Hemco 3.10.1 #17
Open
Hemco 3.10.1 #17
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
.readthedocs.yaml - Now request Python 3.12 for ReadTheDocs builds docs/requirements.txt - Update to more recent Python package versions for ReadTheDocs builds CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
.github/stale.yml - Updated the list of label names for to account for the recent change in GitHub label names in the HEMCO repo. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
.github/no-response.yml .github/stale.yml - Removed .github/workflows/stale.yml - Configuration file for GitHub "stale" action, which replaces StaleBot. Use the most recent list of issue/PR labels to never be marked stale. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR geoschem#274 (Replace stalebot with "stale" GitHub action, by @yantosca) into the HEMCO "no-diff-to-benchmark" development stream. This PR updates the list of label names for issues/PRs that should not be marked stale, and also switches from the old "stalebot" to the new "stale" GitHub action. Signed-off-by: Bob Yantosca <[email protected]>
AUTHORS.txt - Added Simon Branford, Yidan Tang, Karn Vohra, Haihui Zhu to the list of GEOS-Chem developers Signed-off-by: Bob Yantosca <[email protected]>
Here we have updated the Github issue template files to utilize forms. This involves using YAML configuration files instead of markdown. This should make issue submissions easier for users and will ensure users provide the required information. Note that issue forms are not supported for pull requests currently. The pull request form here has been cleaned up slightly. Addresses feature request geoschem/geos-chem#1831. Signed-off-by: Melissa Sulprizio <[email protected]>
This merge brings PR geoschem#276 (Update Github issue templates to use issue forms, by @msulprizio) into the HEMCO "no-diff-to-benchmark development stream. This PR uses dropdown menus and boxes to ensure that users provide the required information in the geoschem/HEMCO issue tracker. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings the HEMCO "no-diff-to-benchmark" development stream into the HEMCO 3.9.0 development stream. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings the HEMCO documentation branch into the HEMCO 3.9.0 develompent stream, in anticipation of the 3.9.0 release. Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the HEMCO superproject about the following commits that were pushed to the geos-chem-shared-docs repository cbfb5cb Update bibliography, bug fixes in supplemental guides 6b6ea17 Fix incorrect references in history-diag-guide.rst 3d827c3 Added extra named anchors in history-diag-guide.rst 41266ed Merge branch 'feature/history-guide' 285d590 Remove reference to BPCH_DIAG in customize-guide.rst These are all documentation-related updates in anticipation of the GEOS-Chem 14.4.0 and HEMCO 3.9.0 releases. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings all of the updates for HEMCO 3.9.0 that were added to the dev/3.9.0 branch into the main branch, in anticipation of the 3.9.0 release. Signed-off-by: Bob Yantosca <[email protected]>
Changed version numbers to 3.9.0 in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py - src/Core/hco_error_mod.F90 Signed-off-by: Bob Yantosca <[email protected]>
.github/workflows/stale.yml - The exempt-issue-labels YAML tag should have had a comma-separated list of labels not to be marked stale. We had used a YAML sequence, which caused the GitHub "Mark stale issues" to fail. Now fixed. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR geoschem#280 (Now use comma-separated list for exempt-issue-labels YAML tag in stale.yml, by @yantosca) into the HEMCO "no-diff-to-benchmark" development stream. This PR fixes a bug which caused the "Mark stale issues" GitHub action to fail due to an improperly formatted YAML file. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings the no-diff-to-benchmark branch into the main branch in anticipation of the HEMCO 3.9.1 release. Signed-off-by: Bob Yantosca <[email protected]>
Changed version numbers in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py - src/Core/hco_error_mod.F90 Signed-off-by: Bob Yantosca <[email protected]>
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 <[email protected]>
docs/source/hco-config - Fixed a few broken :literal: tags CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
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 <[email protected]>
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 <[email protected]>
- Added checklists - Updated broken links - Added link to GitHub pull request doc Signed-off-by: Bob Yantosca <[email protected]>
Signed-off-by: Bob Yantosca <[email protected]>
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 <[email protected]>
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 <[email protected]>
.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 <[email protected]>
CHANGELOG.md - Added a note about fixing the pressure issue in HEMCO standalone Signed-off-by: Bob Yantosca <[email protected]>
src/Core/hco_geotools_mod.F90 - Check if PSFC (surface pressure) is in hPa on the first call to HCO_CalcVertGrid. Use a SAVEd logical flag (DO_SCALE_PSFC) to denote if we need to convert from hPa to Pa. - Add code to convert PSFC from hPa to Pa on each timestep, depending on the value of DO_SCALE_PSFC - Updated comments Signed-off-by: Bob Yantosca <[email protected]>
…alone) This merge brings PR # (Fix inconsistent pressure units in HEMCO standalone, by @yantosca) into the HEMCO 3.10.0 development stream. This PR implements a fix for the bug described by @yuanjianz in issue geoschem#277. Signed-off-by: Bob Yantosca <[email protected]>
src/Extensions/hcox_finn_mod.F90 src/Extensions/hcox_gfed_include_gfed4.H - Updated with new emission factors (cf Kelvin Bates) for new species introduced in K. Travis et al 2023 (see PR #2318) CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
src/Extensions/hcox_gfed_include_gfed4.H - Species ACR should use index geoschem#41 but was assigned with index geoschem#36. This caused RCHO to be overwritten, causing an indexing error. Signed-off-by: Bob Yantosca <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
The warnings count is removed since it is not used now that we do not write to a dedicated HEMCO log. It also has limited value since not all warnings are important, e.g. unit mismatch of '1' vs 'mol mol-1'. Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
HCO_WARNING, like HCO_MSG, will not cause the model to fail and therefore does not RC passed as an argument. Signed-off-by: Lizzie Lundgren <[email protected]>
This generally makes the log looks cleaner. Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
…xibility_in_hemco Improve log flexibility in HEMCO
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Fixes to build and run in GEOS
docs/source/geos-chem-shared-docs - Submodule update: Added KPP-Standalone Supplemental Guide (bc4d75c) docs/source/index.rst - Added KPP-Standalone Supplemental Guide to toctree CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the HEMCO superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 18712bb Add extra examples to supplemental-guides/error-guide.rst This update adds documentation for additional common errors to the "Understanding what error messages mean" supplemental guide. Signed-off-by: Bob Yantosca <[email protected]>
docs/source/hco-ref-guide/hemco-config.rst - Updated the documentation for HEMCO 3.10.1, namely: - * sends logfile output to stdout - A file name sends logfile output to that file - When using CESM, logfile output goes to "atm.log" CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
This merge brings the dev/no-diff-to-benchmark branch commits into the HEMCO 3.10.1 release branch, in anticipation of the 3.10.1 release. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings ReadTheDocs documentation updates for HEMCO 3.10.1 (in the docs/dev branch) into the release/3.10.1 branch. Signed-off-by: Bob Yantosca <[email protected]>
Updated version numbers in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py - src/Core/hco_error_mod.F90 Updated docs/source/geos-chem-shared-docs submodule hash to 18712bb Please see the CHANGELOG.md for updates included in this version. Signed-off-by: Bob Yantosca <[email protected]>
viral211
approved these changes
Jan 16, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Name and Institution (Required)
Name: Lizzie Lundgren
Institution: Harvard University
Describe the update
This PR updates HEMCO to 3.10.1. See HEMCO
CHANGELOG.mdfor description of changes.