poetry update & new version

.github/workflows/tests.yaml

@@ -82,6 +82,7 @@ jobs:
           git config --global user.email [email protected]
           git config --global init.defaultBranch "main"
       - name: prepare repo
+        continue-on-error: true
         run: |
           git clone https://github.com/PythonFZ/IPS-Examples
           cd IPS-Examples

ipsuite/calculators/apax_jax_md.py

@@ -4,7 +4,9 @@
 import typing
 
 import ase.io
+import h5py
 import yaml
+import znh5md
 import zntrack.utils
 from zntrack import dvc, zn
 
@@ -92,5 +94,13 @@ def run(self):
     @functools.cached_property
     def atoms(self) -> typing.List[ase.Atoms]:
         # filename should be changeable
-        with self.state.fs.open((self.sim_dir / "md.traj").as_posix()) as f:
-            return list(ase.io.iread(f))
+        def file_handle(filename):
+            file = self.state.fs.open(filename, "rb")
+            return h5py.File(file)
+
+        return znh5md.ASEH5MD(
+            self.sim_dir / "md.h5",
+            format_handler=functools.partial(
+                znh5md.FormatHandler, file_handle=file_handle
+            ),
+        ).get_atoms_list()

ipsuite/configuration_comparison/base.py

@@ -118,7 +118,6 @@ class ConfigurationComparison(base.IPSNode):
 
     Attributes
     ----------
-        hash used to use this Node as zn.Nodes()
     reference: typing.Union[utils.helpers.UNION_ATOMS_OR_ATOMS_LST,
      utils.types.SupportsAtoms]
         reference configurations to compare analyte to

ipsuite/configuration_selection/base.py

@@ -1,7 +1,6 @@
 """Base Node for ConfigurationSelection."""
 import logging
 import typing
-import uuid
 
 import ase
 import znflow
@@ -27,7 +26,6 @@ class ConfigurationSelection(base.ProcessAtoms):
 
     """
 
-    _hash = zntrack.zn.outs()
     exclude_configurations: typing.Union[
         typing.Dict[str, typing.List[int]], base.protocol.HasSelectedConfigurations
     ] = zntrack.zn.deps(None)
@@ -47,7 +45,6 @@ def _post_init_(self):
 
     def run(self):
         """ZnTrack Node Run method."""
-        self._hash = str(uuid.uuid4())
         if self.exclude is not None:
             if self.exclude_configurations is None:
                 self.exclude_configurations = {}

ipsuite/data_loading/add_data_h5md.py

@@ -1,7 +1,6 @@
 """Load Data directly from a H5MD trajectory file."""
 import functools
 import typing
-import uuid
 
 import ase
 import h5py
@@ -15,11 +14,10 @@ class AddDataH5MD(base.IPSNode):
     """Load Data directly from a H5MD trajectory file."""
 
     file = zntrack.dvc.deps()
-    _hash = zntrack.zn.outs()
     _atoms = None
 
     def run(self):
-        self._hash = str(uuid.uuid4())  # we must have an output
+        pass
 
     @property
     def atoms(self) -> typing.List[ase.Atoms]:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ipsuite"
-version = "0.1.0a3"
+version = "0.1.0a4"
 description = "A suite of tools for machine learned interatomic potentials."
 authors = ["zincwarecode <[email protected]>"]
 keywords = ["data-version-control", "machine-learning", "reproducibility", "interatomic potentials"]
@@ -9,12 +9,12 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 # tensorflow-io-gcs-filesystem
-python = ">=3.10,<3.12"
+python = ">=3.10,<3.11"
 # temporary version constraints
 libclang = "^15"
 
 znh5md = "^0.1.6a0"
-zntrack = "^0.6.0a5"
+zntrack = "^0.6.3a1"
 
 ase = "^3.22.1"
 
@@ -40,7 +40,7 @@ xmltodict = "^0.13.0"
 
 nequip = { version = "^0.5.6", optional = true }
 apax = { git = "https://github.com/apax-hub/apax.git", rev = "dev", optional = true}
-rdkit = "^2022.9.5"
+rdkit = "^2023"
 lazy-loader = "^0.2"
 znflow = "^0.1.11"
 

tests/integration/calculators/apax_md_minimal.yaml

@@ -1,3 +1,6 @@
 temperature: 1
-duration: 2.5
-n_inner: 1
+duration: 3 #fs
+n_inner: 1 # compiled innner steps
+dt: 0.5 # fs
+dr_threshold: 0.5 # Neighborlist skin
+sampling_rate: 1

tests/integration/configuration_selection/test_index.py

@@ -11,9 +11,6 @@
 def test_direct_selection(proj_w_data, eager, data_style):
     proj, data = proj_w_data
 
-    if eager:
-        for node in data:
-            node.load()
     with proj:
         if data_style == "lst":
             _data = data
@@ -38,6 +35,10 @@ def test_direct_selection(proj_w_data, eager, data_style):
             name="selection2",
         )
 
+    if eager:
+        for node in data:
+            node.load()
+
     proj.run(eager=eager)
     if not eager:
         selection.load()

tests/test_atomsuite.py → tests/test_ipsuite.py

@@ -4,7 +4,7 @@
 
 def test_version():
     """Test 'IPSuite' version."""
-    assert ips.__version__ == "0.1.0a3"
+    assert ips.__version__ == "0.1.0a4"
 
 
 def test_node_imports():