Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Release 2.4.0 #457

Merged
merged 5 commits into from
May 20, 2024
Merged

Release 2.4.0 #457

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
fb804ed
Error to warning (#445)
InnocentBug Mar 25, 2024
306428c
Merge pull request #450 from C-Accel-CRIPT/release-v2.3.0
InnocentBug Apr 1, 2024
dd4004f
Update search, so it works with the new `after` syntax. (#456)
InnocentBug May 17, 2024
78cd694
version bump
InnocentBug May 20, 2024
4693b7c
do changelog
InnocentBug May 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,9 @@
"Doctests",
"linenums",
"XLYOFNOQVPJJNP",
"CRIPTUUID"
"CRIPTUUID",
"rootdir",
"startswith",
"pluggy"
]
}
96 changes: 91 additions & 5 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Loading
Loading