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@InnocentBug InnocentBug released this 01 Apr 18:56
v2.3.0
6f574d7
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Version 2.3.0

New Features:

  • cript.API objects now have a DataSchema attribute called schema, representing the JSON schema for node validation.
    • This includes the ability to enable and disable node validation.
  • cript.API objects now have logger attributes from the Python logging module to control logging flows.
  • Refactor of Paginator:
    • New Paginator objects for accessing data from the CRIPT data bank via search.
    • Paginator are now Python iterators. You can use for node in paginator: ... directly.
    • Paginator now return cript.Node objects natively.
    • JSON response can be requested from Paginator alternatively. This is helpful for internal work and debugging.
  • Additional information is added to the logging message when nodes are validated. For primary nodes, name is displayed; for others, the UUID is displayed.
  • HTTP requests are now optimized, leaving connections open and grouping requests for better performance.
  • A native iterator for nodes is now offered. It iterates in depth-first order over all child nodes of the root node. Cycles are automatically broken, and every node is visited exactly once.
  • Materials with no identifier issue a warning to users.
  • Debugging messages show full API requests and responses for debugging.
  • Automated UUID caching for nodes can now be explicitly circumvented when using cript.load_nodes_from_json. Mostly useful for development.

Known Issues and Bugs:

  • Saving projects is not supported. Temporarily, you can use get_expanded_json to store a JSON representation of projects, which can be uploaded into CRIPT at a later time.
  • BigSMILES search patterns are not supported.
  • Searching for more than 1000 pages (10000 entries) is not supported.
  • Permission settings in CRIPT do not influence the behavior of the SDK objects.
  • Tests that require valid tokens (like saving or searching) are not included in CI/CD tests.

Bugfixes:

  • cript.load_nodes_from_json can now load JSON files that store different nodes in lists or dictionaries.
  • Not all nodes were correctly validated at all times, especially if instantiated from JSON. All nodes are automatically validated now.
  • The documentation has been updated to remove certain mistakes.
  • Users can have only one Python object with the same UUID to avoid mis-updates. This did not work in all cases, but it works in all cases now.

Breaking Changes:

  • cript.API() objects no longer have functions related to JSON schema validation. Please use the new DataSchema class instead. The DataSchema class can be accessed via the schema property of the API class.
  • Indirect logging control via the API is defunct. Please use the direct access to the logger attribute of API classes to control logging output.
  • The SDK used to use identifier dictionaries for material identifiers. This is updated to use individual attributes of the material node. This is consistent with the JSON schema and front-end but is a breaking change to older SDK versions and the original CRIPT publication.
  • Projects were checked to ensure the presence of material and computation in Experiments. These errors were converted into warnings.

Health Report

=============================================================================================== test session starts ===============================================================================================
platform linux -- Python 3.11.2, pytest-7.4.3
plugins: cov-4.1.0
collected 124 items

tests/test_node_util.py ........... [ 8%]
tests/api/test_api.py ..... [ 12%]
tests/api/test_db_schema.py ..... [ 16%]
tests/api/test_search.py .....F [ 21%]
tests/nodes/test_utils.py .. [ 23%]
tests/nodes/primary_nodes/test_collection.py .....F [ 28%]
tests/nodes/primary_nodes/test_computation.py .....F [ 33%]
tests/nodes/primary_nodes/test_computational_process.py ....F [ 37%]
tests/nodes/primary_nodes/test_data.py ....F [ 41%]
tests/nodes/primary_nodes/test_experiment.py ....F [ 45%]
tests/nodes/primary_nodes/test_inventory.py ..F [ 47%]
tests/nodes/primary_nodes/test_material.py ...F [ 50%]
tests/nodes/primary_nodes/test_process.py .....F [ 55%]
tests/nodes/primary_nodes/test_project.py ...F [ 58%]
tests/nodes/primary_nodes/test_reference.py ......F [ 64%]
tests/nodes/subobjects/test_algorithm.py ..F [ 66%]
tests/nodes/subobjects/test_citation.py ..F [ 69%]
tests/nodes/subobjects/test_computational_forcefield.py ..F [ 71%]
tests/nodes/subobjects/test_condition.py ..F [ 74%]
tests/nodes/subobjects/test_equipment.py ..F [ 76%]
tests/nodes/subobjects/test_ingredient.py ..F [ 79%]
tests/nodes/subobjects/test_parameter.py ..F [ 81%]
tests/nodes/subobjects/test_property.py ..F [ 83%]
tests/nodes/subobjects/test_quantity.py ..F [ 86%]
tests/nodes/subobjects/test_software.py ...F [ 89%]
tests/nodes/subobjects/test_software_configuration.py ..F [ 91%]
tests/nodes/supporting_nodes/test_file.py ..s....F [ 98%]
tests/nodes/supporting_nodes/test_user.py .. [100%]
============================================================================================= short test summary info =============================================================================================
FAILED tests/api/test_search.py::test_api_search_bigsmiles - cript.nodes.exceptions.CRIPTJsonDeserializationError: JSON deserialization failed for node type Material with JSON str: Material
FAILED tests/nodes/primary_nodes/test_collection.py::test_integration_collection - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_computation.py::test_integration_computation - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_computational_process.py::test_integration_computational_process - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_data.py::test_integration_data - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_experiment.py::test_integration_experiment - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_inventory.py::test_integration_inventory - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_material.py::test_integration_material - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_process.py::test_integration_complex_process - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_project.py::test_integration_project - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/primary_nodes/test_reference.py::test_integration_reference - IndexError: list index out of range
FAILED tests/nodes/subobjects/test_algorithm.py::test_integration_algorithm - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_citation.py::test_integration_citation - IndexError: list index out of range
FAILED tests/nodes/subobjects/test_computational_forcefield.py::test_integration_computational_forcefield - AttributeError: 'NoneType' object has no attribute 'description'
FAILED tests/nodes/subobjects/test_condition.py::test_integration_process_condition - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_equipment.py::test_integration_equipment - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_ingredient.py::test_integration_ingredient - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_parameter.py::test_integration_parameter - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_property.py::test_integration_material_property - IndexError: list index out of range
FAILED tests/nodes/subobjects/test_quantity.py::test_integration_quantity - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_software.py::test_integration_software - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/subobjects/test_software_configuration.py::test_integration_software_configuration - AttributeError: 'list' object has no attribute 'starts with'
FAILED tests/nodes/supporting_nodes/test_file.py::test_integration_file - AttributeError: 'list' object has no attribute 'starts with'
======================================================================== 23 failed, 100 passed, 1 skipped, 1 warning in 905.51s (0:15:05) =========================================================================
Assets 2