def get_documentation():
doc = str(Coefficients.__doc__)
valid_values = str([option.name for option in CoefficientPlottingSetting])[1:-1].replace("'", "`")
mapping = {
"For options see :py:obj:`~source.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting`.":
f"Valid values are: {valid_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(SequenceCountEncoder.__doc__)
valid_field_values = str(Repertoire.FIELDS)[1:-1].replace("'", "`")
mapping = {
"Valid comparison value can be any repertoire field name.": f"Valid values are {valid_field_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(Word2VecEncoder.__doc__)
valid_values = str([model_type.name for model_type in ModelType])[1:-1].replace("'", "`")
mapping = {
"Valid values for this parameter are names of the ModelType enum.": f"Valid values are {valid_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(SVM.__doc__)
mapping = {
"For usage instructions, check :py:obj:`~immuneML.ml_methods.SklearnMethod.SklearnMethod`.": SklearnMethod.get_usage_documentation("SVM"),
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(LogisticRegression.__doc__)
mapping = {
"For usage instructions, check :py:obj:`~source.ml_methods.SklearnMethod.SklearnMethod`.":
SklearnMethod.get_usage_documentation("LogisticRegression"),
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(SplitConfig.__doc__)
mapping = {
"split_strategy (SplitType)": "split_strategy",
"reports (ReportConfig)": "reports",
"manual_config (:py:obj:`~immuneML.hyperparameter_optimization.config.ManualSplitConfig.ManualSplitConfig`)": "manual_config",
"leave_one_out_config (:py:obj:`~immuneML.hyperparameter_optimization.config.LeaveOneOutConfig.LeaveOneOutConfig`)": "leave_one_out_config"
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(MatchedRegexEncoder.__doc__)
chain_values = str([region_type.value for region_type in Chain])[1:-1].replace("'", "`")
mapping = {
"The chains are specified by their three letter code, see :py:obj:`~immuneML.data_model.receptor.receptor_sequence.Chain.Chain`.": f"The chains are specified by their three letter code, valid values are: {chain_values}.",
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(RandomForestClassifier.__doc__)
mapping = {
"For usage instructions, check :py:obj:`~source.ml_methods.SklearnMethod.SklearnMethod`.":
SklearnMethod.get_usage_documentation("RandomForestClassifier"),
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(AtchleyKmerEncoder.__doc__)
valid_values = str([item.name for item in RelativeAbundanceType])[1:-1].replace("'", "`")
mapping = {
"how to compute abundance term for k-mers":
f"how to compute abundance term for k-mers; valid values are {valid_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(ReportConfig.__doc__)
mapping = {
"data_splits (dict)": "data_splits",
"models (dict)": "models",
"data (dict)": "data",
"encoding (dict)": "encoding"
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(DuplicateSequenceFilter.__doc__)
mapping = {
"Valid options are defined by the CountAggregationFunction enum.": f"Valid values are: {[e.name for e in CountAggregationFunction]}.",
"Valid options are defined by the SequenceType enum.": f"Valid values are: {[e.name for e in SequenceType]}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(DatasetExportInstruction.__doc__)
valid_strategy_values = ReflectionHandler.all_nonabstract_subclass_basic_names(DataExporter, "Exporter", "dataset_export/")
valid_strategy_values = str(valid_strategy_values)[1:-1].replace("'", "`")
mapping = {
"Valid formats are class names of any non-abstract class inheriting "
":py:obj:`~immuneML.IO.dataset_export.DataExporter.DataExporter`.": f"Valid values are: {valid_strategy_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(IGoRImport.__doc__)
region_type_values = str([region_type.name for region_type in RegionType])[1:-1].replace("'", "`")
repertoire_fields = list(Repertoire.FIELDS)
repertoire_fields.remove("region_types")
mapping = {
"Valid values for region_type are the names of the :py:obj:`~immuneML.data_model.receptor.RegionType.RegionType` enum.": f"Valid values are {region_type_values}.",
"Valid immuneML fields that can be specified here are defined by Repertoire.FIELDS": f"Valid immuneML fields that can be specified here are {repertoire_fields}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(OLGAImport.__doc__)
region_type_values = str([
region_type.name for region_type in RegionType
])[1:-1].replace("'", "`")
mapping = {
"Valid values for region_type are the names of the :py:obj:`~immuneML.data_model.receptor.RegionType.RegionType` enum.":
f"Valid values are {region_type_values}.",
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(DistanceEncoder.__doc__)
valid_values = [metric.name for metric in DistanceMetricType]
valid_values = str(valid_values)[1:-1].replace("'", "`")
valid_field_values = str(Repertoire.FIELDS)[1:-1].replace("'", "`")
mapping = {
"Names of different distance metric types are allowed values in the specification.": f"Valid values are: {valid_values}.",
"Valid values include any repertoire attribute (sequence, amino acid sequence, V gene etc).":
f"Valid values are {valid_field_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(FeatureValueBarplot.__doc__)
error_bar = DocEnumHelper.get_enum_names(ErrorBarMeaning)
panel_layout = DocEnumHelper.get_enum_names_and_values(PanelLayoutType)
panel_axis_scales = DocEnumHelper.get_enum_names_and_values(PanelAxisScalesType)
panel_label_switch_type = DocEnumHelper.get_enum_names_and_values(PanelLabelSwitchType)
mapping = {
"For options see :py:obj:`~source.visualization.ErrorBarMeaning.ErrorBarMeaning`.": f"Valid values are: {error_bar}.",
"For options see :py:obj:`~source.visualization.PanelLayoutType.PanelLayoutType`.": f"Valid values are: {panel_layout}",
"For options see :py:obj:`~source.visualization.PanelAxisScalesType.PanelAxisScalesType`.": f"Valid values are: {panel_axis_scales}",
"For options see :py:obj:`~source.visualization.PanelLabelSwitchType.PanelLabelSwitchType`.": f"Valid values are: {panel_label_switch_type}"
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
initial_doc = str(Signal.__doc__)
valid_implanting_values = str(
ReflectionHandler.all_nonabstract_subclass_basic_names(
SignalImplantingStrategy, 'Implanting',
'signal_implanting_strategy/'))[1:-1].replace("'", "`")
docs_mapping = {
"Valid values for this argument are class names of different signal implanting strategies.":
f"Valid values are: {valid_implanting_values}"
}
doc = update_docs_per_mapping(initial_doc, docs_mapping)
return doc
def get_documentation():
doc = str(Motif.__doc__)
valid_strategy_values = ReflectionHandler.all_nonabstract_subclass_basic_names(
MotifInstantiationStrategy, "Instantiation",
"motif_instantiation_strategy/")
valid_strategy_values = str(valid_strategy_values)[1:-1].replace(
"'", "`")
chain_values = str([name for name in Chain])[1:-1].replace("'", "`")
mapping = {
"It should be one of the classes inheriting MotifInstantiationStrategy.":
f"Valid values are: {valid_strategy_values}.",
"The value should be an instance of :py:obj:`~source.data_model.receptor.receptor_sequence.Chain.Chain`.":
f"Valid values are: {chain_values}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(SingleLineReceptorImport.__doc__)
valid_chain_names = str([item.name for item in Chain])[1:-1].replace("'", "`")
valid_chain_pair_names = str([item.name for item in ChainPair])[1:-1].replace("'", "`")
region_type_values = str([region_type.name for region_type in RegionType])[1:-1].replace("'", "`")
mapping = {
"The possible names that can be filled in for <chain> are given in :py:obj:`~immuneML.data_model.receptor.receptor_sequence.Chain.Chain`":
f"The possible names that can be filled in for <chain> are: {valid_chain_names}.",
"Valid values for receptor_chains are the names of the :py:obj:`~immuneML.data_model.receptor.ChainPair.ChainPair` enum.":
f"Valid values for receptor_chains are: {valid_chain_pair_names}.",
"Valid values for region_type are the names of the :py:obj:`~immuneML.data_model.receptor.RegionType.RegionType` enum.": f"Valid values are {region_type_values}.",
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(MiXCRImport.__doc__)
region_type_values = str([
region_type.name
for region_type in MiXCRImport.SEQUENCE_NAME_MAP.keys()
])[1:-1].replace("'", "`")
repertoire_fields = list(Repertoire.FIELDS)
repertoire_fields.remove("region_types")
mapping = {
"Valid values for region_type are defined in MiXCRImport.SEQUENCE_NAME_MAP.":
f"Valid values are {region_type_values}.",
"Valid immuneML fields that can be specified here are defined by Repertoire.FIELDS":
f"Valid immuneML fields that can be specified here are {repertoire_fields}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc
def get_documentation():
doc = str(TrainMLModelInstruction.__doc__)
valid_values = str([metric.name.lower() for metric in Metric])[1:-1].replace("'", "`")
valid_strategies = str(ReflectionHandler.all_nonabstract_subclass_basic_names(HPOptimizationStrategy, "",
"hyperparameter_optimization/strategy/"))[1:-1]\
.replace("'", "`")
mapping = {
"dataset (Dataset)": "dataset",
"hp_strategy (HPOptimizationStrategy)": "strategy",
"hp_settings": "settings",
"assessment (SplitConfig)": "assessment",
"selection (SplitConfig)": "selection",
"optimization_metric (Metric)": "optimization_metric",
"label_configuration (LabelConfiguration)": "labels (list)",
"data_reports": "reports",
"a list of metrics": f"a list of metrics ({valid_values})",
"a metric to use for optimization": f"a metric to use for optimization (one of {valid_values})",
"Valid values are objects of any class inheriting :py:obj:`~immuneML.hyperparameter_optimization.strategy."
"HPOptimizationStrategy.HPOptimizationStrategy`.": f"Valid values are: {valid_strategies}.",
"the reports to be specified here have to be :py:obj:`~immuneML.reports.train_ml_model_reports.TrainMLModelReport.TrainMLModelReport` reports.": f"the reports that can be provided here are :ref:`{TrainMLModelReport.get_title()}`."
}
doc = update_docs_per_mapping(doc, mapping)
return doc