Preparation for release.

Add missing check that positive attribute is consistent with sign implied by standard_name from #30
cedadev · Mar 21, 2018 · 77f35c5 · 77f35c5
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diff --git a/CHANGES.md b/CHANGES.md
@@ -3,6 +3,18 @@
 See https://github.com/cedadev/cf-checker/milestones?state=closed for full details of each release.
 
 -----------------------------------------------------------------
+## March 2018
+
+CF Checker release 3.1.0
+
+This is a development release to include addition checks for CF-1.7 comformance.
+
+### Other Noteworthy Changes
+
+[#35](https://github.com/cedadev/cf-checker/issues/35): Improve execution speed
+
+[#29](https://github.com/cedadev/cf-checker/issues/29): Include checks against region names table
+
 ## 03.05.2017
 
 CF Checker release 3.0.1

diff --git a/README.md b/README.md
@@ -42,14 +42,17 @@ Alternatively, to install from source:
 
 ## Running the CF Checker
 
-`cfchecks [-a area_types.xml] [-s standard_names.xml] [-t cache_time_days ] [-v CFVersion] [-x] [--cachedir <dir>] file1 [file2...]`
+`cfchecks [-a <area-types.xml>] [-r <regions.xml>] [-s <std_names.xml>] [-v <CFVersion>] [-x] [-t <cache_time_days>] file1 [file2...]`
+
+For further details and for other available command line options please see the help by running `cfchecks -h`
 
 ### Environment Variables
 
 The following parameters can be set on the command-line or through environment variables:
 
-1. `CF_STANDARD_NAMES` (or CL option `-s`) : The path or URL to the CF standard names table
-2. `CF_AREA_TYPES` or (CL option `-a`) : The path or URL to the CF area types tables
+1. `CF_STANDARD_NAMES` or (CL option `-s`) : The path or URL to the CF standard names table
+2. `CF_AREA_TYPES` or (CL option `-a`) : The path or URL to the CF area types table
+3. `CF_REGION_NAMES` or (CL option `-r`): The path or URL to the CF region names table
 
 ### Wrapper script
 
@@ -64,7 +67,7 @@ The wrapper is maintained by CEDA and not by NCAS CMS.
 
 ### Running the Test script
 
-In the release tarball there is a `test_files` directory containing a `test.sh` script which runs a series of test files through the CF Checker and confirms the checker is working as expected.  It is a very elementary system, which will be rewritten soon.  Before running it you will need to edit the location of the cfchecker script in the `tests.sh` file:
+In the release tarball there is a `test_files` directory containing a `test.sh` script which runs a series of test files through the CF Checker and confirms the checker is working as expected.  It is a very elementary system, which will be rewritten soon.  Before running it you will need to edit the location of the cfchecks script in the `tests.sh` file:
 
     cfchecker="<location of cfchecks>"
 

diff --git a/src/cfchecker/__init__.py b/src/cfchecker/__init__.py
@@ -1 +1 @@
-__version__ = '3.0.6-dev'
+__version__ = '3.1.0-rc1'
diff --git a/src/cfchecker/cfchecks.py b/src/cfchecker/cfchecks.py
@@ -2664,6 +2664,14 @@ def chkDescription(self, varName):
                   else:
                       self._add_error("No region names specified", varName, code="3.3")
 
+              if hasattr(var, 'positive'):
+                  # Check that positive attribute is consistent with sign implied by standard_name
+                  if (re.match("height", name, re.I) and not re.match("up", var.positive, re.I)) or \
+                          (re.match("depth", name, re.I) and not re.match("down", var.positive, re.I)):
+                      self._add_warn("Positive attribute inconsistent with sign conventions implied by the standard_name",
+                                     varName, code="4.3")
+
+
   #---------------------------------  
   def getStringValue(self, varName):
   #---------------------------------

diff --git a/test_files/CF_1_0_OK.check b/test_files/CF_1_0_OK.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CF_1_0_OK.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 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
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CF_1_7.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.7
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Area Type Table Version 7 (14 March 2018)
@@ -20,6 +20,8 @@ ERROR: (5): co-ordinate variable not monotonic
 ------------------
 Checking variable: depth
 ------------------
+WARN: (4.3): Positive attribute inconsistent with sign conventions implied by the standard_name
+ERROR: (3.1): Units are not consistent with those given in the standard_name table.
 ERROR: (5): co-ordinate variable not monotonic
 
 ------------------
@@ -128,6 +130,6 @@ 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
+ERRORS detected: 25
+WARNINGS given: 4
 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
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM018_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM021_test1.check b/test_files/CRM021_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM021_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM024_test1.check b/test_files/CRM024_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM024_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM026_test2.check b/test_files/CRM026_test2.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM026_test2.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM027_test1.check b/test_files/CRM027_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM027_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM027_test2.check b/test_files/CRM027_test2.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM027_test2.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM028_test1.check b/test_files/CRM028_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM028_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM032_test1.check b/test_files/CRM032_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM032_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM033_test1.check b/test_files/CRM033_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM033_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM035.check b/test_files/CRM035.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM035.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM037.check b/test_files/CRM037.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM037.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM038.check b/test_files/CRM038.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM038.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/CRM041.check b/test_files/CRM041.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: CRM041.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/GregRappa.check b/test_files/GregRappa.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: GregRappa.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/Trac020_test1.check b/test_files/Trac020_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: Trac020_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/Trac020_test2.check b/test_files/Trac020_test2.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: Trac020_test2.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/Trac022.check b/test_files/Trac022.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: Trac022.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/Trac049_test1.check b/test_files/Trac049_test1.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: Trac049_test1.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.4
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Area Type Table Version 7 (14 March 2018)

diff --git a/test_files/Trac049_test2.check b/test_files/Trac049_test2.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: Trac049_test2.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.4
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Area Type Table Version 7 (14 March 2018)

diff --git a/test_files/UpgradeVn.pl b/test_files/UpgradeVn.pl
@@ -13,7 +13,7 @@
 #           Before running simply alter the variables $checkerVN and
 #           $standardNameVN as appropriate.
 #-------------------------------------------------------------------------- 
-$checkerVN="3.0.6-dev";
+$checkerVN="3.1.0-rc1";
 $standardNameVN="50 (2018-03-14T11:01:19Z)";
 $areaTypeVN="7 (14 March 2018)";
 

diff --git a/test_files/badc_units.check b/test_files/badc_units.check
@@ -1,7 +1,7 @@
 
 CHECKING NetCDF FILE: badc_units.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 
 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
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: cell_measures.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/cell_methods.check b/test_files/cell_methods.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: cell_methods.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/complex.check b/test_files/complex.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: complex.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/example_5.10.check b/test_files/example_5.10.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: example_5.10.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.7
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Area Type Table Version 7 (14 March 2018)

diff --git a/test_files/example_6.2.check b/test_files/example_6.2.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: example_6.2.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.7
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Area Type Table Version 7 (14 March 2018)

diff --git a/test_files/flag_tests.check b/test_files/flag_tests.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: flag_tests.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.3
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/formula_terms.check b/test_files/formula_terms.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: formula_terms.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/hfogo_O1_labelVariable_KT.check b/test_files/hfogo_O1_labelVariable_KT.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: hfogo_O1_labelVariable_KT.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.0
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Standardized Region Name Table Version 2 (12 June 2013)

diff --git a/test_files/issue27.check b/test_files/issue27.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: issue27.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.6
 Using Standard Name Table Version 50 (2018-03-14T11:01:19Z)
 Using Area Type Table Version 7 (14 March 2018)

diff --git a/test_files/stdName_test.check b/test_files/stdName_test.check
@@ -1,6 +1,6 @@
 CHECKING NetCDF FILE: stdName_test.nc
 =====================
-Using CF Checker Version 3.0.6-dev
+Using CF Checker Version 3.1.0-rc1
 Checking against CF Version CF-1.7
 Using Standard Name Table Version 2 (2006-09-26T18:12:43Z)
 Using Area Type Table Version 7 (14 March 2018)