Merge branch 'release_05'

ECP-CANDLE · Jun 6, 2022 · f6a3da8 · f6a3da8
2 parents 7d50c4f + b6ab4ff
commit f6a3da8
Showing 1 changed file with 49 additions and 49 deletions.
diff --git a/common/parsing_utils.py b/common/parsing_utils.py
@@ -19,48 +19,48 @@
  "name": "config_file",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "specify model configuration file",
+ "help": "Specify alternate model configuration file",
  },
  {
  "name": "data_type",
  "abv": "d",
  "type": str,
  "default": argparse.SUPPRESS,
  "choices": ["f16", "f32", "f64"],
- "help": "default floating point.",
+ "help": "Specify default floating points precision",
  },
  {
  "name": "rng_seed",
  "abv": "r",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "random number generator seed.",
+ "help": "Random number generator seed",
  },
  {
  "name": "train_bool",
  "type": hutils.str2bool,
  "default": True,
- "help": "train model.",
+ "help": "Flag to toggle model training",
  },
  {
  "name": "eval_bool",
  "type": hutils.str2bool,
  "default": argparse.SUPPRESS,
- "help": "evaluate model (use it for inference).",
+ "help": "Flag to evaluate model (use it for inference).",
  },
  {
  "name": "timeout",
  "action": "store",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "seconds allowed to train model (default: no timeout).",
+ "help": "Maximum time in seconds allowed to train model (default: no timeout).",
  },
  {
  "name": "gpus",
  "nargs": "+",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "set IDs of GPUs to use.",
+ "help": "Set IDs of GPUs to use.",
  },
  {
  "name": "profiling",
@@ -77,64 +77,64 @@
  "abv": "s",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "file path to save model snapshots.",
+ "help": "File path to save model snapshots.",
  },
  {
  "name": "model_name",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "specify model name to use when building filenames for saving.",
+ "help": "Specify model name to use when building filenames for saving.",
  },
  {
  "name": "home_dir",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "set home directory.",
+ "help": "Set home directory.",
  },
  {
  "name": "train_data",
  "action": "store",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "training data filename.",
+ "help": "Training data filename.",
  },
  {
  "name": "val_data",
  "action": "store",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "validation data filename.",
+ "help": "Validation data filename.",
  },
  {
  "name": "test_data",
  "type": str,
  "action": "store",
  "default": argparse.SUPPRESS,
- "help": "testing data filename.",
+ "help": "Testing data filename.",
  },
  {
  "name": "output_dir",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "output directory.",
+ "help": "Set output directory.",
  },
  {
  "name": "data_url",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "set data source url.",
+ "help": "Set data source url.",
  },
  {
  "name": "experiment_id",
  "type": str,
  "default": "EXP000",
- "help": "set the experiment unique identifier.",
+ "help": "Set the experiment unique identifier.",
  },
  {
  "name": "run_id",
  "type": str,
  "default": "RUN000",
- "help": "set the run unique identifier.",
+ "help": "Set the run unique identifier.",
  },
 ]
 
@@ -144,7 +144,7 @@
  "abv": "v",
  "type": hutils.str2bool,
  "default": False,
- "help": "increase output verbosity.",
+ "help": "Increase output verbosity.",
  },
  {"name": "logfile", "abv": "l", "type": str, "default": None, "help": "log file"},
 ]
@@ -155,19 +155,19 @@
  "type": str,
  "default": argparse.SUPPRESS,
  "choices": ["minabs", "minmax", "std", "none"],
- "help": "type of feature scaling; 'minabs': to [-1,1]; 'minmax': to [0,1], 'std': standard unit normalization; 'none': no normalization.",
+ "help": "Type of feature scaling; 'minabs': to [-1,1]; 'minmax': to [0,1], 'std': standard unit normalization; 'none': no normalization.",
  },
  {
  "name": "shuffle",
  "type": hutils.str2bool,
  "default": False,
- "help": "randomly shuffle data set (produces different training and testing partitions each run depending on the seed)",
+ "help": "Randomly shuffle data set (produces different training and testing partitions each run depending on the seed)",
  },
  {
  "name": "feature_subsample",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "number of features to randomly sample from each category (cellline expression, drug descriptors, etc), 0 means using all features",
+ "help": "Number of features to randomly sample from each category (cellline expression, drug descriptors, etc), 0 means using all features",
  },
 ]
 
@@ -176,83 +176,83 @@
  "name": "dense",
  "nargs": "+",
  "type": int,
- "help": "number of units in fully connected layers in an integer array.",
+ "help": "Number of units in fully connected layers in an integer array.",
  },
  {
  "name": "conv",
  "nargs": "+",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "integer array describing convolution layers: conv1_filters, conv1_filter_len, conv1_stride, conv2_filters, conv2_filter_len, conv2_stride ....",
+ "help": "Integer array describing convolution layers: conv1_filters, conv1_filter_len, conv1_stride, conv2_filters, conv2_filter_len, conv2_stride ....",
  },
  {
  "name": "locally_connected",
  "type": hutils.str2bool,
  "default": argparse.SUPPRESS,
- "help": "use locally connected layers instead of convolution layers.",
+ "help": "Use locally connected layers instead of convolution layers.",
  },
  {
  "name": "activation",
  "abv": "a",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "keras activation function to use in inner layers: relu, tanh, sigmoid...",
+ "help": "Activation function to use in inner layers: relu, tanh, sigmoid...",
  },
  {
  "name": "out_activation",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "keras activation function to use in out layer: softmax, linear, ...",
+ "help": "Activation function to use in out layer: softmax, linear, ...",
  },
  {
  "name": "lstm_size",
  "nargs": "+",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "integer array describing size of LSTM internal state per layer.",
+ "help": "Integer array describing size of LSTM internal state per layer.",
  },
  {
  "name": "recurrent_dropout",
  "action": "store",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "ratio of recurrent dropout.",
+ "help": "Ratio of recurrent dropout.",
  },
  {
  "name": "dropout",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "ratio of dropout used in fully connected layers.",
+ "help": "Ratio of dropout used in fully connected layers.",
  },
  {
  "name": "pool",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "pooling layer length.",
+ "help": "Pooling layer length.",
  },
  {
  "name": "batch_normalization",
  "type": hutils.str2bool,
  "default": argparse.SUPPRESS,
- "help": "use batch normalization.",
+ "help": "Use batch normalization.",
  },
  {
  "name": "loss",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "keras loss function to use: mse, ...",
+ "help": "Loss function to use: mse, ...",
  },
  {
  "name": "optimizer",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "keras optimizer to use: sgd, rmsprop, ...",
+ "help": "Optimizer to use: sgd, rmsprop, ...",
  },
  {
  "name": "metrics",
  "type": str,
  "default": argparse.SUPPRESS,
- "help": "metrics to evaluate performance: accuracy, ...",
+ "help": "Metrics to evaluate performance: accuracy, ...",
  },
 ]
 
@@ -262,33 +262,33 @@
  "type": int,
  "abv": "e",
  "default": argparse.SUPPRESS,
- "help": "number of training epochs.",
+ "help": "Number of training epochs.",
  },
  {
  "name": "batch_size",
  "type": int,
  "abv": "z",
  "default": argparse.SUPPRESS,
- "help": "batch size.",
+ "help": "Batch size.",
  },
  {
  "name": "learning_rate",
  "abv": "lr",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "overrides the learning rate for training.",
+ "help": "Overrides the default learning rate for training.",
  },
  {
  "name": "early_stop",
  "type": hutils.str2bool,
  "default": argparse.SUPPRESS,
- "help": "activates keras callback for early stopping of training in function of the monitored variable specified.",
+ "help": "Activates keras callback for early stopping of training in function of the monitored variable specified.",
  },
  {
  "name": "momentum",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "overrides the momentum to use in the SGD optimizer when training.",
+ "help": "Overrides the default momentum to use in the SGD optimizer when training.",
  },
  {
  "name": "initialization",
@@ -303,43 +303,43 @@
  "lecun_uniform",
  "he_normal",
  ],
- "help": "type of weight initialization; 'constant': to 0; 'uniform': to [-0.05,0.05], 'normal': mean 0, stddev 0.05; 'glorot_uniform': [-lim,lim] with lim = sqrt(6/(fan_in+fan_out)); 'lecun_uniform' : [-lim,lim] with lim = sqrt(3/fan_in); 'he_normal' : mean 0, stddev sqrt(2/fan_in).",
+ "help": "Type of weight initialization; 'constant': to 0; 'uniform': to [-0.05,0.05], 'normal': mean 0, stddev 0.05; 'glorot_uniform': [-lim,lim] with lim = sqrt(6/(fan_in+fan_out)); 'lecun_uniform' : [-lim,lim] with lim = sqrt(3/fan_in); 'he_normal' : mean 0, stddev sqrt(2/fan_in).",
  },
  {
  "name": "val_split",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "fraction of data to use in validation.",
+ "help": "Fraction of data to use in validation.",
  },
  {
  "name": "train_steps",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "overrides the number of training batches per epoch if set to nonzero.",
+ "help": "Overrides the number of training batches per epoch if set to nonzero.",
  },
  {
  "name": "val_steps",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "overrides the number of validation batches per epoch if set to nonzero.",
+ "help": "Overrides the number of validation batches per epoch if set to nonzero.",
  },
  {
  "name": "test_steps",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "overrides the number of test batches per epoch if set to nonzero.",
+ "help": "Overrides the number of test batches per epoch if set to nonzero.",
  },
  {
  "name": "train_samples",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "overrides the number of training samples if set to nonzero.",
+ "help": "Overrides the number of training samples if set to nonzero.",
  },
  {
  "name": "val_samples",
  "type": int,
  "default": argparse.SUPPRESS,
- "help": "overrides the number of validation samples if set to nonzero.",
+ "help": "Overrides the number of validation samples if set to nonzero.",
  },
 ]
 
@@ -362,19 +362,19 @@
  "name": "clr_base_lr",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "Base lr for cycle lr.",
+ "help": "Base lr for cyclic lr.",
  },
  {
  "name": "clr_max_lr",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "Max lr for cycle lr.",
+ "help": "Max lr for cyclic lr.",
  },
  {
  "name": "clr_gamma",
  "type": float,
  "default": argparse.SUPPRESS,
- "help": "Gamma parameter for learning cycle LR.",
+ "help": "Gamma parameter for cyclic LR.",
  },
 ]