings, mirrored from the official LLVM repo: http
 optional = false
 python-versions = "*"
 files = [
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@@ -3183,13 +3173,13 @@ files = [
 
 [[package]]
 name = "mako"
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+version = "1.3.8"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
 optional = true
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -3311,52 +3301,45 @@ files = [
 
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 name = "matplotlib"
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+version = "3.10.0"
 description = "Python plotting package"
 optional = false
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 ]
 
 [package.dependencies]
@@ -3371,7 +3354,7 @@ pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
 [package.extras]
-dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6,!=2.13.3)", "setuptools (>=64)", "setuptools_scm (>=7)"]
+dev = ["meson-python (>=0.13.1,<0.17.0)", "pybind11 (>=2.13.2,!=2.13.3)", "setuptools (>=64)", "setuptools_scm (>=7)"]
 
 [[package]]
 name = "matplotlib-inline"
@@ -3475,9 +3458,9 @@ files = [
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
-    {version = ">=1.23.3", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
     {version = ">=1.21.2", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
+    {version = ">=1.23.3", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
+    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
 ]
 
 [package.extras]
@@ -3485,13 +3468,13 @@ dev = ["absl-py", "pyink", "pylint (>=2.6.0)", "pytest", "pytest-xdist"]
 
 [[package]]
 name = "mlflow"
-version = "2.18.0"
+version = "2.19.0"
 description = "MLflow is an open source platform for the complete machine learning lifecycle"
 optional = true
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -3506,7 +3489,7 @@ Jinja2 = [
 ]
 markdown = ">=3.3,<4"
 matplotlib = "<4"
-mlflow-skinny = "2.18.0"
+mlflow-skinny = "2.19.0"
 numpy = "<3"
 pandas = "<3"
 pyarrow = ">=4.0.0,<19"
@@ -3519,23 +3502,23 @@ waitress = {version = "<4", markers = "platform_system == \"Windows\""}
 aliyun-oss = ["aliyunstoreplugin"]
 databricks = ["azure-storage-file-datalake (>12)", "boto3 (>1)", "botocore", "google-cloud-storage (>=1.30.0)"]
 extras = ["azureml-core (>=1.2.0)", "boto3", "botocore", "google-cloud-storage (>=1.30.0)", "kubernetes", "prometheus-flask-exporter", "pyarrow", "pysftp", "requests-auth-aws-sigv4", "virtualenv"]
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+gateway = ["aiohttp (<4)", "boto3 (>=1.28.56,<2)", "fastapi (<1)", "pydantic (>=1.0,<3)", "slowapi (>=0.1.9,<1)", "tiktoken (<1)", "uvicorn[standard] (<1)", "watchfiles (<2)"]
+genai = ["aiohttp (<4)", "boto3 (>=1.28.56,<2)", "fastapi (<1)", "pydantic (>=1.0,<3)", "slowapi (>=0.1.9,<1)", "tiktoken (<1)", "uvicorn[standard] (<1)", "watchfiles (<2)"]
 jfrog = ["mlflow-jfrog-plugin"]
-langchain = ["langchain (>=0.1.0,<=0.3.7)"]
+langchain = ["langchain (>=0.1.0,<=0.3.9)"]
 mlserver = ["mlserver (>=1.2.0,!=1.3.1)", "mlserver-mlflow (>=1.2.0,!=1.3.1)"]
 sqlserver = ["mlflow-dbstore"]
 xethub = ["mlflow-xethub"]
 
 [[package]]
 name = "mlflow-skinny"
-version = "2.18.0"
+version = "2.19.0"
 description = "MLflow is an open source platform for the complete machine learning lifecycle"
 optional = true
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -3544,7 +3527,7 @@ click = ">=7.0,<9"
 cloudpickle = "<4"
 databricks-sdk = ">=0.20.0,<1"
 gitpython = ">=3.1.9,<4"
-importlib-metadata = ">=3.7.0,<4.7.0 || >4.7.0,<9"
+importlib_metadata = ">=3.7.0,<4.7.0 || >4.7.0,<9"
 opentelemetry-api = ">=1.9.0,<3"
 opentelemetry-sdk = ">=1.9.0,<3"
 packaging = "<25"
@@ -3557,10 +3540,10 @@ sqlparse = ">=0.4.0,<1"
 aliyun-oss = ["aliyunstoreplugin"]
 databricks = ["azure-storage-file-datalake (>12)", "boto3 (>1)", "botocore", "google-cloud-storage (>=1.30.0)"]
 extras = ["azureml-core (>=1.2.0)", "boto3", "botocore", "google-cloud-storage (>=1.30.0)", "kubernetes", "prometheus-flask-exporter", "pyarrow", "pysftp", "requests-auth-aws-sigv4", "virtualenv"]
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-genai = ["aiohttp (<4)", "boto3 (>=1.28.56,<2)", "fastapi (<1)", "pydantic (>=1.0,<3)", "slowapi (>=0.1.9,<1)", "tiktoken (<1)", "uvicorn[standard] (<1)", "watchfiles (<1)"]
+gateway = ["aiohttp (<4)", "boto3 (>=1.28.56,<2)", "fastapi (<1)", "pydantic (>=1.0,<3)", "slowapi (>=0.1.9,<1)", "tiktoken (<1)", "uvicorn[standard] (<1)", "watchfiles (<2)"]
+genai = ["aiohttp (<4)", "boto3 (>=1.28.56,<2)", "fastapi (<1)", "pydantic (>=1.0,<3)", "slowapi (>=0.1.9,<1)", "tiktoken (<1)", "uvicorn[standard] (<1)", "watchfiles (<2)"]
 jfrog = ["mlflow-jfrog-plugin"]
-langchain = ["langchain (>=0.1.0,<=0.3.7)"]
+langchain = ["langchain (>=0.1.0,<=0.3.9)"]
 mlserver = ["mlserver (>=1.2.0,!=1.3.1)", "mlserver-mlflow (>=1.2.0,!=1.3.1)"]
 sqlserver = ["mlflow-dbstore"]
 xethub = ["mlflow-xethub"]
@@ -4027,13 +4010,13 @@ PyYAML = ">=5.1.0"
 
 [[package]]
 name = "opentelemetry-api"
-version = "1.28.2"
+version = "1.29.0"
 description = "OpenTelemetry Python API"
 optional = true
 python-versions = ">=3.8"
 files = [
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@@ -4042,34 +4025,34 @@ importlib-metadata = ">=6.0,<=8.5.0"
 
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+version = "1.29.0"
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 typing-extensions = ">=3.7.4"
 
 [[package]]
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+version = "0.50b0"
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 [package.dependencies]
 deprecated = ">=1.2.6"
-opentelemetry-api = "1.28.2"
+opentelemetry-api = "1.29.0"
 
 [[package]]
 name = "opt-einsum"
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 [package.dependencies]
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     {version = ">=1.22.4", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
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 pytz = ">=2020.1"
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 [[package]]
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+    {file = "tensorstore-0.1.71-cp313-cp313-macosx_10_14_x86_64.whl", hash = "sha256:31e39ed7d374f43e45bff52611bad99315c577b44c099b2f6837b801b3467645"},
+    {file = "tensorstore-0.1.71-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:de8843fb3462899de7bcdeeaccb92303a9d61006bc36364deb4a88df46320ba4"},
+    {file = "tensorstore-0.1.71-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6276e279b45eb5d9b95c4df3e7956255f414fd4b128d2de16d8aecde86c36357"},
+    {file = "tensorstore-0.1.71-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:52b546f076b2c3bf217c60f05de4124cc1197ce92f8e826e7ec73ae324074a5a"},
+    {file = "tensorstore-0.1.71-cp313-cp313-win_amd64.whl", hash = "sha256:ecf4feb574051f40e81572ea2ff8e5895b2980c5dd3b29fe81c70d25e42d3b6a"},
+    {file = "tensorstore-0.1.71.tar.gz", hash = "sha256:5c37c7b385517b568282a7aedded446216335d0cb41187c93c80b53596c92c96"},
 ]
 
 [package.dependencies]
@@ -7248,13 +7242,13 @@ files = [
 
 [[package]]
 name = "znflow"
-version = "0.2.2"
+version = "0.2.3"
 description = "A general purpose framework for building and running computational graphs."
 optional = true
 python-versions = "<4.0,>=3.9"
 files = [
-    {file = "znflow-0.2.2-py3-none-any.whl", hash = "sha256:0fd83ba42235a1448a347aff1cba83d618a693199d592054d6c540ac18546c28"},
-    {file = "znflow-0.2.2.tar.gz", hash = "sha256:04cea6d52983824888ca6b441aabd686dd88900be69dcb372045e6ae401ac21b"},
+    {file = "znflow-0.2.3-py3-none-any.whl", hash = "sha256:10f3f743a5877214a5f71e860663852e40a6e1f85b2d1d4d469213b42ec4ed07"},
+    {file = "znflow-0.2.3.tar.gz", hash = "sha256:c7997be3080c6c25c4d2a79204b6705a5ab93a761098610e2230b79d67ac68c6"},
 ]
 
 [package.dependencies]
@@ -7265,13 +7259,13 @@ dask = ["dask (>=2024,<2025)", "distributed (>=2024,<2025)"]
 
 [[package]]
 name = "znh5md"
-version = "0.4.0"
+version = "0.4.2"
 description = "ASE Interface for the H5MD format."
 optional = false
 python-versions = "<4.0,>=3.10"
 files = [
-    {file = "znh5md-0.4.0-py3-none-any.whl", hash = "sha256:9bf905f85076937dc4dc76a09875e234404cc551dd95b8705a3f597b519bb96f"},
-    {file = "znh5md-0.4.0.tar.gz", hash = "sha256:18979d3f9b7ff12e1a6147a82abdd63f2aacf9537b5ed9235f16027471a5b1e9"},
+    {file = "znh5md-0.4.2-py3-none-any.whl", hash = "sha256:e264461a2b24acbeeabd863a3b8edc9df69854cec510ebd61d7a0fa52abe8989"},
+    {file = "znh5md-0.4.2.tar.gz", hash = "sha256:ff52a1037e148d64a5d8634def87f476549a6c4e645a29a2dff2b0f992d2a895"},
 ]
 
 [package.dependencies]
@@ -7293,13 +7287,13 @@ files = [
 
 [[package]]
 name = "zntrack"
-version = "0.8.0"
+version = "0.8.1"
 description = "Create, Run and Benchmark DVC Pipelines in Python"
 optional = true
 python-versions = "<4,>=3.10"
 files = [
-    {file = "zntrack-0.8.0-py3-none-any.whl", hash = "sha256:8b1d3e98b026ad3312bddf7ef8cef6ba56455c542be0163629daf1214500a205"},
-    {file = "zntrack-0.8.0.tar.gz", hash = "sha256:5ad0dd4ec517880cb49ac794e0ff990b7dc2ba8395f1b3d9326998ecb69ebe97"},
+    {file = "zntrack-0.8.1-py3-none-any.whl", hash = "sha256:7483d08dc6a8c0b9b58754f58d241c38113b51dd3beb62e3041b35ae612fc9b0"},
+    {file = "zntrack-0.8.1.tar.gz", hash = "sha256:4f39da4f1db02c6cfc9d516c6d60f1e6705bc427e96423ecbc33ba96da068a55"},
 ]
 
 [package.dependencies]
@@ -7309,7 +7303,7 @@ pyyaml = ">=6,<7"
 tqdm = ">=4,<5"
 typer = ">=0.13,<0.14"
 znfields = ">=0.1.2,<0.2.0"
-znflow = ">=0.2.2,<0.3.0"
+znflow = ">=0.2.3,<0.3.0"
 znjson = ">=0.2,<0.3"
 
 [extras]
@@ -7319,4 +7313,4 @@ zntrack = ["zntrack"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<4.0"
-content-hash = "195093fecebea1b7b6ee157538bd2e15563507a8b8997eb86ba14f080bf724af"
+content-hash = "2b6d2f5977b582394ca6d800a957dbad1165414962bcb566248c96a8495cef8e"
diff --git a/pyproject.toml b/pyproject.toml
index 76e9efae..fa9c6c6c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ znh5md = "^0.4"
 pydantic = "^2.3.0"
 jax = "^0.4.25"
 orbax-checkpoint = "0.5.16"
-flax = "0.8.4"
+flax = "^0.10.1"
 uncertainty-toolbox = "^0.1.1"
 e3x = "^1.0.2"
 vesin = "^0.2.0"
diff --git a/tests/nodes/test_n_model.py b/tests/nodes/test_n_model.py
index e5e01853..2ffbf9f9 100644
--- a/tests/nodes/test_n_model.py
+++ b/tests/nodes/test_n_model.py
@@ -62,7 +62,7 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose):
     save_config_with_seed(tmp_path / "example2.yaml", seed=2)
 
     proj = zntrack.Project(automatic_node_names=True)
-    thermostat = ips.calculators.LangevinThermostat(
+    thermostat = ips.LangevinThermostat(
         time_step=1.0, temperature=100.0, friction=0.01
     )
     with proj:
@@ -74,7 +74,7 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose):
             data=data.frames, validation_data=data.frames, config="example2.yaml"
         )
         ensemble = ApaxEnsemble(models=[model1, model2])
-        md = ips.calculators.ASEMD(
+        md = ips.ASEMD(
             data=data.frames,
             model=ensemble,
             thermostat=thermostat,
@@ -82,22 +82,22 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose):
             sampling_rate=1,
         )
 
-        uncertainty_selection = ips.configuration_selection.ThresholdSelection(
-            data=md, n_configurations=1, threshold=0.0001
+        uncertainty_selection = ips.ThresholdSelection(
+            data=md.frames, n_configurations=1, threshold=0.0001
         )
 
         selection_batch_size = 3
         kernel_selection = apax.nodes.BatchKernelSelection(
-            data=md.atoms,
+            data=md.frames,
             train_data=data.frames,
             models=[model1, model2],
             n_configurations=selection_batch_size,
             processing_batch_size=4,
         )
 
-        prediction = ips.analysis.Prediction(data=kernel_selection.frames, model=ensemble)
-        analysis = ips.analysis.PredictionMetrics(
-            x=kernel_selection.frames, y=prediction.atoms
+        prediction = ips.Prediction(data=kernel_selection.frames, model=ensemble)
+        analysis = ips.PredictionMetrics(
+            x=kernel_selection.frames, y=prediction.frames
         )
 
     proj.repro()
@@ -110,7 +110,7 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose):
 
     assert atoms.get_potential_energy() < 0
 
-    uncertainties = [x.calc.results["energy_uncertainty"] for x in md.atoms]
-    assert [md.atoms[np.argmax(uncertainties)]] == uncertainty_selection.atoms
+    uncertainties = [x.calc.results["energy_uncertainty"] for x in md.frames]
+    assert [md.frames[np.argmax(uncertainties)]] == uncertainty_selection.frames
 
     assert len(kernel_selection.frames) == selection_batch_size