C-Accel-CRIPT · InnocentBug · May 20, 2024 · Mar 25, 2024 · Apr 1, 2024 · May 17, 2024
diff --git a/.github/workflows/tests.yml b/.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/

diff --git a/.trunk/configs/.cspell.json b/.trunk/configs/.cspell.json
@@ -123,6 +123,9 @@
  "Doctests",
  "linenums",
  "XLYOFNOQVPJJNP",
- "CRIPTUUID"
+ "CRIPTUUID",
+ "rootdir",
+ "startswith",
+ "pluggy"
  ]
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,94 @@
 # CRIPT Python SDK Changelog
 
+## 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.
+
+### Health Report
+
+````shell
+=============================================================================================== test session starts ===============================================================================================
+platform linux -- Python 3.11.2, pytest-7.4.3, pluggy-1.3.0
+rootdir: /home/ludwig/git/Python-SDK
+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 ..
+
+FAILED tests/nodes/primary_nodes/test_collection.py::test_integration_collection - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_computation.py::test_integration_computation - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_computational_process.py::test_integration_computational_process - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_data.py::test_integration_data - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_experiment.py::test_integration_experiment - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_inventory.py::test_integration_inventory - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_material.py::test_integration_material - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_process.py::test_integration_complex_process - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/primary_nodes/test_project.py::test_integration_project - AttributeError: 'list' object has no attribute 'startswith'
+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 'startswith'
+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 'startswith'
+FAILED tests/nodes/subobjects/test_equipment.py::test_integration_equipment - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/subobjects/test_ingredient.py::test_integration_ingredient - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/subobjects/test_parameter.py::test_integration_parameter - AttributeError: 'list' object has no attribute 'startswith'
+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 'startswith'
+FAILED tests/nodes/subobjects/test_software.py::test_integration_software - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/subobjects/test_software_configuration.py::test_integration_software_configuration - AttributeError: 'list' object has no attribute 'startswith'
+FAILED tests/nodes/supporting_nodes/test_file.py::test_integration_file - AttributeError: 'list' object has no attribute 'startswith'
+======================================================================== 22 failed, 101 passed, 1 skipped, 1 warning in 1506.18s (0:25:06) ========================================================================
+
+
+
 ## Version 2.3.0
 
-**New Features:**
+### 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.
@@ -19,22 +105,22 @@
 - 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:**
+### 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:**
+### 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:**
+### 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.
@@ -102,4 +188,4 @@ FAILED tests/nodes/subobjects/test_software.py::test_integration_software - Attr
 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) =========================================================================
-```
+````
diff --git a/README.md b/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/)
 

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = cript
-version = 2.3.0
+version = 2.4.0
 description = CRIPT Python SDK
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -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

diff --git a/src/cript/api/api.py b/src/cript/api/api.py
@@ -258,6 +258,9 @@ def _init_logger(self, log_level=logging.INFO) -> None:
 
  logger.setLevel(log_level)
 
+ # Activate Warning handling
+ logging.captureWarnings(True)
+
  # Create a console handler
  console_handler = logging.StreamHandler()
 
@@ -784,35 +787,32 @@ def search(
  node_type = node_type.node_type_snake_case
 
  api_endpoint: str = ""
- page_number: Union[int, None] = None
-
+ limit_node_fetches: Optional[int] = None
  if search_mode == SearchModes.NODE_TYPE:
  api_endpoint = f"/search/{node_type}"
- page_number = 0
+ value_to_search = ""
 
  elif search_mode == SearchModes.CONTAINS_NAME:
  api_endpoint = f"/search/{node_type}"
- page_number = 0
 
  elif search_mode == SearchModes.EXACT_NAME:
  api_endpoint = f"/search/exact/{node_type}"
- page_number = None
+ limit_node_fetches = 1
 
  elif search_mode == SearchModes.UUID:
  api_endpoint = f"/{node_type}/{value_to_search}"
  # putting the value_to_search in the URL instead of a query
  value_to_search = ""
- page_number = None
+ limit_node_fetches = 1
 
  elif search_mode == SearchModes.BIGSMILES:
  api_endpoint = "/search/bigsmiles/"
- page_number = 0
 
  # error handling if none of the API endpoints got hit
  else:
  raise RuntimeError("Internal Error: Failed to recognize any search modes. Please report this bug on https://github.com/C-Accel-CRIPT/Python-SDK/issues.")
 
- return Paginator(api=self, url_path=api_endpoint, page_number=page_number, query=value_to_search)
+ return Paginator(api=self, url_path=api_endpoint, query=value_to_search, limit_node_fetches=limit_node_fetches)
 
  def delete(self, node) -> None:
  """