Merge branch 'dev/14.4.0' into dev/no-diff-to-benchmark

.github/workflows/stale.yml

@@ -0,0 +1,38 @@
+# This workflow warns and then closes issues that have had no activity for a specified amount of time.
+#
+# You can adjust the behavior by modifying this file.
+# For more information, see:
+# https://github.com/actions/stale
+name: Mark stale issues
+
+on:
+  schedule:
+  - cron: '0 0 * * *' # Run every night at midnight
+
+jobs:
+  stale:
+
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+
+    steps:
+    - uses: actions/stale@v5
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-label: 'stale'
+        exempt-issue-labels:
+          - 'category: Discussion'
+          - 'category: Feature Request'
+          - 'deferred'
+          - 'help needed: Open Research Problem'
+          - 'help needed: Request Input from Community'
+          - 'never stale'
+          - 'TODO: Documentation'
+        days-before-issue-stale: 30
+        days-before-issue-close: 7
+        stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.'
+        close-issue-message: 'Closing due to inactivity'
+        days-before-pr-stale: -1
+        days-before-pr-close: -1

.gitmodules

@@ -20,7 +20,7 @@
 	path = src/GCHP_GridComp/GEOSChem_GridComp/geos-chem
 	url = https://github.com/geoschem/geos-chem.git
 [submodule "HEMCO"]
-	path = src/GCHP_GridComp/HEMCO_GridComp/HEMCO
+	path = src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO
 	url = https://github.com/geoschem/HEMCO.git
 [submodule "yaFyaml"]
 	path = src/yaFyaml
@@ -32,5 +32,8 @@
 	path = docs/source/geos-chem-shared-docs
 	url = https://github.com/geoschem/geos-chem-shared-docs.git
 [submodule "Cloud-J"]
-	path = src/GCHP_GridComp/Cloud-J
+	path = src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J
 	url = https://github.com/geoschem/Cloud-J
+[submodule "HETP"]
+	path = src/GCHP_GridComp/GEOSChem_GridComp/HETP
+	url = https://github.com/geoschem/HETerogeneous-vectorized-or-Parallel.git

CHANGELOG.md

@@ -2,18 +2,37 @@
 
 This file documents all notable changes to the GCHP wrapper repository starting in version 14.0.0. See also CHANGELOG files for individual submodules, such as:
 - src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/CHANGELOG.md
-- src/GCHP_GridComp/HEMCO_GridComp/HEMCO/CHANGELOG.md
+- src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/CHANGELOG.md
+- src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J/CHANGELOG.md
+- src/GCHP_GridComp/GEOSChem_GridComp/HETP/CHANGELOG.md
 - src/MAPL/CHANGELOG.md
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - TBD
+### Added
+- GitHub Action config file `.github/workflows/stale.yml`, which replaces StaleBot
+- Added git submodule HETP for aerosol thermodynamics in GEOS-Chem
+
+### Changed
+- Updated GEOS-Chem submodule to 14.4.0
+- Updated HEMCO submodule to 3.9.0
+- Changed subdirectory name HEMCO_GridComp to HEMCO since not its own gridded component
+- Moved HEMCO and Cloud-J submodules from GCHP_GridComp to GCHP_GridComp/GEOSChem_GridComp where they are used
+
+### Removed
+- GitHub config files `.github/stale.yml` and `.github/no-response.yml`
+
 ## [14.3.1] - 2024-04-02
 ### Added
 - Now print container name being read by ExtData when `CAP.EXTDATA` is set to `DEBUG` in `logging.yml`
 - Added new pre-processer setting GCHP_WRAPPER for use in submodules
 - Added PLEadv export to FV3 submodule for inclusion in GCHP HISTORY.rc files
+- Added git submodule for HETP aerosol thermodynamics
 
 ### Changed
+- Updated GEOS-Chem submodule to 14.3.1
+- Updated HEMCO submodule to 3.8.1
 - Now use short names for submodules (i.e. without the path) in `.gitmodules`
 
 ### Fixed

src/GCHP_GridComp/CMakeLists.txt

@@ -5,35 +5,23 @@
 #---------------
 set(FV_PRECISION           R8    ) # FV3 precision is R8
 set(GCHP_WRAPPER           TRUE  ) # GCHP model configuration
-set(CLOUDJ_EXTERNAL_CONFIG TRUE  ) # Not Cloud-J standalone
-set(HEMCO_EXTERNAL_CONFIG  TRUE  ) # Not HEMCO standalone
 set(GC_EXTERNAL_CONFIG     TRUE  ) # Not GEOS-Chem Classic
 set(MAPL_ESMF              TRUE  ) # HEMCO and GEOS-Chem will use MAPL/ESMF
 set(MAPL_ACG ${CMAKE_CURRENT_SOURCE_DIR}/../MAPL/Apps/mapl_acg.pl)
 
-#---------------
-# Add FV3
-#---------------
+#-------------------------------------------
+# Add DYNAMICS gridded component (advection)
+#-------------------------------------------
 add_subdirectory(FVdycoreCubed_GridComp EXCLUDE_FROM_ALL)
 
-#---------------
-# Add Cloud-J
-#---------------
-add_subdirectory(Cloud-J EXCLUDE_FROM_ALL)
-
-#---------------
-# Add HEMCO
-#---------------
-add_subdirectory(HEMCO_GridComp EXCLUDE_FROM_ALL)
-
-#---------------
-# Add GEOS-Chem
-#---------------
+#-------------------------------------------
+# Add GCHPchem gridded component (GEOS-Chem)
+#-------------------------------------------
 add_subdirectory(GEOSChem_GridComp EXCLUDE_FROM_ALL)
 
-#---------------
-# Add GCHPctmEnv
-#---------------
+#----------------------------------------------------
+# Add GCHPctmEnv gridded component (pre-advection)
+#----------------------------------------------------
 add_subdirectory(GCHPctmEnv_GridComp EXCLUDE_FROM_ALL)
 
 #--------------------------------

src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt

@@ -19,13 +19,19 @@ set(FASTJX OFF CACHE BOOL
 
 # Local variables
 set(GC_EXTERNAL_CONFIG      TRUE)
+set(CLOUDJ_EXTERNAL_CONFIG  TRUE) # Not Cloud-J standalone
+set(HETP_EXTERNAL_CONFIG    TRUE) # Not HETP standalone test
+set(HEMCO_EXTERNAL_CONFIG   TRUE) # Not HEMCO standalone
 set(GTMM                    FALSE)
 set(MECH "fullchem" CACHE STRING "Name of the chemistry mechanism to use")
 set(GCHP                    TRUE)
 set(MODEL_GCHP              TRUE)
 set(MODEL_GCHPCTM           TRUE)
 
 # Add directories to build
+add_subdirectory(Cloud-J EXCLUDE_FROM_ALL)
+add_subdirectory(HETP EXCLUDE_FROM_ALL)
+add_subdirectory(HEMCO EXCLUDE_FROM_ALL)
 add_subdirectory(geos-chem EXCLUDE_FROM_ALL)
 
 # Configure build properties for GEOS-Chem

src/GCHP_GridComp/HEMCO_GridComp/CMakeLists.txt → src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/CMakeLists.txt

@@ -1,4 +1,4 @@
-# HEMCO_GridComp/CMakeLists.txt
+# HEMCO/CMakeLists.txt
 
 add_subdirectory(HEMCO EXCLUDE_FROM_ALL)