Develop #276
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Develop #276
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…d more self documenting
Setup all nodes
if there is no URL/UID then the URL/UID string is empty
remove disclaimer from README
* refactored all of SDK to use `identifier` instead of `identifiers` * updated documentation and code examples to use `identifier` * updated tests to use `identifier` * all tests are passing * removed unneeded test for test_file.py * fixed broken vocab links within documentation * fixed broken vocab links within documentation * formatted with black
A little small section that CRIPT only works in USA, so users are aware
* upgraded mypy, found errors, fixed errors * formatted with black
* upgraded documentation with many search examples and changed `value_to_search` from `Union[None, str]` to `Optional[str],` * added `BIG_SMILES` to `SearchModes` and added documentation * wrote `test_api_search_bigsmiles` * added `"BCDB"` to .cspell.json * feature: search by bigsmiles and test for it are done! * changing `BIG_SMILES` to `BIGSMILES` * formatted with black
upgraded requirements
* Catching and identifying the situations where a duplicate Name is the issue in a save * introduce an inherent Error for duplicated names * upgrading reliability and no reference to namespaces anymore.
* fixed `_API_TIMEOUT` circular import error * formatted with black * added type hinting to `_API_TIMEOUT`
* fixed SearchMode from `BIG_SMILES` to `BIGSMILES` * after refactoring this was left out, but it is now tested and working * changed timeout from `25` to `90` * I think it might still be too small
…tting any SearchModes (#305) Gave some more context as to what could be happening for the user and helping the user report it to us. Using else instead of an `if` to catch all cases not caught by the `if`
…on (#303) * added `name` to file node docs attributes table * updated file docs JSON representation
fixed `BIGSMILES` search test
lowering coverage CI because it does not account for integration tests
* upgrade paginator.py error handling for response JSON conversion * added new variable for JSON response `api_response` added comments explaining the error handling * formatted with trunk
* started working on delete
* wrote basic delete method
* not tested yet
* wrote basic refresh
* not tested yet
* wrote test for refresh
* but not finished yet
* setup `_set_logger` method for `cript.API`
* added `Notes` to delete docstrings
* refactored `logger` and `verbose`
* removed unused imports and formatted with black
* ignoring mypy error
mypy says that the `logger: logging.Logger = None` this cannot be None because you said it should be `logging.Logger` but before it is initialized it would be None.
Don't want to type it as `Optional` because it should always exist and it is not Optional, so just ignoring the error for now.
* formatting with black and removing unused imports
* removing `cript.API.refresh()` method for now
will add in later if needed
* format with trunk
* changed logging format of `cript.API.delete`
* changed the error for paginator from generic `Exception` to `APIError`
* wrote `DELETE` for test_project.py
* wrote out logic for `integrate_delete_node_helper`
* wrote out logic and docstrings for `integrate_delete_node_helper`
* wrote notes for future upgrades
* ready to write tests for every node
* updated `test_project.py` comment
* added type hinting to paginator.py `response`
* wrote out `delete_integration_node_helper`
* wrote out full test function for `delete_integration_node_helper` in integration_test_helper.py
* cleaned up test_project.py test code
> wrote a small snippet for my printing JSON preference
* updated comments
* updated `test_integration_collection`
* wrote Delete integration test for collection
* wrote Delete integration test for experiment
* wrote Delete integration test for process
* wrote Delete integration test for computation
* fixed `delete integration function` imports for tests since it is not a package
* wrote Delete integration test for data
* wrote Delete integration test for inventory
* wrote Delete integration test for file
* wrote Delete integration test for algorithm
* updated docstrings for clarity in `delete_integration_node_helper`
* wrote Delete integration test for citation
passing successfully!
* wrote Delete integration test for condition
passing successfully!
* wrote Delete integration test for equipment
passing successfully!
* wrote Delete integration test for ingredient
passing successfully!
* wrote Delete integration test for parameter
passing successfully!
* wrote Delete integration test for quantity
passing successfully!
* wrote Delete integration test for Software
passing successfully!
* wrote Delete integration test for Software
passing successfully!
* wrote Delete integration test for Software
passing successfully!
* wrote Delete integration test for Reference
passing successfully!
* upgraded/refactored `APIError`
* `APIError` did not have as much information and was unhelpful in debugging
* gave it more information and made it much more helpful for users to read and for us to debug
* bug fix: changed delete URL to `node_type_snake_case` instead of node_type
* `node_type` was not working for `Computational_Forcefield` because API Endpoint expected snake_case
* wrote and successfully passing computational_forcefield DELETE
* wrote and successfully passing `computational_process` DELETE
* upgraded paginator errors
* wrote DELETE tests for `material`, `project`, `property`
API is having trouble with them
* fixed mypy static typing errors
* formatted with black
* removed unused import
* formatted with trunk
* formatted with trunk
* fixed imports with isort
* formatted with trunk
* working on fixing CI issues
* optimizing imports
* upgraded documentation for `cript.API.delete()`
* trunk fmt
* updated `cript.API.delete()` documentation
* updated host documentation in `cript.API`
* upgraded documentation for `cript.API.verobose`
added example code and example log
* fixed `BIGSMILES` search test
* removed `Navid log style` from integration_test_helper.py
added comments to code for clarity
* formatted with trunk
* importing `Optional` to cript/api/exceptions.py
* formatted with trunk
* added `timeout` to `requests.delete()`
* fixed import error
* formatted with trunk
* making trunk happy
---------
Co-authored-by: Ludwig Schneider <[email protected]>
* upgraded error for `get_vocab_by_category()` * formatted with trunk
…figuration-test Updated delete `software_configuration` integration test to expect deletion and not an API error
fixed test_computational_forcefield.py file name typo
upgraded packages in `requirements.txt` and `setup.cfg`
|
closing this in favor of new PR for a new release of v2.1.0 |
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Description
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Checklist
CONTRIBUTORS.md) in the pull request source branch.