From bf1ee8ee03c623d5151330b7264e3dd031a65aaa Mon Sep 17 00:00:00 2001
From: Javier Vegas-Regidor <javier.vegas@bsc.es>
Date: Wed, 9 Dec 2020 09:49:51 +0100
Subject: [PATCH 1/3] Fix latest version and cdo interpolation

---
 earthdiagnostics/data_convention.py      |  3 +++
 earthdiagnostics/ocean/interpolatecdo.py | 25 +++++++++++++++++++-----
 2 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/earthdiagnostics/data_convention.py b/earthdiagnostics/data_convention.py
index 5e4dd4b5..c6bb6aab 100644
--- a/earthdiagnostics/data_convention.py
+++ b/earthdiagnostics/data_convention.py
@@ -896,6 +896,9 @@ class Cmor3Convention(DataConvention):
             if not os.path.isdir(base_path):
                 base_path = base_path.replace(
                     '/original_files/cmorfiles/', '/cmorfiles/')
+            if not os.path.isdir(base_path):
+                base_path = base_path.replace(
+                    '/cmorfiles/', '/diags/')
             versions = os.listdir(base_path)
             versions.sort(reverse=True)
             self.config.cmor.version = versions[0]
diff --git a/earthdiagnostics/ocean/interpolatecdo.py b/earthdiagnostics/ocean/interpolatecdo.py
index 3de0f28a..42dd17a9 100644
--- a/earthdiagnostics/ocean/interpolatecdo.py
+++ b/earthdiagnostics/ocean/interpolatecdo.py
@@ -1,6 +1,7 @@
 # coding=utf-8
 """CDO-based interpolation"""
 import os
+from cdo import CDOException
 
 import numpy as np
 
@@ -399,11 +400,25 @@ class InterpolateCDO(Diagnostic):
         handler.close()
 
         temp = TempFile.get()
-        Utils.cdo().remap(
-            ",".join((self.grid.split("_")[0], self.weights)),
-            input=variable_file,
-            output=temp,
-        )
+        try:
+            Utils.cdo().remap(
+                ",".join((self.grid.split("_")[0], self.weights)),
+                input=variable_file,
+                output=temp,
+            )
+        except CDOException as ex:
+            msg = (
+                '(cdf_put_vara_double): NetCDF: Numeric '
+                'conversion not representable'
+            )
+            if msg not in ex.msg:
+                raise
+            Utils.cdo().remap(
+                ",".join((self.grid.split("_")[0], self.weights)),
+                input=variable_file,
+                output=temp,
+                options='-b F64'
+            )
 
         handler = Utils.open_cdf(temp)
         if units:
-- 
GitLab


From 012685ce27fdf6211bf1a1f3e7ceb91bb45e3a66 Mon Sep 17 00:00:00 2001
From: Javier Vegas-Regidor <javier.vegas@bsc.es>
Date: Thu, 10 Dec 2020 11:52:36 +0100
Subject: [PATCH 2/3] Fix invalid values in density

---
 earthdiagnostics/ocean/density.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/earthdiagnostics/ocean/density.py b/earthdiagnostics/ocean/density.py
index d4d4aea4..69b070c4 100644
--- a/earthdiagnostics/ocean/density.py
+++ b/earthdiagnostics/ocean/density.py
@@ -134,7 +134,7 @@ class Density(Diagnostic):
                     np.full(bigthetao.shape[1:],
                             ref_pressure, dtype=np.float32)
                 ))
-            sigma_values = np.stack(sigma_values)
+            sigma_values = np.ma.masked_invalid(np.stack(sigma_values))
             sigma_cube = bigthetao.copy(sigma_values)
             sigma_cube.var_name = f'sigma{sigma}'
             sigma_cube.standard_name = 'sea_water_sigma_theta'
@@ -144,7 +144,7 @@ class Density(Diagnostic):
             )
             sigma_cube.units = 'kg m-3'
             temp = TempFile.get()
-            iris.save(sigma_cube, temp, zlib=True)
+            iris.save(sigma_cube, temp, zlib=True, fill_value=1e20)
             del sigma_cube
             del sigma_values
             self.sigma[sigma].set_local_file(temp)
-- 
GitLab


From f9549907daad181668b3b3c1e1588d326f2e1aa2 Mon Sep 17 00:00:00 2001
From: Javier Vegas-Regidor <javier.vegas@bsc.es>
Date: Thu, 10 Dec 2020 15:35:47 +0100
Subject: [PATCH 3/3] Bump version

---
 VERSION            | 2 +-
 doc/source/conf.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/VERSION b/VERSION
index 87ce4929..444877d4 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.5.2
+3.5.3
diff --git a/doc/source/conf.py b/doc/source/conf.py
index e939abc0..9e05183a 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -65,7 +65,7 @@ copyright = u"2020, BSC-CNS Earth Sciences Department"
 # The short X.Y version.
 version = "3.5"
 # The full version, including alpha/beta/rc tags.
-release = "3.5.1"
+release = "3.5.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-- 
GitLab