Work around imports shadowing built ins

Use alternate/alias name.
Use method instead of function.
Change some logic to use different functions with same result.

sapphire/analysis/calibration.py

@@ -10,7 +10,7 @@
 from datetime import datetime, timedelta
 from itertools import chain, combinations, tee
 
-from numpy import abs, arange, histogram, isnan, linspace, nan, percentile, sqrt, std, sum
+from numpy import absolute, arange, histogram, isnan, linspace, nan, percentile, sqrt, std
 from scipy.optimize import curve_fit
 
 from ..api import Station
@@ -60,7 +60,7 @@ def determine_detector_timing_offsets(events, station=None):
         offsets[detector_id], _ = determine_detector_timing_offset(dt, dz)
 
     # If all except reference are nan, make reference nan.
-    if sum(isnan(offsets)) == 3:
+    if sum(isnan(offset) for offset in offsets) == 3:
         offsets = [nan, nan, nan, nan]
 
     # Try to make detector 2 the reference point, if it is not nan.
@@ -80,8 +80,8 @@ def determine_detector_timing_offset(dt, dz=0):
              the error of the mean.
 
     """
-    dt_filter = abs(dt + dz / c) < 100
-    if not sum(dt_filter):
+    dt_filter = absolute(dt + dz / c) < 100
+    if not dt_filter.sum():
         return nan, nan
     p = round_in_base(percentile(dt.compress(dt_filter), [0.5, 99.5]), 2.5)
     bins = arange(p[0] + 1.25, p[1], 2.5)
@@ -369,7 +369,7 @@ def fit_timing_offset(dt, bins):
         popt, pcov = curve_fit(gauss, x, y, p0=(len(dt), 0.0, std(dt)), sigma=sigma, absolute_sigma=False)
         offset = popt[1]
         width = popt[2]
-        offset_error = width / sqrt(sum(y))
+        offset_error = width / sqrt(y.sum())
     except (RuntimeError, TypeError):
         offset, offset_error = nan, nan
     return offset, offset_error
@@ -389,7 +389,7 @@ def determine_best_reference(filters):
 
     for detector_id in ids:
         idx = [j for j in ids if j != detector_id]
-        lengths.append(sum(filters[detector_id] & (filters[idx[0]] | filters[idx[1]] | filters[idx[2]])))
+        lengths.append((filters[detector_id] & (filters[idx[0]] | filters[idx[1]] | filters[idx[2]])).sum())
     return lengths.index(max(lengths))
 
 

sapphire/tests/analysis/test_calibration.py

@@ -7,7 +7,7 @@
 
 import tables
 
-from numpy import all, array, isnan, nan, random, std
+from numpy import array, isnan, nan, random, std
 
 from sapphire import HiSPARCNetwork, HiSPARCStations
 from sapphire.analysis import calibration
@@ -33,8 +33,9 @@ def test_determine_detector_timing_offsets(self):
     @patch.object(calibration, 'fit_timing_offset')
     def test_determine_detector_timing_offset(self, mock_fit):
         # Empty list
-        offset = calibration.determine_detector_timing_offset(array([]))
-        self.assertTrue(all(isnan(offset)))
+        offset, error = calibration.determine_detector_timing_offset(array([]))
+        self.assertTrue(isnan(offset))
+        self.assertTrue(isnan(error))
 
         dt = array([-10, 0, 10])
         dz = 0.6
@@ -74,8 +75,9 @@ def test_determine_station_timing_offset(self, mock_fit, mock_percentile):
         dzc = dz / c
 
         # Empty list
-        offset = calibration.determine_station_timing_offset([])
-        self.assertTrue(all(isnan(offset)))
+        offset, error = calibration.determine_station_timing_offset([])
+        self.assertTrue(isnan(offset))
+        self.assertTrue(isnan(error))
 
         # Good result
         mock_fit.return_value = (1.0, 5.0)

sapphire/tests/validate_results.py

@@ -2,8 +2,8 @@
 
 import tables
 
-from numpy import all, array
-from numpy.testing import assert_array_almost_equal
+from numpy import array
+from numpy.testing import assert_array_almost_equal, assert_equal
 
 
 def validate_results(test, expected_path, actual_path):
@@ -92,7 +92,7 @@ def validate_vlarrays(test, expected_node, actual_node):
         f"VLArrays '{expected_node._v_pathname}' do not have the same shape.",
     )
     for expected_array, actual_array in zip(expected_node, actual_node):
-        test.assertTrue(all(expected_array == actual_array), f"VLArrays '{expected_node._v_pathname}' do not match.")
+        assert_equal(actual_array, expected_array, f"VLArrays '{expected_node._v_pathname}' do not match.")
 
 
 def validate_arrays(test, expected_node, actual_node):

sapphire/utils.py

@@ -10,7 +10,7 @@
 from functools import wraps
 from os import environ
 
-from numpy import arcsin, ceil, floor, pi, round, sin, sqrt
+from numpy import arcsin, around, ceil, floor, pi, sin, sqrt
 from progressbar import ETA, Bar, Percentage, ProgressBar
 from scipy.stats import norm
 
@@ -73,7 +73,7 @@ def floor_in_base(value, base):
 def round_in_base(value, base):
     """Get nearest multiple of base to the value"""
 
-    return base * round(value / base)
+    return base * around(value / base)
 
 
 def closest_in_list(value, items):