use find_spec() instead
WARNI...
# questionsr
Rosana EL-JURDI
10/08/2023, 9:09 PMuse find_spec() instead
WARNING FileFinder.find_loader() is warnings.py:109
deprecated and slated for removal
in Python 3.12; use find_spec()
instead
WARNING the load_module() method is warnings.py:109
deprecated and slated for removal
in Python 3.12; use exec_module()
instead
WARNING find_module() is deprecated and warnings.py:109
slated for removal in Python 3.12;
use find_spec() instead
WARNING FileFinder.find_loader() is warnings.py:109
deprecated and slated for removal
in Python 3.12; use find_spec()
instead
WARNING the load_module() method is warnings.py:109
deprecated and slated for removal
in Python 3.12; use exec_module()
instead
Backend TkAgg is interactive backend. Turning interactive mode on.
================================================================== short test summary info ===================================================================
ERROR src/tests/test_Registration.py - TypeError: AbstractRunner.run() missing 1 required positional argument: 'catalog'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
===================================================================== 1 error in 59.49s ======================================================================
root@c747eee1a373:/usr/src/app#
j
Juan Luis
10/09/2023, 8:25 AMhi @Rosana EL-JURDI ! What version of Kedro and Python are you using?
r
Rosana EL-JURDI
10/09/2023, 9:02 AMkedro, version 0.18.11
Rosana EL-JURDI
10/09/2023, 9:03 AMPython 3.10.11
j
Juan Luis
10/09/2023, 9:12 AMI think the problem is in your
src/tests/test_Registration.pyrunner.run(pipeline)runner.run(pipeline, catalog)r
Rosana EL-JURDI
10/09/2023, 9:13 AMyes I know, the test needs a catalogue
Rosana EL-JURDI
10/09/2023, 9:14 AMbut I do not know how to feed the original catalogue to the test
Rosana EL-JURDI
10/09/2023, 9:14 AMI tried with kedro.context but
Rosana EL-JURDI
10/09/2023, 9:14 AMI think it isnt compatible with my version of kedro
Rosana EL-JURDI
10/09/2023, 9:16 AMThis is the error I am currently running into:
---------- coverage: platform linux, python 3.10.11-final-0 ----------
Name Stmts Miss Cover Missing
----------------------------------------------------------------------------------------------------
src/ai4pet_tracking/__init__.py 1 0 100%
src/ai4pet_tracking/__main__.py 30 30 0% 4-47
src/ai4pet_tracking/datasets/__init__.py 0 0 100%
src/ai4pet_tracking/datasets/nifti_dataset.py 21 21 0% 1-34
src/ai4pet_tracking/datasets/npy_dataset.py 17 17 0% 1-28
src/ai4pet_tracking/datasets/sitk_transform_dataset.py 10 10 0% 1-16
src/ai4pet_tracking/pipeline_registry.py 10 10 0% 2-21
src/ai4pet_tracking/pipelines/Registration/Registration_Functions.py 119 119 0% 2-277
src/ai4pet_tracking/pipelines/Registration/__init__.py 3 3 0% 6-10
src/ai4pet_tracking/pipelines/Registration/base_registrator.py 26 26 0% 1-119
src/ai4pet_tracking/pipelines/Registration/demons_registrator.py 54 54 0% 1-201
src/ai4pet_tracking/pipelines/Registration/nodes.py 111 111 0% 6-281
src/ai4pet_tracking/pipelines/Registration/pipeline.py 6 6 0% 5-17
src/ai4pet_tracking/pipelines/Registration/rigid_registrator.py 49 49 0% 1-130
src/ai4pet_tracking/pipelines/__init__.py 0 0 100%
src/ai4pet_tracking/pipelines/dataloader/__init__.py 3 0 100%
src/ai4pet_tracking/pipelines/dataloader/nodes.py 35 19 46% 57-184, 205-211
src/ai4pet_tracking/pipelines/dataloader/pipeline.py 4 1 75% 12
src/ai4pet_tracking/pipelines/dataloader/transforms.py 51 41 20% 20-21, 27-38, 55-125
src/ai4pet_tracking/pipelines/dataloader/utils.py 15 15 0% 3-46
src/ai4pet_tracking/settings.py 3 3 0% 25-28
----------------------------------------------------------------------------------------------------
TOTAL 568 535 6%
========================================================================== short test summary info ===========================================================================
ERROR src/tests/test_Registration.py - TypeError: ConfigLoader.__init__() got an unexpected keyword argument 'config_file'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================== 1 error in 4.29s ==============================================================================
Rosana EL-JURDI
10/09/2023, 9:17 AMThis is the script:
import pytest
from kedro.runner.sequential_runner import SequentialRunner
from kedro.config import ConfigLoader
from src.ai4pet_tracking.pipelines.dataloader.nodes import create_dataloaders
from kedro.pipeline import Pipeline, node, pipeline
from kedro.io import DataCatalog
from kedro.config import ConfigLoader
# Load catalog configuration from catalog.yml
conf_loader = ConfigLoader(config_file="catalog/usr/src/app/conf/base/catalog/Registration.yml")
catalog_config = conf_loader.get("catalog*")
# Create DataCatalog using the loaded catalog configuration
data_catalog = DataCatalog.from_config(catalog_config)
# Define your pipeline
def create_pipeline(data_catalog, **kwargs):
return Pipeline([
node(
func=create_dataloaders,
inputs=...
# Add more nodes as needed
])
test_pipeline = create_pipeline(data_catalog)
j
Juan Luis
10/09/2023, 12:20 PMlet's continue that in the other thread https://kedro-org.slack.com/archives/C03RKP2LW64/p1696852857693499?thread_ts=1696842604.595909&cid=C03RKP2LW64
r
Rosana EL-JURDI
10/09/2023, 12:22 PMHello,