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Update to 1.0.1 #454

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Update to 1.0.1 #454

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78fbdea
Update to 1.0.1
InnocentBug Apr 24, 2024
0c01e51
update python version
InnocentBug Apr 24, 2024
63e2e99
run new version on 3.9
InnocentBug Apr 24, 2024
ce28a85
3.10
InnocentBug Apr 24, 2024
c86e042
fix oversight
InnocentBug Apr 24, 2024
6b06b8c
fixing docs
InnocentBug Apr 24, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
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Expand Up @@ -35,7 +35,7 @@ jobs:

matrix:
os: [ubuntu-latest, macos-latest]
python-version: [3.8, 3.12]
python-version: ["3.10", 3.12]

env:
CRIPT_HOST: https://lb-stage.mycriptapp.org/
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -3,7 +3,7 @@
[![License](./CRIPT_full_logo_colored_transparent.png)](https://github.com/C-Accel-CRIPT/Python-SDK/blob/develop/LICENSE.md)

[![License](https://img.shields.io/github/license/C-Accel-CRIPT/cript?style=flat-square)](https://github.com/C-Accel-CRIPT/Python-SDK/blob/develop/LICENSE.md)
[![Python](https://img.shields.io/badge/Language-Python%203.8+-blue?style=flat-square&logo=python)](https://www.python.org/)
[![Python](https://img.shields.io/badge/Language-Python%203.10+-blue?style=flat-square&logo=python)](https://www.python.org/)
[![Code style is black](https://img.shields.io/badge/Code%20Style-black-000000.svg?style=flat-square&logo=python)](https://github.com/psf/black)
[![Link to CRIPT website](https://img.shields.io/badge/platform-criptapp.org-blueviolet?style=flat-square)](https://criptapp.org/)
[![Using Pytest](https://img.shields.io/badge/Dependencies-pytest-green?style=flat-square&logo=Pytest)](https://docs.pytest.org/en/7.2.x/)
Expand Down Expand Up @@ -36,7 +36,7 @@ The CRIPT Python SDK allows programmatic access to the [CRIPT platform](https://

## Installation

CRIPT Python SDK requires Python 3.8+
CRIPT Python SDK requires Python 3.10+

The latest released of CRIPT Python SDK is available on [Python Package Index (PyPI)](https://pypi.org/project/cript/)

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4 changes: 2 additions & 2 deletions setup.cfg
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Expand Up @@ -14,13 +14,13 @@ classifiers =
Topic :: Scientific/Engineering
Programming Language :: Python :: 3
Programming Language :: Python :: 3 :: Only
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.10

[options]
package_dir =
=src
packages = find:
python_requires = >=3.8
python_requires = >=3.10
include_package_data = True
install_requires =
requests==2.31.0
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2 changes: 1 addition & 1 deletion src/cript/nodes/primary_nodes/computation_process.py
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Expand Up @@ -521,7 +521,7 @@ def property(self) -> List[Any]:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.23, unit="J")
>>> my_computation_process.property = [my_property] # doctest: +SKIP
Returns
Expand Down
2 changes: 1 addition & 1 deletion src/cript/nodes/primary_nodes/material.py
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Expand Up @@ -540,7 +540,7 @@ def property(self) -> List[Any]:
... name="my component material 1",
... smiles = "component 1 smiles",
... )
>>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.23, unit="J")
>>> my_material.property = [my_property]

Returns
Expand Down
2 changes: 1 addition & 1 deletion src/cript/nodes/primary_nodes/process.py
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Expand Up @@ -580,7 +580,7 @@ def property(self) -> List[Any]:
--------
>>> import cript
>>> my_process = cript.Process(name="my process name", type="affinity_pure")
>>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.23, unit="J")
>>> my_process.property = [my_property]

Returns
Expand Down
34 changes: 17 additions & 17 deletions src/cript/nodes/subobjects/property.py
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Expand Up @@ -38,7 +38,7 @@ class Property(UUIDBaseNode):

| attribute | type | example | description | required | vocab |
|--------------------|-------------------|-----------------------------------------|------------------------------------------------------------------------------|----------|-------|
| key | str | modulus_shear | type of property | True | True |
| key | str | enthalpy | type of property | True | True |
| type | str | min | type of value stored | True | True |
| value | Any | 1.23 | value or quantity | True | |
| unit | str | gram | unit for value | True | |
Expand All @@ -58,10 +58,10 @@ class Property(UUIDBaseNode):
## JSON Representation
```json
{
"key":"modulus_shear",
"key":"enthalpy",
"node":["Property"],
"type":"value",
"unit":"GPa",
"unit":"J",
"value":5.0
"uid":"_:bc3abb68-25b5-4144-aa1b-85d82b7c77e1",
"uuid":"bc3abb68-25b5-4144-aa1b-85d82b7c77e1",
Expand Down Expand Up @@ -149,7 +149,7 @@ def __init__(
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")

Returns
-------
Expand Down Expand Up @@ -197,7 +197,7 @@ def key(self) -> str:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.key = "angle_rdist"

Returns
Expand Down Expand Up @@ -236,7 +236,7 @@ def type(self) -> str:
Examples
---------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.type = "max"

Returns
Expand Down Expand Up @@ -285,7 +285,7 @@ def set_value(self, new_value: Union[Number, str, None], new_unit: str) -> None:
Examples
---------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.set_value(new_value=1, new_unit="gram")

Parameters
Expand Down Expand Up @@ -345,7 +345,7 @@ def set_uncertainty(self, new_uncertainty: Optional[Number], new_uncertainty_typ
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.set_uncertainty(new_uncertainty=2, new_uncertainty_type="fwhm")

Returns
Expand Down Expand Up @@ -380,7 +380,7 @@ def component(self) -> List[Union[Material, UIDProxy]]:
Examples
---------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_material = cript.Material(name="my material", bigsmiles = "123456")
>>> my_property.component = [my_material]

Expand Down Expand Up @@ -418,7 +418,7 @@ def structure(self) -> str:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.structure = "{[][$][C:1][C:1][$],[$][C:2][C:2]([C:2])[$][]}"

Returns
Expand Down Expand Up @@ -457,7 +457,7 @@ def method(self) -> str:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.method = "ASTM_D3574_Test_A"

Returns
Expand Down Expand Up @@ -494,7 +494,7 @@ def sample_preparation(self) -> Union[Process, None, UIDProxy]:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_process = cript.Process(name="my process name", type="affinity_pure")
>>> my_property.sample_preparation = my_process

Expand Down Expand Up @@ -532,7 +532,7 @@ def condition(self) -> List[Union[Condition, UIDProxy]]:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_condition = cript.Condition(key="atm", type="max", value=1)
>>> my_property.condition = [my_condition]

Expand Down Expand Up @@ -570,7 +570,7 @@ def data(self) -> List[Union[Data, UIDProxy]]:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_file = cript.File(
... name="my file node name",
... source="https://criptapp.org",
Expand Down Expand Up @@ -615,7 +615,7 @@ def computation(self) -> List[Union[Computation, UIDProxy]]:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_computation = cript.Computation(name="my computation name", type="analysis")
>>> my_property.computation = [my_computation]

Expand Down Expand Up @@ -653,7 +653,7 @@ def citation(self) -> List[Union[Citation, UIDProxy]]:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> title = (
... "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: "
... "Soft coarse grained Monte-Carlo Acceleration (SOMA)"
Expand Down Expand Up @@ -707,7 +707,7 @@ def notes(self) -> str:
Examples
--------
>>> import cript
>>> my_property = cript.Property(key="air_flow", type="min", value=1.00, unit="gram")
>>> my_property = cript.Property(key="enthalpy", type="min", value=1.00, unit="J")
>>> my_property.notes = "these are my notes"

Returns
Expand Down
12 changes: 6 additions & 6 deletions tests/fixtures/primary_nodes.py
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Expand Up @@ -25,7 +25,7 @@ def simple_project_node(simple_collection_node) -> cript.Project:
def complex_project_dict(complex_collection_node, simple_material_node, complex_user_node) -> dict:
project_dict = {"node": ["Project"]}
project_dict["locked"] = True
project_dict["model_version"] = "1.0.0"
project_dict["model_version"] = "1.0.1"
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I would advise you dont pin the model_version to a specific version as it is populated automatically on the latest version.

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great idea, how do we know which one is the newest version?

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also this is probably only a work around.

We need a general scheme to update nodes from one version to the newest version automatically.

In this case this is very simple, but it can get more complicated easily.

Do you have ideas how this can be done?

I was thinking something along the Go philosophy that any change needs to have an automatic port option.
Otherwise we will have nodes that we can't process anymore since they are going out of date.

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You can get the latest version from the /schema endpoint at `#/defs/ModelVersion", but I think you are looking too much into it, I think the datamodel as of now wont have major changes that will need transformations, the only changes that will be periodical is from the controlled vocabulary which is also embedded in the jsonschema hence bumping the version number. It should work fine if you remove the model_version attribute altogether.

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can you approve pls

project_dict["updated_by"] = json.loads(copy.deepcopy(complex_user_node).get_expanded_json())
project_dict["created_by"] = json.loads(complex_user_node.get_expanded_json())
project_dict["public"] = True
Expand Down Expand Up @@ -60,7 +60,7 @@ def fixed_cyclic_project_node() -> cript.Project:
project_json_string += '"created_at": "2024-03-12 15:58:12.486673",\n'
project_json_string += '"updated_at": "2024-03-12 15:58:12.486681",\n'
project_json_string += '"email": "test@emai.com",\n'
project_json_string += '"model_version": "1.0.0",\n'
project_json_string += '"model_version": "1.0.1",\n'
project_json_string += '"orcid": "0000-0002-0000-0000",\n'
project_json_string += '"picture": "/my/picture/path",\n'
project_json_string += '"username": "testuser"\n'
Expand All @@ -72,13 +72,13 @@ def fixed_cyclic_project_node() -> cript.Project:
project_json_string += '"created_at": "2024-03-12 15:58:12.486673",\n'
project_json_string += '"updated_at": "2024-03-12 15:58:12.486681",\n'
project_json_string += '"email": "test@emai.com",\n'
project_json_string += '"model_version": "1.0.0",\n'
project_json_string += '"model_version": "1.0.1",\n'
project_json_string += '"orcid": "0000-0002-0000-0000",\n'
project_json_string += '"picture": "/my/picture/path",\n'
project_json_string += '"username": "testuser"\n'
project_json_string += "},\n"
project_json_string += '"locked": true,\n'
project_json_string += '"model_version": "1.0.0",\n'
project_json_string += '"model_version": "1.0.1",\n'
project_json_string += '"public": true,\n'
project_json_string += '"name": "my project name",\n'
project_json_string += '"notes": "my project notes",\n'
Expand Down Expand Up @@ -126,7 +126,7 @@ def fixed_cyclic_project_node() -> cript.Project:
project_json_string += '"node": ["Property"],\n'
project_json_string += '"uid": "_:fc504202-6fdd-43c7-830d-40c7d3f0cb8c",\n'
project_json_string += '"uuid": "fc504202-6fdd-43c7-830d-40c7d3f0cb8c",\n'
project_json_string += '"key": "modulus_shear",\n'
project_json_string += '"key": "enthalpy",\n'
project_json_string += '"type": "value",\n'
project_json_string += '"value": 5.0,\n'
project_json_string += '"unit": "GPa",\n'
Expand Down Expand Up @@ -213,7 +213,7 @@ def fixed_cyclic_project_node() -> cript.Project:
project_json_string += '"node": ["Property"],\n'
project_json_string += '"uid": "_:fde629f5-8d3a-4546-8cd3-9de63b990187",\n'
project_json_string += '"uuid": "fde629f5-8d3a-4546-8cd3-9de63b990187",\n'
project_json_string += '"key": "modulus_shear",\n'
project_json_string += '"key": "enthalpy",\n'
project_json_string += '"type": "value",\n'
project_json_string += '"value": 5.0,\n'
project_json_string += '"unit": "GPa",\n'
Expand Down
8 changes: 4 additions & 4 deletions tests/fixtures/subobjects.py
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Expand Up @@ -122,7 +122,7 @@ def complex_property_node(complex_material_node, complex_condition_node, complex
a maximal property sub-object with all possible fields filled
"""
my_complex_property = cript.Property(
key="modulus_shear",
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how did you know to change this keyword ?
was this info from an error message like in the error message for model 1.0.0?

key="enthalpy",
type="value",
value=5.0,
unit="GPa",
Expand All @@ -144,7 +144,7 @@ def complex_property_node(complex_material_node, complex_condition_node, complex
def complex_property_dict(complex_material_node, complex_condition_dict, complex_citation_dict, complex_data_node, simple_process_node, simple_computation_node) -> dict:
ret_dict = {
"node": ["Property"],
"key": "modulus_shear",
"key": "enthalpy",
"type": "value",
"value": 5.0,
"unit": "GPa",
Expand All @@ -165,7 +165,7 @@ def complex_property_dict(complex_material_node, complex_condition_dict, complex
@pytest.fixture(scope="function")
def simple_property_node() -> cript.Property:
my_property = cript.Property(
key="modulus_shear",
key="enthalpy",
type="value",
value=5.0,
unit="GPa",
Expand All @@ -177,7 +177,7 @@ def simple_property_node() -> cript.Property:
def simple_property_dict() -> dict:
ret_dict = {
"node": ["Property"],
"key": "modulus_shear",
"key": "enthalpy",
"type": "value",
"value": 5.0,
"unit": "GPa",
Expand Down
2 changes: 1 addition & 1 deletion tests/fixtures/supporting_nodes.py
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Expand Up @@ -63,7 +63,7 @@ def complex_local_file_node(tmp_path_factory) -> cript.File:
def complex_user_dict() -> dict:
user_dict = {"node": ["User"]}
user_dict["created_at"] = str(datetime.datetime.now())
user_dict["model_version"] = "1.0.0"
user_dict["model_version"] = "1.0.1"
user_dict["picture"] = "/my/picture/path"
user_dict["updated_at"] = str(datetime.datetime.now())
user_dict["username"] = "testuser"
Expand Down
2 changes: 1 addition & 1 deletion tests/nodes/primary_nodes/test_material.py
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Expand Up @@ -34,7 +34,7 @@ def test_create_complex_material(cript_api, simple_material_node, simple_computa
component = [simple_material_node]
forcefield = simple_computational_forcefield_node

my_property = [cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")]
my_property = [cript.Property(key="rho_z", type="min", value=1.23, unit="gram")]

my_material = cript.Material(
name=material_name,
Expand Down
4 changes: 2 additions & 2 deletions tests/nodes/subobjects/test_property.py
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Expand Up @@ -20,8 +20,8 @@ def test_json(complex_property_node, complex_property_dict):


def test_setter_getter(complex_property_node, simple_material_node, simple_process_node, complex_condition_node, simple_data_node, simple_computation_node, complex_citation_node):
complex_property_node.key = "modulus_loss"
assert complex_property_node.key == "modulus_loss"
complex_property_node.key = "rho_z"
assert complex_property_node.key == "rho_z"

complex_property_node.type = "min"
assert complex_property_node.type == "min"
Expand Down
2 changes: 1 addition & 1 deletion tests/nodes/test_utils.py
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Expand Up @@ -35,7 +35,7 @@ def test_load_node_from_json_dict_argument() -> None:
"uuid": material_uuid,
"name": material_name,
"notes": material_notes,
"property": [{"node": ["Property"], "uid": "_:aedce614-7acb-49d2-a2f6-47463f15b707", "uuid": "aedce614-7acb-49d2-a2f6-47463f15b707", "key": "modulus_shear", "type": "value", "value": 5.0, "unit": "GPa"}],
"property": [{"node": ["Property"], "uid": "_:aedce614-7acb-49d2-a2f6-47463f15b707", "uuid": "aedce614-7acb-49d2-a2f6-47463f15b707", "key": "enthalpy", "type": "value", "value": 5.0, "unit": "GPa"}],
"computational_forcefield": {"node": ["ComputationalForcefield"], "uid": "_:059952a3-20f2-4739-96bd-a5ea43068065", "uuid": "059952a3-20f2-4739-96bd-a5ea43068065", "key": "amber", "building_block": "atom"},
"keyword": ["acetylene"],
"bigsmiles": material_bigsmiles,
Expand Down
12 changes: 6 additions & 6 deletions tests/test_node_util.py
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Expand Up @@ -33,8 +33,8 @@ def test_uid_deserialization(simple_algorithm_node, complex_parameter_node, simp
material = cript.Material(name="my material", bigsmiles="{[][$]CC[$][]}")

computation = cript.Computation(name="my computation name", type="analysis")
property1 = cript.Property("modulus_shear", "value", 5.0, "GPa", computation=[computation])
property2 = cript.Property("modulus_loss", "value", 5.0, "GPa", computation=[computation])
property1 = cript.Property("enthalpy", "value", 5.0, "GPa", computation=[computation])
property2 = cript.Property("rho_z", "value", 5.0, "GPa", computation=[computation])
material.property = [property1, property2]

material2 = cript.load_nodes_from_json(material.json)
Expand All @@ -50,7 +50,7 @@ def test_uid_deserialization(simple_algorithm_node, complex_parameter_node, simp
"node": ["Property"],
"uid": "_:82e7270e-9f35-4b35-80a2-faa6e7f670be",
"uuid": "82e7270e-9f35-4b35-80a2-faa6e7f670be",
"key": "modulus_shear",
"key": "enthalpy",
"type": "value",
"value": 5.0,
"unit": "GPa",
Expand All @@ -60,7 +60,7 @@ def test_uid_deserialization(simple_algorithm_node, complex_parameter_node, simp
"node": ["Property"],
"uid": "_:fc4dfa5e-742c-4d0b-bb66-2185461f4582",
"uuid": "fc4dfa5e-742c-4d0b-bb66-2185461f4582",
"key": "modulus_loss",
"key": "rho_z",
"type": "value",
"value": 5.0,
"unit": "GPa",
Expand Down Expand Up @@ -92,7 +92,7 @@ def test_uid_deserialization(simple_algorithm_node, complex_parameter_node, simp
# ],
# "uid": "_:82e7270e-9f35-4b35-80a2-faa6e7f670be",
# "uuid": "82e7270e-9f35-4b35-80a2-faa6e7f670be",
# "key": "modulus_shear",
# "key": "enthalpy",
# "type": "value",
# "value": 5.0,
# "unit": "GPa",
Expand All @@ -111,7 +111,7 @@ def test_uid_deserialization(simple_algorithm_node, complex_parameter_node, simp
# ],
# "uid": "_:fc4dfa5e-742c-4d0b-bb66-2185461f4582",
# "uuid": "fc4dfa5e-742c-4d0b-bb66-2185461f4582",
# "key": "modulus_loss",
# "key": "rho_z",
# "type": "value",
# "value": 5.0,
# "unit": "GPa",
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