Merge remote-tracking branch 'origin/update-schema' into search-after

.github/workflows/tests.yml

@@ -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/

README.md

@@ -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/)
@@ -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/)
 

setup.cfg

@@ -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

src/cript/nodes/primary_nodes/computation_process.py

@@ -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

src/cript/nodes/primary_nodes/material.py

@@ -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

src/cript/nodes/primary_nodes/process.py

@@ -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

src/cript/nodes/subobjects/property.py

@@ -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 | |
@@ -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",
@@ -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
  -------
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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]
 
@@ -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
@@ -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
@@ -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
 
@@ -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]
 
@@ -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",
@@ -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]
 
@@ -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)"
@@ -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

tests/fixtures/primary_nodes.py

@@ -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"
  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
@@ -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'
@@ -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'
@@ -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'
@@ -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'

tests/fixtures/subobjects.py

@@ -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",
+ key="enthalpy",
  type="value",
  value=5.0,
  unit="GPa",
@@ -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",
@@ -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",
@@ -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",

tests/fixtures/supporting_nodes.py

@@ -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"

tests/nodes/primary_nodes/test_material.py

@@ -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,

tests/nodes/subobjects/test_property.py

@@ -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"

tests/nodes/test_utils.py

@@ -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,

tests/test_node_util.py

@@ -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)
@@ -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",
@@ -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",
@@ -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",
@@ -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",