def testOverrideValues(self):
config_flags.DEFINE_config_file('config')
with self.assertRaisesWithLiteralMatch(
config_flags.UnparsedFlagError,
'The flag has not been parsed yet'):
flags.FLAGS['config'].override_values # pylint: disable=pointless-statement
original_float = -1.0
original_dictfloat = -2.0
config = ml_collections.ConfigDict({
'integer': -1,
'float': original_float,
'dict': {
'float': original_dictfloat
}
})
integer_override = 0
dictfloat_override = 1.1
values = _parse_flags(
'./program --test_config={} --test_config.integer={} '
'--test_config.dict.float={}'.format(_TEST_CONFIG_FILE,
integer_override,
dictfloat_override))
config.update_from_flattened_dict(
values['test_config'].override_values)
self.assertEqual(config['integer'], integer_override)
self.assertEqual(config['float'], original_float)
self.assertEqual(config['dict']['float'], dictfloat_override)
def testIsConfigFile(self):
config_flags.DEFINE_config_file('is_a_config_flag')
flags.DEFINE_integer('not_a_config_flag', -1, '')
self.assertTrue(
config_flags.is_config_flag(flags.FLAGS['is_a_config_flag']))
self.assertFalse(
config_flags.is_config_flag(flags.FLAGS['not_a_config_flag']))
def _parse_flags(command,
default=None,
config=None,
lock_config=True,
required=False):
"""Parses arguments simulating sys.argv."""
if config is not None and default is not None:
raise ValueError('If config is supplied a default should not be.')
# Storing copy of the old sys.argv.
old_argv = list(sys.argv)
# Overwriting sys.argv, as sys has a global state it gets propagated.
# The module shlex is useful here because it splits the input similar to
# sys.argv. For instance, string arguments are not split by space.
sys.argv = shlex.split(command)
# Actual parsing.
values = flags.FlagValues()
if config is None:
config_flags.DEFINE_config_file('test_config',
default=default,
flag_values=values,
lock_config=lock_config)
else:
config_flags.DEFINE_config_dict('test_config',
config=config,
flag_values=values,
lock_config=lock_config)
if required:
flags.mark_flag_as_required('test_config', flag_values=values)
values(sys.argv)
# Going back to original values.
sys.argv = old_argv
return values
from absl import logging # pylint: disable=unused-import
from ml_collections.config_flags import config_flags
from ipagnn.lib import path_utils
from ipagnn.lib import setup
from ipagnn.workflows import analysis_workflows
DEFAULT_DATA_DIR = os.path.expanduser(os.path.join('~', 'tensorflow_datasets'))
DEFAULT_CONFIG = 'ipagnn/config/config.py'
flags.DEFINE_string('data_dir', DEFAULT_DATA_DIR, 'Where to place the data.')
flags.DEFINE_string('run_dir', '/tmp/learned_interpreters/default/',
'The directory to use for this run of the experiment.')
config_flags.DEFINE_config_file(name='config',
default=DEFAULT_CONFIG,
help_string='config file')
FLAGS = flags.FLAGS
def main(argv):
del argv # Unused.
data_dir = FLAGS.data_dir
xm_parameters = {}
run_dir = path_utils.expand_run_dir(FLAGS.run_dir, xm_parameters)
config = FLAGS.config
override_values = FLAGS['config'].override_values
run_configuration = setup.configure(data_dir, run_dir, config,
override_values, xm_parameters)
# Lint as: python3
"""Example of ConfigDict usage.
This example includes loading a ConfigDict in FLAGS, locking it, type
safety, iteration over fields, checking for a particular field, unpacking with
`**`, and loading dictionary from string representation.
"""
from absl import app
from absl import flags
from ml_collections.config_flags import config_flags
import yaml
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file(
'my_config', default='ml_collections/config_dict/examples/config.py')
def dummy_function(string, **unused_kwargs):
return 'Hello {}'.format(string)
def print_section(name):
print()
print()
print('-' * len(name))
print(name.upper())
print('-' * len(name))
print()
from tensorflow.io import gfile
import datasets
import transformers
from transformers import BertTokenizerFast
import ml_collections
from ml_collections.config_flags import config_flags
FLAGS = flags.FLAGS
flags.DEFINE_string(
'output_dir', None,
'The output directory where the model checkpoints will be written.')
config_flags.DEFINE_config_file('config', None, 'Hyperparameter configuration')
def get_config():
config = FLAGS.config
hf_config = transformers.AutoConfig.from_pretrained(config.init_checkpoint)
assert hf_config.model_type == 'bert', 'Only BERT is supported.'
model_config = ml_collections.ConfigDict({
'vocab_size':
hf_config.vocab_size,
'hidden_size':
hf_config.hidden_size,
'num_hidden_layers':
hf_config.num_hidden_layers,
'num_attention_heads':
hf_config.num_attention_heads,
import tensorflow as tf
from tensorflow.io import gfile
import uncertainty_baselines as ub
import checkpoint_utils # local file import from baselines.jft
import data_uncertainty_utils # local file import from baselines.jft
import input_utils # local file import from baselines.jft
import preprocess_utils # local file import from baselines.jft
import train_utils # local file import from baselines.jft
import ood_utils # local file import from experimental.near_ood.vit
# TODO(dusenberrymw): Open-source remaining imports.
fewshot = None
config_flags.DEFINE_config_file('config',
None,
'Training configuration.',
lock_config=True)
flags.DEFINE_string('output_dir', default=None, help='Work unit directory.')
flags.DEFINE_integer('num_cores',
default=None,
help='Unused. How many devices being used.')
flags.DEFINE_boolean('use_gpu',
default=None,
help='Unused. Whether or not running on GPU.')
flags.DEFINE_string('tpu', None,
'Unused. Name of the TPU. Only used if use_gpu is False.')
FLAGS = flags.FLAGS
def main(config, output_dir):
from ml_collections.config_flags import config_flags
from tensorflow.io import gfile
import data
import modeling
import training
FLAGS = flags.FLAGS
flags.DEFINE_string(
"output_dir",
None,
"The output directory where the model checkpoints will be written.",
)
config_flags.DEFINE_config_file("config", None, "Hyperparameter configuration")
def get_config():
config = FLAGS.config
hf_config = transformers.AutoConfig.from_pretrained(config.init_checkpoint)
assert hf_config.model_type == "bert", "Only BERT is supported."
model_config = ml_collections.ConfigDict({
"vocab_size":
hf_config.vocab_size,
"hidden_size":
hf_config.hidden_size,
"num_hidden_layers":
hf_config.num_hidden_layers,
"num_attention_heads":
hf_config.num_attention_heads,
from abstract_nas.train import train
from abstract_nas.zoo import utils as zoo_utils
_MAX_NUM_TRIALS = flags.DEFINE_integer("max_num_trials", 50,
"The total number of trials to run.")
_RESULTS_DIR = flags.DEFINE_string(
"results_dir", "", "The directory in which to write the results.")
_WRITE_CHECKPOINTS = flags.DEFINE_bool(
"checkpoints", False, "Whether to checkpoint the evolved models.")
_STUDY_NAME = flags.DEFINE_string(
"study_name", "abstract_nas_demo",
"The name of this study, used for writing results.")
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file("config")
def save_results(population):
"""Saves results as csv."""
results_dir = _RESULTS_DIR.value
study_name = _STUDY_NAME.value
if not results_dir:
logging.warn("No results_dir defined, so skipping saving results.")
return
results_filename = f"{results_dir}/{study_name}.csv"
if os.path.exists(results_filename):
logging.warn("Results file %s already exists, so skipping saving results.",
results_filename)
return
from absl import flags
import gym
import matplotlib.pyplot as plt
from ml_collections.config_flags import config_flags
import torch
from wrappers import wrapper_from_config
import xmagical
from xmagical.utils import KeyboardEnvInteractor
FLAGS = flags.FLAGS
flags.DEFINE_string("embodiment", None, "The agent embodiment.")
config_flags.DEFINE_config_file(
"config",
"configs/rl/default.py",
"File path to the training hyperparameter configuration.",
lock_config=True,
)
flags.mark_flag_as_required("embodiment")
def make_env():
xmagical.register_envs()
embodiment_name = FLAGS.embodiment.capitalize()
env = gym.make(f"SweepToTop-{embodiment_name}-State-Allo-TestLayout-v0")
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
env = wrapper_from_config(FLAGS.config, env, device)
return env
from cascaded_networks.datasets.dataset_handler import DataHandler
from cascaded_networks.models import densenet
from cascaded_networks.models import resnet
from cascaded_networks.modules import eval_handler
from cascaded_networks.modules import losses
from cascaded_networks.modules import train_handler
from cascaded_networks.modules import utils
# Setup Flags
FLAGS = flags.FLAGS
flags.DEFINE_string('gcs_path', None, 'gcs_path dir')
flags.DEFINE_bool('hyper_param_sweep', None, 'conducting hyperparam sweep')
flags.DEFINE_integer('n_gpus', None, 'Number of GPUs')
config_flags.DEFINE_config_file(
name='config',
default=None,
help_string='Path to the Training configuration.')
def main(_):
config = FLAGS.config
if config.debug:
config.epochs = 5
# Make reproducible
utils.make_reproducible(config.random_seed)
# Parse GCS bucket path
gcs_subpath = config.local_output_dir
import os
import sys
import wandb
import pytorch_lightning as pl
from datasets import load_dataset
from utils.wandb import get_experiments, load_model
from attack import trainer
# args
from absl import app
from absl import flags
from ml_collections.config_flags import config_flags
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file("config", default="config.py:attack")
def model_name(args):
n = args.prior + '_' + args.arc_type + '_' + str(args.z_dim)
return n
def cli_main(_):
pl.seed_everything(1234)
if "absl.logging" in sys.modules:
import absl.logging
absl.logging.set_verbosity("info")
absl.logging.set_stderrthreshold("info")
'preds_col', None,
'Name to use for the DeepNull prediction column. If unspecified, will be '
'the target column name with "_deepnull" suffix added.')
_NUM_FOLDS = flags.DEFINE_integer(
'num_folds', 5, 'The number of cross-validation folds to use.')
_SEED = flags.DEFINE_integer('seed', None, 'Random seed to use.')
_LOGDIR = flags.DEFINE_string(
'logdir', '/tmp', 'Directory in which to write temporary outputs.')
_VERBOSE = flags.DEFINE_boolean(
'verbose', False, 'If True, prints verbose model training output.')
# N.B.: ml_collections v0.1.0 does not return from this function. When an update
# is released on PyPI, use the same structure as the above flags.
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file(
'model_config', None,
'Specifies the model config file to use. If unspecified, defaults to the '
'MLP-based TF model used for all main results of the DeepNull paper.')
def main(argv: Sequence[str]) -> None:
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
tf.random.set_seed(_SEED.value)
logging.info('Loading data from %s', _INPUT_TSV.value)
input_df, binary_col_map = data.load_plink_or_bolt_file(
path_or_buf=_INPUT_TSV.value, missing_value=_MISSING_VALUE.value)
if FLAGS.model_config is None:
full_config = config.get_config('deepnull')
else:
from absl import app
from absl import logging
from ml_collections.config_flags import config_flags
from stable_transfer.classification import accuracy
from stable_transfer.classification import gbc
from stable_transfer.classification import hscore
from stable_transfer.classification import leep
from stable_transfer.classification import logme
from stable_transfer.classification import nleep
from stable_transfer.classification import transfer_experiment
_CONFIG_DIR = './'
_CONFIG = config_flags.DEFINE_config_file(
'my_config',
f'{_CONFIG_DIR}/stable_transfer/classification/config_transfer_experiment.py',
)
def run_experiment(experiment):
"""Run the experiment defined in the config file."""
if experiment.config.experiment.metric == 'accuracy':
return accuracy.get_test_accuracy(experiment)
if experiment.config.experiment.metric == 'leep':
return leep.get_train_leep(experiment)
if experiment.config.experiment.metric == 'logme':
return logme.get_train_logme(experiment)
if experiment.config.experiment.metric == 'hscore':
return hscore.get_train_hscore(experiment)
if experiment.config.experiment.metric == 'nleep':
return nleep.get_train_nleep(experiment)
def testModuleName(self):
config_flags.DEFINE_config_file('flag')
argv_0 = './program'
_parse_flags(argv_0)
self.assertIn(flags.FLAGS['flag'],
flags.FLAGS.flags_by_module_dict()[argv_0])
import torch
# project
from path_handler import model_path
from model import get_model
import dataset
import trainer
import tester
# args
from absl import app
from absl import flags
from ml_collections.config_flags import config_flags
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file("config", default="config.py")
def main(_):
if "absl.logging" in sys.modules:
import absl.logging
absl.logging.set_verbosity("info")
absl.logging.set_stderrthreshold("info")
config = FLAGS.config
print(config)
# Set the seed
torch.manual_seed(config.seed)
from importlib import import_module
from absl import flags
from ml_collections.config_flags import config_flags
# Configure model
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file('model')
def load_model():
module_path, class_name = FLAGS.model.constructor.rsplit('.', 1)
module = import_module(module_path)
learner = getattr(module, class_name)
return learner(**FLAGS.model.hparams)
r"""Example of basic DEFINE_flag_dict usage.
To run this example with basic config file:
python define_config_dict_basic.py -- \
--my_config=ml_collections/config_flags/examples/config.py
\
--my_config.field1=8 --my_config.nested.field=2.1 \
--my_config.tuple='(1, 2, (1, 2))'
To run this example with parameterised config file:
python define_config_dict_basic.py -- \
--my_config=ml_collections/config_flags/examples/parameterised_config.py:linear
\
--my_config.model_config.output_size=256'
"""
# pylint: enable=line-too-long
from absl import app
from ml_collections.config_flags import config_flags
_CONFIG = config_flags.DEFINE_config_file('my_config')
def main(_):
print(_CONFIG.value)
if __name__ == '__main__':
app.run(main)
To run this example with basic config file:
python define_config_dict_basic.py -- \
--my_config=ml_collections/config_flags/examples/config.py
\
--my_config.field1=8 --my_config.nested.field=2.1 \
--my_config.tuple='(1, 2, (1, 2))'
To run this example with parameterised config file:
python define_config_dict_basic.py -- \
--my_config=ml_collections/config_flags/examples/parameterised_config.py:linear
\
--my_config.model_config.output_size=256'
"""
# pylint: enable=line-too-long
from absl import app
from absl import flags
from ml_collections.config_flags import config_flags
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file('my_config')
def main(_):
print(FLAGS.my_config)
if __name__ == '__main__':
app.run(main)
# pylint: disable=line-too-long
flags.DEFINE_string(
'query', None, 'natural language description of the desired object.'
'can also be specified in the config file')
flags.DEFINE_integer('seed', 0,
'random seed. change to get a different generation')
flags.DEFINE_string('executable_name', 'train',
'executable name. [train|eval]')
flags.DEFINE_string('experiment_dir', 'results', 'experiment output directory')
flags.DEFINE_string('work_unit_dir', None,
'work unit output directory within experiment_dir')
flags.DEFINE_string('config_json', None,
'hyperparameter file to read in .json')
flags.DEFINE_string('extra_args_json_str', None, 'extra args to pass in')
config_flags.DEFINE_config_file('config', lock_config=False)
FLAGS = flags.FLAGS
# pylint: enable=line-too-long
def main(executable_dict, argv):
del argv
work_unit = platform.work_unit()
tf.enable_v2_behavior()
# Hide any GPUs form TensorFlow. Otherwise TF might reserve memory and make
# it unavailable to JAX.
tf.config.experimental.set_visible_devices([], 'GPU')
host_id = jax.host_id()
n_host = jax.host_count()
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Training and evaluation for NCSNv3."""
from . import ncsn_lib
from absl import app
from absl import flags
from ml_collections.config_flags import config_flags
import tensorflow as tf
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file("config",
None,
"Training configuration.",
lock_config=True)
flags.DEFINE_string("workdir", None, "Work unit directory.")
flags.DEFINE_string("mode", "train", "Running mode: train or eval")
flags.DEFINE_string("eval_folder", "eval",
"The folder name for storing evaluation results")
flags.mark_flags_as_required(["workdir", "config"])
def main(argv):
del argv
tf.config.experimental.set_visible_devices([], "GPU")
if FLAGS.mode == "train":
ncsn_lib.train(FLAGS.config, FLAGS.workdir)
elif FLAGS.mode == "eval":
ncsn_lib.evaluate(FLAGS.config, FLAGS.workdir, FLAGS.eval_folder)
from jax.flatten_util import ravel_pytree
from ml_collections.config_flags import config_flags
import numpy as np
import scipy.linalg
import adversarial
import data as data_loader
import model
from norm import norm_f
from norm import norm_type_dual
import optim
import summary as summary_tools
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file('config', None, 'Config file name.')
def evaluate_risks(data, predict_f, loss_f, model_param):
"""Returns the risk of a model for various loss functions.
Args:
data: An array of data samples for approximating the risk.
predict_f: Function that predicts labels given input.
loss_f: Function that outputs model's specific loss function.
model_param: Model parameters.
Returns:
Dictionary of risks for following loss functions:
(model's loss, 0/1, adversarial risk wrt a single norm-ball).
"""
import jax.numpy as jnp
from ml_collections.config_flags import config_flags
import numpy as np
import optax
import pandas as pd
from sklearn import metrics
import tensorflow as tf
import tensorflow_datasets as tfds
from tensorflow_probability.substrates import jax as tfp
from counterfactual_fairness import adult
from counterfactual_fairness import causal_network
from counterfactual_fairness import utils
from counterfactual_fairness import variational
FLAGS = flags.FLAGS
config_flags.DEFINE_config_file('config', 'adult_pscf_config.py',
'Training configuration.')
LOG_EVERY = 100
# These are all aliases to callables which will return instances of
# particular distribution modules, or a Node itself. This is used to make
# subsequent code more legible.
Node = causal_network.Node
Gaussian = causal_network.Gaussian
MLPMultinomial = causal_network.MLPMultinomial
def build_input(train_data: pd.DataFrame,
batch_size: int,
training_steps: int,
shuffle_size: int = 10000):