Updated ReadTheDocs documentation for the 14.5.0 release

CHANGELOG.md CMakeLists.txt docs/source/conf.py src/GEOS-Chem/CHANGELOG.md src/GEOS-Chem/KPP/fullchem/CHANGELOG_fullchem.md - Updated version numbers from 14.4.3 to 14.5.0 docs/requirements.txt - Update Python package jinja2 needed for ReadTheDocs from 3.1.3 to 3.1.4 (fixes a security issue) docs/source/getting-started/*.rst docs/source/user-guide/*.rst docs/source/geos-chem-shared-docs - Updated documentation for 14.5.0. Includes: - New documentation for the GEOS-Chem Input Data portal on AWS - Corresponding updates to the dry-run simulation docs - Moved doc common to GCClassic, GCHP, HEMCO to geos-chem-shared-docs - Added warnings in doc about GEOS-FP convection update on 6/1/20 - Updated links and references - Text formatting updates (indentation, trimmed whitespace, etc.) src/GCHP_GridComp/GEOSChem_GridComp/geos-chem - Submodule update (updated version numbers to 14.5.0) Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Nov 8, 2024 · 35acd2b · 35acd2b
2 parents 9761e0c + 103ebc6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,14 +9,20 @@ 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).
 
-## [Unreleased] - TBD
+## [14.5.0] - 2024-11-08
+### Added
+- Added documentation about GEOS convection change affecting meteorology starting June 1, 2020
+
 ### Changed
 - Updated GEOS-Chem to 14.5.0
 - Updated HEMCO to 3.10.0
 - Updated Cloud-J to 8.0.1
 
 ### Fixed
 - Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run
+- Updated compiler requirements to specify max GNU version is 12
+- Updated documentation for version 14.5.0
+- Updated `docs/requirements.txt` to use `jinja2==3.1.4` (fixes a security issue)
 
 ## [14.4.3] - 2024-08-13
 ### Changed

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required (VERSION 3.13)
 project (gchp_ctm
-  VERSION 14.4.3
+  VERSION 14.5.0
   LANGUAGES Fortran CXX C
 )
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -12,4 +12,4 @@ sphinxcontrib-bibtex==2.6.2
 sphinx-autobuild==2021.3.14
 recommonmark==0.7.1
 docutils==0.20.1
-jinja2==3.1.3
+jinja2==3.1.4
diff --git 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 = '14.4.3'
+release = '14.5.0'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs
diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst
@@ -24,14 +24,14 @@ will automatically initialize and update all the submodules:
 
 .. code-block:: console
 
-   gcuser:~$ git clone --recurse-submodules https://github.com/geoschem/GCHP.git ~/GCHP
-   gcuser:~$ cd ~/GCHP
+   $ git clone --recurse-submodules https://github.com/geoschem/GCHP.git ~/GCHP
+   $ cd ~/GCHP
 
 Upon download you will have the most recently released version. You can check what this is by printing the last commit in the git log and scanning the output for tag.
 
 .. code-block:: console
 
-   gcuser:~/GCHP$ git log -n 1
+   $ git log -n 1
 
 .. tip::
 
@@ -40,17 +40,17 @@ Upon download you will have the most recently released version. You can check wh
 
    .. code-block:: console
 
-      gcuser:~/GCHP$ git checkout tags/14.0.0                  # Points HEAD to the tag "14.0.0"
-      gcuser:~/GCHP$ git branch version_14.0.0                 # Creates a new branch at tag "14.0.0"
-      gcuser:~/GCHP$ git checkout version_14.0.0               # Checks out the version_14.0.0 branch
-      gcuser:~/GCHP$ git submodule update --init --recursive   # Reverts submodules to the "14.0.0" tag
+      $ git checkout tags/14.0.0                  # Points HEAD to the tag "14.0.0"
+      $ git branch version_14.0.0                 # Creates a new branch at tag "14.0.0"
+      $ git checkout version_14.0.0               # Checks out the version_14.0.0 branch
+      $ git submodule update --init --recursive   # Reverts submodules to the "14.0.0" tag
 
    You can do this for any tag in the version history.   For a list of
    all tags, type:
 
    .. code-block:: console
 
-      gcuser:~/GCHP$ git tag
+      $ git tag
 
    If you have any unsaved changes, make sure you commit those to a
    branch prior to updating versions.
@@ -65,8 +65,17 @@ the prompts:
 
 .. code-block:: console
 
-   gcuser:~/GCHP$ cd run/
-   gcuser:~/GCHP$ ./createRunDir.sh
+   $ cd run/
+   $ ./createRunDir.sh
+
+.. important::
+
+   The convection scheme used for GEOS-FP met generation changed
+   from RAS to Grell-Freitas with impact on GEOS-FP meteorology
+   files starting June 1, 2020, specifically enhanced vertical
+   transport. If you plan to do simulations across this boundary
+   consider using MERRA2 instead. For more information see
+   `GEOS-Chem GitHub issue #1409 <https://github.com/geoschem/geos-chem/issues/1409/>`__.
 
 =======================
 3. Configure your build
@@ -83,15 +92,15 @@ guide we will do both, starting with building from the source code.
 
 .. code-block:: console
 
-   gcuser:~/GCHP$ mkdir ~/GCHP/build
-   gcuser:~/GCHP$ cd ~/GCHP/build
+   $ mkdir ~/GCHP/build
+   $ cd ~/GCHP/build
 
 Initialize your build directory by running :program:`cmake`, passing it the path to your source code.
 Make sure you have loaded all libraries required for GCHP prior to this step.
 
 .. code-block:: console
 
-   gcuser:~/GCHP/build$ cmake ~/GCHP
+   $ cmake ~/GCHP
 
 Now you can configure :ref:`build options <gchp_build_options>`.
 These are persistent settings that are saved to your build directory.
@@ -103,7 +112,7 @@ the run directory you created in Step 2.
 
 .. code-block:: console
 
-   gcuser:~/GCHP/build$ cmake . -DRUNDIR="/path/to/your/run/directory"
+   $ cmake . -DRUNDIR="/path/to/your/run/directory"
 
 .. note::
    The :literal:`.` in the :program:`cmake` command above is
@@ -116,23 +125,23 @@ symbolic link in the run directory:
 
 .. code-block:: console
 
-   gcuser:/path/to/your/run/directory/$ cd build
-   gcuser:/path/to/your/run/directory/build$ cmake ../CodeDir -DRUNDIR=..
+   $ cd /path/to/your/run/directory/build
+   $ cmake ../CodeDir -DRUNDIR=..
 
 GEOS-Chem has a number of optional compiler flags you can add
 here. For example, to compile with RRTMG:
 
 .. code-block:: console
 
-   gcuser:/path/to/your/run/directory/build$ cmake ../CodeDir -DRUNDIR=.. -DRRTMG=y
+   $ cmake ../CodeDir -DRUNDIR=.. -DRRTMG=y
 
 A useful compiler option is to build in debug mode. Doing this is a
 good idea if you encountered a segmentation fault in a previous run
 and need more information about where the error happened and why.
 
 .. code-block:: console
 
-   gcuser:/path/to/your/run/directory/build$ cmake ../CodeDir -DRUNDIR=.. -DCMAKE_BUILD_TYPE=Debug
+   $ cmake ../CodeDir -DRUNDIR=.. -DCMAKE_BUILD_TYPE=Debug
 
 See the GEOS-Chem documentation for more information on compiler flags.
 
@@ -147,14 +156,15 @@ available. Do this with the :literal:`-j` flag:
 
 .. code-block:: console
 
-   gcuser:~/GCHP/build$ make -j
+   $ cd ~/GCHP/build   # Skip if you are already here
+   $ make -j
 
 Upon successful compilation, install the compiled executable to your
 run directory (or directories):
 
 .. code-block:: console
 
-   gcuser:~/GCHP/build$ make install
+   $ make install
 
 This copies :file:`bin/gchp` and supplemental files to your run directory.
 
@@ -180,7 +190,7 @@ Now, navigate to your run directory:
 
 .. code-block:: console
 
-   $ cd path/to/your/run/directory
+   $ cd /path/to/your/run/directory
 
 Commonly changed simulation settings, such as grid resolution, run
 duration, and number of cores, are set in

diff --git a/docs/source/getting-started/requirements.rst b/docs/source/getting-started/requirements.rst
@@ -19,7 +19,7 @@ following software:
 * Compilers (C, C++, and Fortran):
 
    * Intel compilers versions 2019-2021, or
-   * GNU compilers version ≥ 10
+   * GNU compilers versions ≥ 10 and < 13
 
 * MPI (Message Passing Interface)
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -77,12 +77,12 @@ 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
    supplement/stretched-grid.rst
    supplement/satellite-overpass.rst
+   geos-chem-shared-docs/doc/gcid-portal-overview.rst
    geos-chem-shared-docs/supplemental-guides/bashdatacatalog.rst
    geos-chem-shared-docs/supplemental-guides/history-diag-guide.rst
    geos-chem-shared-docs/supplemental-guides/netcdf-guide.rst