Merge branch 'MITgcm:master' into nc-grdchk+prof

doc/tag-index

@@ -1,6 +1,12 @@
     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".
+
 checkpoint69c (2024/12/06)
 o pkg/mom_common,fluxform,vecinv:
   - remove ISOTROPIC_COS_SCALING code from pkg/mom_vecinv/mom_vi_hdissip.F (was

tools/do_tst_2+2

@@ -271,12 +271,12 @@ if test "x$ADDRESS" != xNONE -a "x$ADDRESS" != x ; then
       fi
     fi
     if test "x$SENDCMD" != x ; then
-        SendOpt='' ; headCMD=`echo $SENDCMD | awk '{print $1}'`
-        if test $headCMD != 'scp' ; then SendOpt='-s MITgcm-test -m 3555000' ; fi
-        #echo " run: $SENDCMD $SendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES"
+        sendOpt='' ; nb=`echo $SENDCMD | grep -c '\<scp\>'`
+        if [ $nb -eq 0 ] ; then sendOpt='-s MITgcm-test -m 3555000' ; fi
+        #echo " run: $SENDCMD $sendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES"
         tar -cf  ${SAVDIR}/${DRESULTS}".tar" $DRESULTS > /dev/null 2>&1 \
             && gzip  ${SAVDIR}/${DRESULTS}".tar" \
-            && $SENDCMD $SendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESS
+            && $SENDCMD $sendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESS
         out=$?
         if test "x$out" != x0 ; then
             echo

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)
 

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)
 

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"],
 )

verification/testreport

@@ -1051,7 +1051,6 @@ scandirs()
     fi
 }
 
-
 check_eedata()
 {
     # check_eedata eedata size.h
@@ -1094,7 +1093,6 @@ check_eedata()
 
 ###############################################################################
 
-
 #  Default properties
 debug=0
 verbose=1
@@ -1907,14 +1905,14 @@ if test "x$ADDRESSES" = xNONE -o "x$ADDRESSES" = x ; then
     echo "No results email was sent."
 else
     if test "x$SENDCMD" != x ; then
-	SendOpt='' ; headCMD=`echo $SENDCMD | awk '{print $1}'`
-	if test $headCMD != 'scp' ; then SendOpt='-s MITgcm-test -m 3555000' ; fi
+	sendOpt='' ; nb=`echo $SENDCMD | grep -c '\<scp\>'`
+	if [ $nb -eq 0 ] ; then sendOpt='-s MITgcm-test -m 3555000' ; fi
 	if [ $verbose -gt 1 ]; then
-	   echo " run: $SENDCMD $SendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES"
+	   echo " run: $SENDCMD $sendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES"
 	fi
 	tar -cf ${SAVDIR}/${DRESULTS}".tar" $DRESULTS > /dev/null 2>&1 \
 	    && gzip ${SAVDIR}/${DRESULTS}".tar" \
-	    && $SENDCMD $SendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES
+	    && $SENDCMD $sendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
 	    echo