Merge pull request #44 from GEOS-ESM/develop

Release v2.0.0

.github/workflows/changelog-enforcer.yml

@@ -0,0 +1,22 @@
+name: "Enforce Changelog"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: dangoslen/changelog-enforcer@v3
+      with:
+        changeLogPath: 'CHANGELOG.md'
+        skipLabels: 'Skip Changelog,0 diff trivial,automatic,dependencies,github_actions'
+        missingUpdateErrorMessage: >
+            No update to CHANGELOG.md found! Please add a changelog
+            entry to it describing your change.  Please note that the
+            keepachangelog (https://keepachangelog.com) format is
+            used. If your change is very trivial not applicable for a
+            changelog entry, add a 'Skip Changelog' label to the pull
+            request to skip the changelog enforcer.
+

.github/workflows/validate_yaml_files.yml

@@ -0,0 +1,31 @@
+---
+
+# Based on code from https://github.com/marketplace/actions/yaml-lint
+
+name: Yaml Lint
+
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+# This validation is equivalent to running on the command line:
+#   yamllint -d relaxed --no-warnings
+# and is controlled by the .yamllint.yml file
+jobs:
+  validate-YAML:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - id: yaml-lint
+        name: yaml-lint
+        uses: ibiqlik/action-yamllint@v3
+        with:
+          no_warnings: true
+          format: colored
+          config_file: .yamllint.yml
+
+      - uses: actions/upload-artifact@v3
+        if: always()
+        with:
+          name: yamllint-logfile
+          path: ${{ steps.yaml-lint.outputs.logfile }}

.yamllint.yml

@@ -0,0 +1,29 @@
+---
+
+extends: default
+
+rules:
+  braces:
+    level: warning
+    max-spaces-inside: 1
+  brackets:
+    level: warning
+    max-spaces-inside: 1
+  colons:
+    level: warning
+  commas:
+    level: warning
+  comments: disable
+  comments-indentation: disable
+  document-start: disable
+  empty-lines:
+    level: warning
+  hyphens:
+    level: warning
+  indentation:
+    level: warning
+    indent-sequences: consistent
+  line-length:
+    level: warning
+    allow-non-breakable-inline-mappings: true
+  truthy: disable

CHANGELOG.md

@@ -8,8 +8,29 @@
 
 ### Changed
 
+
+## [v2.0.0] - 2023-05-17
+
+### Added
+
+- Added changelog enforcer
+
+### Changed
+
+- Updated to use latest components (matching GEOSgcm v10.25.0)
+- Wholesale conversion to python3. Changes to all python scripts, and CMakelists with f2py compilation
+- the components.yaml now imports the GMAOpyobs repository, which replaces the legacy GMAO_pyobs directory
+- The GMAO_pyobs3 directory is no longer needed
+- A new directory called GMAO_aeropyobs has been added to share. This includes python utilities that require MAPL or GFIO that were previously in GMAO_pyobs. 
+- There may still be issues related to byte-to-string conversions that require fixing, but will need to be fixed as they are encountered.
+- Added GMAOpyobs v1.0.1 to components.yaml
+- Updated MAPL to v2.39.9
+
 ## [v1.0.0] - 2022-06-17
-Converted to mepo, cmake, and v3 giant files
+
+### Changed
+
+- Converted to mepo, cmake, and v3 giant files
 
 ### Added
 
@@ -18,12 +39,13 @@ Converted to mepo, cmake, and v3 giant files
 - legacy MAPL_Base/Python/MAPL into latest MAPL on develop branch
 
 ### Fixed
+
 - Moved src/GMAO_Shared to src/Shared/GMAO_Shared
 - obs_aod codes now work with v3 giant files
 
 ## [0.99.0] - 2020-03-23
 
-Intial GitHub release.
+Initial GitHub release.
 
 ### Added
   - Open source license

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   AeroApps
-  VERSION 1.0
+  VERSION 2.0.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")

components.yaml

@@ -5,23 +5,28 @@ AeroApps:
 env:
   local: ./env@
   remote: ../ESMA_env.git
-  tag: v3.2.2
+  tag: v4.8.0
   develop: main
 
 cmake:
   local: ./cmake@
   remote: ../ESMA_cmake.git
-  tag: v3.4.7
+  tag: v3.28.0
   develop: develop
 
 ecbuild:
   local: ./cmake@/ecbuild@
   remote: ../ecbuild.git
-  tag: geos/v1.0.6
+  tag: geos/v1.3.0
 
 MAPL:
   local: ./src/Shared/GMAO_Shared/MAPL@
   remote: ../MAPL.git
-  tag: v2.6.9
+  tag: v2.39.0
   develop: develop
 
+GMAOpyobs:
+  local: ./src/Shared/GMAO_Shared/GMAO_pyobs@
+  remote: ../GMAOpyobs.git
+  tag: v1.0.1
+  develop: develop

src/Applications/GAAS_App/aeronet_all.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """
 Splits AERONET into synoptic chunks.
 """
@@ -17,7 +17,7 @@ def makethis_dir(path):
     if path != '':
         rc = os.system('mkdir -p '+path)
         if rc:
-            raise IOError, "could not create directory "+path
+            raise IOError("could not create directory "+path)
 
 if __name__ == "__main__":
 
@@ -28,16 +28,16 @@ def makethis_dir(path):
     onehour = timedelta(seconds=60*60)
 
     if len(sys.argv)<2:
-        print "Usage:"
-        print "        aeronet4_all.py  year1 [year2]"
+        print("Usage:")
+        print("        aeronet4_all.py  year1 [year2]")
         sys.exit(1)
     else:
         y1 = sys.argv[1]
         if len(sys.argv)>2:
             y2 = sys.argv[2]
         else:
             y2 = y1
-        Years = range(int(y1),int(y2)+1)
+        Years = list(range(int(y1),int(y2)+1))
 
     # Loop over years
     # ---------------
@@ -49,7 +49,7 @@ def makethis_dir(path):
 
             today = tyme0 + (doy-1) * oneday
 
-            print 'Day: ', today
+            print('Day: ', today)
 
             # Read AERONET for this day
             # -------------------------

src/Applications/GAAS_App/aod_data.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import os, sys
 
 def aod_type(dataID, stdoutFLG=True):
@@ -115,19 +115,19 @@ def aod_filter(classlist_string, stdoutFLG=True):
     scriptname = os.path.basename(sys.argv[0])
 
     if len(sys.argv) < 2:
-        print("\nusage: {0} routineName input_parameters".format(scriptname))
-        print( " routineName options = {0}\n\n".format(routineList.keys()))
+        print(("\nusage: {0} routineName input_parameters".format(scriptname)))
+        print(( " routineName options = {0}\n\n".format(list(routineList.keys()))))
         exit()
 
     routineName = sys.argv[1]
-    if routineName not in routineList.keys():
+    if routineName not in list(routineList.keys()):
         raise Exception("Error. Unknown routine name: {0}".format(routineName))
     routine = routineList[routineName]
 
     if len(sys.argv) < 3:
         scriptname = os.path.basename(sys.argv[0])
-        print("\nusage: {0} {1} input_parameters".format(scriptname, routineName))
-        print(routineList[routineName].__doc__)
+        print(("\nusage: {0} {1} input_parameters".format(scriptname, routineName)))
+        print((routineList[routineName].__doc__))
         exit()
 
     routineList[routineName](*sys.argv[2:])

src/Applications/GAAS_App/avhrr_all.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """
 Splits AVHRR into synoptic chunks.
 """
@@ -14,16 +14,16 @@
     onehour = timedelta(seconds=60*60)
 
     if len(sys.argv)<2:
-        print "Usage:"
-        print "        avhrr_all.py  year1 [year2]"
+        print("Usage:")
+        print("        avhrr_all.py  year1 [year2]")
         sys.exit(1)
     else:
         y1 = sys.argv[1]
         if len(sys.argv)>2:
             y2 = sys.argv[2]
         else:
             y2 = y1
-        Years = range(int(y1),int(y2)+1)
+        Years = list(range(int(y1),int(y2)+1))
 
     # Loop over years
     # ---------------
@@ -42,5 +42,5 @@
 
                 cmd = 'python avhrr_l2a.py -v asc %d %d'%(nymd,nhms)
 
-                print cmd
+                print(cmd)
                 os.system(cmd)

src/Applications/GAAS_App/avhrr_l2a.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -W ignore::DeprecationWarning
 
 """
@@ -54,10 +54,10 @@
     i = 0
     for orbit in cf('AVHRR_L2A_ORBITS').split(','):
         cmd = "patmosx_l2a.py %s %s %s %s"%(Options,orbit,nymd,nhms)
-        print cmd
+        print(cmd)
         if not options.dryrun:
             if system(cmd):
-                raise ValueError, "patmosx_l2a.py failed for %s on %s %s"%(orbit,nymd,nhms)
+                raise ValueError("patmosx_l2a.py failed for %s on %s %s"%(orbit,nymd,nhms))
 
         i += 1
 

src/Applications/GAAS_App/avhrr_nnr.py

@@ -77,7 +77,7 @@ def _getInputs(self):
         for inputName in self.net.InputNames:
 
             if self.verbose>0:
-                print 'Getting NN input ',inputName
+                print('Getting NN input ',inputName)
 
             # Retrieve input
             # --------------
@@ -114,15 +114,15 @@ def apply(self,nnFile='/nobackup/NNR/Net/nnr_001b.avhrr_Tau.net'):
             return # no good data to work with
 
         if len(self.net.TargetNames)>1:
-            raise ValueError, 'Strange, more than one predictor'
+            raise ValueError('Strange, more than one predictor')
 
         # Evaluate NN on inputs
         # ---------------------
         targets = self.net(self._getInputs())
 
         name = self.net.TargetNames[0]
         if self.verbose>0:
-            print "Evaluating NNR for <%s> with Log-AOD = "%name, self.net.laod 
+            print("Evaluating NNR for <%s> with Log-AOD = "%name, self.net.laod) 
 
         # Output is always AOD
         # --------------------