Merge pull request #39 from cedadev/cf1_7

Further CF-1.7 checks
cedadev · Feb 28, 2018 · b66e954 · b66e954
2 parents a162a9f + b7ed52f
commit b66e954
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Showing 37 changed files with 501 additions and 87 deletions.
diff --git a/src/cfchecker/cfchecks.py b/src/cfchecker/cfchecks.py
diff --git a/test_files/CF_1_0_OK.check b/test_files/CF_1_0_OK.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CF_1_0_OK.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/CF_1_7.check b/test_files/CF_1_7.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CF_1_7.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.7
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Area Type Table Version 6 (22 February 2017)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
@@ -11,7 +11,6 @@ ERROR: (2.6.3): Variable external_var2 named as an external variable must not be
 ------------------
 Checking variable: lat
 ------------------
-ERROR: (5): co-ordinate variable not monotonic
 
 ------------------
 Checking variable: lon
@@ -65,6 +64,70 @@ Checking variable: arv4
 ERROR: (2.5.1): actual_range attribute must be of same type as variable arv4
 ERROR: (2.5.1): actual_range values must be greater than or equal to 15.0 (valid_min)
 
-ERRORS detected: 14
-WARNINGS given: 0
-INFORMATION messages: 0
+------------------
+Checking variable: current_speed_qc
+------------------
+WARN: (3.3): Use of standard_name modifier status_flag is deprecated
+
+------------------
+Checking variable: current_speed_qc2
+------------------
+WARN: (3.3): Use of standard_name modifier number_of_observations is deprecated
+
+------------------
+Checking variable: n_heat_transport
+------------------
+
+------------------
+Checking variable: geo_region
+------------------
+ERROR: (3.3): Invalid region name: dummy_ocean
+
+------------------
+Checking variable: lev
+------------------
+ERROR: (4.3.3): Standard name of variable PS inconsistent with that of lev
+ERROR: (4.3.3): PTOP is not declared as a variable
+ERROR: (5): co-ordinate variable not monotonic
+
+------------------
+Checking variable: PS
+------------------
+
+------------------
+Checking variable: sigma
+------------------
+ERROR: (4.3.3): Formula term dummy not present in formula for ocean_sigma_coordinate
+ERROR: (4.3.3): Standard names of formula_terms variables are inconsistent/invalid
+ERROR: (5): co-ordinate variable not monotonic
+
+------------------
+Checking variable: var2
+------------------
+INFO: (3.1): No units attribute set.  Please consider adding a units attribute for completeness.
+
+------------------
+Checking variable: var3
+------------------
+INFO: (3.1): No units attribute set.  Please consider adding a units attribute for completeness.
+
+------------------
+Checking variable: sigma2
+------------------
+WARN: (3.1): units attribute should be present
+ERROR: (4.3.3): computed_standard_name attribute is only allowed on a coordinate variable which has a formula_terms attribute
+ERROR: (5): co-ordinate variable not monotonic
+
+------------------
+Checking variable: temp
+------------------
+
+------------------
+Checking variable: crs
+------------------
+ERROR: (5.6): Attribute longitude_of_prime_meridian of incorrect data type (Appendix F)
+ERROR: (5.6): reference_ellipsoid_name, prime_meridian_name, horizontal_datum_name and geographic_crs_name must all be definied if any one is defined
+
+ERRORS detected: 24
+WARNINGS given: 3
+INFORMATION messages: 2
diff --git a/test_files/CF_1_7.nc.gz b/test_files/CF_1_7.nc.gz
diff --git a/test_files/CRM018_test1.check b/test_files/CRM018_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM018_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (2.6.1): No 'Conventions' attribute present

diff --git a/test_files/CRM021_test1.check b/test_files/CRM021_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM021_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/CRM024_test1.check b/test_files/CRM024_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM024_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 ERROR: (2.6.1): This netCDF file does not appear to contain CF Convention data.

diff --git a/test_files/CRM026_test2.check b/test_files/CRM026_test2.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM026_test2.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/CRM027_test1.check b/test_files/CRM027_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM027_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (7.1): Data for variable time lies outside cell boundaries

diff --git a/test_files/CRM027_test2.check b/test_files/CRM027_test2.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM027_test2.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (7.1): Data for variable time lies outside cell boundaries

diff --git a/test_files/CRM028_test1.check b/test_files/CRM028_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM028_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (2.6.1): No 'Conventions' attribute present

diff --git a/test_files/CRM032_test1.check b/test_files/CRM032_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM032_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 ERROR: (2.6.1): This netCDF file does not appear to contain CF Convention data.

diff --git a/test_files/CRM033_test1.check b/test_files/CRM033_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM033_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (2.6.1): No 'Conventions' attribute present

diff --git a/test_files/CRM035.check b/test_files/CRM035.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM035.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (2.6.1): No 'Conventions' attribute present

diff --git a/test_files/CRM037.check b/test_files/CRM037.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM037.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/CRM038.check b/test_files/CRM038.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM038.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/CRM041.check b/test_files/CRM041.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: CRM041.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/GregRappa.check b/test_files/GregRappa.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: GregRappa.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/Trac020_test1.check b/test_files/Trac020_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: Trac020_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/Trac020_test2.check b/test_files/Trac020_test2.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: Trac020_test2.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 

diff --git a/test_files/Trac022.check b/test_files/Trac022.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: Trac022.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (2.6.1): No 'Conventions' attribute present

diff --git a/test_files/Trac049_test1.check b/test_files/Trac049_test1.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: Trac049_test1.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.4
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Area Type Table Version 6 (22 February 2017)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 

diff --git a/test_files/Trac049_test2.check b/test_files/Trac049_test2.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: Trac049_test2.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.4
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Area Type Table Version 6 (22 February 2017)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 

diff --git a/test_files/UpgradeVn.pl b/test_files/UpgradeVn.pl
@@ -14,7 +14,7 @@
 #           $standardNameVN as appropriate.
 #-------------------------------------------------------------------------- 
 $checkerVN="3.0.6-dev";
-$standardNameVN="48 (2017-11-28T15:32:48Z)";
+$standardNameVN="49 (2018-02-13T08:44:33Z)";
 
 $TEST_FILES_DIR="/home/ros/puma2/git-projects/cf-checker/test_files";
 chdir $TEST_FILES_DIR or die "Failed to cd to $TEST_FILES_DIR: $!\n";

diff --git a/test_files/badc_units.check b/test_files/badc_units.check
@@ -2,7 +2,7 @@
 CHECKING NetCDF FILE: badc_units.nc
 =====================
 Using CF Checker Version 3.0.6-dev
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 
 WARNING (7.1): Data for variable time lies outside cell boundaries
 

diff --git a/test_files/cell_measures.check b/test_files/cell_measures.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: cell_measures.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 ERROR: (7.1): Incorrect dimensions for boundary variable: lon_vertices

diff --git a/test_files/cell_methods.check b/test_files/cell_methods.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: cell_methods.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 ERROR: (7.1): Incorrect dimensions for boundary variable: lon_vertices

diff --git a/test_files/complex.check b/test_files/complex.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: complex.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.0
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
 WARN: (2.6.1): No 'Conventions' attribute present

diff --git a/test_files/example_5.10.check b/test_files/example_5.10.check
@@ -0,0 +1,51 @@
+CHECKING NetCDF FILE: example_5.10.nc
+=====================
+Using CF Checker Version 3.0.6-dev
+Checking against CF Version CF-1.7
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
+Using Area Type Table Version 6 (22 February 2017)
+Using Standardized Region Name Table Version 2 (12 June 2013)
+
+
+------------------
+Checking variable: x
+------------------
+ERROR: (5): co-ordinate variable not monotonic
+
+------------------
+Checking variable: y
+------------------
+ERROR: (5): co-ordinate variable not monotonic
+
+------------------
+Checking variable: z
+------------------
+ERROR: (5): co-ordinate variable not monotonic
+
+------------------
+Checking variable: lat
+------------------
+
+------------------
+Checking variable: lon
+------------------
+
+------------------
+Checking variable: temp
+------------------
+
+------------------
+Checking variable: pres
+------------------
+
+------------------
+Checking variable: crsOSGB
+------------------
+
+------------------
+Checking variable: crsWGS84
+------------------
+
+ERRORS detected: 3
+WARNINGS given: 0
+INFORMATION messages: 0
diff --git a/test_files/example_5.10.nc.gz b/test_files/example_5.10.nc.gz
diff --git a/test_files/example_6.2.check b/test_files/example_6.2.check
@@ -2,7 +2,7 @@ CHECKING NetCDF FILE: example_6.2.nc
 =====================
 Using CF Checker Version 3.0.6-dev
 Checking against CF Version CF-1.7
-Using Standard Name Table Version 48 (2017-11-28T15:32:48Z)
+Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
 Using Area Type Table Version 6 (22 February 2017)
 Using Standardized Region Name Table Version 2 (12 June 2013)
 
@@ -14,7 +14,6 @@ Checking variable: n_heat_transport
 ------------------
 Checking variable: time
 ------------------
-ERROR: (5): co-ordinate variable not monotonic
 
 ------------------
 Checking variable: lat
@@ -24,6 +23,6 @@ Checking variable: lat
 Checking variable: geo_region
 ------------------
 
-ERRORS detected: 1
+ERRORS detected: 0
 WARNINGS given: 0
 INFORMATION messages: 0
diff --git a/test_files/example_6.2.nc.gz b/test_files/example_6.2.nc.gz