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Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment. #8561

Merged
merged 10 commits into from
Jul 9, 2024
Merged

Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment. #8561

merged 10 commits into from
Jul 9, 2024

Commits on Jul 9, 2024

  1. Updated Python and PyMC, removed TensorFlow, and added PyTorch in Doc… 

    …ker and conda environments. Notable environment changes: python 3.6.10 -> 3.10.13, pymc 3.1 -> 5.10.0, theano 1.0.4 -> pytensor 2.18.1, added pytorch 2.1.0, removed tensorflow 1.15.0 and other CNN dependencies, added libblas-dev to the base Docker.
    @samuelklee
    samuelklee committed Jul 9, 2024
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  2. Updated gCNV code to account for changes from PyMC3/Theano to PyMC/Py… 

    …Tensor.
    @samuelklee
    samuelklee committed Jul 9, 2024
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  3. Updated gCNV integration tests.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  4. Updated gCNV WDL tests.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  5. Updated other tests and tools affected by environment changes.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  6. Reverted posterior sampling to online implementation.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  7. Updated localDevCondaEnv task in build.gradle.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  8. Addressed review comments and cleaned up TODOs.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  9. Released gatkbase-3.3.0 and updated Dockerfile.

    @samuelklee
    samuelklee committed Jul 9, 2024
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  10. Added DeprecatedFeature tags to CNNScoreVariants, CNNVariantTrain, an… 

    …d CNNVariantWriteTensors.
    @samuelklee
    samuelklee committed Jul 9, 2024
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