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Deployment testing #569

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May 24, 2024
Merged

Deployment testing #569

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b1ddf02
redeploy
lucidtronix May 23, 2024
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lucidtronix May 24, 2024
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lucidtronix May 24, 2024
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17 changes: 5 additions & 12 deletions notebooks/ML4H_Model_Factory_Intro.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -29,25 +29,18 @@
"import sys\n",
"import pickle\n",
"import gzip\n",
"from typing import List, Dict, Callable\n",
"from collections import defaultdict, Counter\n",
"from typing import Dict\n",
"\n",
"import h5py\n",
"import numpy as np\n",
"\n",
"\n",
"from ml4h.defines import StorageType\n",
"from ml4h.arguments import parse_args\n",
"from ml4h.TensorMap import TensorMap, Interpretation\n",
"from ml4h.tensor_generators import test_train_valid_tensor_generators\n",
"from ml4h.models.train import train_model_from_generators\n",
"from ml4h.models.model_factory import make_multimodal_multitask_model\n",
"from ml4h.models.inspect import plot_and_time_model\n",
"from ml4h.recipes import compare_multimodal_scalar_task_models, train_multimodal_multitask\n",
"\n",
"%matplotlib inline\n",
"import matplotlib.pyplot as plt\n",
"from matplotlib import gridspec"
"%matplotlib inline"
]
},
{
Expand Down Expand Up @@ -203,7 +196,7 @@
"sys.argv = ['train', \n",
" '--tensors', HD5_FOLDER, \n",
" '--input_tensors', 'mnist.mnist_image',\n",
" '--output_tensors', 'mnit.mnist_label',\n",
" '--output_tensors', 'mnist.mnist_label',\n",
" '--batch_size', '16',\n",
" '--epochs', '12',\n",
" '--output_folder', OUTPUT_FOLDER,\n",
Expand All @@ -215,7 +208,7 @@
"sys.argv = ['train',\n",
" '--tensors', HD5_FOLDER,\n",
" '--input_tensors', 'mnist.mnist_image',\n",
" '--output_tensors', 'mnit.mnist_label',\n",
" '--output_tensors', 'mnist.mnist_label',\n",
" '--activation', 'mish',\n",
" '--dense_blocks', '64', '64', '64',\n",
" '--batch_size', '16',\n",
Expand Down Expand Up @@ -243,7 +236,7 @@
"sys.argv = ['compare_scalar', \n",
" '--tensors', HD5_FOLDER, \n",
" '--input_tensors', 'mnist.mnist_image',\n",
" '--output_tensors', 'mnit.mnist_label',\n",
" '--output_tensors', 'mnist.mnist_label',\n",
" '--id', 'mnist_model_comparison',\n",
" '--output_folder', OUTPUT_FOLDER,\n",
" '--model_files', f'{OUTPUT_FOLDER}learn_2d_cnn/learn_2d_cnn.h5',\n",
Expand Down
8 changes: 4 additions & 4 deletions setup.py
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Expand Up @@ -3,17 +3,17 @@

here = pathlib.Path(__file__).parent.resolve()
# Get the requirements from the requirements file
requirements = (here / 'docker/vm_boot_images/config/tensorflow-requirements.txt').read_text(encoding='utf-8')
#requirements = (here / 'docker/vm_boot_images/config/tensorflow-requirements.txt').read_text(encoding='utf-8')
long_description = (here / 'README.md').read_text(encoding='utf-8')
setup(
name='ml4h',
version='0.0.12',
version='0.0.13',
description='Machine Learning for Health python package',
long_description=long_description, # Optional
long_description_content_type='text/markdown',
url='https://github.com/broadinstitute/ml4h',
python_requires='>=3.6',
#install_requires=["ml4ht", "tensorflow", "pytest", "numcodecs"], # requirements
install_requires=requirements,
install_requires=["ml4ht", "tensorflow", "pytest", "numcodecs"], # requirements
#install_requires=requirements,
packages=find_packages(),
)
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