def make_simulation_docs(path: Path):
instantiations = ReflectionHandler.all_nonabstract_subclasses(
MotifInstantiationStrategy, "Instantiation",
"motif_instantiation_strategy/")
instantiations = [
DocumentationFormat(inst,
inst.__name__.replace('Instantiation', ""),
DocumentationFormat.LEVELS[2])
for inst in instantiations
]
implanting_strategies = ReflectionHandler.all_nonabstract_subclasses(
SignalImplantingStrategy, 'Implanting',
'signal_implanting_strategy/')
implanting_strategies = [
DocumentationFormat(implanting,
implanting.__name__.replace('Implanting', ""),
DocumentationFormat.LEVELS[2])
for implanting in implanting_strategies
]
classes_to_document = [DocumentationFormat(Motif, Motif.__name__, DocumentationFormat.LEVELS[1])] + instantiations + \
[DocumentationFormat(Signal, Signal.__name__, DocumentationFormat.LEVELS[1])] + implanting_strategies + \
[DocumentationFormat(Implanting, Implanting.__name__, DocumentationFormat.LEVELS[1])]
file_path = path / "simulation.rst"
with file_path.open("w") as file:
for doc_format in classes_to_document:
write_class_docs(doc_format, file)
def generate_docs(path: Path):
inst_path = PathBuilder.build(path / "instructions")
instructions = sorted(ReflectionHandler.all_nonabstract_subclasses(
Instruction, "Instruction", subdirectory='instructions/'),
key=lambda x: x.__name__)
inst_paths = {}
for instruction in instructions:
instruction_name = instruction.__name__[:-11]
if hasattr(InstructionParser,
f"make_{instruction_name.lower()}_docs"):
fn = getattr(InstructionParser,
f"make_{instruction_name.lower()}_docs")
file_path = fn(inst_path)
else:
file_path = InstructionParser.make_docs(
instruction, instruction_name, inst_path)
inst_paths[instruction_name] = file_path
inst_file_path = inst_path / "instructions.rst"
with inst_file_path.open('w') as file:
for key, item in inst_paths.items():
lines = f"{key}\n---------------------------\n.. include:: {os.path.relpath(item, EnvironmentSettings.source_docs_path)}\n"
file.writelines(lines)
def make_reports_docs(path: Path):
filename = "reports.rst"
file_path = path / filename
with file_path.open("w") as file:
pass
for report_type_class in [
DataReport, EncodingReport, MLReport, TrainMLModelReport,
MultiDatasetReport
]:
with file_path.open("a") as file:
doc_format = DocumentationFormat(
cls=report_type_class,
cls_name=f"**{report_type_class.get_title()}**",
level_heading=DocumentationFormat.LEVELS[1])
write_class_docs(doc_format, file)
subdir = DefaultParamsLoader.convert_to_snake_case(
report_type_class.__name__) + "s"
classes = ReflectionHandler.all_nonabstract_subclasses(
report_type_class, "", f"reports/{subdir}/")
make_docs(path, classes, filename, "", "a")
def parse_commandline_arguments(args):
ReflectionHandler.get_classes_by_partial_name("", "ml_methods/")
ml_method_names = [
cl.__name__
for cl in ReflectionHandler.all_nonabstract_subclasses(MLMethod)
] + ["SimpleLogisticRegression"]
parser = argparse.ArgumentParser(
description="tool for building immuneML Galaxy YAML from arguments")
parser.add_argument(
"-o",
"--output_path",
required=True,
help="Output location for the generated yaml file (directiory).")
parser.add_argument(
"-f",
"--file_name",
default="specs.yaml",
help=
"Output file name for the yaml file. Default name is 'specs.yaml' if not specified."
)
parser.add_argument(
"-l",
"--labels",
required=True,
help=
"Which metadata labels should be predicted for the dataset (separated by comma)."
)
parser.add_argument(
"-m",
"--ml_methods",
nargs="+",
choices=ml_method_names,
required=True,
help="Which machine learning methods should be applied.")
parser.add_argument("-t",
"--training_percentage",
type=float,
required=True,
help="The percentage of data used for training.")
parser.add_argument(
"-c",
"--split_count",
type=int,
required=True,
help=
"The number of times to repeat the training process with a different random split of the data."
)
parser.add_argument(
"-s",
"--sequence_type",
choices=["complete", "subsequence"],
default=["subsequence"],
nargs="+",
help="Whether complete CDR3 sequences are used, or k-mer subsequences."
)
parser.add_argument(
"-p",
"--position_type",
choices=["invariant", "positional"],
nargs="+",
help=
"Whether IMGT-positional information is used for k-mers, or the k-mer positions are position-invariant."
)
parser.add_argument("-g",
"--gap_type",
choices=["gapped", "ungapped"],
nargs="+",
help="Whether the k-mers contain gaps.")
parser.add_argument("-k", "--k", type=int, nargs="+", help="K-mer size.")
parser.add_argument("-kl",
"--k_left",
type=int,
nargs="+",
help="Length before gap when k-mers are used.")
parser.add_argument("-kr",
"--k_right",
type=int,
nargs="+",
help="Length after gap when k-mers are used.")
parser.add_argument("-gi",
"--min_gap",
type=int,
nargs="+",
help="Minimal gap length when gapped k-mers are used.")
parser.add_argument("-ga",
"--max_gap",
type=int,
nargs="+",
help="Maximal gap length when gapped k-mers are used.")
parser.add_argument(
"-r",
"--reads",
choices=[ReadsType.UNIQUE.value, ReadsType.ALL.value],
nargs="+",
default=[ReadsType.UNIQUE.value],
help=
"Whether k-mer counts should be scaled by unique clonotypes or all observed receptor sequences"
)
return parser.parse_args(args)
def make_preprocessing_docs(path: Path):
classes = ReflectionHandler.all_nonabstract_subclasses(
Preprocessor, "", "preprocessing/")
make_docs(path, classes, "preprocessings.rst", "")
def make_ml_methods_docs(path: Path):
classes = ReflectionHandler.all_nonabstract_subclasses(
MLMethod, "", "ml_methods/")
make_docs(path, classes, "ml_methods.rst", "")
def make_dataset_docs(path: Path):
import_classes = ReflectionHandler.all_nonabstract_subclasses(
DataImport, "Import", "dataset_import/")
make_docs(path, import_classes, "datasets.rst", "Import")
