diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index b1d319f..990090e 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [macos-latest, ubuntu-latest, windows-latest] - python: ["3.9", "3.10"] + python: ["3.11", "3.12"] steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml index 5bcbb6d..4a48197 100644 --- a/.github/workflows/publish_docs.yml +++ b/.github/workflows/publish_docs.yml @@ -13,7 +13,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9 + python-version: 3.11 - name: Install pip run: | diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 65a296f..4a4eaca 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -16,14 +16,14 @@ jobs: fail-fast: false matrix: include: - - { python-version: "3.10", os: ubuntu-latest, session: "pre-commit" } - - { python-version: "3.10", os: ubuntu-latest, session: "safety" } - - { python-version: "3.10", os: ubuntu-latest, session: "mypy" } - - { python-version: "3.10", os: ubuntu-latest, session: "tests" } - - { python-version: "3.10", os: windows-latest, session: "tests" } - - { python-version: "3.10", os: ubuntu-latest, session: "typeguard" } - - { python-version: "3.10", os: ubuntu-latest, session: "xdoctest" } - - { python-version: "3.10", os: ubuntu-latest, session: "docs-build" } + - { python-version: "3.11", os: ubuntu-latest, session: "pre-commit" } + - { python-version: "3.11", os: ubuntu-latest, session: "safety" } + - { python-version: "3.11", os: ubuntu-latest, session: "mypy" } + - { python-version: "3.11", os: ubuntu-latest, session: "tests" } + - { python-version: "3.11", os: windows-latest, session: "tests" } + - { python-version: "3.11", os: ubuntu-latest, session: "typeguard" } + - { python-version: "3.11", os: ubuntu-latest, session: "xdoctest" } + - { python-version: "3.11", os: ubuntu-latest, session: "docs-build" } env: NOXSESSION: ${{ matrix.session }} diff --git a/docs/API.rst b/docs/API.rst deleted file mode 100644 index cb55f7e..0000000 --- a/docs/API.rst +++ /dev/null @@ -1,29 +0,0 @@ -.. module:: drevalpy - -.. automodule:: drevalpy - :noindex: - -API -=== - -Import DrEvalPy using - -.. code-block:: python - - import drevalpy as dep - -.. - Models module: :code:`models` - ------------------------- - - .. module:: devalpy.models - - .. currentmodule:: drevalpy - - Available models - ~~~~~~~~~~~~~~~~ - - .. autosummary:: - :toctree: api/models - - models.baselines \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 491b879..75cc372 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -16,9 +16,7 @@ from jinja2.defaults import DEFAULT_FILTERS -import drevalpy - -sys.path.insert(0, os.path.abspath("../")) +sys.path.insert(0, os.path.abspath("..")) # -- General configuration --------------------------------------------- @@ -58,9 +56,9 @@ # the built documents. # # The short X.Y version. -version = drevalpy.__version__ +version = "1.0.10" # The full version, including alpha/beta/rc tags. -release = drevalpy.__version__ +release = "1.0.10" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/requirements.txt b/docs/requirements.txt index 521aa7c..9cd98f2 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,4 @@ -sphinx-autobuild==2024.10.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -sphinx-autodoc-typehints==2.3.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -sphinx-click==6.0.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -sphinx-rtd-theme==3.0.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" --e . +sphinx-autobuild==2024.10.3 ; python_version >= "3.11" and python_version < "3.13" +sphinx-autodoc-typehints==2.5.0 ; python_version >= "3.11" and python_version < "3.13" +sphinx-click==6.0.0 ; python_version >= "3.11" and python_version < "3.13" +sphinx-rtd-theme==3.0.2 ; python_version >= "3.11" and python_version < "3.13" diff --git a/drevalpy/datasets/curvecurator.py b/drevalpy/datasets/curvecurator.py new file mode 100644 index 0000000..f6ed52e --- /dev/null +++ b/drevalpy/datasets/curvecurator.py @@ -0,0 +1,224 @@ +""" +Contains all function required for CurveCurator fitting. + +CurveCurator publication: +Bayer, F.P., Gander, M., Kuster, B. et al. CurveCurator: a recalibrated F-statistic to assess, +classify, and explore significance of dose–response curves. Nat Commun 14, 7902 (2023). +https://doi-org.eaccess.tum.edu/10.1038/s41467-023-43696-z + +CurveCurator applies a recalibrated F-statistic for p-value estimation of 4-point log-logistic +regression fits. In drevalpy, this can be used to generate training data with higher quality, since +quality measures, such as p-value, R2, or relevance score can be used to filter out viability +measurements of low quality. +""" + +import subprocess +from pathlib import Path + +import numpy as np +import pandas as pd +import toml + +from ..pipeline_function import pipeline_function + + +def _prepare_raw_data(curve_df: pd.DataFrame, output_dir: str | Path): + required_columns = ["dose", "response", "sample", "drug"] + if not all([col in curve_df.columns for col in required_columns]): + raise ValueError("Missing columns in viability data. Required columns are {required_columns}.") + if "replicate" in curve_df.columns: + required_columns.append("replicate") + curve_df = curve_df[required_columns] + n_replicates = 1 + conc_columns = ["dose"] + has_multicol_index = False + if "replicate" in curve_df.columns: + n_replicates = curve_df["replicate"].nunique() + conc_columns.append("replicate") + has_multicol_index = True + + df = curve_df.pivot(index=["sample", "drug"], columns=conc_columns, values="response") + + for i in range(n_replicates): + df.insert(0, (0.0, n_replicates - i), 1.0) + + concentrations = df.columns.sort_values() + df = df[concentrations] + + experiments = np.arange(df.shape[1]) + df.insert(0, "Name", df.index.map(lambda x: f"{x[0]}|{x[1]}")) + df.columns = ["Name"] + [f"Raw {i}" for i in experiments] + + curvecurator_folder = Path(output_dir) + curvecurator_folder.mkdir(exist_ok=True, parents=True) + df.to_csv(curvecurator_folder / "curvecurator_input.tsv", sep="\t", index=False) + + if has_multicol_index: + doses = [pair[0] for pair in concentrations] + else: + doses = concentrations.to_list() + return len(experiments), doses, n_replicates, len(df) + + +def _prepare_toml(filename: str, n_exp: int, n_replicates: int, doses: list[float], dataset_name: str, cores: int): + config = { + "Meta": { + "id": filename, + "description": dataset_name, + "condition": "drug", + "treatment_time": "72 h", + }, + "Experiment": { + "experiments": range(n_exp), + "doses": doses, + "dose_scale": "1e-06", + "dose_unit": "M", + "control_experiment": [i for i in range(n_replicates)], + "measurement_type": "OTHER", + "data_type": "OTHER", + "search_engine": "OTHER", + "search_engine_version": "0", + }, + "Paths": { + "input_file": "curvecurator_input.tsv", + "curves_file": "curves.txt", + "normalization_file": "norm.txt", + "mad_file": "mad.txt", + "dashboard": "dashboard.html", + }, + "Processing": { + "available_cores": cores, + "max_missing": max(len(doses) - 5, 0), + "imputation": False, + "normalization": False, + }, + "Curve Fit": { + "type": "OLS", + "speed": "exhaustive", + "max_iterations": 1000, + "interpolation": False, + "control_fold_change": True, + }, + "F Statistic": { + "optimized_dofs": True, + "alpha": 0.05, + "fc_lim": 0.45, + }, + } + return config + + +def _exec_curvecurator(output_dir: Path): + command = ["CurveCurator", str(output_dir / "config.toml"), "--mad"] + process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + process.communicate() + + +def _calc_ic50(model_params_df: pd.DataFrame): + """ + Calculate the IC50 from a fitted model. + + This function expects a dataframe that was processed in the postprocess function, containing + the columns "Front", "Back", "Slope", "pEC50". It calculates the IC50 for all the models in the + dataframe in closed form and adds the column IC50_curvecurator to the input dataframe. + + :param model_params_df: a dataframe containing the fitted parameters + """ + + def ic50(front, back, slope, pec50): + return (np.log10((front - back) / (0.5 + back)) - slope * pec50) / slope + + front = model_params_df["Front"].values + back = model_params_df["Back"].values + slope = model_params_df["Slope"].values + pec50 = model_params_df["pEC50"].values + + model_params_df["IC50_curvecurator"] = ic50(front, back, slope, pec50) + + +@pipeline_function +def preprocess(input_file: str | Path, output_dir: str | Path, dataset_name: str, cores: int): + """ + Preprocess raw viability data and create config.toml for use with CurveCurator. + + :param input_file: Path to csv file containing the raw viability data + :param output_dir: Path to store all the files to, including the preprocessed data, the config.toml + for CurveCurator, CurveCurator's output files, and the postprocessed data + :param dataset_name: Name of the dataset + :param cores: The number of cores to be used for fitting the curves using CurveCurator. + This parameter is written into the config.toml, but it is min of the number of curves to fit + and the number given (min(n_curves, cores)) + """ + input_file = Path(input_file) + output_dir = Path(output_dir) + curve_df = pd.read_csv(input_file) + + n_exp, doses, n_replicates, n_curves_to_fit = _prepare_raw_data(curve_df, output_dir) + cores = min(n_curves_to_fit, cores) + + config = _prepare_toml(input_file.name, n_exp, n_replicates, doses, dataset_name, cores) + with open(output_dir / "config.toml", "w") as f: + toml.dump(config, f) + + +@pipeline_function +def postprocess(output_folder: str | Path, dataset_name: str): + """ + Postprocess CurveCurator output file. + + This function reads the curves.txt file created by CurveCurator, which contains the + fitted curve parameters and postprocesses it to be used by drevalpy. + + :param output_folder: Path to the output folder of CurveCurator containin the curves.txt file. + :param dataset_name: The name of the dataset, will be used to prepend the postprocessed .csv file + """ + output_folder = Path(output_folder) + required_columns = { + "Name": "Name", + "pEC50": "pEC50", + "pEC50 Error": "pEC50Error", + "Curve Slope": "Slope", + "Curve Front": "Front", + "Curve Back": "Back", + "Curve Fold Change": "FoldChange", + "Curve AUC": "AUC", + "Curve R2": "R2", + "Curve P_Value": "pValue", + "Curve Relevance Score": "RelevanceScore", + "Curve F_Value": "fValue", + "Curve Log P_Value": "negLog10pValue", + "Signal Quality": "SignalQuality", + "Curve RMSE": "RMSE", + "Curve F_Value SAM Corrected": "fValueSAMCorrected", + "Curve Regulation": "Regulation", + } + fitted_curve_data = pd.read_csv(Path(output_folder) / "curves.txt", sep="\t", usecols=required_columns).rename( + columns=required_columns + ) + fitted_curve_data[["cell_line_id", "drug_id"]] = fitted_curve_data.Name.str.split("|", expand=True) + fitted_curve_data["EC50_curvecurator"] = np.power( + 10, -fitted_curve_data["pEC50"].values + ) # in CurveCurator 10^-pEC50 = EC50 + _calc_ic50(fitted_curve_data) + fitted_curve_data.to_csv(output_folder / f"{dataset_name}.csv", index=None) + + +def fit_curves(input_file: str | Path, output_dir: str | Path, dataset_name: str, cores: int): + """ + Fit curves for provided raw viability data. + + This functions reads viability data in a predefined input format, preprocesses the data + to be readable by CurveCurator, fits curves to the data using CurveCurator, and postprocesses + the fitted data to a format required by drevalpy. + + :param input_file: Path to the file containing the raw viability data + :param output_dir: Path to store all the files to, including the preprocessed data, the config.toml + for CurveCurator, CurveCurator's output files, and the postprocessed data + :param dataset_name: The name of the dataset, will be used to prepend the postprocessed .csv file + :param cores: The number of cores to be used for fitting the curves using CurveCurator. + This parameter is written into the config.toml, but it is min of the number of curves to fit + and the number given (min(n_curves, cores)) + """ + preprocess(input_file, output_dir, dataset_name, cores) + _exec_curvecurator(Path(output_dir)) + postprocess(output_dir, dataset_name) diff --git a/drevalpy/datasets/dataset.py b/drevalpy/datasets/dataset.py index 394c438..528e8f6 100644 --- a/drevalpy/datasets/dataset.py +++ b/drevalpy/datasets/dataset.py @@ -66,7 +66,10 @@ class DrugResponseDataset(Dataset): @classmethod def from_csv( - cls: type["DrugResponseDataset"], input_file: str | Path, dataset_name: str = "unknown" + cls: type["DrugResponseDataset"], + input_file: str | Path, + dataset_name: str = "unknown", + measure: str = "response", ) -> "DrugResponseDataset": """ Load a dataset from a csv file. @@ -80,6 +83,7 @@ def from_csv( :param input_file: Path to the csv file containing the data to be loaded :param dataset_name: Optional name to associate the dataset with, default = "unknown" + :param measure: The name of the column containing the measure to predict, default = "response" :returns: DrugResponseDataset object containing data from provided csv file. """ @@ -89,7 +93,7 @@ def from_csv( else: predictions = None return cls( - response=data["response"].values, + response=data[measure].values, cell_line_ids=data["cell_line_id"].values, drug_ids=data["drug_id"].values, predictions=predictions, diff --git a/drevalpy/datasets/loader.py b/drevalpy/datasets/loader.py index 396d32a..8ad8055 100644 --- a/drevalpy/datasets/loader.py +++ b/drevalpy/datasets/loader.py @@ -1,23 +1,30 @@ """Contains functions to load the GDSC1, GDSC2, CCLE, and Toy datasets.""" import os +from pathlib import Path from typing import Callable import pandas as pd from ..pipeline_function import pipeline_function +from .curvecurator import fit_curves from .dataset import DrugResponseDataset from .utils import download_dataset def load_gdsc1( - path_data: str = "data", file_name: str = "response_GDSC1.csv", dataset_name: str = "GDSC1" + path_data: str = "data", + measure: str = "LN_IC50", + file_name: str = "response_GDSC1.csv", + dataset_name: str = "GDSC1", ) -> DrugResponseDataset: """ Loads the GDSC1 dataset. :param path_data: Path to the dataset. :param file_name: File name of the dataset. + :param measure: The name of the column containing the measure to predict, default = "LN_IC50" + :param dataset_name: Name of the dataset. :return: DrugResponseDataset containing response, cell line IDs, and drug IDs. """ @@ -29,30 +36,36 @@ def load_gdsc1( response_data["DRUG_NAME"] = response_data["DRUG_NAME"].str.replace(",", "") return DrugResponseDataset( - response=response_data["LN_IC50"].values, + response=response_data[measure].values, cell_line_ids=response_data["CELL_LINE_NAME"].values, drug_ids=response_data["DRUG_NAME"].values, dataset_name=dataset_name, ) -def load_gdsc2(path_data: str = "data", file_name: str = "response_GDSC2.csv"): +def load_gdsc2(path_data: str = "data", measure: str = "LN_IC50", file_name: str = "response_GDSC2.csv"): """ Loads the GDSC2 dataset. :param path_data: Path to the dataset. :param file_name: File name of the dataset. + :param measure: The name of the column containing the measure to predict, default = "LN_IC50" + :return: DrugResponseDataset containing response, cell line IDs, and drug IDs. """ - return load_gdsc1(path_data=path_data, file_name=file_name, dataset_name="GDSC2") + return load_gdsc1(path_data=path_data, measure=measure, file_name=file_name, dataset_name="GDSC2") -def load_ccle(path_data: str = "data", file_name: str = "response_CCLE.csv") -> DrugResponseDataset: +def load_ccle( + path_data: str = "data", measure: str = "LN_IC50", file_name: str = "response_CCLE.csv" +) -> DrugResponseDataset: """ Loads the CCLE dataset. :param path_data: Path to the dataset. :param file_name: File name of the dataset. + :param measure: The name of the column containing the measure to predict, default = "LN_IC50" + :return: DrugResponseDataset containing response, cell line IDs, and drug IDs. """ dataset_name = "CCLE" @@ -64,34 +77,49 @@ def load_ccle(path_data: str = "data", file_name: str = "response_CCLE.csv") -> response_data["DRUG_NAME"] = response_data["DRUG_NAME"].str.replace(",", "") return DrugResponseDataset( - response=response_data["LN_IC50"].values, + response=response_data[measure].values, cell_line_ids=response_data["CELL_LINE_NAME"].values, drug_ids=response_data["DRUG_NAME"].values, dataset_name=dataset_name, ) -def load_toy(path_data: str = "data") -> DrugResponseDataset: +def load_toy(path_data: str = "data", measure: str = "response") -> DrugResponseDataset: """ Loads small Toy dataset, subsampled from GDSC1. :param path_data: Path to the dataset. + :param measure: The name of the column containing the measure to predict, default = "response" + :return: DrugResponseDataset containing response, cell line IDs, and drug IDs. """ dataset_name = "Toy_Data" + measure = "response" # overwrite this explicitly to avoid problems, should be changed in the future path = os.path.join(path_data, dataset_name, "toy_data.csv") if not os.path.exists(path): download_dataset(dataset_name, path_data, redownload=True) response_data = pd.read_csv(path) return DrugResponseDataset( - response=response_data["response"].values, + response=response_data[measure].values, cell_line_ids=response_data["cell_line_id"].values, drug_ids=response_data["drug_id"].values, dataset_name=dataset_name, ) +def load_custom(path_data: str | Path, measure: str = "response") -> DrugResponseDataset: + """ + Load custom dataset. + + :param path_data: Path to location of custom dataset + :param measure: The name of the column containing the measure to predict, default = "response" + + :return: DrugResponseDataset containing response, cell line IDs, and drug IDs + """ + return DrugResponseDataset.from_csv(path_data, measure=measure) + + AVAILABLE_DATASETS: dict[str, Callable] = { "GDSC1": load_gdsc1, "GDSC2": load_gdsc2, @@ -101,16 +129,45 @@ def load_toy(path_data: str = "data") -> DrugResponseDataset: @pipeline_function -def load_dataset(dataset_name: str, path_data: str = "data") -> DrugResponseDataset: +def load_dataset( + dataset_name: str, path_data: str = "data", measure: str = "response", curve_curator: bool = False, cores: int = 1 +) -> DrugResponseDataset: """ Load a dataset based on the dataset name. - :param dataset_name: The name of the dataset to load ('GDSC1', 'GDSC2', 'CCLE', or 'Toy_Data'). - :param path_data: The path to the dataset. + :param dataset_name: The name of the dataset to load. Can be one of ('GDSC1', 'GDSC2', 'CCLE', or 'Toy_Data') + to download provided datasets, or any other name to allow for custom datasets. + :param path_data: The parent path in which custom or downloaded datasets should be located, or in which raw + viability data is to be found for fitting with CurveCurator (see param curve_curator for details). + The location of the datasets are resolved by //.csv. + :param measure: The name of the column containing the measure to predict, default = "response". + If curve_curator is True, this measure is appended with "_curvecurator", e.g. "response_curvecurator" to + distinguish between measures provided by the original source of a dataset, or the measures fit by + CurveCurator. + :param curve_curator: If True, the measure is appended with "_curvecurator". + If a custom dataset_name was provided, this will invoke the fitting procedure of raw viability data, + which is expected to exist at //_raw.csv. The fitted dataset will + be stored in the same folder, in a file called .csv + :param cores: Number of cores to use for CurveCurator fitting. Only used when curve_curator is True, default = 1 :return: A DrugResponseDataset containing response, cell line IDs, drug IDs, and dataset name. - :raises ValueError: If the dataset name is unknown. + :raises FileNotFoundError: If the custom dataset or raw viability data could not be found at the given path. """ - if dataset_name in AVAILABLE_DATASETS: - return AVAILABLE_DATASETS[dataset_name](path_data) # type: ignore + if curve_curator: + measure += "_curvecurator" + input_file = Path(path_data) / dataset_name / f"{dataset_name}_raw.csv" else: - raise ValueError(f"Unknown dataset name: {dataset_name}") + input_file = Path(path_data) / dataset_name / f"{dataset_name}.csv" + + if dataset_name in AVAILABLE_DATASETS: + return AVAILABLE_DATASETS[dataset_name](path_data, measure) # type: ignore + + if input_file.is_file(): + if curve_curator: + fit_curves( + input_file=input_file, + output_dir=input_file.parent, + dataset_name=dataset_name, + cores=cores, + ) + return load_custom(Path(path_data) / dataset_name / f"{dataset_name}.csv", measure=measure) + raise FileNotFoundError(f"Custom dataset does not exist at given path: {input_file}") diff --git a/drevalpy/utils.py b/drevalpy/utils.py index a4c7df7..0962407 100644 --- a/drevalpy/utils.py +++ b/drevalpy/utils.py @@ -126,6 +126,21 @@ def get_parser() -> argparse.ArgumentParser: default=False, help="Whether to run " "CurveCurator " "to sort out " "non-reactive " "curves", ) + + parser.add_argument( + "--curve_curator_cores", + type=int, + default=1, + help="Max. number of cores used to fit curves with CurveCurator following min(cores, #curves to fit).", + ) + + parser.add_argument( + "--measure", + type=str, + default="LN_IC50", + help="The drug response measure used as prediction target. Can be one of ['LN_IC50', 'response']", + ) + parser.add_argument( "--overwrite", action="store_true", @@ -170,8 +185,7 @@ def check_arguments(args) -> None: :param args: arguments passed from the command line :raises AssertionError: if any of the arguments is invalid - :raises NotImplementedError: because CurveCurator is not implemented yet - :raises ValueError: if the number of cross-validation splits is less than 1 + :raises ValueError: if the number of cross-validation splits or curve_curator_cores is less than 1 """ if not args.models: raise AssertionError("At least one model must be specified") @@ -212,7 +226,7 @@ def check_arguments(args) -> None: os.makedirs(args.path_data, exist_ok=True) if args.n_cv_splits <= 1: - raise ValueError("Number of cross-validation splits must be greater than 1") + raise ValueError("Number of cross-validation splits must be greater than 1.") # TODO Allow for custom randomization tests maybe via config file if args.randomization_mode[0] != "None": @@ -221,9 +235,15 @@ def check_arguments(args) -> None: "At least one invalid randomization mode. Available randomization modes are SVCC, " "SVRC, SVSC, SVRD" ) if args.curve_curator: - raise NotImplementedError("CurveCurator not implemented") + if args.curve_curator_cores < 1: + raise ValueError("Number of cores for CurveCurator must be greater than 0.") + + if args.measure not in ["LN_IC50", "response"]: + raise ValueError("Only 'LN_IC50' and 'response' are currently available as a drug response measure.") + if args.response_transformation not in ["None", "standard", "minmax", "robust"]: raise AssertionError("Invalid response_transformation. Choose from None, standard, minmax, robust") + if args.optim_metric not in AVAILABLE_METRICS: raise AssertionError( f"Invalid optim_metric for hyperparameter tuning. Choose from" f" {list(AVAILABLE_METRICS.keys())}" @@ -243,6 +263,9 @@ def main(args) -> None: dataset_name=args.dataset_name, cross_study_datasets=args.cross_study_datasets, path_data=args.path_data, + measure=args.measure, + curve_curator=args.curve_curator, + cores=args.curve_curator_cores, ) models = [MODEL_FACTORY[model] for model in args.models] @@ -279,20 +302,43 @@ def main(args) -> None: def get_datasets( - dataset_name: str, cross_study_datasets: list, path_data: str = "data" + dataset_name: str, + cross_study_datasets: list, + path_data: str = "data", + measure: str = "response", + curve_curator: bool = False, + cores: int = 1, ) -> tuple[DrugResponseDataset, Optional[list[DrugResponseDataset]]]: """ Load the response data and cross-study datasets. - :param dataset_name: name of the dataset - :param cross_study_datasets: list of cross-study datasets - :param path_data: path to the data directory, default is "data" + :param dataset_name: The name of the dataset to load. Can be one of ('GDSC1', 'GDSC2', 'CCLE', or 'Toy_Data') + to download provided datasets, or any other name to allow for custom datasets. + :param cross_study_datasets: list of cross-study datasets. CurveCurator is not applicable to these. If you wish + to provide custom cross_study_datasets, you have to invoke curve fitting manually using + drevalpy.datasets.curvecurator.fit_curves + :param path_data: The parent path in which custom or downloaded datasets should be located, or in which raw + viability data is to be found for fitting with CurveCurator (see param curve_curator for details). + The location of the datasets are resolved by //.csv. + :param measure: The name of the column containing the measure to predict, default = "response". + If curve_curator is True, this measure is appended with "_curvecurator", e.g. "response_curvecurator" to + distinguish between measures provided by the original source of a dataset, or the measures fit by + CurveCurator. + :param curve_curator: If True, the measure is appended with "_curvecurator". + If a custom dataset_name was provided, this will invoke the fitting procedure of raw viability data, + which is expected to exist at //_raw.csv. The fitted dataset will + be stored in the same folder, in a file called .csv + :param cores: Number of cores to use for CurveCurator fitting. Only used when curve_curator is True, default = 1 :returns: response data and, potentially, cross-study datasets """ # PIPELINE: LOAD_RESPONSE - response_data = load_dataset(dataset_name=dataset_name, path_data=path_data) + response_data = load_dataset( + dataset_name=dataset_name, path_data=path_data, measure=measure, curve_curator=curve_curator, cores=cores + ) - cross_study_datasets = [load_dataset(dataset_name=dn, path_data=path_data) for dn in cross_study_datasets] + cross_study_datasets = [ + load_dataset(dataset_name=dn, path_data=path_data, measure=measure) for dn in cross_study_datasets + ] return response_data, cross_study_datasets diff --git a/noxfile.py b/noxfile.py index fc5cb95..dfc9e41 100644 --- a/noxfile.py +++ b/noxfile.py @@ -18,7 +18,7 @@ sys.exit(1) package = "drevalpy" -python_versions = ["3.10", "3.11"] +python_versions = ["3.11", "3.12"] nox.options.sessions = ( "pre-commit", "safety", @@ -147,7 +147,7 @@ def mypy(session: Session) -> None: """ args = session.posargs or ["drevalpy", "tests", "docs/conf.py"] session.install(".") - session.install("mypy", "pytest", "types-requests", "types-attrs", "types-PyYAML") + session.install("mypy", "pytest", "types-requests", "types-attrs", "types-PyYAML", "types-toml") session.run("mypy", *args) @@ -158,7 +158,7 @@ def tests(session: Session) -> None: :param session: The Session object. """ - session.install(".") + session.install(".[fit]") session.install("coverage[toml]", "pytest", "pygments") try: session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs) @@ -194,7 +194,7 @@ def typeguard(session: Session) -> None: :param session: The Session object. 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line-length = 120 diff --git a/requirements.txt b/requirements.txt index e7afaf4..6606cf0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,86 +1,159 @@ -aiohappyeyeballs==2.4.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -aiohttp==3.11.4 ; python_version >= "3.9" and python_full_version <= "3.13.0" -aiosignal==1.3.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -async-timeout==5.0.1 ; python_version >= "3.9" and python_version < "3.11" -attrs==24.2.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -certifi==2024.8.30 ; python_version >= "3.9" and python_full_version <= "3.13.0" -charset-normalizer==3.4.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -click==8.1.7 ; python_version >= "3.9" and python_full_version <= "3.13.0" -colorama==0.4.6 ; python_version >= "3.9" and python_full_version <= "3.13.0" and platform_system == "Windows" -contourpy==1.3.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -cycler==0.12.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -filelock==3.16.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -flaky==3.8.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -fonttools==4.55.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -frozenlist==1.5.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -fsspec==2024.10.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -fsspec[http]==2024.10.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -idna==3.10 ; python_version >= "3.9" and python_full_version <= "3.13.0" -importlib-resources==6.4.5 ; python_version >= "3.9" and python_full_version <= "3.13.0" -jinja2==3.1.4 ; python_version >= "3.9" and python_full_version <= "3.13.0" -joblib==1.4.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -jsonschema-specifications==2024.10.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -jsonschema==4.23.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -kiwisolver==1.4.7 ; python_version >= "3.9" and python_full_version <= "3.13.0" -lightning-utilities==0.11.8 ; python_version >= "3.9" and python_full_version <= "3.13.0" -markupsafe==3.0.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -matplotlib==3.9.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -mpmath==1.3.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -msgpack==1.1.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -multidict==6.1.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -networkx==3.2.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -numpy==1.26.4 ; python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cublas-cu12==12.1.3.1 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cuda-cupti-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cuda-nvrtc-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cuda-runtime-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cudnn-cu12==9.1.0.70 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cufft-cu12==11.0.2.54 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-curand-cu12==10.3.2.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cusolver-cu12==11.4.5.107 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-cusparse-cu12==12.1.0.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-nccl-cu12==2.20.5 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-nvjitlink-cu12==12.6.77 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -nvidia-nvtx-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -packaging==24.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pandas-flavor==0.6.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pandas==2.2.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -patsy==1.0.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pillow==11.0.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pingouin==0.5.5 ; python_version >= "3.9" and python_full_version <= "3.13.0" -plotly==5.24.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -propcache==0.2.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -protobuf==5.28.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -psutil==6.1.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pyarrow==18.0.0 ; sys_platform != "darwin" and python_version >= "3.9" and python_full_version <= "3.13.0" or platform_machine != "x86_64" and python_version >= "3.9" and python_full_version <= "3.13.0" -pyparsing==3.2.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pytorch-lightning==2.4.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pytz==2024.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -pyyaml==6.0.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -ray[tune]==2.39.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -referencing==0.35.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -requests==2.32.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -rpds-py==0.21.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -scikit-learn==1.5.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -scipy==1.13.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -seaborn==0.13.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -setuptools==75.5.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -six==1.16.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -statsmodels==0.14.4 ; python_version >= "3.9" and python_full_version <= "3.13.0" -sympy==1.13.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -tabulate==0.9.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -tenacity==9.0.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -tensorboardx==2.6.2.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -threadpoolctl==3.5.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -torch-geometric==2.6.1 ; python_version >= "3.9" and python_full_version <= "3.13.0" -torch==2.4.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -torchmetrics==1.6.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -tqdm==4.67.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -triton==3.0.0 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version < "3.13" and python_version >= "3.9" -typing-extensions==4.12.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -tzdata==2024.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -urllib3==2.2.3 ; python_version >= "3.9" and python_full_version <= "3.13.0" -xarray==2024.7.0 ; python_version >= "3.9" and python_full_version <= "3.13.0" -yarl==1.17.2 ; python_version >= "3.9" and python_full_version <= "3.13.0" -zipp==3.21.0 ; python_version >= "3.9" and python_version < "3.10" +aiohappyeyeballs==2.4.3 ; python_version >= "3.11" and python_version < "3.13" +aiohttp==3.11.7 ; python_version >= "3.11" and python_version < "3.13" +aiosignal==1.3.1 ; python_version >= "3.11" and python_version < "3.13" +alabaster==1.0.0 ; python_version >= "3.11" and python_version < "3.13" +anyio==4.6.2.post1 ; python_version >= "3.11" and python_version < "3.13" +argcomplete==3.5.1 ; python_version >= "3.11" and python_version < "3.13" +attrs==24.2.0 ; python_version >= "3.11" and python_version < "3.13" +babel==2.16.0 ; python_version >= "3.11" and python_version < "3.13" +bandit==1.7.10 ; python_version >= "3.11" and python_version < "3.13" +black==24.10.0 ; python_version >= "3.11" and python_version < "3.13" +bokeh==3.4.3 ; python_version >= "3.11" and python_version < "3.13" +certifi==2024.8.30 ; python_version >= "3.11" and python_version < "3.13" +cfgv==3.4.0 ; python_version >= "3.11" and python_version < "3.13" +charset-normalizer==3.4.0 ; python_version >= "3.11" and python_version < "3.13" +click==8.1.7 ; python_version >= "3.11" and python_version < "3.13" +colorama==0.4.6 ; python_version >= "3.11" and python_version < "3.13" +colorlog==6.9.0 ; python_version >= "3.11" and python_version < "3.13" +contourpy==1.3.1 ; python_version >= "3.11" and python_version < "3.13" +curve-curator==0.5.1 ; python_version >= "3.11" and python_version < "3.13" +cycler==0.12.1 ; python_version >= "3.11" and python_version < "3.13" +darglint==1.8.1 ; python_version >= "3.11" and python_version < "3.13" +distlib==0.3.9 ; python_version >= "3.11" and python_version < "3.13" +docutils==0.21.2 ; python_version >= "3.11" and python_version < "3.13" +filelock==3.16.1 ; python_version >= "3.11" and python_version < "3.13" +flake8-bandit==4.1.1 ; python_version >= "3.11" and python_version < "3.13" +flake8-bugbear==24.10.31 ; python_version >= "3.11" and python_version < "3.13" +flake8-docstrings==1.7.0 ; python_version >= "3.11" and python_version < "3.13" +flake8-rst-docstrings==0.3.0 ; python_version >= "3.11" and python_version < "3.13" +flake8==7.1.1 ; python_version >= "3.11" and python_version < "3.13" +flaky==3.8.1 ; python_version >= "3.11" and python_version < "3.13" +fonttools==4.55.0 ; python_version >= "3.11" and python_version < "3.13" +frozenlist==1.5.0 ; python_version >= "3.11" and python_version < "3.13" +fsspec==2024.10.0 ; python_version >= "3.11" and python_version < "3.13" +fsspec[http]==2024.10.0 ; python_version >= "3.11" and python_version < "3.13" +h11==0.14.0 ; python_version >= "3.11" and python_version < "3.13" +identify==2.6.3 ; python_version >= "3.11" and python_version < "3.13" +idna==3.10 ; python_version >= "3.11" and python_version < "3.13" +imagesize==1.4.1 ; python_version >= "3.11" and python_version < "3.13" +importlib-resources==6.4.5 ; python_version >= "3.11" and python_version < "3.13" +iniconfig==2.0.0 ; python_version >= "3.11" and python_version < "3.13" +isort==5.13.2 ; python_version >= "3.11" and python_version < "3.13" +jinja2==3.1.4 ; python_version >= "3.11" and python_version < "3.13" +joblib==1.4.2 ; python_version >= "3.11" and python_version < "3.13" +jsonschema-specifications==2024.10.1 ; python_version >= "3.11" and python_version < "3.13" +jsonschema==4.23.0 ; python_version >= "3.11" and python_version < "3.13" +kiwisolver==1.4.7 ; python_version >= "3.11" and python_version < "3.13" +lightning-utilities==0.11.9 ; python_version >= "3.11" and python_version < "3.13" +markdown-it-py==3.0.0 ; python_version >= "3.11" and python_version < "3.13" +markupsafe==3.0.2 ; python_version >= "3.11" and python_version < "3.13" +matplotlib==3.9.2 ; python_version >= "3.11" and python_version < "3.13" +mccabe==0.7.0 ; python_version >= "3.11" and python_version < "3.13" +mdurl==0.1.2 ; python_version >= "3.11" and python_version < "3.13" +mpmath==1.3.0 ; python_version >= "3.11" and python_version < "3.13" +msgpack==1.1.0 ; python_version >= "3.11" and python_version < "3.13" +multidict==6.1.0 ; python_version >= "3.11" and python_version < "3.13" +mypy-extensions==1.0.0 ; python_version >= "3.11" and python_version < "3.13" +networkx==3.4.2 ; python_version >= "3.11" and python_version < "3.13" +nodeenv==1.9.1 ; python_version >= "3.11" and python_version < "3.13" +nox-poetry==1.0.3 ; python_version >= "3.11" and python_version < "3.13" +nox==2024.10.9 ; python_version >= "3.11" and python_version < "3.13" +numpy==1.26.4 ; python_version >= "3.11" and python_version < "3.13" +nvidia-cublas-cu12==12.1.3.1 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cuda-cupti-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cuda-nvrtc-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cuda-runtime-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cudnn-cu12==9.1.0.70 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cufft-cu12==11.0.2.54 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-curand-cu12==10.3.2.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cusolver-cu12==11.4.5.107 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-cusparse-cu12==12.1.0.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-nccl-cu12==2.20.5 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-nvjitlink-cu12==12.6.85 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +nvidia-nvtx-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.11" and python_version < "3.13" +packaging==24.2 ; python_version >= "3.11" and python_version < "3.13" +pandas-flavor==0.6.0 ; python_version >= "3.11" and python_version < "3.13" +pandas==2.2.3 ; python_version >= "3.11" and python_version < "3.13" +pathspec==0.12.1 ; python_version >= "3.11" and python_version < "3.13" +patsy==1.0.1 ; python_version >= "3.11" and python_version < "3.13" +pbr==6.1.0 ; python_version >= "3.11" and python_version < "3.13" +pep8-naming==0.14.1 ; python_version >= "3.11" and python_version < "3.13" +pillow==11.0.0 ; python_version >= "3.11" and python_version < "3.13" +pingouin==0.5.5 ; python_version >= "3.11" and python_version < "3.13" +platformdirs==4.3.6 ; python_version >= "3.11" and python_version < "3.13" +plotly==5.24.1 ; python_version >= "3.11" and python_version < "3.13" +pluggy==1.5.0 ; python_version >= "3.11" and python_version < "3.13" +pre-commit-hooks==5.0.0 ; python_version >= "3.11" and python_version < "3.13" +pre-commit==4.0.1 ; python_version >= "3.11" and python_version < "3.13" +propcache==0.2.0 ; python_version >= "3.11" and python_version < "3.13" +protobuf==5.28.3 ; python_version >= "3.11" and python_version < "3.13" +psutil==6.1.0 ; python_version >= "3.11" and python_version < "3.13" +pyarrow==18.1.0 ; sys_platform != "darwin" and python_version >= "3.11" and python_version < "3.13" or platform_machine != "x86_64" and python_version >= "3.11" and python_version < "3.13" +pycodestyle==2.12.1 ; python_version >= "3.11" and python_version < "3.13" +pydocstyle==6.3.0 ; python_version >= "3.11" and python_version < "3.13" +pyflakes==3.2.0 ; python_version >= "3.11" and python_version < "3.13" +pygments==2.18.0 ; python_version >= "3.11" and python_version < "3.13" +pyparsing==3.2.0 ; python_version >= "3.11" and python_version < "3.13" +pytest==7.4.4 ; python_version >= "3.11" and python_version < "3.13" +python-dateutil==2.9.0.post0 ; python_version >= "3.11" and python_version < "3.13" +pytorch-lightning==2.4.0 ; python_version >= "3.11" and python_version < "3.13" +pytz==2024.2 ; python_version >= "3.11" and python_version < "3.13" +pyupgrade==3.19.0 ; python_version >= "3.11" and python_version < "3.13" +pyyaml==6.0.2 ; python_version >= "3.11" and python_version < "3.13" +ray[tune]==2.39.0 ; python_version >= "3.11" and python_version < "3.13" +referencing==0.35.1 ; python_version >= "3.11" and python_version < "3.13" +requests==2.32.3 ; python_version >= "3.11" and python_version < "3.13" +restructuredtext-lint==1.4.0 ; python_version >= "3.11" and python_version < "3.13" +rich==13.9.4 ; python_version >= "3.11" and python_version < "3.13" +rpds-py==0.21.0 ; python_version >= "3.11" and python_version < "3.13" +ruamel-yaml-clib==0.2.12 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.11" +ruamel-yaml==0.18.6 ; python_version >= "3.11" and python_version < "3.13" +scikit-learn==1.5.2 ; python_version >= "3.11" and python_version < "3.13" +scipy==1.14.1 ; python_version >= "3.11" and python_version < "3.13" +seaborn==0.13.2 ; python_version >= "3.11" and python_version < "3.13" +setuptools==75.6.0 ; python_version >= "3.11" and python_version < "3.13" +six==1.16.0 ; python_version >= "3.11" and python_version < "3.13" +sniffio==1.3.1 ; python_version >= "3.11" and python_version < "3.13" +snowballstemmer==2.2.0 ; python_version >= "3.11" and python_version < "3.13" +sphinx-autobuild==2024.10.3 ; python_version >= "3.11" and python_version < "3.13" +sphinx-autodoc-typehints==2.5.0 ; python_version >= "3.11" and python_version < "3.13" +sphinx-click==6.0.0 ; python_version >= "3.11" and python_version < "3.13" +sphinx-rtd-theme==3.0.2 ; python_version >= "3.11" and python_version < "3.13" +sphinx==8.1.3 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-applehelp==2.0.0 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-devhelp==2.0.0 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-htmlhelp==2.1.0 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-jquery==4.1 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-qthelp==2.0.0 ; python_version >= "3.11" and python_version < "3.13" +sphinxcontrib-serializinghtml==2.0.0 ; python_version >= "3.11" and python_version < "3.13" +starlette==0.41.3 ; python_version >= "3.11" and python_version < "3.13" +statsmodels==0.14.4 ; python_version >= "3.11" and python_version < "3.13" +stevedore==5.4.0 ; python_version >= "3.11" and python_version < "3.13" +sympy==1.13.3 ; python_version >= "3.11" and python_version < "3.13" +tabulate==0.9.0 ; python_version >= "3.11" and python_version < "3.13" +tenacity==9.0.0 ; python_version >= "3.11" and python_version < "3.13" +tensorboardx==2.6.2.2 ; python_version >= "3.11" and python_version < "3.13" +threadpoolctl==3.5.0 ; python_version >= "3.11" and python_version < "3.13" +tokenize-rt==6.1.0 ; python_version >= "3.11" and python_version < "3.13" +toml==0.10.2 ; python_version >= "3.11" and python_version < "3.13" +tomlkit==0.13.2 ; python_version >= "3.11" and python_version < "3.13" +torch-geometric==2.6.1 ; python_version >= "3.11" and python_version < "3.13" +torch==2.4.0 ; python_version >= "3.11" and python_version < "3.13" +torchmetrics==1.6.0 ; python_version >= "3.11" and python_version < "3.13" +tornado==6.4.2 ; python_version >= "3.11" and python_version < "3.13" +tqdm==4.67.1 ; python_version >= "3.11" and python_version < "3.13" +triton==3.0.0 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version < "3.13" and python_version >= "3.11" +types-pyyaml==6.0.12.20240917 ; python_version >= "3.11" and python_version < "3.13" +types-requests==2.32.0.20241016 ; python_version >= "3.11" and python_version < "3.13" +types-toml==0.10.8.20240310 ; python_version >= "3.11" and python_version < "3.13" +typing-extensions==4.12.2 ; python_version >= "3.11" and python_version < "3.13" +tzdata==2024.2 ; python_version >= "3.11" and python_version < "3.13" +urllib3==2.2.3 ; python_version >= "3.11" and python_version < "3.13" +uvicorn==0.32.1 ; python_version >= "3.11" and python_version < "3.13" +virtualenv==20.28.0 ; python_version >= "3.11" and python_version < "3.13" +watchfiles==1.0.0 ; python_version >= "3.11" and python_version < "3.13" +websockets==14.1 ; python_version >= "3.11" and python_version < "3.13" +xarray==2024.11.0 ; python_version >= "3.11" and python_version < "3.13" +xyzservices==2024.9.0 ; python_version >= "3.11" and python_version < "3.13" +yarl==1.18.0 ; python_version >= "3.11" and python_version < "3.13" diff --git a/setup.cfg b/setup.cfg index 93ebefd..6ab92a9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -14,5 +14,5 @@ max-complexity = 10 docstring-convention = google per-file-ignores = tests/*:S101,S301,S403 - drevalpy/datasets/toy.py:S403,S301 + drevalpy/datasets/curvecurator.py:S404,S603 docstring_style = sphinx diff --git a/tests/CTRPv2_sample_test/CTRPv2_sample_test_raw.csv b/tests/CTRPv2_sample_test/CTRPv2_sample_test_raw.csv new file mode 100644 index 0000000..8af4b0a --- /dev/null +++ b/tests/CTRPv2_sample_test/CTRPv2_sample_test_raw.csv @@ -0,0 +1,113 @@ +,dose,response,sample,drug,replicate +8390,0.002,1.0955079850281488,2004,afatinib,1 +8391,0.002,0.9369539186580808,2004,afatinib,2 +8392,0.0041,0.8294920158973823,2004,afatinib,1 +8393,0.0041,0.9105435966967405,2004,afatinib,2 +8394,0.0081,1.0098562889944274,2004,afatinib,1 +8395,0.0081,1.0455847467457329,2004,afatinib,2 +8396,0.016,0.7997383630343657,2004,afatinib,1 +8397,0.016,0.8839888023747461,2004,afatinib,2 +8398,0.032,0.8273100425752845,2004,afatinib,1 +8399,0.032,0.8408964152537145,2004,afatinib,2 +8400,0.065,0.8947769516844151,2004,afatinib,1 +8401,0.065,1.042899400329442,2004,afatinib,2 +8402,0.13,1.0853798270461994,2004,afatinib,1 +8403,0.13,0.917576278566009,2004,afatinib,2 +8404,0.26,0.672870137616213,2004,afatinib,1 +8405,0.26,0.5671884265995343,2004,afatinib,2 +8406,0.52,0.7038305298908818,2004,afatinib,1 +8407,0.52,0.7630238195861496,2004,afatinib,2 +8408,1.0,0.7775460358825583,2004,afatinib,1 +8409,1.0,0.7411821282906099,2004,afatinib,2 +8410,2.1,0.7033915944835474,2004,afatinib,1 +8411,2.1,0.6444766524849002,2004,afatinib,2 +8412,4.2,0.5389786383267785,2004,afatinib,1 +8413,4.2,0.4623316390568497,2004,afatinib,2 +8414,8.3,0.1767766952966369,2004,afatinib,1 +8415,8.3,0.25366563664522,2004,afatinib,2 +8416,17.0,0.0616822841178651,2004,afatinib,1 +8417,17.0,0.0207175900046665,2004,afatinib,2 +8418,33.0,0.0303954671066339,2004,afatinib,1 +8419,33.0,0.0209486342434427,2004,afatinib,2 +8420,66.0,0.0114302439117525,2004,afatinib,1 +8421,66.0,0.0172411521881556,2004,afatinib,2 +10938,0.002,1.0731858962374974,2004,lapatinib,1 +10939,0.002,1.1915999762950489,2004,lapatinib,2 +10940,0.0041,0.9126920057518458,2004,lapatinib,1 +10941,0.0041,1.007025349315796,2004,lapatinib,2 +10942,0.0081,0.7846928718872889,2004,lapatinib,1 +10943,0.0081,1.146232732176102,2004,lapatinib,2 +10944,0.016,1.0700809956566426,2004,lapatinib,1 +10945,0.016,1.163603870176683,2004,lapatinib,2 +10946,0.032,0.9392037019011334,2004,lapatinib,1 +10947,0.032,1.061003929954875,2004,lapatinib,2 +10948,0.065,0.9427714662399728,2004,lapatinib,1 +10949,0.065,0.925240293045082,2004,lapatinib,2 +10950,0.13,0.8787349618012162,2004,lapatinib,1 +10951,0.13,1.0684356354627889,2004,lapatinib,2 +10952,0.26,1.1941631870745897,2004,lapatinib,1 +10953,0.26,1.1120333073823458,2004,lapatinib,2 +10954,0.52,0.8703695562159134,2004,lapatinib,1 +10955,0.52,1.4400311304072253,2004,lapatinib,2 +10956,1.0,1.0551733260722722,2004,lapatinib,1 +10957,1.0,1.0025227668357692,2004,lapatinib,2 +10958,2.1,1.2177348208537884,2004,lapatinib,1 +10959,2.1,1.0322339596514074,2004,lapatinib,2 +10960,4.2,0.8959561310220235,2004,lapatinib,1 +10961,4.2,1.1028984805171396,2004,lapatinib,2 +10962,8.3,0.6167680767672187,2004,lapatinib,1 +10963,8.3,0.5458589076649897,2004,lapatinib,2 +10964,17.0,0.2506941089752694,2004,lapatinib,1 +10965,17.0,0.2895732015486608,2004,lapatinib,2 +10966,33.0,0.02948244534048,2004,lapatinib,1 +10967,33.0,0.0204607097356807,2004,lapatinib,2 +10968,66.0,0.8762412270452258,2004,lapatinib,1 +10969,66.0,0.8129282899636412,2004,lapatinib,2 +12457260,0.002,1.025928365774697,LC1F,afatinib,1 +12457261,0.002,0.6766585868878507,LC1F,afatinib,2 +12457262,0.0041,1.444529833683516,LC1F,afatinib,1 +12457263,0.0041,0.5180272874509741,LC1F,afatinib,2 +12457264,0.0081,0.4746710604752596,LC1F,afatinib,1 +12457265,0.0081,1.1920956518590946,LC1F,afatinib,2 +12457266,0.016,0.875330654293931,LC1F,afatinib,1 +12457267,0.016,0.8643574745348869,LC1F,afatinib,2 +12457268,0.032,0.5833363976667916,LC1F,afatinib,1 +12457269,0.032,0.3755299817352323,LC1F,afatinib,2 +12457270,0.065,0.5921358059268162,LC1F,afatinib,1 +12457271,0.065,0.3942000870281391,LC1F,afatinib,2 +12457272,0.13,0.972668431366438,LC1F,afatinib,1 +12457273,0.13,0.3570009949212661,LC1F,afatinib,2 +12457274,0.26,0.222518933313124,LC1F,afatinib,1 +12457275,0.26,0.4652248288515076,LC1F,afatinib,2 +12457276,0.52,0.4733568156183569,LC1F,afatinib,1 +12457277,0.52,0.7747485205636878,LC1F,afatinib,2 +12457278,1.0,0.874299815700005,LC1F,afatinib,1 +12457279,1.0,0.4989613594995253,LC1F,afatinib,2 +12457280,2.1,0.4266130490560336,LC1F,afatinib,1 +12457281,2.1,0.7323981235615232,LC1F,afatinib,2 +12457282,4.2,0.3612325994808814,LC1F,afatinib,1 +12457283,4.2,0.2242220399155036,LC1F,afatinib,2 +12457284,8.3,0.5695522088920328,LC1F,afatinib,1 +12457285,8.3,0.4490661864419671,LC1F,afatinib,2 +12457286,17.0,0.1640264068239951,LC1F,afatinib,1 +12457287,17.0,0.8542320898502386,LC1F,afatinib,2 +12457288,33.0,0.0726446317198823,LC1F,afatinib,1 +12457289,33.0,0.593286146203179,LC1F,afatinib,2 +12457290,66.0,0.0564454068844888,LC1F,afatinib,1 +12457291,66.0,0.0905588846596799,LC1F,afatinib,2 +12457569,0.002,0.6217471954827811,LC1F,lapatinib,1 +12457570,0.002,0.5792668457284896,LC1F,lapatinib,2 +12457571,0.0041,0.5893105503848409,LC1F,lapatinib,1 +12457572,0.0041,0.421031476804208,LC1F,lapatinib,2 +12457573,0.0081,0.7349917696370422,LC1F,lapatinib,1 +12457574,0.0081,0.6763303497309292,LC1F,lapatinib,2 +12457575,0.016,0.7469585019797846,LC1F,lapatinib,1 +12457576,0.016,0.4986156256760348,LC1F,lapatinib,2 +12457577,0.032,0.6383413456828999,LC1F,lapatinib,1 +12457578,0.032,0.5027105948821384,LC1F,lapatinib,2 +12457579,0.065,0.5600393097018835,LC1F,lapatinib,1 +12457580,0.065,0.3498964663987989,LC1F,lapatinib,2 +12457581,0.13,0.6767993087159954,LC1F,lapatinib,1 +12457582,0.13,0.3866231687276585,LC1F,lapatinib,2 +12457583,0.26,0.4310717725087979,LC1F,lapatinib,1 +12457584,0.26,0.3112185588455425,LC1F,lapatinib,2 diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 96eb38c..35ab3f5 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -1,7 +1,7 @@ """Tests for the DrugResponseDataset and the FeatureDataset class.""" -import os import tempfile +from pathlib import Path import networkx as nx import numpy as np @@ -9,6 +9,7 @@ from flaky import flaky from drevalpy.datasets.dataset import DrugResponseDataset, FeatureDataset +from drevalpy.datasets.loader import load_dataset from drevalpy.utils import get_response_transformation # Tests for the DrugResponseDataset class @@ -27,12 +28,13 @@ def test_response_dataset_load() -> None: drug_ids=data["drug_id"], response=data["response"], ) - dataset.save("dataset.csv") + dataset_path = Path("dataset.csv") + dataset.save(dataset_path) del dataset # Load the dataset - dataset = DrugResponseDataset.from_csv("dataset.csv") + dataset = DrugResponseDataset.from_csv(dataset_path) - os.remove("dataset.csv") + dataset_path.unlink() # Check if the dataset loaded correctly assert np.array_equal(dataset.cell_line_ids, data["cell_line_id"]) @@ -40,6 +42,21 @@ def test_response_dataset_load() -> None: assert np.allclose(dataset.response, data["response"]) +def test_fitting_and_loading_custom_dataset(): + """Test CurveCurator fitting of raw viability dataset and loading it.""" + dataset_name = "CTRPv2_sample_test" + load_dataset( + dataset_name=dataset_name, + path_data=str(Path(__file__).parent), + measure="IC50", + curve_curator=True, + cores=200, + ) + for f in (Path(__file__).parent / dataset_name).glob("*"): + if f.name != f"{dataset_name}_raw.csv": + f.unlink() + + def test_response_dataset_add_rows() -> None: """Test if the add_rows method works correctly.""" dataset1 = DrugResponseDataset( diff --git a/tests/test_run_suite.py b/tests/test_run_suite.py index f309ced..7573e9c 100644 --- a/tests/test_run_suite.py +++ b/tests/test_run_suite.py @@ -24,6 +24,8 @@ "n_trials_robustness": 2, "cross_study_datasets": ["GDSC1"], "curve_curator": False, + "curve_curator_cores": 1, + "measure": "LN_IC50", "overwrite": False, "optim_metric": "RMSE", "n_cv_splits": 2,