diff --git a/notebooks/ML4H_Model_Factory_Intro.ipynb b/notebooks/ML4H_Model_Factory_Intro.ipynb index 81c9f9b5a..9726e738e 100644 --- a/notebooks/ML4H_Model_Factory_Intro.ipynb +++ b/notebooks/ML4H_Model_Factory_Intro.ipynb @@ -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" ] }, { @@ -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", @@ -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", @@ -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", diff --git a/setup.py b/setup.py index 94f5b602d..defb204f1 100644 --- a/setup.py +++ b/setup.py @@ -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(), )