From 9c77f3023ecbbb35b7df48b492085b6abc9c1116 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 8 Jul 2024 13:34:18 -0400 Subject: [PATCH 01/18] GEOS-Chem submod update: Merge PR #2363 (Update setCommonRunSettings.sh) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 8554d3a30 Merge PR #2363 (Update setCommonRunSettings.sh.template) This PR implements a hotfix for an issue where GCHP simulations always "thought" that they were using mass fluxes regardless of the met field option chosen. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index dd859ee45..8554d3a30 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit dd859ee45494af71d29f0877f359ff571f697b67 +Subproject commit 8554d3a30312c28d51452d6da471661eaa1b2a3e From 6eb11101a5f0d94f41c96d8a51e736c47c47f74b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Jul 2024 14:24:44 -0400 Subject: [PATCH 02/18] GEOS-Chem submod update: Merge PR #2342 and Cloud-J PR #17 This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: f78052f59 Merge PR #2342 (Read number of levels with clouds into Cloud-J) and to the geoschem/Cloud-J repository: 2d75997 Merge pull request #17 from geoschem/feature/set_levels_with_cloud_from_parent_model 8a3b925 Update .zenodo.json; add license badge to README d93a5aa Add Zenodo file for DOI generation 42b31ea Update version and add release date for 7.7.1 c9cbe9a Update README.md These PRs allow you to specify the number of levels with cloud for Cloud-J. This number is different depending on which instance of GEOS-Chem you are using (GCClassic, GCHP, CESM, WRF-GC, etc). Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J | 2 +- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J index 3162ea8ba..2d7599717 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J +++ b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J @@ -1 +1 @@ -Subproject commit 3162ea8baa9ab69c3b8473270abc0188ad54501b +Subproject commit 2d75997172ec4af590b1aba65d9ebf65773a4bf2 diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 8554d3a30..f78052f59 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 8554d3a30312c28d51452d6da471661eaa1b2a3e +Subproject commit f78052f598e27b699fc535d8477fa7ddf062a8d0 From 530da55175e01f70152e6037529582ef98b428e4 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Jul 2024 16:29:30 -0400 Subject: [PATCH 03/18] geos-chem-shared-docs update: Updated "View related documentation" tables This commit informs the GCHP superproject about the following updates that were pushed to the geos-chem-shared-docs repository: 65d9a1f Updated the "View Related Documentation" supplemental guide This removes the "GEOS-Chem on the cloud" entry from the list of related documentation, and also updates the legacy documentation archive. Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index cbfb5cb7e..65d9a1ff6 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit cbfb5cb7ea3b20921fb1cb156ba8ab468d54364d +Subproject commit 65d9a1ff6dc44a9e479b4903bb36e83272d01aa3 From 493b4fdb84eebec9d22e0c1db93994ca2c42feda Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Jul 2024 17:32:01 -0400 Subject: [PATCH 04/18] Submod updates: Merge GEOS-Chem PR #2353 and Cloud-J PR #19 This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 5b3987feb Merge PR #2353 (Cloud-J error handling) And to the geoschem/Cloud-J repository: 5eabcbe Merge pull request #19 from geoschem/feature/error_handling These PRs return the error code from Cloud-J all the way out to the main program, where the simulation can be terminated gracefully. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J | 2 +- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J index 2d7599717..5eabcbe1b 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J +++ b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J @@ -1 +1 @@ -Subproject commit 2d75997172ec4af590b1aba65d9ebf65773a4bf2 +Subproject commit 5eabcbe1b12f674a24f6afa85a63ba8c0e3884fa diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index f78052f59..5b3987feb 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit f78052f598e27b699fc535d8477fa7ddf062a8d0 +Subproject commit 5b3987febe19a1d6042331c78ed438f49bbc2cd1 From a96673e85e98b0944e1cb05164aa22ece3bbbb90 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Wed, 10 Jul 2024 14:01:06 -0400 Subject: [PATCH 05/18] GEOS-Chem submod update: Merge PR #2366 (CESM spectral-element dyn core) Signed-off-by: Lizzie Lundgren --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 5b3987feb..9e8e300d1 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 5b3987febe19a1d6042331c78ed438f49bbc2cd1 +Subproject commit 9e8e300d1022d6d19c66ebdd49b7b6e42b9677d4 From 2fd25ee78a5abac2ca1a788f4055932fc2cbbdab Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Wed, 10 Jul 2024 16:49:52 -0400 Subject: [PATCH 06/18] Submod updates: Merge MAPL PRs #35 and #36 (prefetch debug; hflux bug fix) hflux is horizontal flux regridding. Signed-off-by: Lizzie Lundgren --- src/MAPL | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MAPL b/src/MAPL index 850f20a9b..231d53cc0 160000 --- a/src/MAPL +++ b/src/MAPL @@ -1 +1 @@ -Subproject commit 850f20a9b7b78f8cf58fe4516e49ea2b0d50e31f +Subproject commit 231d53cc0b14dc3275cac2867ddb9e15adbc8877 From 95a745c0d5e84b91e023b7747b32d3c2bfb2b31f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 11 Jul 2024 10:53:39 -0400 Subject: [PATCH 07/18] GEOS-Chem submod update: Merge PR #2369 (Fixes for satellite diags) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 7e4001658 Merge PR #2369 (Fix several issues with satellite diagnostics) This PR resolves several outstanding issues with the GEOS-Chem Classic satellite diagnostics. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 9e8e300d1..7e4001658 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 9e8e300d1022d6d19c66ebdd49b7b6e42b9677d4 +Subproject commit 7e4001658a2ce00af9b7bb73e3a4a3b2dbaae20e From c0b538fef352b1a4b339ab44b356befd3bedd410 Mon Sep 17 00:00:00 2001 From: Yidan Tang Date: Fri, 12 Jul 2024 11:50:17 -0500 Subject: [PATCH 08/18] Add docs geos-chem-input-data-on-aws.rst to supplemental-guides. Signed-off-by: Yidan Tang --- docs/source/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/index.rst b/docs/source/index.rst index 3369aac6a..5af027817 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -77,6 +77,7 @@ use Spack to install GCHP's dependencies if needed. geos-chem-shared-docs/supplemental-guides/load-libraries-guide.rst geos-chem-shared-docs/supplemental-guides/spack-guide.rst + geos-chem-shared-docs/supplemental-guides/geos-chem-input-data-on-aws.rst supplement/setting-up-aws-parallelcluster.rst supplement/caching-input-data.rst supplement/containers.rst From 481ea943bd2745c47784b23b4d8d36c7d3467079 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 12 Jul 2024 13:57:23 -0400 Subject: [PATCH 09/18] Throw a CMake error if FAST-JX is used for any mech except Hg src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt - Add an if block to throw a fatal error if the FASTJX compile option is selected for fullchem, custom, or carbon simulations. Fullchem and custom mechanisms use Cloud-J. We still need to use the FAST-JX photolysis scheme with Hg pending input file updates. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 14 +++++++++----- src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt | 8 ++++++++ 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ca2dc5a2..d2cd39021 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,14 +1,18 @@ # Changelog 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/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 +- `src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/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 +### Changed +- CMake now throws an error if FAST-JX is used with any other mechanism than Hg + ## [14.4.1] - 2024-06-28 ### Fixed - Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt b/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt index 1036e4ec4..48ea0fbb0 100755 --- a/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt +++ b/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt @@ -147,3 +147,11 @@ gc_pretty_print(VARIABLE RRTMG IS_BOOLEAN) gc_pretty_print(VARIABLE GTMM IS_BOOLEAN) gc_pretty_print(VARIABLE LUO_WETDEP IS_BOOLEAN) gc_pretty_print(VARIABLE FASTJX IS_BOOLEAN) + +# Throw an error unless we are using the Hg mechanism, +# The fullchem & custom mechanisms now use Cloud-J! +if(${FASTJX}) + if(NOT ${MECH} MATCHES "Hg") + message(FATAL_ERROR "FASTJX can only be used with the Hg mechanism!") + endif() +endif() From 7c5bd90c2972a97215d78ab5d1908111a5a6c459 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 12 Jul 2024 14:38:58 -0400 Subject: [PATCH 10/18] GEOS-Chem submod update: Add doc about input data on AWS cloud This commit informs the GCClassic superproject about the following updates that were pushed to geos-chem-shared-docs: c061f07 Add documentation and tutorial for GEOS-Chem input data on AWS. - supplemental-guides/geos-chem-input-data-on-aws.rst is the main page. - why-on-cloud.rst, data-on-aws.rst and getting-started-aws.rst are sub-pages. Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 65d9a1ff6..c061f07e8 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 65d9a1ff6dc44a9e479b4903bb36e83272d01aa3 +Subproject commit c061f07e88ebf30719dfed76282e7aeac79ae0ad From 0d5ecb3509adc4d7dc51e6717fd419e8ef7f752a Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Fri, 12 Jul 2024 15:06:11 -0400 Subject: [PATCH 11/18] Cloud-J submod update: Update to version 7.7.2 release Signed-off-by: Lizzie Lundgren --- CHANGELOG.md | 4 ++++ src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ca2dc5a2..e252d1fee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,10 @@ This file documents all notable changes to the GCHP wrapper repository starting 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). +## [14.4.2] - TBD +### Changed +- Updated Cloud-J submodule to 7.7.2 + ## [14.4.1] - 2024-06-28 ### Fixed - Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J index 5eabcbe1b..37a4ece35 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J +++ b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J @@ -1 +1 @@ -Subproject commit 5eabcbe1b12f674a24f6afa85a63ba8c0e3884fa +Subproject commit 37a4ece3580a9a8ce64d9fbd03c699cd116c6d80 From 094f53b90430fadb40f28dfdf95087ceff6377af Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 12 Jul 2024 15:21:06 -0400 Subject: [PATCH 12/18] GEOS-Chem submod update: Merge PR #2372 (Disable MEGAN in non-bmk sims) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 03287a67a Merge PR #2372 (Turn off MEGAN extension for non-benchmark sims) This PR disables the MEGAN extension for all fullchem sims except benchmark. (Excluding GCAP2 simulations.) Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 7e4001658..03287a67a 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 7e4001658a2ce00af9b7bb73e3a4a3b2dbaae20e +Subproject commit 03287a67a368663bd393b777c1f9e1dc0d486ee6 From cfa2e4e3b6c5616e2de829691aaed627863d6217 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 15 Jul 2024 17:41:59 -0400 Subject: [PATCH 13/18] geos-chem-shared-docs update: Update photolysis sectin in Using KPP guide This commit informs the GCHP superproject about the following updates that were made in the geos-chem-shared-docs submodule ce3c86a Update Photolysis section in using-kpp-with-gc.rst Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index c061f07e8..ce3c86acc 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit c061f07e88ebf30719dfed76282e7aeac79ae0ad +Subproject commit ce3c86accdcd73d3c3a46e41be1fcc09775200dd From 16e7d7f5e6bc46f0884bdab27239418620863ae9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 16 Jul 2024 10:34:52 -0400 Subject: [PATCH 14/18] HEMCO submod update: Merge PR #282 (Remove manual InvMEGAN diags) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/HEMCO repository: 40066bc Merge PR #282 (Remove manual InvMEGAN diagnostics) This PR removes obsolete manual diagnostics from the MEGAN extension. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO b/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO index 2192e0e88..40066bc98 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO +++ b/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO @@ -1 +1 @@ -Subproject commit 2192e0e88ee5f20fcd3bae71b613a902ec4c31ba +Subproject commit 40066bc98a4a7c883b1d51ec50bf5c6c586b8885 From 1cc504c1d9d1bc879f7449646e7875f836360d3f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 16 Jul 2024 11:21:27 -0400 Subject: [PATCH 15/18] GEOS-Chem submod update: Merge PR #2379 (Disable FAST-JX except for Hg) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 0147de618 Merge PR #2379 (Disable FAST-JX except for Hg simulation) This PR adds a runtime error trap to disable FAST-JX for all simulations except Hg. Eventually Hg will use Cloud-J pending an update. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 03287a67a..0147de618 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 03287a67a368663bd393b777c1f9e1dc0d486ee6 +Subproject commit 0147de618006e0f082389414b949afb24b02a94f From 123284069c9d2652df73a64ea6cba04a45bb607e Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Tue, 16 Jul 2024 13:09:17 -0400 Subject: [PATCH 16/18] GEOS-Chem submod update: merge PR #2375 (standard emissions in CESM) Signed-off-by: Lizzie Lundgren --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 0147de618..b9cf9816b 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 0147de618006e0f082389414b949afb24b02a94f +Subproject commit b9cf9816bf2aedbb6fb3c199ff02d694c7f9bac8 From 3b6859971daba335f40f1057d48c5cf4aa822e42 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 18 Jul 2024 17:01:52 -0400 Subject: [PATCH 17/18] Update CONTRIBUTING.md - Fixed broken links to external docs - Instruct users to update the CHANGELOG.md file Signed-off-by: Bob Yantosca --- CONTRIBUTING.md | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 61b29a79f..ff32b7ec2 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -5,20 +5,21 @@ Thank you for looking into contributing to GEOS-Chem! GEOS-Chem is a grass-roots Updates to the GEOS-Chem model benefit both you and the [entire GEOS-Chem community](https://geoschem.github.io/people.html). You benefit through [coauthorship and citations](https://geoschem.github.io/new-developments.html). Priority development needs are identified at GEOS-Chem users' meetings with updates between meetings based on [GEOS-Chem Steering Committee (GCSC)](https://geoschem.github.io/steering-committee.html) input through [Working Groups](https://geoschem.github.io/working-groups.html). ## We use GitHub and ReadTheDocs -We use GitHub to host the GCHP source code, to track issues, user questions, and feature requests, and to accept pull requests: [https://github.com/geoschem/GCHP](https://github.com/geoschem/GCHP). Please help out as you can in response to issues and user questions. +We use GitHub to host the GEOS-Chem Classic source code, to track issues, user questions, and feature requests, and to accept pull requests: [https://github.com/geoschem/geos-chem](https://github.com/geoschem/geos-chem). Please help out as you can in response to issues and user questions. -GCHP Classic documentation can be found at [gchp.readthedocs.io](https://geos-chem.readthedocs.io). +GCHP documentation can be found at [gchp.readthedocs.io](https://geos-chem.readthedocs.io). ## When should I submit updates? -Submit bug fixes right away, as these will be given the highest priority. Please see "Support Guidelines" for more information. +Submit bug fixes right away, as these will be given the highest +priority. Please see **[Support Guidelines](https://gchp.readthedocs.io/en/latest/reference/SUPPORT.html)** for more information. Submit updates (code and/or data) for mature model developments once you have submitted a paper on the topic. Your Working Group chair can offer guidance on the timing of submitting code for inclusion into GEOS-Chem. The practical aspects of submitting code updates are listed below. ## How can I submit updates? -We use [GitHub Flow](https://guides.github.com/introduction/flow/index.html), so all changes happen through pull requests. This workflow is [described here](https://guides.github.com/introduction/flow/index.html). +We use **GitHub Flow**, so all changes happen through [pull requests](https://help.github.com/articles/creating-a-pull-request/). This workflow is [described here](https://docs.github.com/en/get-started/using-github/github-flow). As the author you are responsible for: - Testing your changes @@ -33,11 +34,12 @@ As the author you are responsible for: 4. [Fork the relevant GEOS-Chem repositories](https://help.github.com/articles/fork-a-repo/) into your Github account. 5. Clone your forks of the GEOS-Chem repositories to your computer system. 6. Add your modifications into a [new branch](https://git-scm.com/book/en/v2/Git-Branching-Branches-in-a-Nutshell) off the **main** branch. - 7. Test your update thoroughly and make sure that it works. For structural updates we recommend performing a difference test (i.e. testing against the prior version) in order to ensure that identical results are obtained). - 8. Review the coding conventions and checklists for code and data updates listed below. - 9. Create a [pull request in GitHub](https://help.github.com/articles/creating-a-pull-request/). - 10. The [GEOS-Chem Support Team](https://geoschem.github.io/support-team.html) will add your updates into the development branch for an upcoming GEOS-Chem version. They will also validate your updates with [benchmark simulations](http://wiki.geos-chem.org/GEOS-Chem_benchmarking). - 11. If the benchmark simulations reveal a problem with your update, the GCST will request that you take further corrective action. + 7. Add a sentence to the `CHANGELOG.md` file describing your update. + 8. Test your update thoroughly and make sure that it works. For structural updates we recommend performing a difference test (i.e. testing against the prior version) in order to ensure that identical results are obtained). + 9. Review the coding conventions and checklists for code and data updates listed below. + 10. Create a [pull request in GitHub](https://help.github.com/articles/creating-a-pull-request/). + 11. The [GEOS-Chem Support Team](https://geoschem.github.io/support-team.html) will add your updates into the development branch for an upcoming GEOS-Chem version. They will also validate your updates with [benchmark simulations](http://wiki.geos-chem.org/GEOS-Chem_benchmarking). + 12. If the benchmark simulations reveal a problem with your update, the GCST will request that you take further corrective action. ### Coding conventions The GEOS-Chem codebase dates back several decades and includes contributions from many people and multiple organizations. Therefore, some inconsistent conventions are inevitable, but we ask that you do your best to be consistent with nearby @@ -48,8 +50,9 @@ code. 1. Use Fortran-90 free format instead of Fortran-77 fixed format. 2. Include thorough comments in all submitted code. 3. Include full citations for references at the top of relevant source code modules. - 4. Remove extraneous code updates (e.g. testing options, other science). - 5. Submit any related code or configuration files for [GCHP](https://gchp.readthedocs.io) along with code or configuration files for [GEOS-Chem Classic](https://geos-chem.readthedocs.io). + 4. Check that you have updated the `CHANGELOG.md` file. + 5. Remove extraneous code updates (e.g. testing options, other science). + 6. Submit any related code or configuration files for [GCHP](https://gchp.readthedocs.io) along with code or configuration files for [GEOS-Chem Classic](https://geos-chem.readthedocs.io). ### Checklist for submitting data files From 856010810a7b32d3df695a4802dd65868f9a5a8b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 24 Jul 2024 14:50:14 -0400 Subject: [PATCH 18/18] GCHP 14.4.2 release Changed version numbers in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py Submodule versions have now been updated to: - GEOS-Chem (Science Codebase) 14.4.2 - HEMCO 3.9.2 - Cloud-J 7.7.2 See CHANGELOG.md for a list of updates in this version. Signed-off-by: Bob Yantosca --- CHANGELOG.md | 2 +- CMakeLists.txt | 2 +- docs/source/conf.py | 2 +- src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO | 2 +- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e2cec652e..68de2b11b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ This file documents all notable changes to the GCHP wrapper repository starting 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). -## [14.4.2] - TBD +## [14.4.2] - 2024-07-24 ### Changed - Updated Cloud-J submodule to 7.7.2 - Disable support for FAST-JX for all simulations except Hg diff --git a/CMakeLists.txt b/CMakeLists.txt index 69094cb9d..4e8240076 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,6 +1,6 @@ cmake_minimum_required (VERSION 3.13) project (gchp_ctm - VERSION 14.4.1 + VERSION 14.4.2 LANGUAGES Fortran CXX C ) diff --git a/docs/source/conf.py b/docs/source/conf.py index 10288b259..3bf48d972 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,7 +23,7 @@ author = 'GEOS-Chem Support Team' # The full version, including alpha/beta/rc tags -release = '14.4.1' +release = '14.4.2' # -- General configuration --------------------------------------------------- diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO b/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO index 40066bc98..e68ebae6e 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO +++ b/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO @@ -1 +1 @@ -Subproject commit 40066bc98a4a7c883b1d51ec50bf5c6c586b8885 +Subproject commit e68ebae6ed8286e09f3a18fd505873bce074edfa diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index b9cf9816b..6a26a6bab 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit b9cf9816bf2aedbb6fb3c199ff02d694c7f9bac8 +Subproject commit 6a26a6bab094dd8230247aeeb9a252b53c543417