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From af82c757b7cdd78556563af10ee08f013b784002 Mon Sep 17 00:00:00 2001
From: Paul Kienzle <pkienzle@nist.gov>
Date: Tue, 21 May 2024 17:26:18 -0400
Subject: [PATCH] acknowledge bad values in wsolve ci/pi tests
---
bumps/wsolve.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/bumps/wsolve.py b/bumps/wsolve.py
index 3f48344b..fb4b1aeb 100644
--- a/bumps/wsolve.py
+++ b/bumps/wsolve.py
@@ -435,7 +435,7 @@ def test():
# Uncomment these to show target values
# print "Tp = [%.16g, %.16g]"%(p[0],p[1])
# print "Tdp = [%.16g, %.16g]"%(dp[0],dp[1])
- # print "Tpi,Tci = %.16g, %.16g"%(pi,ci)
+ # "Tpi,Tci = %.16g, %.16g"%(pi,ci)
Tp = np.array([7.787249069840737, 1.503992847461524])
Tdp = np.array([1.522338103010216, 2.117633626902384])
Tpi, Tci = 7.611128464981324, 2.342860389884832
@@ -446,8 +446,9 @@ def test():
pierr = np.abs(pi - Tpi)
assert perr < 1e-14, "||p-Tp||=%g" % perr
assert dperr < 1e-14, "||dp-Tdp||=%g" % dperr
- assert cierr < 1e-14, "||ci-Tci||=%g" % cierr
- assert pierr < 1e-14, "||pi-Tpi||=%g" % pierr
+ # Target values are only accurate to 9 digits for scipy < 1.13
+ assert cierr < 1e-8, "||ci-Tci||=%g" % cierr
+ assert pierr < 1e-8, "||pi-Tpi||=%g" % pierr
assert_array_almost_equal_nulp(py, poly(px), nulp=8)
if __name__ == "__main__":
From fa00b9499e8ef89e779a54085c6d2d9d3e8c72b3 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 17 Jun 2024 14:59:42 -0400
Subject: [PATCH 1/3] use np.asarray(... type=float) instead of np.asfarray
---
bumps/simplex.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bumps/simplex.py b/bumps/simplex.py
index 09b6ee91..e9485821 100644
--- a/bumps/simplex.py
+++ b/bumps/simplex.py
@@ -141,7 +141,7 @@ def simplex(f, x0=None, bounds=None, radius=0.05,
"""
fcalls, func = wrap_function(f, bounds)
- x0 = np.asfarray(x0).flatten()
+ x0 = np.asarray(x0, dtype=float).flatten()
# print "x0",x0
N = len(x0)
rank = len(x0.shape)
From 7e8e792d1a115788322ec00094f964b12e61e4f4 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 17 Jun 2024 15:00:10 -0400
Subject: [PATCH 2/3] use np.nan instead of (now removed) np.NaN
---
bumps/dream/formatnum.py | 10 +++++-----
bumps/dream/walk.py | 4 ++--
bumps/fitproblem.py | 6 +++---
bumps/formatnum.py | 10 +++++-----
4 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/bumps/dream/formatnum.py b/bumps/dream/formatnum.py
index 2ee6036e..dd74833f 100644
--- a/bumps/dream/formatnum.py
+++ b/bumps/dream/formatnum.py
@@ -41,7 +41,7 @@
from __future__ import division
import math
-from numpy import isinf, isnan, inf, NaN
+from numpy import isinf, isnan, inf, nan
__all__ = ['format_value', 'format_uncertainty',
'format_uncertainty_compact', 'format_uncertainty_pm',
@@ -295,10 +295,10 @@ def test_compact():
# non-finite values
assert value_str(-inf, None) == "-inf"
assert value_str(inf, None) == "inf"
- assert value_str(NaN, None) == "NaN"
+ assert value_str(nan, None) == "NaN"
# bad or missing uncertainty
- assert value_str(-1.23567, NaN) == "-1.23567"
+ assert value_str(-1.23567, nan) == "-1.23567"
assert value_str(-1.23567, -inf) == "-1.23567"
assert value_str(-1.23567, -0.1) == "-1.23567"
assert value_str(-1.23567, 0) == "-1.23567"
@@ -427,10 +427,10 @@ def test_pm():
# non-finite values
assert value_str(-inf, None) == "-inf"
assert value_str(inf, None) == "inf"
- assert value_str(NaN, None) == "NaN"
+ assert value_str(nan, None) == "NaN"
# bad or missing uncertainty
- assert value_str(-1.23567, NaN) == "-1.23567"
+ assert value_str(-1.23567, nan) == "-1.23567"
assert value_str(-1.23567, -inf) == "-1.23567"
assert value_str(-1.23567, -0.1) == "-1.23567"
assert value_str(-1.23567, 0) == "-1.23567"
diff --git a/bumps/dream/walk.py b/bumps/dream/walk.py
index 833cbb62..950e5a3b 100644
--- a/bumps/dream/walk.py
+++ b/bumps/dream/walk.py
@@ -10,12 +10,12 @@
__all__ = ["walk"]
-from numpy import asarray, ones_like, NaN, isnan
+from numpy import asarray, ones_like, nan, isnan
from . import util
-def walk(n=1000, mu=0, sigma=1, alpha=0.01, s0=NaN):
+def walk(n=1000, mu=0, sigma=1, alpha=0.01, s0=nan):
"""
Mean reverting random walk.
diff --git a/bumps/fitproblem.py b/bumps/fitproblem.py
index 7753bcf4..896f808f 100644
--- a/bumps/fitproblem.py
+++ b/bumps/fitproblem.py
@@ -59,7 +59,7 @@
import warnings
import numpy as np
-from numpy import inf, isnan, NaN
+from numpy import inf, isnan, nan
from . import parameter, bounds as mbounds
from .parameter import to_dict
@@ -510,7 +510,7 @@ def _nllf_components(self):
info = (traceback.format_exc(),
parameter.summarize(self._parameters))
logging.error("\n".join(info))
- return NaN, NaN, NaN
+ return nan, nan, nan
def __call__(self, pvec=None):
"""
@@ -772,7 +772,7 @@ def nllf_scale(problem):
measurements. To first approximation, the uncertainty in $\chi^2_N$
is $k/(n-k)$
"""
- dof = getattr(problem, 'dof', np.NaN)
+ dof = getattr(problem, 'dof', np.nan)
if dof <= 0 or np.isnan(dof) or np.isinf(dof):
return 1., 0.
else:
diff --git a/bumps/formatnum.py b/bumps/formatnum.py
index 3075f618..f0da2b51 100644
--- a/bumps/formatnum.py
+++ b/bumps/formatnum.py
@@ -41,7 +41,7 @@
from __future__ import division
import math
-from numpy import isinf, isnan, inf, NaN
+from numpy import isinf, isnan, inf, nan
__all__ = ['format_value', 'format_uncertainty',
'format_uncertainty_compact', 'format_uncertainty_pm',
@@ -294,10 +294,10 @@ def test_compact():
# non-finite values
assert value_str(-inf, None) == "-inf"
assert value_str(inf, None) == "inf"
- assert value_str(NaN, None) == "NaN"
+ assert value_str(nan, None) == "NaN"
# bad or missing uncertainty
- assert value_str(-1.23567, NaN) == "-1.23567"
+ assert value_str(-1.23567, nan) == "-1.23567"
assert value_str(-1.23567, -inf) == "-1.23567"
assert value_str(-1.23567, -0.1) == "-1.23567"
assert value_str(-1.23567, 0) == "-1.23567"
@@ -426,10 +426,10 @@ def test_pm():
# non-finite values
assert value_str(-inf, None) == "-inf"
assert value_str(inf, None) == "inf"
- assert value_str(NaN, None) == "NaN"
+ assert value_str(nan, None) == "NaN"
# bad or missing uncertainty
- assert value_str(-1.23567, NaN) == "-1.23567"
+ assert value_str(-1.23567, nan) == "-1.23567"
assert value_str(-1.23567, -inf) == "-1.23567"
assert value_str(-1.23567, -0.1) == "-1.23567"
assert value_str(-1.23567, 0) == "-1.23567"
From 891f759b49fdd7939c103761de8478881a7ca326 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 17 Jun 2024 15:43:27 -0400
Subject: [PATCH 3/3] use np.asmatrix instead of np.mat (deprecated alias)
---
bumps/pytwalk.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bumps/pytwalk.py b/bumps/pytwalk.py
index 021c3408..ceacedd4 100644
--- a/bumps/pytwalk.py
+++ b/bumps/pytwalk.py
@@ -14,7 +14,7 @@
__all__ = ["pytwalk"]
from numpy.random import uniform, normal
-from numpy import ones, zeros, cumsum, shape, mat, cov, mean, ceil, matrix, sqrt
+from numpy import ones, zeros, cumsum, shape, asmatrix as mat, cov, mean, ceil, matrix, sqrt
from numpy import floor, exp, log, sum, pi, arange
# Some auxiliary functions and constants
|