Update MITgcmutils for numpy 2.0.0 and bug fix (MITgcm#897)

* Update MITgcmutils for numpy 2.0.0 * Fix two bugs * MITgcmutils now always requires matplotlib * adjust warning statement * Bump MITgcmutils version number * MITgcmutils: fix bug in negative salinity check * document fix in utils/python --------- Co-authored-by: Martin Losch <[email protected]> Co-authored-by: Jean-Michel Campin <[email protected]>
jahn · Dec 18, 2024 · 83a5371 · 83a5371
1 parent c908a60
commit 83a5371
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Showing 4 changed files with 31 additions and 31 deletions.
diff --git a/doc/tag-index b/doc/tag-index
@@ -1,6 +1,8 @@
     Notes on tags used in MITgcmUV
     ==============================
 
+o utils/python:
+  - make MITgcmutils compatible with numpy 2.0.0 again.
 o testreport:
  - improve way of sending results tar file with "scp", now allowing to combine
    "ssh" then "scp".

diff --git a/utils/python/MITgcmutils/MITgcmutils/conversion.py b/utils/python/MITgcmutils/MITgcmutils/conversion.py
@@ -43,14 +43,14 @@ def pfromz(rC, rF0=0.0, lat=None, rhoConst=1.0275e+3, eosRefP0=1.01325e+5,
     >>> pfromz(-1000,lat=[70,90])
     1009.6304, 1010.2562
     """
-    z = np.asfarray(rC)
+    z = np.asarray(rC, dtype=np.float64)
 
     assert np.all(z<=0), 'input_error: values cannot be positive'
 
     if lat is None:
         gravity = 9.81
     else:
-        lat = np.asfarray(lat)
+        lat = np.asarray(lat, dtype=np.float64)
         if lat.ndim == 1 and z.ndim == 1:
             lat,z = np.meshgrid(lat,z)
 

diff --git a/utils/python/MITgcmutils/MITgcmutils/density.py b/utils/python/MITgcmutils/MITgcmutils/density.py
@@ -37,9 +37,10 @@
 def _check_salinity(s):
 
     sneg = s<0
-    if not np.any(sneg):
-        warnings.warn('found negative salinity values, reset them to NaN')
-        # s[sneg] = np.NaN
+    if np.any(sneg):
+        warnings.warn('found negative salinity values')
+        # warnings.warn('found negative salinity values, reset them to nan')
+        # s[sneg] = np.nan
 
     return s
 
@@ -105,8 +106,8 @@ def linear(salt,theta,
     """
 
     # make sure arguments are floating point
-    s = np.asfarray(salt)
-    t = np.asfarray(theta)
+    s = np.asarray(salt, dtype=np.float64)
+    t = np.asarray(theta, dtype=np.float64)
 
     _check_dimensions(s,t)
 
@@ -152,8 +153,8 @@ def poly3(poly3,salt,theta):
     - Converted to python by Gavilan on 2024-07-18
     """
     # make sure arguments are floating point
-    s = np.asfarray(salt)
-    t = np.asfarray(theta)
+    s = np.asarray(salt, dtype=np.float64)
+    t = np.asarray(theta, dtype=np.float64)
     coeffs=poly3[:,3:]
 
 
@@ -249,9 +250,9 @@ def jmd95(salt,theta,p):
     """
 
     # make sure arguments are floating point
-    s = np.asfarray(salt)
-    t = np.asfarray(theta)
-    p = np.asfarray(p)
+    s = np.asarray(salt, dtype=np.float64)
+    t = np.asarray(theta, dtype=np.float64)
+    p = np.asarray(p, dtype=np.float64)
 
     _check_dimensions(s,t,p)
 
@@ -299,9 +300,9 @@ def bulkmodjmd95(salt,theta,p):
     """ Compute bulk modulus
     """
     # make sure arguments are floating point
-    s = np.asfarray(salt)
-    t = np.asfarray(theta)
-    p = np.asfarray(p)
+    s = np.asarray(salt, dtype=np.float64)
+    t = np.asarray(theta, dtype=np.float64)
+    p = np.asarray(p, dtype=np.float64)
 
     # coefficients in pressure coordinates for
     # 3. secant bulk modulus K of fresh water at p = 0
@@ -424,9 +425,9 @@ def unesco(salt,theta,p):
     """
 
     # make sure arguments are floating point
-    s = np.asfarray(salt)
-    t = np.asfarray(theta)
-    p = np.asfarray(p)
+    s = np.asarray(salt, dtype=np.float64)
+    t = np.asarray(theta, dtype=np.float64)
+    p = np.asarray(p, dtype=np.float64)
 
     _check_dimensions(s,t,p)
 
@@ -473,9 +474,9 @@ def bulkmodunesco(salt,theta,p):
     """ Compute bulk modulus
     """
     # make sure arguments are floating point
-    s = np.asfarray(salt)
-    t = np.asfarray(theta)
-    p = np.asfarray(p)
+    s = np.asarray(salt, dtype=np.float64)
+    t = np.asarray(theta, dtype=np.float64)
+    p = np.asarray(p, dtype=np.float64)
 
     # 3. secant bulk modulus K of fresh water at p = 0
     eosJMDCKFw = [   1.965221e+04,
@@ -600,7 +601,7 @@ def mdjwf(salt,theta,p,epsln=0):
     """
 
     # make sure arguments are floating point
-    s = np.asarray(s, dtype=np.float64)
+    s = np.asarray(salt, dtype=np.float64)
     t = np.asarray(theta, dtype=np.float64)
     p = np.asarray(p, dtype=np.float64)
 
@@ -667,7 +668,7 @@ def mdjwf(salt,theta,p,epsln=0):
     )
 
     denom = 1.0/(epsln+den)
-    rho = rhoNum*denom
+    rho = num*denom
 
     return rho
 
@@ -704,9 +705,9 @@ def teos10(salt,theta,p,epsln=0):
     """
 
     # make sure arguments are floating point
-    sa = np.asfarray(salt)
-    ct = np.asfarray(theta)
-    p = np.asfarray(p)
+    sa = np.asarray(salt, dtype=np.float64)
+    ct = np.asarray(theta, dtype=np.float64)
+    p = np.asarray(p, dtype=np.float64)
 
     _check_dimensions(sa,ct,p)
 

diff --git a/utils/python/MITgcmutils/setup.py b/utils/python/MITgcmutils/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="MITgcmutils",
-    version="0.2",
+    version="0.2.1",
     author="MITgcm Developers and Contributors",
     author_email="[email protected]",
     description="Python utilities for MITgcm",
@@ -19,8 +19,5 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    install_requires=["numpy"],
-    extras_require={
-        "plot":  ["matplotlib"],
-    }
+    install_requires=["numpy","matplotlib"],
 )