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Resync main with develop #458

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Resync main with develop #458

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8a3aba2
Merge pull request #334 from C-Accel-CRIPT/develop
nh916 Sep 12, 2023
f5126a6
Merge pull request #400 from C-Accel-CRIPT/develop
nh916 Nov 17, 2023
9a6f28d
Merge pull request #417 from C-Accel-CRIPT/develop
nh916 Nov 17, 2023
75a2ffc
Merge pull request #420 from C-Accel-CRIPT/develop
nh916 Nov 28, 2023
97c7f9c
Merge pull request #447 from C-Accel-CRIPT/release-v2.3.0
InnocentBug Apr 1, 2024
6f574d7
Merge pull request #451 from C-Accel-CRIPT/release-v2.3.0
InnocentBug Apr 1, 2024
2a3fd65
Error to warning (#445)
InnocentBug Mar 25, 2024
3dad218
Update search, so it works with the new `after` syntax. (#456)
InnocentBug May 17, 2024
9fd6a58
version bump
InnocentBug May 20, 2024
cf7f6b0
do changelog
InnocentBug May 20, 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/
Expand Down
5 changes: 4 additions & 1 deletion .trunk/configs/.cspell.json
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Expand Up @@ -123,6 +123,9 @@
"Doctests",
"linenums",
"XLYOFNOQVPJJNP",
"CRIPTUUID"
"CRIPTUUID",
"rootdir",
"startswith",
"pluggy"
]
}
96 changes: 91 additions & 5 deletions CHANGELOG.md
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@@ -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.
Expand All @@ -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.
Expand Down Expand Up @@ -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) =========================================================================
```
````
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/)

Expand Down
6 changes: 3 additions & 3 deletions setup.cfg
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@@ -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
Expand All @@ -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
Expand Down
16 changes: 8 additions & 8 deletions src/cript/api/api.py
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Expand Up @@ -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()

Expand Down Expand Up @@ -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:
"""
Expand Down
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