SYMBOL INDEX (794 symbols across 112 files)

FILE: downloads-generation/allele_sequences/filter_sequences.py
  function run (line 26) | def run():

FILE: downloads-generation/allele_sequences/make_allele_sequences.py
  function normalize_allele_name_optional (line 37) | def normalize_allele_name_optional(s):
  function run (line 40) | def run():

FILE: downloads-generation/allele_sequences/select_alleles_to_disambiguate.py
  function run (line 27) | def run():

FILE: downloads-generation/analysis_predictor_info/generate_artifacts.py
  function run (line 106) | def run():
  function do_job (line 246) | def do_job(tasks, constant_data=GLOBAL_DATA):

FILE: downloads-generation/analysis_predictor_info/generate_model_selection_with_decoys.py
  function run (line 41) | def run():

FILE: downloads-generation/analysis_predictor_info/predict_on_model_selection_data.py
  function do_predict (line 57) | def do_predict(predictor, key, sub_df, constant_data=None):
  function run (line 69) | def run():

FILE: downloads-generation/data_curated/curate.py
  function normalize_allele_name_or_return_unknown (line 15) | def normalize_allele_name_or_return_unknown(s):
  function load_data_kim2014 (line 88) | def load_data_kim2014(filename):
  function load_data_systemhc_atlas (line 110) | def load_data_systemhc_atlas(filename, min_probability=0.99):
  function load_data_iedb (line 139) | def load_data_iedb(iedb_csv, include_qualitative=True):
  function load_data_additional_ms (line 252) | def load_data_additional_ms(filename):
  function run (line 276) | def run():

FILE: downloads-generation/data_curated/curate_ms_by_pmid.py
  function normalize_allele_name_or_return_unknown (line 17) | def normalize_allele_name_or_return_unknown(s):
  function load (line 61) | def load(filenames, **kwargs):
  function debug (line 74) | def debug(*filenames):
  function handle_pmid_27600516 (line 80) | def handle_pmid_27600516(filename):
  function handle_pmid_23481700 (line 115) | def handle_pmid_23481700(filename):
  function handle_pmid_24616531 (line 154) | def handle_pmid_24616531(filename):
  function handle_pmid_25576301 (line 177) | def handle_pmid_25576301(filename):
  function handle_pmid_26992070 (line 246) | def handle_pmid_26992070(*filenames):
  function handle_pmid_27412690 (line 307) | def handle_pmid_27412690(filename):
  function handle_pmid_28832583 (line 359) | def handle_pmid_28832583(*filenames):
  function handle_pmid_31495665 (line 470) | def handle_pmid_31495665(filename):
  function handle_pmid_27869121 (line 656) | def handle_pmid_27869121(filename):
  function handle_pmid_31154438 (line 711) | def handle_pmid_31154438(*filenames):
  function handle_pmid_31844290 (line 767) | def handle_pmid_31844290(*filenames):
  function make_expression_groups (line 865) | def make_expression_groups(dataset_identifier, df, groups):
  function handle_expression_GSE113126 (line 877) | def handle_expression_GSE113126(*filenames):
  function handle_expression_expression_atlas_22460905 (line 900) | def handle_expression_expression_atlas_22460905(filename):
  function handle_expression_human_protein_atlas (line 939) | def handle_expression_human_protein_atlas(*filenames):
  function make_expression_mixtures (line 995) | def make_expression_mixtures(expression_df):
  function run (line 1027) | def run():

FILE: downloads-generation/data_evaluation/join_with_precomputed.py
  function load_results (line 31) | def load_results(dirname, result_df=None, columns=None):
  function run (line 67) | def run():

FILE: downloads-generation/data_evaluation/make_benchmark.py
  function run (line 63) | def run():

FILE: downloads-generation/data_evaluation/split_by_sample.py
  function run (line 30) | def run():

FILE: downloads-generation/data_mass_spec_annotated/annotate.py
  function run (line 51) | def run():

FILE: downloads-generation/data_predictions/run_predictors.py
  function load_results (line 97) | def load_results(dirname, result_df=None, dtype="float32"):
  function run (line 140) | def run(argv=sys.argv[1:]):
  function do_predictions_mhctools (line 361) | def do_predictions_mhctools(work_item_dicts, constant_data=None):
  function do_predictions_mhcflurry (line 444) | def do_predictions_mhcflurry(work_item_dicts, constant_data=None):

FILE: downloads-generation/data_predictions/write_allele_list.py
  function run (line 24) | def run():

FILE: downloads-generation/data_predictions/write_proteome_peptides.py
  function run (line 51) | def run():

FILE: downloads-generation/data_references/process.py
  function run (line 41) | def run():

FILE: downloads-generation/models_class1/write_validation_data.py
  function run (line 49) | def run(argv):

FILE: downloads-generation/models_class1_kim_benchmark/curate.py
  function normalize_allele_name_or_return_unknown (line 13) | def normalize_allele_name_or_return_unknown(s):
  function load_data_kim2014 (line 71) | def load_data_kim2014(filename):
  function load_data_systemhc_atlas (line 92) | def load_data_systemhc_atlas(filename, min_probability=0.99):
  function load_data_abelin_mass_spec (line 120) | def load_data_abelin_mass_spec(filename):
  function load_data_iedb (line 143) | def load_data_iedb(iedb_csv, include_qualitative=True, include_mass_spec...
  function run (line 232) | def run():

FILE: downloads-generation/models_class1_kim_benchmark/write_validation_data.py
  function run (line 49) | def run(argv):

FILE: downloads-generation/models_class1_pan/reassign_mass_spec_training_data.py
  function go (line 21) | def go(args):

FILE: downloads-generation/models_class1_pan_variants/exclude_data_from_training.py
  function normalize_allele_name_or_return_unknown (line 13) | def normalize_allele_name_or_return_unknown(s):
  function load_30377561 (line 49) | def load_30377561(filename):
  function go (line 83) | def go(args):

FILE: downloads-generation/models_class1_pan_variants/generate_hyperparameters.py
  function transform_to_single_hidden (line 26) | def transform_to_single_hidden(hyperparameters):
  function transform_to_no_pretrain (line 35) | def transform_to_no_pretrain(hyperparameters):
  function transform_to_compact_peptide (line 41) | def transform_to_compact_peptide(hyperparameters):

FILE: downloads-generation/models_class1_presentation/make_train_data.py
  function run (line 63) | def run():

FILE: downloads-generation/models_class1_processing/annotate_hits_with_expression.py
  function run (line 33) | def run():

FILE: downloads-generation/models_class1_processing/generate_hyperparameters.base.py
  function hyperparrameters_grid (line 26) | def hyperparrameters_grid():

FILE: downloads-generation/models_class1_processing/generate_hyperparameters.variants.py
  function transform (line 26) | def transform(kind, hyperparameters):

FILE: downloads-generation/models_class1_processing/make_train_data.py
  function do_process_samples (line 79) | def do_process_samples(samples, constant_data=None):
  function run (line 166) | def run():

FILE: downloads-generation/random_peptide_predictions/random_predictions.py
  function run (line 25) | def run():

FILE: mhcflurry/allele_encoding.py
  class AlleleEncoding (line 6) | class AlleleEncoding(object):
    method __init__ (line 7) | def __init__(self, alleles=None, allele_to_sequence=None, borrow_from=...
    method compact (line 73) | def compact(self):
    method allele_representations (line 89) | def allele_representations(self, encoding_name):
    method fixed_length_vector_encoded_sequences (line 121) | def fixed_length_vector_encoded_sequences(self, encoding_name):

FILE: mhcflurry/amino_acid.py
  function available_vector_encodings (line 82) | def available_vector_encodings():
  function vector_encoding_length (line 94) | def vector_encoding_length(name):
  function index_encoding (line 109) | def index_encoding(sequences, letter_to_index_dict):
  function fixed_vectors_encoding (line 137) | def fixed_vectors_encoding(index_encoded_sequences, letter_to_vector_df):

FILE: mhcflurry/calibrate_percentile_ranks_command.py
  function run (line 130) | def run(argv=sys.argv[1:]):
  function run_class1_presentation_predictor (line 173) | def run_class1_presentation_predictor(args, peptides):
  function run_class1_affinity_predictor (line 233) | def run_class1_affinity_predictor(args, peptides):
  function do_class1_affinity_calibrate_percentile_ranks (line 365) | def do_class1_affinity_calibrate_percentile_ranks(
  function class1_affinity_calibrate_percentile_ranks (line 383) | def class1_affinity_calibrate_percentile_ranks(

FILE: mhcflurry/class1_affinity_predictor.py
  class Class1AffinityPredictor (line 40) | class Class1AffinityPredictor(object):
    method __init__ (line 50) | def __init__(
    method manifest_df (line 128) | def manifest_df(self):
    method clear_cache (line 162) | def clear_cache(self):
    method neural_networks (line 178) | def neural_networks(self):
    method merge (line 193) | def merge(cls, predictors):
    method merge_in_place (line 230) | def merge_in_place(self, others):
    method canonicalize_allele_name (line 285) | def canonicalize_allele_name(self, raw_name):
    method supported_alleles (line 314) | def supported_alleles(self):
    method supported_peptide_lengths (line 330) | def supported_peptide_lengths(self):
    method check_consistency (line 350) | def check_consistency(self):
    method save (line 371) | def save(self, models_dir, model_names_to_write=None, write_metadata=T...
    method load (line 489) | def load(models_dir=None, max_models=None, optimization_level=None):
    method __repr__ (line 681) | def __repr__(self):
    method optimize (line 700) | def optimize(self, warn=True):
    method model_name (line 739) | def model_name(allele, num):
    method weights_path (line 761) | def weights_path(models_dir, model_name):
    method master_allele_encoding (line 777) | def master_allele_encoding(self):
    method fit_allele_specific_predictors (line 793) | def fit_allele_specific_predictors(
    method fit_class1_pan_allele_models (line 933) | def fit_class1_pan_allele_models(
    method add_pan_allele_model (line 1025) | def add_pan_allele_model(self, model, models_dir_for_save=None):
    method percentile_ranks (line 1052) | def percentile_ranks(self, affinities, allele=None, alleles=None, thro...
    method predict (line 1114) | def predict(
    method predict_to_dataframe (line 1164) | def predict_to_dataframe(
    method calibrate_percentile_ranks (line 1462) | def calibrate_percentile_ranks(
    method model_select (line 1614) | def model_select(

FILE: mhcflurry/class1_neural_network.py
  class Class1NeuralNetworkModel (line 44) | class Class1NeuralNetworkModel(nn.Module):
    method __init__ (line 49) | def __init__(
    method _initialize_weights (line 232) | def _initialize_weights(self, init):
    method forward (line 247) | def forward(self, inputs):
    method get_weights_list (line 342) | def get_weights_list(self):
    method set_weights_list (line 358) | def set_weights_list(self, weights, auto_convert_keras=True):
    method to_json (line 632) | def to_json(self):
  class Class1NeuralNetwork (line 686) | class Class1NeuralNetwork(object):
    method apply_hyperparameter_renames (line 796) | def apply_hyperparameter_renames(cls, hyperparameters):
    method __init__ (line 816) | def __init__(self, **hyperparameters):
    method clear_model_cache (line 836) | def clear_model_cache(klass):
    method borrow_cached_network (line 843) | def borrow_cached_network(klass, network_json, network_weights):
    method _parse_keras_json_config (line 880) | def _parse_keras_json_config(cls, config):
    method _create_model_from_config (line 1005) | def _create_model_from_config(cls, config, instance_hyperparameters=No...
    method _create_merged_model_from_config (line 1105) | def _create_merged_model_from_config(cls, config, instance_hyperparame...
    method model_cache_key (line 1164) | def model_cache_key(network_json):
    method keras_network_cache_key (line 1187) | def keras_network_cache_key(network_json):
    method network (line 1193) | def network(self, borrow=False):
    method update_network_description (line 1229) | def update_network_description(self):
    method get_config (line 1290) | def get_config(self):
    method from_config (line 1307) | def from_config(cls, config, weights=None, weights_loader=None):
    method load_weights (line 1347) | def load_weights(self):
    method get_weights (line 1355) | def get_weights(self):
    method get_weights_list (line 1368) | def get_weights_list(self):
    method set_weights_list (line 1379) | def set_weights_list(self, weights, auto_convert_keras=True):
    method __getstate__ (line 1404) | def __getstate__(self):
    method __setstate__ (line 1420) | def __setstate__(self, state):
    method peptides_to_network_input (line 1427) | def peptides_to_network_input(self, peptides):
    method supported_peptide_lengths (line 1448) | def supported_peptide_lengths(self):
    method allele_encoding_to_network_input (line 1463) | def allele_encoding_to_network_input(self, allele_encoding):
    method data_dependent_weights_initialization (line 1487) | def data_dependent_weights_initialization(network, x_dict=None, method...
    method _regularized_parameters (line 1510) | def _regularized_parameters(network):
    method _regularization_penalty (line 1524) | def _regularization_penalty(parameters, l1=0.0, l2=0.0):
    method get_device (line 1539) | def get_device(self):
    method fit_generator (line 1543) | def fit_generator(
    method _create_optimizer (line 1747) | def _create_optimizer(self, network):
    method fit (line 1768) | def fit(
    method predict (line 2171) | def predict(
    method merge (line 2254) | def merge(cls, models, merge_method="average"):
    method make_network (line 2294) | def make_network(
    method clear_allele_representations (line 2339) | def clear_allele_representations(self):
    method set_allele_representations (line 2356) | def set_allele_representations(self, allele_representations, force_sur...
    method _update_embedding (line 2383) | def _update_embedding(self, network, reshaped, force_surgery):
  class MergedClass1NeuralNetwork (line 2421) | class MergedClass1NeuralNetwork(nn.Module):
    method __init__ (line 2426) | def __init__(self, networks, merge_method="average"):
    method forward (line 2431) | def forward(self, inputs):
    method get_weights_list (line 2444) | def get_weights_list(self):
    method set_weights_list (line 2451) | def set_weights_list(self, weights, auto_convert_keras=False):

FILE: mhcflurry/class1_presentation_predictor.py
  class Class1PresentationPredictor (line 36) | class Class1PresentationPredictor(object):
    method __init__ (line 51) | def __init__(
    method supported_alleles (line 72) | def supported_alleles(self):
    method supported_peptide_lengths (line 79) | def supported_peptide_lengths(self):
    method supports_affinity_prediction (line 86) | def supports_affinity_prediction(self):
    method supports_processing_prediction (line 91) | def supports_processing_prediction(self):
    method supports_presentation_prediction (line 98) | def supports_presentation_prediction(self):
    method predict_affinity (line 105) | def predict_affinity(
    method predict_processing (line 264) | def predict_processing(
    method fit (line 323) | def fit(
    method get_model (line 398) | def get_model(self, name=None):
    method predict (line 425) | def predict(
    method predict_sequences (line 598) | def predict_sequences(
    method save (line 856) | def save(
    method load (line 935) | def load(cls, models_dir=None, max_models=None):
    method __repr__ (line 1014) | def __repr__(self):
    method percentile_ranks (line 1020) | def percentile_ranks(self, presentation_scores, throw=True):
    method calibrate_percentile_ranks (line 1044) | def calibrate_percentile_ranks(self, scores, bins=None):

FILE: mhcflurry/class1_processing_neural_network.py
  class Class1ProcessingModel (line 20) | class Class1ProcessingModel(nn.Module):
    method __init__ (line 25) | def __init__(
    method forward (line 117) | def forward(self, inputs):
    method _process_n_flank (line 170) | def _process_n_flank(self, conv_result, peptide_length):
    method _process_c_flank (line 204) | def _process_c_flank(self, conv_result, peptide_length):
    method _max_pool_over_peptide_n (line 237) | def _max_pool_over_peptide_n(self, x, peptide_length):
    method _max_pool_over_peptide_c (line 262) | def _max_pool_over_peptide_c(self, x, peptide_length):
    method _extract_c_cleavage (line 284) | def _extract_c_cleavage(self, x, peptide_length):
    method _extract_c_flank_avg (line 294) | def _extract_c_flank_avg(self, conv_result, peptide_length):
    method _extract_n_flank_avg (line 318) | def _extract_n_flank_avg(self, conv_result):
    method get_weights_list (line 336) | def get_weights_list(self):
    method set_weights_list (line 345) | def set_weights_list(self, weights, auto_convert_keras=True):
    method _reorder_keras_weights (line 399) | def _reorder_keras_weights(self, weights):
  class Class1ProcessingNeuralNetwork (line 452) | class Class1ProcessingNeuralNetwork(object):
    method __init__ (line 513) | def __init__(self, **hyperparameters):
    method sequence_lengths (line 523) | def sequence_lengths(self):
    method get_device (line 540) | def get_device(self):
    method network (line 544) | def network(self):
    method _regularized_parameters (line 568) | def _regularized_parameters(network):
    method _regularization_penalty (line 582) | def _regularization_penalty(parameters, l1=0.0, l2=0.0):
    method update_network_description (line 597) | def update_network_description(self):
    method fit (line 607) | def fit(
    method _create_optimizer (line 835) | def _create_optimizer(self, network):
    method predict (line 855) | def predict(
    method predict_encoded (line 893) | def predict_encoded(
    method network_input (line 947) | def network_input(self, sequences, throw=True):
    method make_network (line 978) | def make_network(
    method __getstate__ (line 1016) | def __getstate__(self):
    method __setstate__ (line 1030) | def __setstate__(self, state):
    method get_weights (line 1036) | def get_weights(self):
    method get_config (line 1048) | def get_config(self):
    method from_config (line 1063) | def from_config(cls, config, weights=None):

FILE: mhcflurry/class1_processing_predictor.py
  class Class1ProcessingPredictor (line 23) | class Class1ProcessingPredictor(object):
    method __init__ (line 29) | def __init__(
    method sequence_lengths (line 60) | def sequence_lengths(self):
    method add_models (line 84) | def add_models(self, models):
    method manifest_df (line 122) | def manifest_df(self):
    method model_name (line 145) | def model_name(num):
    method weights_path (line 161) | def weights_path(models_dir, model_name):
    method predict (line 176) | def predict(
    method predict_to_dataframe (line 215) | def predict_to_dataframe(
    method predict_to_dataframe_encoded (line 245) | def predict_to_dataframe_encoded(
    method check_consistency (line 280) | def check_consistency(self):
    method save (line 294) | def save(self, models_dir, model_names_to_write=None, write_metadata=T...
    method load (line 361) | def load(cls, models_dir=None, max_models=None):
    method __repr__ (line 414) | def __repr__(self):

FILE: mhcflurry/cluster_parallelism.py
  function add_cluster_parallelism_args (line 25) | def add_cluster_parallelism_args(parser):
  function cluster_results_from_args (line 62) | def cluster_results_from_args(
  function cluster_results (line 106) | def cluster_results(
  function worker_entry_point (line 380) | def worker_entry_point(argv=sys.argv[1:]):

FILE: mhcflurry/common.py
  function normalize_allele_name (line 16) | def normalize_allele_name(
  function normalize_pytorch_backend (line 98) | def normalize_pytorch_backend(backend):
  function configure_pytorch (line 123) | def configure_pytorch(backend=None, gpu_device_nums=None, num_threads=No...
  function configure_tensorflow (line 154) | def configure_tensorflow(backend=None, gpu_device_nums=None, num_threads...
  function get_pytorch_device (line 190) | def get_pytorch_device():
  function configure_logging (line 226) | def configure_logging(verbose=False):
  function amino_acid_distribution (line 246) | def amino_acid_distribution(peptides, smoothing=0.0):
  function random_peptides (line 270) | def random_peptides(num, length=9, distribution=None):
  function positional_frequency_matrix (line 306) | def positional_frequency_matrix(peptides):
  function save_weights (line 333) | def save_weights(weights_list, filename):
  function load_weights (line 348) | def load_weights(filename):
  class NumpyJSONEncoder (line 366) | class NumpyJSONEncoder(json.JSONEncoder):
    method default (line 371) | def default(self, obj):

FILE: mhcflurry/custom_loss.py
  function get_loss (line 23) | def get_loss(name):
  class Loss (line 49) | class Loss(object):
    method __init__ (line 61) | def __init__(self, name=None):
    method __str__ (line 64) | def __str__(self):
    method loss (line 67) | def loss(self, y_true, y_pred):
    method get_keras_loss (line 70) | def get_keras_loss(self, reduction="sum_over_batch_size"):
  class StandardKerasLoss (line 83) | class StandardKerasLoss(Loss):
    method __init__ (line 90) | def __init__(self, loss_name="mse"):
    method encode_y (line 96) | def encode_y(y):
  class TransformPredictionsLossWrapper (line 100) | class TransformPredictionsLossWrapper(Loss):
    method __init__ (line 107) | def __init__(
    method encode_y (line 117) | def encode_y(self, *args, **kwargs):
    method loss (line 120) | def loss(self, y_true, y_pred):
  class MSEWithInequalities (line 125) | class MSEWithInequalities(Loss):
    method __init__ (line 154) | def __init__(self):
    method encode_y (line 158) | def encode_y(y, inequalities=None):
    method _max_value (line 162) | def _max_value(values):
    method loss (line 167) | def loss(self, y_true, y_pred):
  class MSEWithInequalitiesAndMultipleOutputs (line 175) | class MSEWithInequalitiesAndMultipleOutputs(Loss):
    method __init__ (line 200) | def __init__(self):
    method encode_y (line 204) | def encode_y(y, inequalities=None, output_indices=None):
    method loss (line 209) | def loss(self, y_true, y_pred):
  class MultiallelicMassSpecLoss (line 226) | class MultiallelicMassSpecLoss(Loss):
    method __init__ (line 234) | def __init__(self, delta=0.2, multiplier=1.0):
    method encode_y (line 240) | def encode_y(y):
    method loss (line 243) | def loss(self, y_true, y_pred):
  function check_shape (line 251) | def check_shape(name, arr, expected_shape):

FILE: mhcflurry/data_dependent_weights_initialization.py
  function svd_orthonormal (line 46) | def svd_orthonormal(shape):
  function get_activations_pytorch (line 72) | def get_activations_pytorch(model, layer_name, x_dict, device=None):
  function get_activations (line 133) | def get_activations(model, layer, X_batch):
  function lsuv_init (line 152) | def lsuv_init(model, batch, verbose=True, margin=0.1, max_iter=100):

FILE: mhcflurry/downloads.py
  function get_downloads_dir (line 34) | def get_downloads_dir():
  function get_current_release (line 41) | def get_current_release():
  function get_downloads_metadata (line 48) | def get_downloads_metadata():
  function get_default_class1_models_dir (line 60) | def get_default_class1_models_dir(test_exists=True):
  function get_default_class1_presentation_models_dir (line 91) | def get_default_class1_presentation_models_dir(test_exists=True):
  function get_default_class1_processing_models_dir (line 123) | def get_default_class1_processing_models_dir(test_exists=True):
  function get_current_release_downloads (line 157) | def get_current_release_downloads():
  function get_path (line 198) | def get_path(download_name, filename='', test_exists=True):
  function configure (line 228) | def configure():

FILE: mhcflurry/downloads_command.py
  function run (line 105) | def run(argv=sys.argv[1:]):
  function mkdir_p (line 122) | def mkdir_p(path):
  function yes_no (line 138) | def yes_no(boolean):
  class TqdmUpTo (line 143) | class TqdmUpTo(tqdm):
    method update_to (line 145) | def update_to(self, b=1, bsize=1, tsize=None):
  function fetch_subcommand (line 159) | def fetch_subcommand(args):
  function info_subcommand (line 273) | def info_subcommand(args):
  function path_subcommand (line 324) | def path_subcommand(args):
  function url_subcommand (line 331) | def url_subcommand(args):

FILE: mhcflurry/encodable_sequences.py
  class EncodingError (line 12) | class EncodingError(ValueError):
    method __init__ (line 16) | def __init__(self, message, supported_peptide_lengths):
  class EncodableSequences (line 23) | class EncodableSequences(object):
    method create (line 35) | def create(klass, sequences):
    method __init__ (line 45) | def __init__(self, sequences):
    method __len__ (line 60) | def __len__(self):
    method variable_length_to_fixed_length_categorical (line 63) | def variable_length_to_fixed_length_categorical(
    method variable_length_to_fixed_length_vector_encoding (line 111) | def variable_length_to_fixed_length_vector_encoding(
    method sequences_to_fixed_length_index_encoded_array (line 187) | def sequences_to_fixed_length_index_encoded_array(

FILE: mhcflurry/ensemble_centrality.py
  function _nanmean_no_warnings (line 10) | def _nanmean_no_warnings(log_values):
  function _nanmedian_no_warnings (line 22) | def _nanmedian_no_warnings(log_values):
  function robust_mean (line 33) | def robust_mean(log_values):

FILE: mhcflurry/fasta.py
  function read_fasta_to_dataframe (line 15) | def read_fasta_to_dataframe(filename, full_descriptions=False):
  class FastaParser (line 37) | class FastaParser(object):
    method __init__ (line 41) | def __init__(self):
    method iterate_over_file (line 45) | def iterate_over_file(self, fasta_path, full_descriptions=False):
    method _current_entry (line 85) | def _current_entry(self):
    method open_file (line 96) | def open_file(fasta_path):
    method _parse_header_id (line 106) | def _parse_header_id(line, full_description=False):

FILE: mhcflurry/flanking_encoding.py
  class FlankingEncoding (line 18) | class FlankingEncoding(object):
    method __init__ (line 31) | def __init__(self, peptides, n_flanks, c_flanks):
    method __len__ (line 51) | def __len__(self):
    method vector_encode (line 57) | def vector_encode(
    method encode (line 115) | def encode(

FILE: mhcflurry/hyperparameters.py
  class HyperparameterDefaults (line 7) | class HyperparameterDefaults(object):
    method __init__ (line 16) | def __init__(self, **defaults):
    method extend (line 19) | def extend(self, other):
    method with_defaults (line 36) | def with_defaults(self, obj):
    method subselect (line 49) | def subselect(self, obj):
    method check_valid_keys (line 59) | def check_valid_keys(self, obj):
    method models_grid (line 72) | def models_grid(self, **kwargs):

FILE: mhcflurry/local_parallelism.py
  function add_local_parallelism_args (line 22) | def add_local_parallelism_args(parser):
  function worker_pool_with_gpu_assignments_from_args (line 76) | def worker_pool_with_gpu_assignments_from_args(args):
  function worker_pool_with_gpu_assignments (line 101) | def worker_pool_with_gpu_assignments(
  function validate_worker_pool_args (line 165) | def validate_worker_pool_args(
  function worker_init_kwargs_for_scheduler (line 193) | def worker_init_kwargs_for_scheduler(
  function make_worker_pool (line 233) | def make_worker_pool(
  function worker_init_entry_point (line 309) | def worker_init_entry_point(
  function worker_init (line 329) | def worker_init(
  class WrapException (line 350) | class WrapException(Exception):
    method __init__ (line 355) | def __init__(self):
    method __str__ (line 359) | def __str__(self):
  function call_wrapped (line 363) | def call_wrapped(function, *args, **kwargs):
  function call_wrapped_kwargs (line 384) | def call_wrapped_kwargs(function, kwargs):

FILE: mhcflurry/percent_rank_transform.py
  class PercentRankTransform (line 8) | class PercentRankTransform(object):
    method __init__ (line 13) | def __init__(self):
    method fit (line 17) | def fit(self, values, bins):
    method transform (line 39) | def transform(self, values):
    method to_series (line 54) | def to_series(self):
    method from_series (line 69) | def from_series(series):

FILE: mhcflurry/predict_command.py
  function run (line 176) | def run(argv=sys.argv[1:]):

FILE: mhcflurry/predict_scan_command.py
  function parse_peptide_lengths (line 185) | def parse_peptide_lengths(value):
  function run (line 202) | def run(argv=sys.argv[1:]):

FILE: mhcflurry/pytorch_layers.py
  function get_activation (line 9) | def get_activation(name):
  class LocallyConnected1D (line 36) | class LocallyConnected1D(nn.Module):
    method __init__ (line 57) | def __init__(self, in_channels, out_channels, input_length, kernel_size,
    method forward (line 82) | def forward(self, x):

FILE: mhcflurry/pytorch_losses.py
  class MSEWithInequalities (line 14) | class MSEWithInequalities(nn.Module):
    method encode_y (line 27) | def encode_y(y, inequalities=None):
    method forward (line 61) | def forward(self, y_pred, y_true, sample_weights=None):
  class MSEWithInequalitiesAndMultipleOutputs (line 108) | class MSEWithInequalitiesAndMultipleOutputs(nn.Module):
    method encode_y (line 119) | def encode_y(y, inequalities=None, output_indices=None):
    method forward (line 149) | def forward(self, y_pred, y_true, sample_weights=None):
  class MultiallelicMassSpecLoss (line 208) | class MultiallelicMassSpecLoss(nn.Module):
    method __init__ (line 223) | def __init__(self, delta=0.2, multiplier=1.0):
    method encode_y (line 229) | def encode_y(y):
    method forward (line 235) | def forward(self, y_pred, y_true, sample_weights=None):
  class StandardLoss (line 288) | class StandardLoss(nn.Module):
    method __init__ (line 295) | def __init__(self, loss_name="mse"):
    method encode_y (line 306) | def encode_y(y):
    method forward (line 310) | def forward(self, y_pred, y_true, sample_weights=None):
  function get_pytorch_loss (line 350) | def get_pytorch_loss(name):

FILE: mhcflurry/random_negative_peptides.py
  class RandomNegativePeptides (line 11) | class RandomNegativePeptides(object):
    method __init__ (line 50) | def __init__(self, **hyperparameters):
    method plan (line 56) | def plan(self, peptides, affinities, alleles=None, inequalities=None):
    method plan_by_length (line 134) | def plan_by_length(self, df_all, df_binders=None, df_nonbinders=None):
    method plan_by_allele (line 165) | def plan_by_allele(self, df_all, df_binders=None, df_nonbinders=None):
    method plan_by_allele_equalize_nonbinders (line 196) | def plan_by_allele_equalize_nonbinders(
    method get_alleles (line 245) | def get_alleles(self):
    method get_peptides (line 262) | def get_peptides(self):
    method get_total_count (line 284) | def get_total_count(self):

FILE: mhcflurry/regression_target.py
  function from_ic50 (line 4) | def from_ic50(ic50, max_ic50=50000.0):
  function to_ic50 (line 23) | def to_ic50(x, max_ic50=50000.0):

FILE: mhcflurry/scoring.py
  function make_scores (line 12) | def make_scores(

FILE: mhcflurry/select_allele_specific_models_command.py
  function run (line 185) | def run(argv=sys.argv[1:]):
  class ScrambledPredictor (line 411) | class ScrambledPredictor(object):
    method __init__ (line 412) | def __init__(self, predictor):
    method predict (line 417) | def predict(self, peptides, allele):
  function model_select (line 426) | def model_select(allele, constant_data=GLOBAL_DATA):
  function cache_encoding (line 490) | def cache_encoding(predictor, peptides):
  class ScoreFunction (line 497) | class ScoreFunction(object):
    method __init__ (line 502) | def __init__(self, function, summary=None):
    method __call__ (line 506) | def __call__(self, *args, **kwargs):
  class CombinedModelSelector (line 510) | class CombinedModelSelector(object):
    method __init__ (line 514) | def __init__(self, model_selectors, weights=None, min_contribution_per...
    method usable_for_allele (line 521) | def usable_for_allele(self, allele):
    method plan_summary (line 526) | def plan_summary(self, allele):
    method score_function (line 529) | def score_function(self, allele, dry_run=False):
  class ConsensusModelSelector (line 580) | class ConsensusModelSelector(object):
    method __init__ (line 585) | def __init__(
    method usable_for_allele (line 602) | def usable_for_allele(self, allele):
    method max_absolute_value (line 605) | def max_absolute_value(self, allele):
    method plan_summary (line 608) | def plan_summary(self, allele):
    method score_function (line 611) | def score_function(self, allele):
  class MSEModelSelector (line 630) | class MSEModelSelector(object):
    method __init__ (line 635) | def __init__(
    method usable_for_allele (line 647) | def usable_for_allele(self, allele):
    method max_absolute_value (line 650) | def max_absolute_value(self, allele):
    method plan_summary (line 656) | def plan_summary(self, allele):
    method score_function (line 659) | def score_function(self, allele):
  class MassSpecModelSelector (line 711) | class MassSpecModelSelector(object):
    method __init__ (line 716) | def __init__(
    method ppv (line 755) | def ppv(y_true, predictions):
    method usable_for_allele (line 761) | def usable_for_allele(self, allele):
    method max_absolute_value (line 765) | def max_absolute_value(self, allele):
    method plan_summary (line 771) | def plan_summary(self, allele):
    method score_function (line 774) | def score_function(self, allele):

FILE: mhcflurry/select_pan_allele_models_command.py
  function mse (line 93) | def mse(
  function run (line 134) | def run(argv=sys.argv[1:]):
  function do_model_select_task (line 296) | def do_model_select_task(item, constant_data=GLOBAL_DATA):
  function model_select (line 302) | def model_select(

FILE: mhcflurry/select_processing_models_command.py
  function run (line 87) | def run(argv=sys.argv[1:]):
  function do_model_select_task (line 229) | def do_model_select_task(item, constant_data=GLOBAL_DATA):
  function model_select (line 233) | def model_select(

FILE: mhcflurry/testing_utils.py
  function startup (line 8) | def startup():
  function cleanup (line 15) | def cleanup():

FILE: mhcflurry/train_allele_specific_models_command.py
  function run (line 131) | def run(argv=sys.argv[1:]):
  function alleles_by_similarity (line 331) | def alleles_by_similarity(allele):
  function train_model (line 345) | def train_model(
  function subselect_df_held_out (line 418) | def subselect_df_held_out(df, recriprocal_held_out_fraction=10, seed=0):

FILE: mhcflurry/train_pan_allele_models_command.py
  function assign_folds (line 134) | def assign_folds(df, num_folds, held_out_fraction, held_out_max):
  function pretrain_data_iterator (line 210) | def pretrain_data_iterator(
  function run (line 263) | def run(argv=sys.argv[1:]):
  function main (line 282) | def main(args):
  function initialize_training (line 296) | def initialize_training(args):
  function train_models (line 424) | def train_models(args):
  function train_model (line 537) | def train_model(

FILE: mhcflurry/train_presentation_models_command.py
  function run (line 66) | def run(argv=sys.argv[1:]):
  function main (line 85) | def main(args):

FILE: mhcflurry/train_processing_models_command.py
  function assign_folds (line 113) | def assign_folds(df, num_folds, held_out_samples):
  function run (line 153) | def run(argv=sys.argv[1:]):
  function main (line 172) | def main(args):
  function initialize_training (line 186) | def initialize_training(args):
  function train_models (line 270) | def train_models(args):
  function train_model (line 378) | def train_model(

FILE: scripts/compare_tf_pytorch_random_outputs.py
  function _json_default (line 94) | def _json_default(value):
  function _self_cmd (line 102) | def _self_cmd(*args: str) -> list[str]:
  function _run_subprocess_json (line 106) | def _run_subprocess_json(cmd: list[str]) -> dict:
  function _run_subprocess (line 115) | def _run_subprocess(cmd: list[str]) -> None:
  function _append_if_set (line 119) | def _append_if_set(cmd: list[str], flag: str, value: str | None) -> None:
  function _repo_root_default (line 124) | def _repo_root_default() -> Path:
  function _random_sequences (line 128) | def _random_sequences(rng: np.random.Generator, lengths: np.ndarray) -> ...
  function _generate_dataset (line 139) | def _generate_dataset(
  function _apply_allele_panel (line 171) | def _apply_allele_panel(
  function cmd_backend_metadata (line 194) | def cmd_backend_metadata(args: argparse.Namespace) -> None:
  function cmd_predict_backend (line 261) | def cmd_predict_backend(args: argparse.Namespace) -> None:
  function _numeric_stats (line 369) | def _numeric_stats(
  function cmd_analyze (line 433) | def cmd_analyze(args: argparse.Namespace) -> None:
  function cmd_run (line 533) | def cmd_run(args: argparse.Namespace) -> None:
  function _add_common_model_dir_args (line 701) | def _add_common_model_dir_args(parser: argparse.ArgumentParser) -> None:
  function build_parser (line 708) | def build_parser() -> argparse.ArgumentParser:
  function main (line 780) | def main() -> None:

FILE: scripts/cross_allele_parity_analysis.py
  function _repo_root_default (line 85) | def _repo_root_default() -> Path:
  function _compare_script_path (line 89) | def _compare_script_path() -> Path:
  function _self_cmd (line 93) | def _self_cmd(*args: str) -> list[str]:
  function _run_subprocess_json (line 97) | def _run_subprocess_json(cmd: list[str]) -> dict:
  function _run_subprocess (line 105) | def _run_subprocess(cmd: list[str]) -> None:
  function _append_if_set (line 109) | def _append_if_set(cmd: list[str], flag: str, value: str | None) -> None:
  function _select_alleles (line 114) | def _select_alleles(
  function _lengths_to_sample (line 149) | def _lengths_to_sample(
  function _random_sequences (line 166) | def _random_sequences(
  function _generate_uniform_peptides (line 189) | def _generate_uniform_peptides(
  function _cross_join_dataset (line 239) | def _cross_join_dataset(peptides_df: pd.DataFrame, alleles: list[str]) -...
  function _pre_run_sanity_checks (line 271) | def _pre_run_sanity_checks(peptides_df: pd.DataFrame, dataset: pd.DataFr...
  function _enforce_presentation_score_requirements (line 290) | def _enforce_presentation_score_requirements(
  function _numeric_output_columns (line 324) | def _numeric_output_columns(df: pd.DataFrame) -> list[str]:
  function _make_diff_frame (line 328) | def _make_diff_frame(merged: pd.DataFrame, numeric_columns: list[str]) -...
  function _per_output_summary (line 340) | def _per_output_summary(diff_df: pd.DataFrame, numeric_columns: list[str...
  function _break_thresholds_for_output (line 360) | def _break_thresholds_for_output(output: str) -> float:
  function _break_analysis (line 368) | def _break_analysis(
  function _plot_output_ranges (line 400) | def _plot_output_ranges(summary_df: pd.DataFrame, out_path: Path) -> None:
  function _plot_row_max_hist (line 437) | def _plot_row_max_hist(row_summary: pd.DataFrame, out_path: Path) -> None:
  function _plot_length_breakdown (line 459) | def _plot_length_breakdown(
  function _safe_plot_name (line 490) | def _safe_plot_name(name: str) -> str:
  function _plot_per_output_hists (line 494) | def _plot_per_output_hists(
  function _write_break_report (line 542) | def _write_break_report(
  function build_parser (line 590) | def build_parser() -> argparse.ArgumentParser:
  function main (line 620) | def main() -> None:

FILE: scripts/extract_high_presentation_fixture.py
  function _collect_model_metadata (line 33) | def _collect_model_metadata() -> dict:
  function build_parser (line 58) | def build_parser() -> argparse.ArgumentParser:
  function main (line 76) | def main() -> None:

FILE: scripts/generate_fixture_error_report.py
  class MetricReport (line 52) | class MetricReport:
    method summary (line 64) | def summary(self) -> dict:
  function build_parser (line 81) | def build_parser() -> argparse.ArgumentParser:
  function _format_number (line 91) | def _format_number(value: float, digits: int = 6) -> str:
  function _format_percent (line 102) | def _format_percent(value: float) -> str:
  function _as_float_array (line 108) | def _as_float_array(values: Iterable[float]) -> np.ndarray:
  function _clip_positive (line 112) | def _clip_positive(values: np.ndarray) -> np.ndarray:
  function _make_error_frame (line 118) | def _make_error_frame(
  function _load_affinity_fixture (line 137) | def _load_affinity_fixture() -> dict:
  function _load_presentation_fixture (line 142) | def _load_presentation_fixture() -> tuple[pd.DataFrame, dict]:
  function _predict_current_outputs (line 149) | def _predict_current_outputs() -> tuple[dict, pd.DataFrame, dict]:
  function _compute_metric_reports (line 290) | def _compute_metric_reports(
  function _axis_range (line 401) | def _axis_range(values: np.ndarray) -> tuple[float, float]:
  function _tick_values (line 411) | def _tick_values(start: float, stop: float, count: int = 5) -> list[float]:
  function _format_tick (line 417) | def _format_tick(value: float, log_scale: bool = False) -> str:
  function _render_scatter_svg (line 423) | def _render_scatter_svg(
  function _render_histogram_svg (line 500) | def _render_histogram_svg(
  function _render_summary_table (line 582) | def _render_summary_table(reports: list[MetricReport]) -> str:
  function _render_top_error_table (line 611) | def _render_top_error_table(report: MetricReport, limit: int = 10) -> str:
  function _render_metric_section (line 641) | def _render_metric_section(report: MetricReport) -> str:
  function _write_outputs (line 691) | def _write_outputs(
  function main (line 925) | def main() -> None:

FILE: scripts/modal_train_mhcflurry.py
  function _install_repo (line 39) | def _install_repo():
  function run_training_job (line 85) | def run_training_job(job: dict) -> dict:
  function main (line 131) | def main(command_template: str, workers: int = 1):

FILE: scripts/plot_fixture_diffs.py
  function load_fixture (line 40) | def load_fixture():
  function generate_predictions (line 47) | def generate_predictions(fixture_df):
  function plot_output (line 136) | def plot_output(col, tf_vals, pt_vals, out_dir):
  function main (line 232) | def main():

FILE: scripts/validate_allele_sequences.py
  function load_raw_csv (line 27) | def load_raw_csv(path):
  function renormalize (line 32) | def renormalize(raw_mapping):
  function main (line 53) | def main():

FILE: test/__init__.py
  function data_path (line 9) | def data_path(name):
  function initialize (line 17) | def initialize():

FILE: test/conftest.py
  function pytest_configure (line 9) | def pytest_configure(config):

FILE: test/expensive_verify_pretrain_optimizable.py
  function verify_optimizable (line 63) | def verify_optimizable():

FILE: test/pytest_helpers.py
  function mhcflurry_cli (line 20) | def mhcflurry_cli(command):
  function eq_ (line 32) | def eq_(a, b, msg=None):
  function assert_less (line 40) | def assert_less(a, b, msg=None):
  function assert_greater (line 48) | def assert_greater(a, b, msg=None):
  function assert_almost_equal (line 56) | def assert_almost_equal(a, b, places=7, msg=None):
  function assert_raises (line 68) | def assert_raises(exc_class, func=None, *args, **kwargs):

FILE: test/test_allele_encoding.py
  function test_allele_encoding_speed (line 9) | def test_allele_encoding_speed():

FILE: test/test_amino_acid.py
  function test_index_and_one_hot_encoding (line 15) | def test_index_and_one_hot_encoding():
  function test_index_encoding_no_downcast_futurewarning (line 54) | def test_index_encoding_no_downcast_futurewarning():

FILE: test/test_api_compat_shims.py
  function test_legacy_configure_tensorflow_entry_point (line 11) | def test_legacy_configure_tensorflow_entry_point():
  function test_legacy_worker_init_signature_kept (line 16) | def test_legacy_worker_init_signature_kept():
  function test_worker_init_preserves_empty_gpu_assignment (line 21) | def test_worker_init_preserves_empty_gpu_assignment(monkeypatch):
  function test_legacy_cache_key_alias (line 37) | def test_legacy_cache_key_alias():
  function test_legacy_get_keras_loss_accessor (line 48) | def test_legacy_get_keras_loss_accessor():
  function test_legacy_get_activations_symbol_kept (line 56) | def test_legacy_get_activations_symbol_kept():

FILE: test/test_calibrate_percentile_ranks_command.py
  function setup_module (line 25) | def setup_module():
  function run_and_check (line 31) | def run_and_check(n_jobs=0, delete=True, additional_args=[]):
  function test_run_serial (line 71) | def test_run_serial():
  function test_run_parallel (line 75) | def test_run_parallel():
  function test_run_cluster_parallelism (line 79) | def test_run_cluster_parallelism(delete=True):

FILE: test/test_changing_allele_representations.py
  function setup_module (line 12) | def setup_module():
  function test_changing_allele_representations (line 60) | def test_changing_allele_representations():

FILE: test/test_class1_affinity_predictor.py
  function setup_teardown (line 25) | def setup_teardown():
  function warn_with_traceback (line 40) | def warn_with_traceback(message, category, filename, lineno, file=None, ...
  function predict_and_check (line 49) | def predict_and_check(
  function test_a1_known_epitopes_in_newly_trained_model (line 69) | def test_a1_known_epitopes_in_newly_trained_model():
  function test_class1_affinity_predictor_a0205_memorize_training_data (line 136) | def test_class1_affinity_predictor_a0205_memorize_training_data():
  function test_no_nans (line 212) | def test_no_nans():
  function test_predict_implementations_equivalent (line 220) | def test_predict_implementations_equivalent():
  function test_no_runtime_warnings_for_unsupported_rows (line 248) | def test_no_runtime_warnings_for_unsupported_rows():

FILE: test/test_class1_neural_network.py
  function setup_teardown (line 20) | def setup_teardown():
  function test_class1_neural_network_a0205_training_accuracy (line 28) | def test_class1_neural_network_a0205_training_accuracy():
  function test_inequalities (line 84) | def test_inequalities():
  function test_basic_training (line 166) | def test_basic_training():
  function test_serialization (line 194) | def test_serialization():
  function test_different_peptide_lengths (line 228) | def test_different_peptide_lengths():
  function test_early_stopping (line 253) | def test_early_stopping():
  function test_batch_normalization (line 276) | def test_batch_normalization():
  function test_dropout (line 296) | def test_dropout():
  function test_multiple_outputs (line 316) | def test_multiple_outputs():

FILE: test/test_class1_pan.py
  function setup_module (line 18) | def setup_module():
  function test_train_simple (line 94) | def test_train_simple():

FILE: test/test_class1_presentation_predictor.py
  function setup_module (line 23) | def setup_module():
  function teardown_module (line 42) | def teardown_module():
  function predictors (line 55) | def predictors():
  function test_basic (line 64) | def test_basic(predictors):
  function test_downloaded_predictor_small (line 166) | def test_downloaded_predictor_small(predictors):
  function test_downloaded_predictor (line 246) | def test_downloaded_predictor(predictors):
  function test_downloaded_predictor_invalid_peptides (line 429) | def test_downloaded_predictor_invalid_peptides(predictors):

FILE: test/test_class1_processing_neural_network.py
  function setup_teardown (line 22) | def setup_teardown():
  function decode_matrix (line 35) | def decode_matrix(array):
  function test_neural_network_input (line 61) | def test_neural_network_input():
  function test_small (line 138) | def test_small():
  function test_more (line 144) | def test_more():
  function test_basic_indexing (line 156) | def test_basic_indexing(num=10000, do_assertions=True, **hyperparameters):
  function train_basic_network (line 177) | def train_basic_network(num, do_assertions=True, is_hit=None, **hyperpar...
  function test_serialization (line 250) | def test_serialization():
  function test_different_peptide_lengths (line 284) | def test_different_peptide_lengths():
  function test_empty_flanks (line 312) | def test_empty_flanks():
  function test_prediction_range (line 335) | def test_prediction_range():

FILE: test/test_class1_processing_predictor.py
  function setup (line 17) | def setup():
  function teardown (line 21) | def teardown():
  function test_basic (line 25) | def test_basic():

FILE: test/test_custom_loss.py
  function setup_module (line 15) | def setup_module():
  function setup_teardown (line 21) | def setup_teardown():
  function evaluate_loss (line 28) | def evaluate_loss(loss_obj, y_true, y_pred):
  function test_mse_with_inequalities (line 47) | def test_mse_with_inequalities(loss_obj=None):
  function test_mse_with_inequalities_and_multiple_outputs (line 93) | def test_mse_with_inequalities_and_multiple_outputs():
  function test_multiallelic_mass_spec_loss (line 155) | def test_multiallelic_mass_spec_loss():
  function test_encode_y_basic (line 226) | def test_encode_y_basic():
  function test_loss_gradient_flow (line 244) | def test_loss_gradient_flow():
  function test_inequality_gradient_respects_constraint (line 262) | def test_inequality_gradient_respects_constraint():

FILE: test/test_doctest.py
  function setup_module (line 20) | def setup_module():
  function test_doctests (line 26) | def test_doctests():

FILE: test/test_download_models_class1.py
  function setup_module (line 17) | def setup_module():
  function teardown_module (line 23) | def teardown_module():
  function downloaded_predictor (line 30) | def downloaded_predictor():
  function predict_and_check (line 34) | def predict_and_check(
  function test_a1_titin_epitope_downloaded_models (line 51) | def test_a1_titin_epitope_downloaded_models(downloaded_predictor):
  function test_a1_mage_epitope_downloaded_models (line 59) | def test_a1_mage_epitope_downloaded_models(downloaded_predictor):
  function test_a2_hiv_epitope_downloaded_models (line 67) | def test_a2_hiv_epitope_downloaded_models(downloaded_predictor):
  function test_caching (line 73) | def test_caching(downloaded_predictor):
  function test_downloaded_predictor_is_serializable (line 84) | def test_downloaded_predictor_is_serializable(downloaded_predictor):
  function test_downloaded_predictor_is_savable (line 99) | def test_downloaded_predictor_is_savable(downloaded_predictor):
  function test_downloaded_predictor_gives_percentile_ranks (line 115) | def test_downloaded_predictor_gives_percentile_ranks(downloaded_predictor):

FILE: test/test_ensemble_centrality.py
  function test_robust_mean (line 10) | def test_robust_mean():
  function test_no_runtime_warnings_for_all_nan_rows (line 33) | def test_no_runtime_warnings_for_all_nan_rows():

FILE: test/test_hyperparameters.py
  function test_all_combinations_of_hyperparameters (line 6) | def test_all_combinations_of_hyperparameters():

FILE: test/test_local_parallelism.py
  function test_worker_init_kwargs_round_robin_across_gpus (line 12) | def test_worker_init_kwargs_round_robin_across_gpus():
  function test_worker_init_kwargs_without_gpu_scheduling_uses_backend (line 27) | def test_worker_init_kwargs_without_gpu_scheduling_uses_backend():
  function test_worker_init_kwargs_normalizes_default_backend_alias (line 40) | def test_worker_init_kwargs_normalizes_default_backend_alias():
  function test_worker_init_kwargs_with_gpus_normalizes_default_backend_alias (line 52) | def test_worker_init_kwargs_with_gpus_normalizes_default_backend_alias():
  function test_backend_default_alias_parses (line 65) | def test_backend_default_alias_parses():
  function test_validate_worker_pool_args_requires_parallelism_for_gpus (line 72) | def test_validate_worker_pool_args_requires_parallelism_for_gpus():
  function test_validate_worker_pool_args_rejects_non_cuda_backends_for_gpus (line 82) | def test_validate_worker_pool_args_rejects_non_cuda_backends_for_gpus():
  function test_validate_worker_pool_args_rejects_invalid_backend (line 92) | def test_validate_worker_pool_args_rejects_invalid_backend():

FILE: test/test_master_compat_predictions.py
  function setup_module (line 34) | def setup_module():
  function teardown_module (line 38) | def teardown_module():
  function _load_model_and_expected (line 42) | def _load_model_and_expected(name):
  function _predict (line 52) | def _predict(config, weights, expected, backend=None):
  function test_predictions_match_expected (line 72) | def test_predictions_match_expected(model_name):
  function test_mps_matches_cpu (line 85) | def test_mps_matches_cpu(model_name):

FILE: test/test_multi_output.py
  function setup_module (line 13) | def setup_module():
  function test_multi_output (line 19) | def test_multi_output(setup_module):

FILE: test/test_network_merging.py
  function setup_module (line 14) | def setup_module():
  function teardown_module (line 22) | def teardown_module():
  function predictors (line 29) | def predictors():
  function test_merge (line 33) | def test_merge(predictors):

FILE: test/test_percent_rank_transform.py
  function test_percent_rank_transform (line 9) | def test_percent_rank_transform():

FILE: test/test_predict_command.py
  function setup_teardown (line 19) | def setup_teardown():
  function test_csv (line 35) | def test_csv():
  function test_no_csv (line 58) | def test_no_csv():

FILE: test/test_predict_scan_command.py
  function setup_module (line 16) | def setup_module():
  function read_output_csv (line 23) | def read_output_csv(filename):
  function test_fasta (line 29) | def test_fasta():
  function test_fasta_50nm (line 56) | def test_fasta_50nm():
  function test_fasta_percentile (line 81) | def test_fasta_percentile():
  function test_commandline_sequences (line 106) | def test_commandline_sequences():

FILE: test/test_pytorch_coverage.py
  function setup_teardown (line 21) | def setup_teardown():
  class TestGetPytorchLoss (line 30) | class TestGetPytorchLoss:
    method test_standard_mse (line 31) | def test_standard_mse(self):
    method test_standard_mae (line 40) | def test_standard_mae(self):
    method test_custom_loss_lookup (line 48) | def test_custom_loss_lookup(self):
    method test_custom_multi_output_lookup (line 54) | def test_custom_multi_output_lookup(self):
    method test_custom_mass_spec_lookup (line 60) | def test_custom_mass_spec_lookup(self):
    method test_unknown_standard_loss_raises (line 65) | def test_unknown_standard_loss_raises(self):
    method test_unknown_custom_loss_raises (line 70) | def test_unknown_custom_loss_raises(self):
  class TestStandardLossWeighted (line 76) | class TestStandardLossWeighted:
    method test_mse_with_sample_weights (line 77) | def test_mse_with_sample_weights(self):
    method test_mae_with_sample_weights (line 87) | def test_mae_with_sample_weights(self):
    method test_mse_column_vector_predictions_do_not_warn (line 96) | def test_mse_column_vector_predictions_do_not_warn(self):
  class TestMSEWithInequalitiesSampleWeights (line 108) | class TestMSEWithInequalitiesSampleWeights:
    method test_weighted_equality_loss (line 109) | def test_weighted_equality_loss(self):
    method test_encode_y_nan_raises (line 121) | def test_encode_y_nan_raises(self):
    method test_encode_y_length_mismatch_raises (line 126) | def test_encode_y_length_mismatch_raises(self):
  class TestMSEMultiOutputSampleWeights (line 132) | class TestMSEMultiOutputSampleWeights:
    method test_weighted_multi_output (line 133) | def test_weighted_multi_output(self):
    method test_encode_y_negative_output_indices_raises (line 144) | def test_encode_y_negative_output_indices_raises(self):
    method test_encode_y_output_indices_shape_mismatch_raises (line 150) | def test_encode_y_output_indices_shape_mismatch_raises(self):
  class TestMultiallelicMassSpecEdgeCases (line 157) | class TestMultiallelicMassSpecEdgeCases:
    method test_no_hits_returns_zero (line 158) | def test_no_hits_returns_zero(self):
    method test_no_decoys_returns_zero (line 167) | def test_no_decoys_returns_zero(self):
  class TestGetActivation (line 180) | class TestGetActivation:
    method test_tanh (line 181) | def test_tanh(self):
    method test_sigmoid (line 187) | def test_sigmoid(self):
    method test_relu (line 192) | def test_relu(self):
    method test_linear_returns_none (line 198) | def test_linear_returns_none(self):
    method test_unknown_raises (line 203) | def test_unknown_raises(self):
  class TestLocallyConnected1D (line 209) | class TestLocallyConnected1D:
    method test_output_shape (line 210) | def test_output_shape(self):
    method test_deterministic_forward (line 219) | def test_deterministic_forward(self):
  class TestEnsembleCentralityEdgeCases (line 236) | class TestEnsembleCentralityEdgeCases:
    method test_robust_mean_falls_back_to_nanmean_for_few_columns (line 237) | def test_robust_mean_falls_back_to_nanmean_for_few_columns(self):
    method test_robust_mean_two_columns (line 244) | def test_robust_mean_two_columns(self):
    method test_robust_mean_all_nan_many_columns (line 250) | def test_robust_mean_all_nan_many_columns(self):
    method test_nanmedian_mixed_nans (line 256) | def test_nanmedian_mixed_nans(self):
    method test_nanmean_single_value_per_row (line 268) | def test_nanmean_single_value_per_row(self):
    method test_centrality_measures_dict (line 276) | def test_centrality_measures_dict(self):
  class TestWeightInitialization (line 284) | class TestWeightInitialization:
    method _make_model (line 285) | def _make_model(self, init):
    method test_glorot_uniform (line 298) | def test_glorot_uniform(self):
    method test_glorot_normal (line 302) | def test_glorot_normal(self):
    method test_he_uniform (line 306) | def test_he_uniform(self):
    method test_he_normal (line 310) | def test_he_normal(self):
    method test_biases_are_zero (line 314) | def test_biases_are_zero(self):
  class TestMergedClass1NeuralNetwork (line 324) | class TestMergedClass1NeuralNetwork:
    method _make_merged (line 325) | def _make_merged(self, merge_method, n_networks=2):
    method test_average (line 343) | def test_average(self):
    method test_sum (line 352) | def test_sum(self):
    method test_concatenate (line 360) | def test_concatenate(self):
    method test_unknown_merge_method_raises (line 368) | def test_unknown_merge_method_raises(self):
    method test_get_set_weights_roundtrip (line 375) | def test_get_set_weights_roundtrip(self):
  class TestSkipConnectionsTopology (line 390) | class TestSkipConnectionsTopology:
    method test_forward_pass (line 391) | def test_forward_pass(self):
    method test_different_from_feedforward (line 408) | def test_different_from_feedforward(self):
  class TestCanonicalizeAlleleName (line 439) | class TestCanonicalizeAlleleName:
    method test_common_alleles_roundtrip (line 440) | def test_common_alleles_roundtrip(self):
    method test_aliases_false_avoids_remapping (line 451) | def test_aliases_false_avoids_remapping(self):
    method test_normalize_raises_on_invalid (line 458) | def test_normalize_raises_on_invalid(self):
    method test_normalize_returns_default_on_invalid (line 463) | def test_normalize_returns_default_on_invalid(self):
    method test_forbidden_substring_raises (line 469) | def test_forbidden_substring_raises(self):
    method test_forbidden_substring_returns_default (line 474) | def test_forbidden_substring_returns_default(self):
  class TestConfigurePyTorch (line 484) | class TestConfigurePyTorch:
    method test_reconfigure_backend (line 485) | def test_reconfigure_backend(self):
    method test_invalid_backend_raises (line 494) | def test_invalid_backend_raises(self):
    method test_default_backend_alias_maps_to_auto (line 499) | def test_default_backend_alias_maps_to_auto(self):
    method test_configure_tensorflow_cpu_backend_maps_to_cpu (line 508) | def test_configure_tensorflow_cpu_backend_maps_to_cpu(self):
    method test_configure_tensorflow_default_alias_maps_to_auto (line 519) | def test_configure_tensorflow_default_alias_maps_to_auto(self):
    method test_configure_tensorflow_gpu_backend_maps_to_gpu (line 530) | def test_configure_tensorflow_gpu_backend_maps_to_gpu(self):

FILE: test/test_pytorch_regressions.py
  function setup_teardown (line 32) | def setup_teardown():
  function _make_simple_affinity_model (line 38) | def _make_simple_affinity_model(**overrides):
  function _make_allele_representations (line 62) | def _make_allele_representations(num_alleles=2):
  function _seed_all (line 66) | def _seed_all(seed=1):
  function test_sample_weights_affect_training (line 72) | def test_sample_weights_affect_training():
  function test_validation_split_is_fixed_when_lr_zero (line 100) | def test_validation_split_is_fixed_when_lr_zero():
  function test_dropout_probability_is_keep_prob (line 122) | def test_dropout_probability_is_keep_prob():
  function test_batch_norm_uses_keras_defaults (line 134) | def test_batch_norm_uses_keras_defaults():
  function test_processing_dropout_is_spatial (line 151) | def test_processing_dropout_is_spatial():
  function test_processing_flank_averages_use_tf_masked_mean_semantics (line 178) | def test_processing_flank_averages_use_tf_masked_mean_semantics():
  function test_mse_with_inequalities_rejects_out_of_range_targets (line 207) | def test_mse_with_inequalities_rejects_out_of_range_targets():
  function test_mse_with_inequalities_rejects_invalid_inequality (line 214) | def test_mse_with_inequalities_rejects_invalid_inequality():
  function test_multiallelic_mass_spec_encode_y_validates_values (line 219) | def test_multiallelic_mass_spec_encode_y_validates_values():
  function test_merge_allele_specific_raises_not_implemented (line 224) | def test_merge_allele_specific_raises_not_implemented():
  function test_merged_network_serialization_preserves_dropout_keep_probability (line 242) | def test_merged_network_serialization_preserves_dropout_keep_probability():
  function test_dense_regularization_excludes_output_layer (line 279) | def test_dense_regularization_excludes_output_layer():
  function test_processing_validation_uses_last_fraction_and_sample_weights (line 311) | def test_processing_validation_uses_last_fraction_and_sample_weights():
  function test_optimizer_defaults_match_keras (line 380) | def test_optimizer_defaults_match_keras():
  function test_weight_and_embedding_updates_preserve_device (line 407) | def test_weight_and_embedding_updates_preserve_device():
  function test_cached_keras_weight_reload_preserves_device (line 459) | def test_cached_keras_weight_reload_preserves_device():
  function test_l1_regularization_changes_weights_even_with_zero_data_loss (line 485) | def test_l1_regularization_changes_weights_even_with_zero_data_loss():

FILE: test/test_random_negative_peptides.py
  function test_random_negative_peptides_by_allele_equalize_nonbinders (line 10) | def test_random_negative_peptides_by_allele_equalize_nonbinders():
  function test_random_negative_peptides_by_allele (line 63) | def test_random_negative_peptides_by_allele():

FILE: test/test_regression_target.py
  function test_regression_target_to_ic50 (line 9) | def test_regression_target_to_ic50():
  function test_ic50_to_regression_target (line 14) | def test_ic50_to_regression_target():

FILE: test/test_released_master_predictions.py
  function setup_module (line 18) | def setup_module():
  function teardown_module (line 22) | def teardown_module():
  function _load_expected (line 26) | def _load_expected(name):
  function test_allele_specific_affinity_predictions (line 32) | def test_allele_specific_affinity_predictions():
  function test_pan_allele_affinity_predictions (line 52) | def test_pan_allele_affinity_predictions():

FILE: test/test_released_predictors_on_hpv_dataset.py
  function data_path (line 19) | def data_path(name):
  function setup_module (line 30) | def setup_module():
  function teardown_module (line 41) | def teardown_module():
  function predictors (line 48) | def predictors():
  function test_on_hpv (line 52) | def test_on_hpv(predictors, df=DF):

FILE: test/test_released_predictors_well_correlated.py
  function setup (line 23) | def setup():
  function setup_teardown (line 34) | def setup_teardown():
  function predictors (line 53) | def predictors():
  function test_correlation (line 57) | def test_correlation(

FILE: test/test_released_presentation_highscore_rows.py
  function setup_module (line 34) | def setup_module():
  function teardown_module (line 38) | def teardown_module():
  function _load_expected (line 42) | def _load_expected():
  function _atol_for_output (line 48) | def _atol_for_output(column):
  function test_expected_data_has_high_and_low_contexts (line 56) | def test_expected_data_has_high_and_low_contexts():
  function test_presentation_predictions (line 72) | def test_presentation_predictions():

FILE: test/test_selected_peptides_csv.py
  function _normalize_allele (line 24) | def _normalize_allele(allele):
  function selected_peptides_predictions (line 36) | def selected_peptides_predictions():
  function test_selected_peptides_mhcflurry_matches_csv (line 64) | def test_selected_peptides_mhcflurry_matches_csv(selected_peptides_predi...
  function test_selected_peptides_netmhcpan_affinity_close (line 93) | def test_selected_peptides_netmhcpan_affinity_close(selected_peptides_pr...

FILE: test/test_speed.py
  function setup_module (line 28) | def setup_module():
  function teardown_module (line 38) | def teardown_module():
  function load_predictors (line 48) | def load_predictors():
  function predictors (line 57) | def predictors():
  function init (line 64) | def init():
  function test_speed_allele_specific (line 68) | def test_speed_allele_specific(predictors, profile=False, num=DEFAULT_NU...
  function test_speed_pan_allele (line 121) | def test_speed_pan_allele(predictors, profile=False, num=DEFAULT_NUM_PRE...

FILE: test/test_train_and_related_commands.py
  function setup_module (line 22) | def setup_module():
  function run_and_check (line 65) | def run_and_check(n_jobs=0):
  function run_and_check_with_model_selection (line 107) | def run_and_check_with_model_selection(n_jobs=1):
  function test_run_parallel (line 169) | def test_run_parallel():
  function test_run_serial (line 174) | def test_run_serial():

FILE: test/test_train_pan_allele_models_command.py
  function setup_module (line 24) | def setup_module():
  function run_and_check (line 138) | def run_and_check(n_jobs=0, delete=True, additional_args=[]):
  function test_run_parallel (line 197) | def test_run_parallel():
  function test_run_serial (line 202) | def test_run_serial():
  function test_run_cluster_parallelism (line 206) | def test_run_cluster_parallelism():

FILE: test/test_train_processing_models_command.py
  function setup_module (line 24) | def setup_module():
  function make_dataset (line 47) | def make_dataset(num=10000):
  function run_and_check (line 83) | def run_and_check(n_jobs=0, additional_args=[], delete=False):
  function Xtest_run_parallel (line 149) | def Xtest_run_parallel():
  function test_run_serial (line 153) | def test_run_serial():

FILE: test/test_training_variants.py
  function setup_teardown (line 21) | def setup_teardown():
  function _seed (line 27) | def _seed(s=42):
  function _make_model (line 33) | def _make_model(**overrides):
  function test_train_with_locally_connected (line 59) | def test_train_with_locally_connected():
  function test_train_with_dropout (line 81) | def test_train_with_dropout():
  function test_train_with_batch_normalization (line 100) | def test_train_with_batch_normalization():
  function test_train_lc_dropout_batchnorm (line 120) | def test_train_lc_dropout_batchnorm():
  function test_train_with_skip_connections (line 143) | def test_train_with_skip_connections():
  function test_train_with_peptide_dense_layers (line 162) | def test_train_with_peptide_dense_layers():
  function test_train_with_optimizer (line 182) | def test_train_with_optimizer(optimizer):
  function test_train_with_l2_regularization (line 202) | def test_train_with_l2_regularization():
  function test_train_with_l1_l2_regularization (line 221) | def test_train_with_l1_l2_regularization():
  function test_train_with_random_negatives (line 241) | def test_train_with_random_negatives():
  function test_train_with_early_stopping (line 261) | def test_train_with_early_stopping():
  function test_serialization_with_lc_dropout_batchnorm (line 285) | def test_serialization_with_lc_dropout_batchnorm():
  function test_train_mixed_lengths_with_lc (line 314) | def test_train_mixed_lengths_with_lc():
  function _random_aa (line 345) | def _random_aa(choices, rng):
  function _generate_a0201_binder (line 349) | def _generate_a0201_binder(rng, length=9):
  function _generate_non_binder (line 357) | def _generate_non_binder(rng, length=9):
  function test_learn_a0201_motif (line 367) | def test_learn_a0201_motif():