diff --git a/auton_survival/__init__.py b/auton_survival/__init__.py index 5ad5028..0c9b28b 100644 --- a/auton_survival/__init__.py +++ b/auton_survival/__init__.py @@ -475,6 +475,3 @@ class is a composite transform that does both Imputing ***and*** Scaling with import warnings from tqdm.auto import tqdm -import logging - -logging.basicConfig() diff --git a/auton_survival/experiments.py b/auton_survival/experiments.py index d64ccfc..0368d74 100644 --- a/auton_survival/experiments.py +++ b/auton_survival/experiments.py @@ -35,9 +35,11 @@ from sklearn.utils import shuffle from tqdm import tqdm -import logging -logger = logging.getLogger(__name__) + +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) class SurvivalRegressionCV: diff --git a/auton_survival/logging.py b/auton_survival/logging.py new file mode 100644 index 0000000..88da5cc --- /dev/null +++ b/auton_survival/logging.py @@ -0,0 +1,3 @@ +import logging + +LOGGER = logging.getLogger("auton_survival") diff --git a/auton_survival/metrics.py b/auton_survival/metrics.py index f241c29..fd886c3 100644 --- a/auton_survival/metrics.py +++ b/auton_survival/metrics.py @@ -32,10 +32,12 @@ from scipy.optimize import fsolve from sklearn.metrics import auc from tqdm import tqdm -import logging + import warnings -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) def treatment_effect( diff --git a/auton_survival/models/cmhe/__init__.py b/auton_survival/models/cmhe/__init__.py index a51546c..9394dcd 100644 --- a/auton_survival/models/cmhe/__init__.py +++ b/auton_survival/models/cmhe/__init__.py @@ -75,7 +75,7 @@ """ -import logging + import numpy as np import torch @@ -85,7 +85,9 @@ from auton_survival.utils import _dataframe_to_array -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) class DeepCoxMixturesHeterogenousEffects: diff --git a/auton_survival/models/cmhe/cmhe_utilities.py b/auton_survival/models/cmhe/cmhe_utilities.py index e16fafc..cdb88d6 100644 --- a/auton_survival/models/cmhe/cmhe_utilities.py +++ b/auton_survival/models/cmhe/cmhe_utilities.py @@ -21,7 +21,7 @@ # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. -import logging + import torch import numpy as np @@ -40,7 +40,9 @@ smooth_bl_survival, ) -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) def get_likelihood(model, breslow_splines, x, t, e, a): diff --git a/auton_survival/models/cph/__init__.py b/auton_survival/models/cph/__init__.py index 859ced5..7b16438 100644 --- a/auton_survival/models/cph/__init__.py +++ b/auton_survival/models/cph/__init__.py @@ -24,7 +24,7 @@ r""" Deep Cox Proportional Hazards Model""" from collections import namedtuple -import logging + import torch import numpy as np import random @@ -37,7 +37,9 @@ from auton_survival.models.utils.recurrent_nn_utils import _get_padded_targets -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) DcphModel = namedtuple("DcphModel", ["module", "breslow"]) diff --git a/auton_survival/models/cph/dcph_utilities.py b/auton_survival/models/cph/dcph_utilities.py index 5cfba3d..2eb080d 100644 --- a/auton_survival/models/cph/dcph_utilities.py +++ b/auton_survival/models/cph/dcph_utilities.py @@ -1,7 +1,7 @@ import torch import numpy as np import pandas as pd -import logging + from sksurv.linear_model.coxph import BreslowEstimator @@ -19,7 +19,9 @@ partial_ll_loss, ) -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) def fit_breslow(model, x, t, e): diff --git a/auton_survival/models/dcm/__init__.py b/auton_survival/models/dcm/__init__.py index b543389..34973b1 100644 --- a/auton_survival/models/dcm/__init__.py +++ b/auton_survival/models/dcm/__init__.py @@ -50,7 +50,7 @@ """ -import logging + import torch import numpy as np @@ -59,7 +59,9 @@ from auton_survival.utils import _dataframe_to_array -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) class DeepCoxMixtures: diff --git a/auton_survival/models/dcm/dcm_utilities.py b/auton_survival/models/dcm/dcm_utilities.py index 5ec9e50..3d04c9b 100644 --- a/auton_survival/models/dcm/dcm_utilities.py +++ b/auton_survival/models/dcm/dcm_utilities.py @@ -1,5 +1,5 @@ import warnings -import logging + from matplotlib.pyplot import get import torch @@ -24,7 +24,9 @@ smooth_bl_survival, ) -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) def get_likelihood(model, breslow_splines, x, t, e): diff --git a/auton_survival/models/dsm/__init__.py b/auton_survival/models/dsm/__init__.py index eb1ce12..520d71c 100644 --- a/auton_survival/models/dsm/__init__.py +++ b/auton_survival/models/dsm/__init__.py @@ -156,7 +156,7 @@ """ -import logging + import torch import numpy as np @@ -183,7 +183,9 @@ __pdoc__["DSMBase"] = False -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) class DSMBase: diff --git a/auton_survival/models/dsm/dsm_utilities.py b/auton_survival/models/dsm/dsm_utilities.py index 34c30cc..0287189 100644 --- a/auton_survival/models/dsm/dsm_utilities.py +++ b/auton_survival/models/dsm/dsm_utilities.py @@ -37,10 +37,11 @@ import numpy as np import gc -import logging -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) def pretrain_dsm( diff --git a/auton_survival/phenotyping.py b/auton_survival/phenotyping.py index 28c48cd..874de71 100644 --- a/auton_survival/phenotyping.py +++ b/auton_survival/phenotyping.py @@ -24,7 +24,7 @@ """Utilities to phenotype individuals based on similar survival characteristics.""" -import logging + from random import random import warnings import numpy as np @@ -38,7 +38,9 @@ from auton_survival.utils import _get_method_kwargs from auton_survival.experiments import CounterfactualSurvivalRegressionCV -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) class Phenotyper: diff --git a/auton_survival/reporting.py b/auton_survival/reporting.py index d317def..c0fa5c9 100644 --- a/auton_survival/reporting.py +++ b/auton_survival/reporting.py @@ -1,4 +1,3 @@ -import logging import numpy as np import pandas as pd @@ -8,7 +7,9 @@ from lifelines.plotting import add_at_risk_counts -logger = logging.getLogger(__name__) +from auton_survival.logging import LOGGER + +logger = LOGGER.getChild(__name__) def plot_kaplanmeier(outcomes, groups=None, plot_counts=False, **kwargs):