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Merge HEMCO develop into main#8

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joewallwork wants to merge 22 commits intomainfrom
develop
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Merge HEMCO develop into main#8
joewallwork wants to merge 22 commits intomainfrom
develop

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This PR updates the main branch of the fetch4:HEMCO repository with the code changes from the project.

The changes include upgrading to a more recent version of HEMCO, accounting for MODEL_GISS preprocessor flags, and a build fix for Intel compilers.

ltmurray and others added 22 commits May 6, 2024 19:50
… for GISS-GC.

The goal is to try to get GISS-GC to run, so we can go back to before this commit, and imeplement a version that does not break GCClassic.

Note, the "GISS_MODEL" mostly robust, it's just edits to where MODEL_CLASSIC lines that are wrong.
This commit addresses the issue in geoschem/HEMCO geoschem#281.

src/Extensions/hcox_megan_mod.F90
- Removed the calls to Diagn_Create for InvMEGAN diagnostics.
  These can be activated by adding the proper entries to the
  HEMCO_Diagn.rc file.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/hco-config
- Fixed a few broken :literal: tags

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR geoschem#282 (Remove InvMEGAN manual diagnostics from
hcox_megan_mod.F90, by @yantosca) into the HEMCO "no-diff-to-benchmark"
development stream.

This PR removes several obsolete manual diagnostics.  The diagnostics can
be scheduled by editing HEMCO_Diagn.rc instead.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
In order to make the HEMCO documentation easier to navigate,
we have done the following:

1. Converted several :option: tags to subsections, with named anchors.
   These will show up in the table of contents in the left nav bar.

2. Updated references to the new subsections accordingly.

3. Updated pages for clarity.  In several locations, use tables
   instead of descriptive paragraph to describe options and the
   behaviors they toggle.

4. Fixed indentation and trimmed trailing whitespace.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
- Added checklists
- Updated broken links
- Added link to GitHub pull request doc

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings documentation updates for the HEMCO 3.9.2 release
from the docs/dev branch into the HEMCO 3.9.2 development stream.

Updates in geos-chem-shared-docs include:
- Updated photolysis section (to reference Cloud-J)
- New Supplemental Guide for GEOS-Chem input data on AWS
- Updated the "View Related documentation" supplemental guide

Updates in docs/source include:
- Changing option tags to subsections in the HEMCO configuration
  documentation and elsewhere, so that they show up in the nav bar
- Updating references from option tags to subsections
- Fixing broken links
- Updating the CONTRIBUTING.md file to instruct users to update
  the CHANGELOG when submitting updates

Also updated the CHANGELOG.md file accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Changed version numbers in:
- CHANGELOG.md
- CMakeLists.txt
- docs/source/conf.py
- src/Core/hco_error_mod.F90

See CHANGELOG.md for a list of updates in this version.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
.github/workflows/stale.yml
- Add brackets around the list for `exempt-issue-labels`.  Verified
  this syntax with the YAML linter yamllint.com.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings the "dev/no-diff-to-benchmark" branch into main
in preparation for the HEMCO 3.9.3 release.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Updated version numbers in:
- CHANGELOG.md
- CMakeLists.txt
- docs/source/conf.py
- src/Core/hco_error_mod.F90

Also updated .release/changeVersionNumbers.sh to echo that the
version numbers were updated in the "CHANGELOG.md" file.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Upgrade `develop` to v14.3.1
… for GISS-GC.

The goal is to try to get GISS-GC to run, so we can go back to before this commit, and imeplement a version that does not break GCClassic.

Note, the "GISS_MODEL" mostly robust, it's just edits to where MODEL_CLASSIC lines that are wrong.
Upgrade `develop` to HEMCO v.3.9.3 (GEOS-Chem v14.4.3)
@joewallwork joewallwork added bug Something isn't working enhancement New feature or request labels Mar 24, 2025
@joewallwork joewallwork self-assigned this Mar 24, 2025
@joewallwork joewallwork requested a review from ltmurray March 24, 2025 14:54
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