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V0.1.2 #55

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kasinadhsarma opened this issue Sep 9, 2024 · 4 comments · Fixed by #59, #64, #68, #72 or #73
Closed

V0.1.2 #55

kasinadhsarma opened this issue Sep 9, 2024 · 4 comments · Fixed by #59, #64, #68, #72 or #73
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(neuroflexenv) ubuntu@ip-10-240-215-184:~/NeuroFlex$ source neuroflexenv/bin/activate && export PYTHONPATH=$(pwd) && pytest tests/ --disable-warnings --maxfail=1
============================= test session starts ==============================
platform linux -- Python 3.12.5, pytest-8.3.2, pluggy-1.5.0
rootdir: /home/ubuntu/NeuroFlex
configfile: pytest.ini
collected 161 items

tests/advanced_models/test_advanced_math_solving.py .ss............ [ 9%]
tests/advanced_models/test_advanced_time_series_analysis.py ............ [ 16%]
............. [ 24%]
tests/advanced_models/test_multi_modal_learning.py ........s. [ 31%]
tests/advanced_models/test_neural_networks.py ...... [ 34%]
tests/advanced_models/test_reinforcement_learning.py ...... [ 38%]
tests/advanced_models/test_reinforcement_learning_advancements.py ...... [ 42%]
...s [ 44%]
tests/cognitive_architectures/test_advanced_thinking.py ........ [ 49%]
tests/cognitive_architectures/test_cognitive_architectures.py .s..s..s [ 54%]
tests/edge_ai/test_edge_ai_optimization.py ..s...ss..s [ 61%]
tests/edge_ai/test_neuromorphic_computing.py ........ [ 66%]
tests/scientific_domains/bioinformatics/test_bioinformatics_integration.py . [ 67%]
.ss. [ 69%]
tests/scientific_domains/bioinformatics/test_ete_integration.py ssssss [ 73%]
tests/scientific_domains/bioinformatics/test_scikit_bio_integration.py s [ 73%]
ss.ss [ 77%]
tests/scientific_domains/biology/test_synthetic_biology_insights.py ...s [ 79%]
s [ 80%]
tests/scientific_domains/test_alphafold_integration.py s.s..s.ss [ 85%]
tests/scientific_domains/test_art_integration.py sssss [ 88%]
tests/scientific_domains/test_google_integration.py ssssssss [ 93%]
tests/scientific_domains/test_math_solvers.py ...... [ 97%]
tests/scientific_domains/test_xarray_integration.py .... [100%]

================ 117 passed, 44 skipped, 28 warnings in 43.45s ================= fixes in future and devlopment
@kasinadhsarma kasinadhsarma self-assigned this Sep 9, 2024
@kasinadhsarma kasinadhsarma added the coder Devin(the software Devloper) label Sep 9, 2024
@kasinadhsarma kasinadhsarma linked a pull request Sep 12, 2024 that will close this issue
Enhance AlphaFold Integration with OpenMM and Unit Tests #59
Merged
@kasinadhsarma kasinadhsarma reopened this Sep 13, 2024
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(neuroflex-env) ubuntu@ip-10-240-234-255:~/NeuroFlex$ pytest
============================= test session starts ==============================
platform linux -- Python 3.8.12, pytest-8.3.3, pluggy-1.5.0
rootdir: /home/ubuntu/NeuroFlex
configfile: pytest.ini
testpaths: tests
collected 184 items

tests/advanced_models/test_advanced_math_solving.py .ss............ [ 8%]
tests/advanced_models/test_advanced_time_series_analysis.py ............ [ 14%]
............. [ 21%]
tests/advanced_models/test_multi_modal_learning.py ........s. [ 27%]
tests/advanced_models/test_neural_networks.py ...... [ 30%]
tests/advanced_models/test_reinforcement_learning.py ...... [ 33%]
tests/advanced_models/test_reinforcement_learning_advancements.py ...... [ 36%]
...s [ 39%]
tests/cognitive_architectures/test_advanced_thinking.py ........ [ 43%]
tests/cognitive_architectures/test_cognitive_architectures.py .s..s..s [ 47%]
tests/edge_ai/test_edge_ai_optimization.py ..s...ss..s [ 53%]
tests/edge_ai/test_neuromorphic_computing.py ........ [ 58%]
tests/scientific_domains/bioinformatics/test_bioinformatics_integration.py . [ 58%]
.ss. [ 60%]
tests/scientific_domains/bioinformatics/test_ete_integration.py ssssss [ 64%]
tests/scientific_domains/bioinformatics/test_scikit_bio_integration.py s [ 64%]
ss.ss [ 67%]
tests/scientific_domains/biology/test_synthetic_biology_insights.py ...s [ 69%]
s [ 70%]
tests/scientific_domains/test_alphafold_integration.py sss.s....s.sss. [ 78%]
tests/scientific_domains/test_art_integration.py sssss [ 80%]
tests/scientific_domains/test_google_integration.py ssssssss [ 85%]
tests/scientific_domains/test_math_solvers.py ...... [ 88%]
tests/scientific_domains/test_xarray_integration.py .... [ 90%]
tests/test_core_components.py ................. [100%]

=============================== warnings summary ===============================
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[arima]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/statespace/sarimax.py:966: UserWarning: Non-stationary starting autoregressive parameters found. Using zeros as starting parameters.
warn('Non-stationary starting autoregressive parameters'

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[arima]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/statespace/sarimax.py:978: UserWarning: Non-invertible starting MA parameters found. Using zeros as starting parameters.
warn('Non-invertible starting MA parameters found.'

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/NeuroFlex/advanced_models/advanced_time_series_analysis.py:213: UserWarning: Non-invertible starting MA parameters found. Using zeros as starting parameters.
warnings.warn("Non-invertible starting MA parameters found. Using zeros as starting parameters.", UserWarning)

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/statespace/mlemodel.py:3015: RuntimeWarning: invalid value encountered in divide
return self.params / self.bse

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/stattools.py:1420: RuntimeWarning: invalid value encountered in divide
test_statistic = numer_squared_sum / denom_squared_sum

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/stattools.py:693: RuntimeWarning: invalid value encountered in divide
acf = avf[: nlags + 1] / avf[0]

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/base/model.py:607: ConvergenceWarning: Maximum Likelihood optimization failed to converge. Check mle_retvals
warnings.warn("Maximum Likelihood optimization failed to "

tests/edge_ai/test_edge_ai_optimization.py::TestEdgeAIOptimization::test_model_compression
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/torch/ao/quantization/observer.py:214: UserWarning: Please use quant_min and quant_max to specify the range for observers. reduce_range will be deprecated in a future release of PyTorch.
warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================ 137 passed, 47 skipped, 27 warnings in 37.31s =================

@kasinadhsarma
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(neuroflex-env) ubuntu@ip-10-240-234-255:~/NeuroFlex$ pytest
============================= test session starts ==============================
platform linux -- Python 3.8.12, pytest-8.3.3, pluggy-1.5.0
rootdir: /home/ubuntu/NeuroFlex
configfile: pytest.ini
testpaths: tests
collected 184 items

tests/advanced_models/test_advanced_math_solving.py ............... [ 8%]
tests/advanced_models/test_advanced_time_series_analysis.py ............ [ 14%]
............. [ 21%]
tests/advanced_models/test_multi_modal_learning.py ........s. [ 27%]
tests/advanced_models/test_neural_networks.py ...... [ 30%]
tests/advanced_models/test_reinforcement_learning.py ...... [ 33%]
tests/advanced_models/test_reinforcement_learning_advancements.py ...... [ 36%]
...s [ 39%]
tests/cognitive_architectures/test_advanced_thinking.py ........ [ 43%]
tests/cognitive_architectures/test_cognitive_architectures.py .s..s..s [ 47%]
tests/edge_ai/test_edge_ai_optimization.py ..s...ss..s [ 53%]
tests/edge_ai/test_neuromorphic_computing.py ........ [ 58%]
tests/scientific_domains/bioinformatics/test_bioinformatics_integration.py . [ 58%]
.ss. [ 60%]
tests/scientific_domains/bioinformatics/test_ete_integration.py ssssss [ 64%]
tests/scientific_domains/bioinformatics/test_scikit_bio_integration.py s [ 64%]
ss.ss [ 67%]
tests/scientific_domains/biology/test_synthetic_biology_insights.py ...s [ 69%]
s [ 70%]
tests/scientific_domains/test_alphafold_integration.py sss.s....s.sss. [ 78%]
tests/scientific_domains/test_art_integration.py sssss [ 80%]
tests/scientific_domains/test_google_integration.py ssssssss [ 85%]
tests/scientific_domains/test_math_solvers.py ...... [ 88%]
tests/scientific_domains/test_xarray_integration.py .... [ 90%]
tests/test_core_components.py ................. [100%]

=============================== warnings summary ===============================
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/NeuroFlex/advanced_models/advanced_time_series_analysis.py:213: UserWarning: Non-invertible starting MA parameters found. Using zeros as starting parameters.
warnings.warn("Non-invertible starting MA parameters found. Using zeros as starting parameters.", UserWarning)

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/statespace/mlemodel.py:3015: RuntimeWarning: invalid value encountered in divide
return self.params / self.bse

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/stattools.py:1420: RuntimeWarning: invalid value encountered in divide
test_statistic = numer_squared_sum / denom_squared_sum

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_valid_methods[sarima]
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_sarima_forecast
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/tsa/stattools.py:693: RuntimeWarning: invalid value encountered in divide
acf = avf[: nlags + 1] / avf[0]

tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order2-seasonal_order2-data2]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
tests/advanced_models/test_advanced_time_series_analysis.py::test_analyze_different_configurations[sarima-order3-seasonal_order3-data3]
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/statsmodels/base/model.py:607: ConvergenceWarning: Maximum Likelihood optimization failed to converge. Check mle_retvals
warnings.warn("Maximum Likelihood optimization failed to "

tests/edge_ai/test_edge_ai_optimization.py::TestEdgeAIOptimization::test_model_compression
/home/ubuntu/NeuroFlex/neuroflex-env/lib/python3.8/site-packages/torch/ao/quantization/observer.py:214: UserWarning: Please use quant_min and quant_max to specify the range for observers. reduce_range will be deprecated in a future release of PyTorch.
warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================ 139 passed, 45 skipped, 25 warnings in 40.29s =================

@kasinadhsarma kasinadhsarma linked a pull request Sep 14, 2024 that will close this issue
Fix pytest errors and update compatibility checks #64
Merged
@kasinadhsarma kasinadhsarma pinned this issue Sep 15, 2024
@kasinadhsarma kasinadhsarma moved this from Done to In Progress in Intro Era Sep 15, 2024
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kasinadhsarma commented Sep 15, 2024 •
edited
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(neuroflex-env) ubuntu@ip-10-240-214-91:~/NeuroFlex$ pytest
============================= test session starts ==============================
platform linux -- Python 3.8.12, pytest-8.3.3, pluggy-1.5.0
rootdir: /home/ubuntu/NeuroFlex
configfile: pytest.ini
testpaths: tests
collected 184 items

tests/advanced_models/test_advanced_math_solving.py ............... [ 8%]
tests/advanced_models/test_advanced_time_series_analysis.py ............ [ 14%]
............. [ 21%]
tests/advanced_models/test_multi_modal_learning.py ........s. [ 27%]
tests/advanced_models/test_neural_networks.py ...... [ 30%]
tests/advanced_models/test_reinforcement_learning.py ...... [ 33%]
tests/advanced_models/test_reinforcement_learning_advancements.py ...... [ 36%]
...s [ 39%]
tests/cognitive_architectures/test_advanced_thinking.py ........ [ 43%]
tests/cognitive_architectures/test_cognitive_architectures.py .s..s..s [ 47%]
tests/edge_ai/test_edge_ai_optimization.py ..s...ss..s [ 53%]
tests/edge_ai/test_neuromorphic_computing.py ........ [ 58%]
tests/scientific_domains/bioinformatics/test_bioinformatics_integration.py . [ 58%]
.ss. [ 60%]
tests/scientific_domains/bioinformatics/test_ete_integration.py ...... [ 64%]
tests/scientific_domains/bioinformatics/test_scikit_bio_integration.py . [ 64%]
..... [ 67%]
tests/scientific_domains/biology/test_synthetic_biology_insights.py ...s [ 69%]
s [ 70%]
tests/scientific_domains/test_alphafold_integration.py sss.s....s.sss. [ 78%]
tests/scientific_domains/test_art_integration.py sssss [ 80%]
tests/scientific_domains/test_google_integration.py ssssssss [ 85%]
tests/scientific_domains/test_math_solvers.py ...... [ 88%]
tests/scientific_domains/test_xarray_integration.py .... [ 90%]
tests/test_core_components.py ................. [100%]

================ 150 passed, 34 skipped, 26 warnings in 50.33s =================

@kasinadhsarma kasinadhsarma linked a pull request Sep 15, 2024 that will close this issue
Enhancements to multi-modal learning and test fixes #68
Merged
@kasinadhsarma
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============================= test session starts ==============================
platform linux -- Python 3.8.18, pytest-8.3.3, pluggy-1.5.0
rootdir: /home/runner/work/NeuroFlex/NeuroFlex
configfile: pytest.ini
collected 216 items
tests/advanced_models/test_advanced_math_solving.py ............... [ 6%]
tests/advanced_models/test_advanced_time_series_analysis.py ............ [ 12%]
............. [ 18%]
tests/advanced_models/test_multi_modal_learning.py ........s. [ 23%]
tests/advanced_models/test_neural_networks.py ...... [ 25%]
tests/advanced_models/test_reinforcement_learning.py ...... [ 28%]
tests/advanced_models/test_reinforcement_learning_advancements.py ...... [ 31%]
...s [ 33%]
tests/ai_ethics/test_ai_ethics.py .....s [ 36%]
tests/cognitive_architectures/test_advanced_thinking.py ........ [ 39%]
tests/cognitive_architectures/test_cognitive_architectures.py .s..s..s [ 43%]
tests/edge_ai/test_edge_ai_optimization.py ..s...ss..s [ 48%]
tests/edge_ai/test_neuromorphic_computing.py ........ [ 52%]
tests/scientific_domains/bioinformatics/test_bioinformatics_integration.py . [ 52%]
.ss. [ 54%]
tests/scientific_domains/bioinformatics/test_ete_integration.py ...... [ 57%]
tests/scientific_domains/bioinformatics/test_scikit_bio_integration.py . [ 57%]
..... [ 60%]
tests/scientific_domains/biology/test_synthetic_biology_insights.py .... [ 62%]
s [ 62%]
tests/scientific_domains/test_alphafold_integration.py sss.s....s.sss. [ 69%]
tests/scientific_domains/test_art_integration.py ..... [ 71%]
tests/scientific_domains/test_google_integration.py ...s.. [ 74%]
tests/scientific_domains/test_math_solvers.py ...... [ 77%]
tests/scientific_domains/test_protein_development.py ......s. [ 81%]
tests/scientific_domains/test_transformers.py .s.s... [ 84%]
tests/scientific_domains/test_xarray_integration.py .... [ 86%]
tests/test_core_components.py ................. [ 93%]
tests/test_security_integration.py ............s [100%]
================ 190 passed, 26 skipped, 57 warnings in 33.79s =================

@github-project-automation github-project-automation bot moved this from In Progress to Done in Intro Era Sep 16, 2024
This was linked to pull requests Sep 16, 2024
Enhance AI ethics tests and refactor SelfCuringRLAgent #72
Merged
Skip tests due to missing AlphaFold data files #73
Merged
Remove protein development LLM #75
Merged
Integrate UnifiedTransformer into NeuroFlex #76
Merged
Integrated AI-driven Security Features into NeuroFlex Project #77
Merged
Merge AI Security Enhancements #78
Merged
Add Comprehensive Documentation #79
Merged
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