From 0e8fe994cc5e8cd1f82ca6b4f81e5c20a9eca151 Mon Sep 17 00:00:00 2001 From: Matteo Fordiani Date: Sat, 18 Nov 2023 16:03:53 +0100 Subject: [PATCH] refactor(logs): add single logger --- auton_survival/__init__.py | 6 ------ auton_survival/experiments.py | 4 +--- auton_survival/logging.py | 4 ++++ auton_survival/metrics.py | 4 +--- auton_survival/models/cmhe/__init__.py | 4 +--- auton_survival/models/cmhe/cmhe_utilities.py | 4 +--- auton_survival/models/cph/__init__.py | 4 +--- auton_survival/models/cph/dcph_utilities.py | 4 +--- auton_survival/models/dcm/__init__.py | 4 +--- auton_survival/models/dcm/dcm_utilities.py | 4 +--- auton_survival/models/dsm/__init__.py | 4 +--- auton_survival/models/dsm/dsm_utilities.py | 4 +--- auton_survival/phenotyping.py | 4 +--- auton_survival/reporting.py | 4 +--- 14 files changed, 16 insertions(+), 42 deletions(-) create mode 100644 auton_survival/logging.py diff --git a/auton_survival/__init__.py b/auton_survival/__init__.py index 5ad5028..e328f34 100644 --- a/auton_survival/__init__.py +++ b/auton_survival/__init__.py @@ -472,9 +472,3 @@ class is a composite transform that does both Imputing ***and*** Scaling with from .models.dcm import DeepCoxMixtures from .models.cph import DeepCoxPH, DeepRecurrentCoxPH from .models.cmhe import DeepCoxMixturesHeterogenousEffects - -import warnings -from tqdm.auto import tqdm -import logging - -logging.basicConfig() diff --git a/auton_survival/experiments.py b/auton_survival/experiments.py index 550e839..85edfbe 100644 --- a/auton_survival/experiments.py +++ b/auton_survival/experiments.py @@ -37,9 +37,7 @@ from tqdm import tqdm -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger class SurvivalRegressionCV: diff --git a/auton_survival/logging.py b/auton_survival/logging.py new file mode 100644 index 0000000..3e5dc48 --- /dev/null +++ b/auton_survival/logging.py @@ -0,0 +1,4 @@ +import logging + +LOGGER_NAME = "auton_survival" +logger = logging.getLogger(LOGGER_NAME) diff --git a/auton_survival/metrics.py b/auton_survival/metrics.py index 4d17d30..05df623 100644 --- a/auton_survival/metrics.py +++ b/auton_survival/metrics.py @@ -35,9 +35,7 @@ import warnings -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger def treatment_effect( diff --git a/auton_survival/models/cmhe/__init__.py b/auton_survival/models/cmhe/__init__.py index 6ffde10..ece2242 100644 --- a/auton_survival/models/cmhe/__init__.py +++ b/auton_survival/models/cmhe/__init__.py @@ -85,9 +85,7 @@ from auton_survival.utils import _dataframe_to_array -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger class DeepCoxMixturesHeterogenousEffects: diff --git a/auton_survival/models/cmhe/cmhe_utilities.py b/auton_survival/models/cmhe/cmhe_utilities.py index fc1da0e..7aed7cf 100644 --- a/auton_survival/models/cmhe/cmhe_utilities.py +++ b/auton_survival/models/cmhe/cmhe_utilities.py @@ -40,9 +40,7 @@ smooth_bl_survival, ) -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger 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 7e64f96..5f002f1 100644 --- a/auton_survival/models/cph/__init__.py +++ b/auton_survival/models/cph/__init__.py @@ -37,9 +37,7 @@ from auton_survival.models.utils.recurrent_nn_utils import _get_padded_targets -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger DcphModel = namedtuple("DcphModel", ["module", "breslow"]) diff --git a/auton_survival/models/cph/dcph_utilities.py b/auton_survival/models/cph/dcph_utilities.py index 5ea6012..f04e957 100644 --- a/auton_survival/models/cph/dcph_utilities.py +++ b/auton_survival/models/cph/dcph_utilities.py @@ -19,9 +19,7 @@ partial_ll_loss, ) -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger def fit_breslow(model, x, t, e): diff --git a/auton_survival/models/dcm/__init__.py b/auton_survival/models/dcm/__init__.py index 7a073a0..668fd0f 100644 --- a/auton_survival/models/dcm/__init__.py +++ b/auton_survival/models/dcm/__init__.py @@ -59,9 +59,7 @@ from auton_survival.utils import _dataframe_to_array -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger class DeepCoxMixtures: diff --git a/auton_survival/models/dcm/dcm_utilities.py b/auton_survival/models/dcm/dcm_utilities.py index 4bd260b..d57b9ef 100644 --- a/auton_survival/models/dcm/dcm_utilities.py +++ b/auton_survival/models/dcm/dcm_utilities.py @@ -24,9 +24,7 @@ smooth_bl_survival, ) -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger 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 6ea1fa1..bc30b78 100644 --- a/auton_survival/models/dsm/__init__.py +++ b/auton_survival/models/dsm/__init__.py @@ -183,9 +183,7 @@ __pdoc__["DSMBase"] = False -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger class DSMBase: diff --git a/auton_survival/models/dsm/dsm_utilities.py b/auton_survival/models/dsm/dsm_utilities.py index 0e0197c..76525a1 100644 --- a/auton_survival/models/dsm/dsm_utilities.py +++ b/auton_survival/models/dsm/dsm_utilities.py @@ -39,9 +39,7 @@ import gc -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger def pretrain_dsm( diff --git a/auton_survival/phenotyping.py b/auton_survival/phenotyping.py index f65e43e..dbe8fac 100644 --- a/auton_survival/phenotyping.py +++ b/auton_survival/phenotyping.py @@ -38,9 +38,7 @@ from auton_survival.utils import _get_method_kwargs from auton_survival.experiments import CounterfactualSurvivalRegressionCV -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger class Phenotyper: diff --git a/auton_survival/reporting.py b/auton_survival/reporting.py index 4dd0fcb..a8d9845 100644 --- a/auton_survival/reporting.py +++ b/auton_survival/reporting.py @@ -7,9 +7,7 @@ from lifelines.plotting import add_at_risk_counts -import logging - -logger = logging.getLogger(__name__) +from auton_survival.logging import logger def plot_kaplanmeier(outcomes, groups=None, plot_counts=False, **kwargs):