From f525fafa102cad9c4b2675da4490c47c2176a76d Mon Sep 17 00:00:00 2001 From: AdriTara Date: Mon, 14 Apr 2025 14:44:10 +0200 Subject: [PATCH] added support for warnings stdlib --- deeptools/SES_scaleFactor.py | 2 ++ deeptools/bamCompare.py | 2 ++ deeptools/bamCoverage.py | 2 ++ deeptools/bamPEFragmentSize.py | 2 ++ deeptools/bigwigAverage.py | 2 ++ deeptools/computeGCBias.py | 2 ++ deeptools/computeMatrixOperations.py | 2 ++ deeptools/correctGCBias.py | 2 ++ deeptools/correlation.py | 2 ++ deeptools/correlation_heatmap.py | 2 ++ deeptools/countReadsPerBin.py | 2 ++ deeptools/getFragmentAndReadSize.py | 2 ++ deeptools/getRatio.py | 2 ++ deeptools/getScaleFactor.py | 2 ++ deeptools/getScorePerBigWigBin.py | 2 ++ deeptools/heatmapper.py | 2 ++ deeptools/heatmapper_utilities.py | 2 ++ deeptools/multiBamSummary.py | 2 ++ deeptools/multiBigwigSummary.py | 2 ++ deeptools/plotCorrelation.py | 2 ++ deeptools/plotCoverage.py | 2 ++ deeptools/plotEnrichment.py | 2 ++ deeptools/plotFingerprint.py | 2 ++ deeptools/plotHeatmap.py | 2 ++ deeptools/plotProfile.py | 2 ++ deeptools/sumCoveragePerBin.py | 2 ++ deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py | 2 ++ deeptools/test/test_countReadsPerBin.py | 2 ++ deeptools/test/test_multiBamSummary.py | 2 ++ deeptools/utilities.py | 2 ++ deeptools/writeBedGraph.py | 2 ++ deeptools/writeBedGraph_bam_and_bw.py | 2 ++ 32 files changed, 64 insertions(+) diff --git a/deeptools/SES_scaleFactor.py b/deeptools/SES_scaleFactor.py index 76194b9ea3..a8a0f72755 100644 --- a/deeptools/SES_scaleFactor.py +++ b/deeptools/SES_scaleFactor.py @@ -3,6 +3,8 @@ import os import numpy as np +import warnings +np.warnings = warnings # own packages from deeptools import bamHandler diff --git a/deeptools/bamCompare.py b/deeptools/bamCompare.py index 223bc06c95..78c17ca8ff 100644 --- a/deeptools/bamCompare.py +++ b/deeptools/bamCompare.py @@ -3,6 +3,8 @@ import argparse # to parse command line arguments import numpy as np +import warnings +np.warnings = warnings import sys # my packages diff --git a/deeptools/bamCoverage.py b/deeptools/bamCoverage.py index acca196fc1..85d94e056a 100644 --- a/deeptools/bamCoverage.py +++ b/deeptools/bamCoverage.py @@ -5,6 +5,8 @@ import argparse import sys import numpy as np +import warnings +np.warnings = warnings from deeptools import writeBedGraph # This should be made directly into a bigWig from deeptools import parserCommon from deeptools.getScaleFactor import get_scale_factor diff --git a/deeptools/bamPEFragmentSize.py b/deeptools/bamPEFragmentSize.py index 9138051717..64fde40204 100755 --- a/deeptools/bamPEFragmentSize.py +++ b/deeptools/bamPEFragmentSize.py @@ -4,6 +4,8 @@ import argparse import sys import numpy as np +import warnings +np.warnings = warnings import matplotlib matplotlib.use('Agg') diff --git a/deeptools/bigwigAverage.py b/deeptools/bigwigAverage.py index 5228ddf08f..c4d73571d7 100644 --- a/deeptools/bigwigAverage.py +++ b/deeptools/bigwigAverage.py @@ -3,6 +3,8 @@ import argparse import sys import numpy as np +import warnings +np.warnings = warnings from deeptools import parserCommon from deeptools import writeBedGraph_bam_and_bw diff --git a/deeptools/computeGCBias.py b/deeptools/computeGCBias.py index f261a9fc14..fcfb6c9510 100755 --- a/deeptools/computeGCBias.py +++ b/deeptools/computeGCBias.py @@ -5,6 +5,8 @@ import multiprocessing import numpy as np +import warnings +np.warnings = warnings import argparse from scipy.stats import poisson import py2bit diff --git a/deeptools/computeMatrixOperations.py b/deeptools/computeMatrixOperations.py index 0224f00a39..b04ed5ddda 100755 --- a/deeptools/computeMatrixOperations.py +++ b/deeptools/computeMatrixOperations.py @@ -2,6 +2,8 @@ import deeptools.heatmapper as heatmapper import deeptoolsintervals.parse as dti import numpy as np +import warnings +np.warnings = warnings import argparse import sys import os diff --git a/deeptools/correctGCBias.py b/deeptools/correctGCBias.py index 1154b93688..489558ff65 100755 --- a/deeptools/correctGCBias.py +++ b/deeptools/correctGCBias.py @@ -11,6 +11,8 @@ import pysam import multiprocessing import numpy as np +import warnings +np.warnings = warnings import argparse from scipy.stats import binom diff --git a/deeptools/correlation.py b/deeptools/correlation.py index 56b8d91d2f..ea14f16ba3 100755 --- a/deeptools/correlation.py +++ b/deeptools/correlation.py @@ -2,6 +2,8 @@ import itertools import copy import numpy as np +import warnings +np.warnings = warnings import scipy.cluster.hierarchy as sch import scipy.stats import matplotlib as mpl diff --git a/deeptools/correlation_heatmap.py b/deeptools/correlation_heatmap.py index 58dbdfbc04..57b73b361a 100644 --- a/deeptools/correlation_heatmap.py +++ b/deeptools/correlation_heatmap.py @@ -3,6 +3,8 @@ from deeptools import cm # noqa: F401 import matplotlib.pyplot as plt import numpy as np +import warnings +np.warnings = warnings import scipy.cluster.hierarchy as sch from matplotlib import rcParams import matplotlib.colors as pltcolors diff --git a/deeptools/countReadsPerBin.py b/deeptools/countReadsPerBin.py index 1e6c78293b..281d270b39 100644 --- a/deeptools/countReadsPerBin.py +++ b/deeptools/countReadsPerBin.py @@ -4,6 +4,8 @@ import sys import multiprocessing import numpy as np +import warnings +np.warnings = warnings # deepTools packages import deeptools.utilities diff --git a/deeptools/getFragmentAndReadSize.py b/deeptools/getFragmentAndReadSize.py index 0cf2dc8eba..49b4b2f725 100644 --- a/deeptools/getFragmentAndReadSize.py +++ b/deeptools/getFragmentAndReadSize.py @@ -1,4 +1,6 @@ import numpy as np +import warnings +np.warnings = warnings # own tools from deeptools import bamHandler diff --git a/deeptools/getRatio.py b/deeptools/getRatio.py index 937cc7c418..91bf21ab12 100644 --- a/deeptools/getRatio.py +++ b/deeptools/getRatio.py @@ -1,4 +1,6 @@ import numpy as np +import warnings +np.warnings = warnings old_settings = np.seterr(all='ignore') diff --git a/deeptools/getScaleFactor.py b/deeptools/getScaleFactor.py index 541b4febdc..094f07f534 100644 --- a/deeptools/getScaleFactor.py +++ b/deeptools/getScaleFactor.py @@ -2,6 +2,8 @@ # -*- coding: utf-8 -*- import numpy as np +import warnings +np.warnings = warnings import deeptools.mapReduce as mapReduce from deeptools import bamHandler from deeptools import utilities diff --git a/deeptools/getScorePerBigWigBin.py b/deeptools/getScorePerBigWigBin.py index 6f0ff45eae..d5fa99b705 100644 --- a/deeptools/getScorePerBigWigBin.py +++ b/deeptools/getScorePerBigWigBin.py @@ -1,5 +1,7 @@ import pyBigWig import numpy as np +import warnings +np.warnings = warnings import os import sys import shutil diff --git a/deeptools/heatmapper.py b/deeptools/heatmapper.py index f86b85e234..23a0fd6436 100644 --- a/deeptools/heatmapper.py +++ b/deeptools/heatmapper.py @@ -2,6 +2,8 @@ import gzip from collections import OrderedDict import numpy as np +import warnings +np.warnings = warnings from copy import deepcopy import pyBigWig diff --git a/deeptools/heatmapper_utilities.py b/deeptools/heatmapper_utilities.py index e63dfb0226..84e8c2d595 100644 --- a/deeptools/heatmapper_utilities.py +++ b/deeptools/heatmapper_utilities.py @@ -1,4 +1,6 @@ import numpy as np +import warnings +np.warnings = warnings import matplotlib matplotlib.use('Agg') matplotlib.rcParams['pdf.fonttype'] = 42 diff --git a/deeptools/multiBamSummary.py b/deeptools/multiBamSummary.py index 981a99e3c2..6f7fceb1ac 100644 --- a/deeptools/multiBamSummary.py +++ b/deeptools/multiBamSummary.py @@ -5,6 +5,8 @@ import sys import argparse import numpy as np +import warnings +np.warnings = warnings import deeptools.countReadsPerBin as countR from deeptools import parserCommon diff --git a/deeptools/multiBigwigSummary.py b/deeptools/multiBigwigSummary.py index 3a5bda19ab..53aaacfc55 100644 --- a/deeptools/multiBigwigSummary.py +++ b/deeptools/multiBigwigSummary.py @@ -5,6 +5,8 @@ import argparse import os.path import numpy as np +import warnings +np.warnings = warnings from deeptools import parserCommon from deeptools.utilities import smartLabels import deeptools.getScorePerBigWigBin as score_bw diff --git a/deeptools/plotCorrelation.py b/deeptools/plotCorrelation.py index 988cf559e2..b6fad4fab5 100644 --- a/deeptools/plotCorrelation.py +++ b/deeptools/plotCorrelation.py @@ -4,6 +4,8 @@ import sys import argparse import numpy as np +import warnings +np.warnings = warnings import matplotlib matplotlib.use('Agg') matplotlib.rcParams['pdf.fonttype'] = 42 diff --git a/deeptools/plotCoverage.py b/deeptools/plotCoverage.py index 464375c7a3..84437f13b5 100755 --- a/deeptools/plotCoverage.py +++ b/deeptools/plotCoverage.py @@ -5,6 +5,8 @@ import sys import argparse import numpy as np +import warnings +np.warnings = warnings import matplotlib matplotlib.use('Agg') diff --git a/deeptools/plotEnrichment.py b/deeptools/plotEnrichment.py index bbd53f90d5..c49698a285 100755 --- a/deeptools/plotEnrichment.py +++ b/deeptools/plotEnrichment.py @@ -4,6 +4,8 @@ import sys import argparse import numpy as np +import warnings +np.warnings = warnings import matplotlib matplotlib.use('Agg') matplotlib.rcParams['pdf.fonttype'] = 42 diff --git a/deeptools/plotFingerprint.py b/deeptools/plotFingerprint.py index a5a468802a..7c12cb6225 100755 --- a/deeptools/plotFingerprint.py +++ b/deeptools/plotFingerprint.py @@ -2,6 +2,8 @@ # -*- coding: utf-8 -*- import numpy as np +import warnings +np.warnings = warnings import argparse import sys import matplotlib diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py index a2149f8299..2ff9489dc7 100755 --- a/deeptools/plotHeatmap.py +++ b/deeptools/plotHeatmap.py @@ -5,6 +5,8 @@ import argparse from collections import OrderedDict import numpy as np +import warnings +np.warnings = warnings import matplotlib matplotlib.use('Agg') matplotlib.rcParams['pdf.fonttype'] = 42 diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py index 7497875f20..82671cc618 100755 --- a/deeptools/plotProfile.py +++ b/deeptools/plotProfile.py @@ -6,6 +6,8 @@ import argparse import numpy as np +import warnings +np.warnings = warnings from math import ceil import matplotlib matplotlib.use('Agg') diff --git a/deeptools/sumCoveragePerBin.py b/deeptools/sumCoveragePerBin.py index 9cde455522..8209da3427 100644 --- a/deeptools/sumCoveragePerBin.py +++ b/deeptools/sumCoveragePerBin.py @@ -1,4 +1,6 @@ import numpy as np +import warnings +np.warnings = warnings import multiprocessing import time diff --git a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py index 076baa2195..425148ccaf 100644 --- a/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py +++ b/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py @@ -1,6 +1,8 @@ import deeptools.bigwigCompare as bwComp import deeptools.multiBigwigSummary as bwCorr import numpy as np +import warnings +np.warnings = warnings import numpy.testing as nt import os.path diff --git a/deeptools/test/test_countReadsPerBin.py b/deeptools/test/test_countReadsPerBin.py index eb09a9684c..19d07a73df 100644 --- a/deeptools/test/test_countReadsPerBin.py +++ b/deeptools/test/test_countReadsPerBin.py @@ -2,6 +2,8 @@ import deeptools.countReadsPerBin as cr import numpy as np +import warnings +np.warnings = warnings import numpy.testing as nt import os.path import pytest diff --git a/deeptools/test/test_multiBamSummary.py b/deeptools/test/test_multiBamSummary.py index c1716352e2..e9d7626404 100644 --- a/deeptools/test/test_multiBamSummary.py +++ b/deeptools/test/test_multiBamSummary.py @@ -1,5 +1,7 @@ import deeptools.multiBamSummary as mbs import numpy as np +import warnings +np.warnings = warnings import numpy.testing as nt import os.path diff --git a/deeptools/utilities.py b/deeptools/utilities.py index 64cc7a75c3..beddddfa55 100755 --- a/deeptools/utilities.py +++ b/deeptools/utilities.py @@ -6,6 +6,8 @@ mpl.use('Agg') from deeptools import cm # noqa: F401 import numpy as np +import warnings +np.warnings = warnings debug = 0 diff --git a/deeptools/writeBedGraph.py b/deeptools/writeBedGraph.py index dd83e9add6..e1e24c4a91 100644 --- a/deeptools/writeBedGraph.py +++ b/deeptools/writeBedGraph.py @@ -2,6 +2,8 @@ import sys import shutil import numpy as np +import warnings +np.warnings = warnings import pyBigWig # own modules diff --git a/deeptools/writeBedGraph_bam_and_bw.py b/deeptools/writeBedGraph_bam_and_bw.py index c3296bc167..2f343cdf92 100644 --- a/deeptools/writeBedGraph_bam_and_bw.py +++ b/deeptools/writeBedGraph_bam_and_bw.py @@ -5,6 +5,8 @@ import shutil import tempfile import numpy as np +import warnings +np.warnings = warnings import sys # NGS packages