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Fix divide-by-zero, deprecation, and futurewarnings #236

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merged 4 commits into from
Oct 8, 2021
Merged

Fix divide-by-zero, deprecation, and futurewarnings #236

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2bd4235
Cover plotlyviz to unix line endings
erooke Oct 6, 2021
a438ffc
Fix deprecation warnings for numpy
erooke Oct 6, 2021
9594c0e
Added random state to AffinityPropogation
erooke Oct 7, 2021
d056782
Silence division by 0 warnings
erooke Oct 7, 2021
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9 changes: 5 additions & 4 deletions kmapper/cover.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ class Cover:

limits: Numpy Array (n_dim,2)
(lower bound, upper bound) for every dimension
If a value is set to `np.float('inf')`, the bound will be assumed to be the min/max value of the dimension
If a value is set to `float('inf')`, the bound will be assumed to be the min/max value of the dimension
Also, if `limits == None`, the limits are defined by the maximum and minimum value of the lens for all dimensions.
i.e. `[[min_1, max_1], [min_2, max_2], [min_3, max_3]]`

Expand Down Expand Up @@ -108,8 +108,8 @@ def _compute_bounds(self, data):
limits_array = np.zeros(self.limits.shape)
limits_array[:, 0] = np.min(data, axis=0)
limits_array[:, 1] = np.max(data, axis=0)
limits_array[self.limits != np.float("inf")] = 0
self.limits[self.limits == np.float("inf")] = 0
limits_array[self.limits != float("inf")] = 0
self.limits[self.limits == float("inf")] = 0
bounds_arr = self.limits + limits_array
""" bounds_arr[i,j] = self.limits[i,j] if self.limits[i,j] == inf
bounds_arr[i,j] = max/min(data[i]) if self.limits == inf """
Expand Down Expand Up @@ -188,7 +188,8 @@ def fit(self, data):
inset = (ranges - inner_range) / 2

# |range| / (2n ( 1 - p))
radius = ranges / (2 * (n_cubes) * (1 - perc_overlap))
with np.errstate(divide='ignore'):
radius = ranges / (2 * (n_cubes) * (1 - perc_overlap))

# centers are fixed w.r.t perc_overlap
zip_items = list(bounds) # work around 2.7,3.4 weird behavior
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