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ReadTheDocs updates for GEOS-Chem Classic 14.5.0 #68

Merged
merged 16 commits into from
Nov 8, 2024
Merged

ReadTheDocs updates for GEOS-Chem Classic 14.5.0 #68

merged 16 commits into from
Nov 8, 2024

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@yantosca yantosca commented Oct 2, 2024 •
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Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

This PR seeks to merge documentation updates for GEOS-Chem 14.5.0 into the dev/14.5.0 branch. We have made the following general updates:

  • Moved documentation for geoschem_config.yml, HEMCO_Diagn.rc, HEMCO_Config.rc, species_database.yml, and the aerosol/chemistry/photolysis configuration files to the https://github.com/geoschem/geos-chem-shared-docs repo.
  • Now point to relocated documentation files in the geos-chem-shared-docs repo
  • Added usage differences between GCHP and GCC for the various documentation files
  • Updated formatting to improve the page rendering and usability (i.e. using .. option:: tags, etc)
  • Flowed the text about the GEOS-Chem Input Data on AWS into the "Download Input Data" section instead of having it as a supplemental guide.
  • Updated the GEOS-Chem dry-run instructions
  • Changed GEOS-Chem version numbers in the relevant files

Related Github Issue

NOTES

Tagging @msulprizio @lizziel @yidant

@yantosca
geos-chem-shared-docs update: Update packages.yaml to GCC 12.2.0
750151f 
Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
Update env files from GNU 10.2.0 to 12.2.0 + related updates
e7efd49 
docs/source/geos-chem-shared-docs
- Fixed broken links in supplemental-guides/spack-guide.rst

docs/source/getting-started/login-env-files-gnu.rst
- Changed label from env-files-gnu10 to env-files-gnu
- Added tip box to build software with Spack if necessary

docs/source/getting-started/login-env-files-intel.rst
- Changed label from _env-files-intel19 to _env-files-intel
- Added tip box to build software with Spack if necessary

docs/source/getting-started/login-env-compilers.rst
docs/source/getting-started/login-env-parallel.rst
- Updated references accordingly

docs/source/getting-started/login-env.rst
- Updated references accordingly
- Added tip box to build software with Spack if necessary

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
geos-chem-shared-docs update: Use [email protected] in load-libraries-guide.rst
03ae9d8 
This commit informs the GCClassic superproject about the following
commits pushed to the geos-chem-shared-docs submodule:

a68981b Update [email protected] -> [email protected] in load-libraries-guide.rst

This updates the GCC compiler version from 10.2.0 to 12.2.0 in the
various documentation pages.

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
Update jinja2 to 3.1.4 in docs/requirements.txt
25bb833 
docs/requirements.txt
- Use jinja 3.1.4 as there is a dependabot security warning for
  the previous version 3.1.3.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
Moved config file doc to geos-chem-shared-docs
3daf9fc 
docs/source/gcclassic-user-guide/geoschem-config.rst
docs/source/gcclassic-user-guide/hemco-config.rst
docs/source/gcclassic-user-guide/hemco-diagn.rst
docs/source/gcclassic-user-guide/phot-chem.rst
docs/source/gcclassic-user-guide/spec-db.rst
- Moved to geos-chem-shared-docs/doc

docs/source/gcclassic-user-guide/config-overview.rst
- Now points to relocated files

docs/source/geos-chem-shared-docs
- Submodule update to

CHANGELOG.md
- Updated accordingly
@yantosca
Updated "Speeding up a slow GEOS-Chem simulation" chapter
f13ea9c 
docs/source/gcclassic-user-guide/run-speedup.rst
- Changed "Use coarser timesteps" to "Use a coarser chemistry timestep"
- Added table of recommended GEOS-Chem Classic timesteps
- Cite Philip et al. 2016
- Added section "Use the Rosenbrock solver w/ auto-reduction"
- Added section "Reduce the amount of files that need to be read"
- Added section "Speeding up GEOS-Chem Classic nested-grid simulations"
- Added subsection "Crop nested-grid meteorology inputs"
- Added subsection "Increase the size of the transport buffer zone"

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
geos-chem-shared-docs update: Add doc about diffs btw GCHP & GCC
440b4d6 
docs/source/geos-chem-shared-docs:
- Added documentation to doc/geoschem-config.rst and doc/hemco-config.rst
  to make the differences between GCHP and GCClassic more explicit.

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
geos-chem-shared-doc update: Fixed typo; Added GCHP vs. GCC diffs
f19794e 
docs/source/geos-chem-shared-docs
- Fixed typo in doc/geoschem-config.rst
- Added GCHP vs. GCC usage difference section in the documentation
  for HEMCO_Diagn.rc

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca added TODO: Documentation Improvements or additions to documentation no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations labels Oct 2, 2024
@yantosca yantosca self-assigned this Oct 2, 2024
@yantosca yantosca added this to the 14.5.0 milestone Oct 2, 2024
This was referenced Oct 2, 2024
Merged
Merged
@yantosca yantosca changed the title ReadTheDocs updates for GEOS-Chem 14.5.0 ReadTheDocs updates for GEOS-Chem Classic 14.5.0 Oct 2, 2024
@yantosca
geos-chem-shared-docs update: GC input data; GCHP History guide
29b8615 
This commit informs the GCClassic superproject about the following
commits that were pushed to the geos-chem-shared-docs repository:

65b2a35 Merge "docs/update_guides_for_gchp" into "main"
7f0cfbb Merge PR #3 (Add doc/tutorial for GEOS-Chem input data on AWS)

These are documentation updates for the 14.5.0 release.

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
RTD Updates: Additional updates for GC Input Data repository
a6973ae 
docs/source/gcclassic-user-guide/download-data.rst
- Removed input-overview.rst from toctree
- Added gcid-repository-overview.rst to toctree
- Added gcid-special-repos.rst to toctree

docs/source/gcclassic-user-guide/dry-run-download.rst
- Add references to pages in geos-chem-shared-docs/doc folder
  pertaining to the GEOS-Chem input data
- Renamed "Choose a data portal" section to "Choose a data repository",
  and updated the data repository descriptions

docs/source/gcclassic-user-guide/gcid-special-repos.rst
- New page describing GEOS-Chem Nested Input Data and
  GCAP 2.0 @ Rochester repositories

docs/source/geos-chem-shared-docs
- Updated submodule hash to commit 09a2f03

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
RTD update: GC data portal doc updates + fixes broken links
a10e19b 
docs/source/gcclassic-user-guide/download-data.rst
- Updated toctree

docs/source/gcclassic-user-guide/dry-run-download.rst
- Terminology change: "repository" -> "portal"
- Simplified "Choose a data portal" section with table

docs/source/gcclassic-user-guide/dry-run.rst
- Removed tip box
- Text formatting update

docs/source/gcclassic-user-guide/gcid-special-repos.rst ->
 renamed to docs/source/gcclassic-user-guide/gcid-special-portals.rst

docs/source/gcclassic-user-guide/input-overview.rst
- Removed (now obsolete)

docs/source/gcclassic-user-guide/restart-files-gc.rst
docs/source/gcclassic-user-guide/restart-files-what.rst
docs/source/gcclassic-user-guide/run-checklist.rst
docs/source/getting-started/disk-space.rst
- Fixed broken links & references
- Text formatting updates

docs/source/getting-started/quick-start.rst
- Fixed broken links & references
- Text formatting updates
- Added attention box for resetting the time cycle flag for SPC_
  in HEMCO_Config.rc

docs/source/geos-chem-shared-docs
- Submodule update with further updates for GEOS-Chem data portals

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca marked this pull request as ready for review November 4, 2024 22:20
@yantosca
Update dry-run download; Add warnings about GEOS-FP
09a5db3 
docs/source/gcclassic-user-guide/dry-run-download.rst
- Reduce indentation for GEOS-Chem data portals & access methods
- Update log.dryrun.unique output to remove obsolete file listings

docs/source/gcclassic-user-guide/run-checklist.rst
docs/source/help-and-reference/known-bugs.rst
- Add "important" box with warning about GEOS-FP convection switch

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca requested a review from lizziel November 5, 2024 17:12
@yantosca
Moved gcid-special-portals.rst to geos-chem-shared-docs/doc
765987a 
docs/source/gcclassic-user-guide/gcid-special-portals.rst
 - Moved to geos-chem-shared-docs/doc/gcid-special-portals.rst

docs/source/gcclassic-user-guide/download-data.rst
- Toctree now points to geoschem-shared-docs/doc/gcid-special-portals.rst

docs/source/gcclassic/dry-run-run.rst
- Add warning box about GEOS-FP convection switch

docs/source/geos-chem-shared-docs
- Submodule update to 54890ed

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
RTD update: Fixed more links/refs and text formatting issues
b81423c 
docs/source/gcclassic-user-guide/compile-cmake.rst
- Add proper indentation to a ".. note::" block

docs/source/gcclassic-user-guide/rundir-carbon.rst
docs/source/gcclassic-user-guide/rundir-fullchem.rst
docs/source/getting-started/quick-start.rst
- Add "important" box about GEOS-FP convection issue
- Trimmed trailing whitespace

docs/source/gcclassic-user-guide/dry-run-download.rst
- Fixed incorrect portal name "geoschem-s3" -> "geoschem+s3"

docs/source/geos-chem-shared-docs
- Submodule update to cd0f4ad (fix broken links & refs)

docs/source/help-and-reference/known-bugs.rst
- Renamed link text to avoid a "duplicate link" warning

docs/source/index.rst
- Removed geos-chem-input-data-on-aws.rst from toctree, as this is now
  moved to geos-chem-shared-docs/doc/gcid-portal-overview.rst

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca
Update warning boxes about GEOS-FP in dry-run & rundir doc
694e24f 
docs/source/gcclassic-user-guide/dry-run-run.rst
docs/source/gcclassic-user-guide/rundir-carbon.rst
docs/source/gcclassic-user-guide/rundir-fullchem.rst
- Edit the "important" box with the warning about GEOS-FP convection
  to make it more clear that the user should choose MERRA-2 to
  avoid discontinuities across June 1, 2020.

docs/source/geos-chem-shared-docs
- Submodule update, now link to GCClassic & HEMCO dry-run-instructions
  from the GEOS-Chem Input Data portal documentation
@yantosca yantosca mentioned this pull request Nov 7, 2024
Merged
@yantosca
Update version numbers to 14.5.0
09b6822 
CHANGELOG.md
CMakeLists.txt
docs/source/conf.py
- Updated version number to 14.5.0, in anticipation of the
  GEOS-Chem Classic 14.5.0 release

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca requested a review from lizziel November 7, 2024 20:22
@yantosca yantosca linked an issue Nov 7, 2024 that may be closed by this pull request
Documentation updates for 14.5.0 #66
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@yantosca yantosca merged commit bef8b4b into dev/14.5.0 Nov 8, 2024
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@yantosca yantosca mentioned this pull request Nov 8, 2024
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@msulprizio msulprizio msulprizio approved these changes

@lizziel lizziel lizziel approved these changes

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no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations TODO: Documentation Improvements or additions to documentation
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Documentation updates for 14.5.0
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@yantosca @lizziel @msulprizio