Version 2.4.0

Version 2.4.0

New Features

• cript.API searches work as intended.
• SDK initiated searches can be controlled and interrupted for large queries.

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.
• 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.
• BigSMILES searches can contain duplicates.

Bug Fixes

• Search is now matched with the API requirements.

Breaking Changes

• The Paginator interface changed to reflect the backend requirements.

Version 2.3.0

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) =========================================================================

v2.2.0

Changes

CI Upgrades

• using Python 12 for CI jobs that require a single python version
• CI runs Python 3.8 and 3.12

Documentation

• added more sections to FAQ docs and fixed spelling errors
• all code examples have been correct and I included CI into it
  • added doctest to all code examples
• added wiki documentation link to README.md
• fixed any missing/broken controlled vocabulary links
• added BaseNode, UUIDBaseNode, and PrimaryBaseNode to documentation
  • in future releases, full documentation will be written for all the methods/functions/attributes of the base classes along with code examples with full doctest
• wrote documentation for CRIPTDuplicateNameError exception & improved error message

Tests

• renamed integrate_nodes_helper to save_integration_node_helper
• reorganizing utility functions into test/utils/
• made tests/ into a package to be easily imported in tests
• created dynamic_material_data fixture for tests
• testing notes attribute within all nodes
• made error documentation headings more standard
  • from "How to Fix" to "Troubleshooting"

API Class

• refactored get_s3_client into a function in a aws_s3_utils.py file
• wrote docs for _prepare_host so it is clearer for future maintenance

Paginator

• improved paginator error if API returns anything other than HTTP 200

Nodes

File Node

• requiring file extension for the node

Material node

• removed redundant Material name getter and setter

General

• upgraded requirements.txt, requirements_docs.txt, requirements_dev.txt
• CRIPT Python SDK requires Python 3.8+ as Python 3.7 has been depreciated
• refactored APIError to be cleaner/more maintainable and gives better error
  • upgraded the documentation for it with Steps to try:
• removed previously unfinished TODO comments

Feature

• wrote API.delete_node_by_uuid(node_type, node_uuid) with docs and tests
• wrote cript.API.get_node_by_uuid(uuid) with full docs and tests
  • reasoning for removing this feature before releasing it
    • essentially it was not robust and will lead to breaking changes in the near future
• load_nodes_from_json works with both str and dict args, updated documentation for that
• added feature to get expanded JSON without UUID
  • wrote feature, wrote comments, documentation, type hinting, doctests, and unit tests
• wrote feature to skip validation
  • useful for when wanting to skip validations that slow the program down

Breaking Changes

The SDK will only work with Python 3.8 or higher as 3.7 has been depreciated

Acknowledgments 🎉

Big thanks to @InnocentBug for volunteering to help with the CRIPT Python SDK since its inception and continuing to add features, improve the SDK, and provide valuable support.

Full Changelog: v2.1.0...v2.2.0

v2.1.0

Release Notes

cript.API.delete()

• Introduced a new feature, cript.API.delete() to delete nodes from the API
  • wrote comprehensive documentation on how to delete a node from the API using the SDK cript.API.delete() method
  • fully tested cript.API.delete() via integration tests covering primary nodes, supporting nodes, and sub-objects.

Documentation

• upgraded/updated documentation for clarity and accuracy
• updated some outdated code examples
• updated outdated or wrong attributes tables
• fixed some broken links to CRIPT controlled vocabulary
• added a warning to the landing page of the CRIPT Python SDK documentation that CRIPT is only available in the USA
  • added that warning to the README as well

BigSmiles Search

• added BIGSMILES SearchMode to the SDK cript.API.search()
  • added some validation and nice error handling for it
  • tested with integration tests to verify and validate that it is working correctly

Material identifiers to identifier

• refactored cript.Material attribute from identifiers to identifier
  • all attributes on all nodes were singular, and this was refactored to be consistent with the rest of the SDK
  • updated documentation, code examples, and all tests for the SDK

cript.API.logger

• upgraded logger code within cript.API to log every time:
  • a node was validated against the DB Schema
  • a file was successfully uploaded to cloud storage
  • a node was successfully deleted from the API
• improved documentation for cript.API.logger and verbose attribute as well
  • provided terminal output examples and code examples for clarity

Error Handling

• found new static type errors with new version of mypy and fixed those
• upgraded error messages for better error handling for many requests including encountering an error when getting the DB Schema, paginator search errors, and cript.API.get_vocab_by_category()
• added better context to cript.API.search() in case an invalid SearchMode was entered
• upgraded API Duplicate Name error message

Miscellaneous

• updated outdated packages
• updated CI/CD and all tests to use staging CRIPT environment
• resolved some trunk CI spelling errors from cspell
• renamed the trunk workflow from CI to Trunk.io to be more descriptive
• added _API_TIMEOUT to all HTTP requests

Notes

• This is the last version of the CRIPT Python SDK that will support Python 3.7
  • Python 3.7 is now deprecated and we encourage everyone to upgrade to Python 3.8 or higher

Credits

Big thanks to @InnocentBug for helping with the CRIPT Python SDK

v2.0.0

What's Changed

• CRIPT Python SDK 2.0 First Release by @nh916 in #272

Full Changelog: https://github.com/C-Accel-CRIPT/Python-SDK/commits/v2.0.0