GCHP 14.7.0 release

.github/workflows/cloud-benchmarking-workflow.yml

@@ -1,57 +1,65 @@
 # Release pipeline:
-# 
+#
 # This pipeline triggers the cloud-based benchmarking workflow
-# upon pushes to the dev environment. The benchmarking workflow 
+# upon pushes to the dev environment. The benchmarking workflow
 # infrastructure code can be found in the following repository:
 # https://github.com/geoschem/gc-cloud-infrastructure
 #
-# This pipeline is triggered by pushes to dev
+# This pipeline is triggered by pushes to dev/* branches.
 #
 # Notes:
 #   - This workflow requires aws credentials necessary to
-#     trigger the benchmarking step function via the aws cli. 
-#     The credentials need step function permissions and can 
-#     be added to the repo as an action secret called 
+#     trigger the benchmarking step function via the aws cli.
+#     The credentials need step function permissions and can
+#     be added to the repo as an action secret called
 #     AWS_SECRET_ACCESS_KEY and AWS_ACCESS_KEY_ID.
 
 name: cloud_benchmarking
 on:
   push:
     branches:
-      - dev**
+      - dev/*
     tags:
       - '*'
   pull_request:
     branches:
-      - dev**
+      - dev/*
 
 jobs:
   trigger_step_function:
     runs-on: ubuntu-latest # aws cli comes pre-installed
     steps:
+
       # for now both use Spot instances -- may need to update to use on demand
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          persist-credentials: false
+
+      # By default we use 1Hr benchmarks
       - name: Set Initial Variables
-        # By default we use 1Hr benchmarks
         run: |
           echo "TIME_PERIOD=1Hr" >> $GITHUB_ENV
           echo "RESOLUTION=24" >> $GITHUB_ENV
-          echo "GITHUB_SHA_SHORT=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV
-          echo "COMMIT_NAME=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV
-      # conditionally overwrite variables if a tag was the triggering event
+          echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV
+          echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV
+
+      # Conditionally overwrite variables if a tag was the triggering event
       - name: Reset Initial Variables for pull request
-        run: |
-          echo "GITHUB_SHA_SHORT=`echo ${{ github.event.pull_request.head.sha }} | cut -c1-7`" >> $GITHUB_ENV
-          echo "COMMIT_NAME=`echo ${{ github.event.pull_request.head.sha }} | cut -c1-7`" >> $GITHUB_ENV
         if: github.event_name == 'pull_request'
+        env:
+          GITHUB_SHA_SHORT: ${{ github.event.pull_request.head.sha }}
+        run: |
+          echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT:0:7}" >> $GITHUB_ENV
+          echo "COMMIT_NAME=${GITHUB_SHA_SHORT:0:7}" >> $GITHUB_ENV
+
+      # We do a 1Month benchmark for tags
       - name: Reset Variables For Tags
-        # We do a 1Month benchmark for tags
+        if: startsWith(github.ref, 'refs/tags/')
         run: |
           echo "TIME_PERIOD=1Mon" >> $GITHUB_ENV
           echo "COMMIT_NAME=${GITHUB_REF##*/}" >> $GITHUB_ENV
-        if: startsWith(github.ref, 'refs/tags/')
+
       - name: Generate Primary Key
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
@@ -62,6 +70,7 @@ jobs:
           cd ${{ github.workspace }}
           echo "DEV_PRIMARY_KEY=gchp-c${RESOLUTION}-${TIME_PERIOD}-`git describe --tags`" >> $GITHUB_ENV
           echo "REF_PRIMARY_KEY=`./.github/workflows/findRefKey.sh ${RESOLUTION} ${TIME_PERIOD} ${GITHUB_SHA}`" >> $GITHUB_ENV
+
       - name: Trigger Step Function
         env:
           # Set config options for aws cli

.github/workflows/lint-ci-workflows.yml

@@ -0,0 +1,77 @@
+# Workflow to run linting checks on source
+name: Lint
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pushes to the "main" or "dev/"* branches,
+  # i.e., PR merges
+  push:
+    branches: [ "main", "dev/*" ]
+
+  # Triggers the workflow on pushes to open pull requests with code changes
+  pull_request:
+    paths:
+      - '.github/workflows/*.yml'
+
+  # Allows you to run this workflow manually from the Actions tab
+  # (usually leave it blank)
+  workflow_dispatch:
+
+# Allow the jobs to read the secret GitHub token
+permissions:
+  contents: read
+
+# Cancel jobs running if new commits are pushed
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+# Workflow run - one or more jobs that can run sequentially or in parallel
+jobs:
+
+  # This workflow contains a single job called "lint"
+  lint:
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Don't quit the Action at the first 
+    strategy:
+      fail-fast: false
+
+    # GitHub secret token
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    # Steps represent a sequence of tasks that will be
+    # executed as part of the job
+    steps:
+
+      # Checks-out your repository under $GITHUB_WORKSPACE,
+      # so your job can access it
+      - name: Checkout code
+        with:
+          persist-credentials: false
+        uses: actions/checkout@v4
+
+      # Installs Python 3.x
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      # Installs Python packages
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m venv ci_venv
+          . ci_venv/bin/activate
+          pip install zizmor==0.9.2
+
+      # Apply GitHub Actions linter, zizmor
+      - name: zizmor
+        if: always()
+        run: |
+          cd ${{ github.workspace }}
+          . ci_venv/bin/activate
+          zizmor .github/workflows/*.yml

.github/workflows/spack-deployment-workflow.yml

@@ -22,7 +22,11 @@ jobs:
     runs-on: ubuntu-latest
     container: continuumio/miniconda3
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
       - name: Get release tag
         id: vars
         run: |

.gitmodules

@@ -7,9 +7,6 @@
 [submodule "ESMA_cmake"]
 	path = ESMA_cmake
 	url = https://github.com/geoschem/ESMA_cmake
-[submodule "gFTL-shared"]
-	path = src/gFTL-shared
-	url = https://github.com/geoschem/gFTL-shared.git
 [submodule "FMS"]
 	path = src/FMS
 	url = https://github.com/geoschem/FMS.git
@@ -22,12 +19,6 @@
 [submodule "HEMCO"]
 	path = src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO
 	url = https://github.com/geoschem/HEMCO.git
-[submodule "yaFyaml"]
-	path = src/yaFyaml
-	url = https://github.com/geoschem/yaFyaml.git
-[submodule "pFlogger"]
-	path = src/pFlogger
-	url = https://github.com/geoschem/pFlogger.git
 [submodule "geos-chem-shared-docs"]
 	path = docs/source/geos-chem-shared-docs
 	url = https://github.com/geoschem/geos-chem-shared-docs.git
@@ -37,3 +28,6 @@
 [submodule "HETP"]
 	path = src/GCHP_GridComp/GEOSChem_GridComp/HETP
 	url = https://github.com/geoschem/HETerogeneous-vectorized-or-Parallel.git
+[submodule "src/GFE"]
+	path = src/GFE
+	url = https://github.com/Goddard-Fortran-Ecosystem/GFE

CHANGELOG.md

@@ -9,6 +9,37 @@ 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).
 
+## [14.7.0] - 2026-02-06
+### Added
+- Added R4 exports in GCHPctmEnv for diagnostics since R8 to R4 conversion in MAPL 2.55 History is broken
+- Added submodule for GFE (Goddard-Fortran-Ecosystem) which includes GMAO libraries yafYaml, pFlogger, gFTL, gFTL-shared, fArgParse, and pFUnit as its own submodules
+- Added connectivity from GEOS-Chem to FV3 dynamics to pass DELP_DRY in GEOS-Chem restart file to advection for restart file species mass conservation
+- Added supplemental guides for GCHP horizontal and vertical grids to ReadTheDocs
+- Added "Particulate matter in GEOS-Chem" supplemental guide to ReadTheDocs
+- Added `docs/read_the_docs_environment.yml` Conda environment file
+
+### Changed
+- Changed minimum CMake version from 3.13 to 3.24
+- Changed minimum ESMF version from 8.4.2 to 8.6.1
+- Updated docs to indicate timing information now printed to allPEs.log
+- Updated docs to include library requirement udunits2 and additional information about stretched grid parameters
+- Updated `lint-ci-workflows` to run on `main` and `dev/*` branches
+- Updated badges on `README.md` and `docs/source/index.rst`
+- Updated submodule ESMA_cmake for GNU Fortran compiler compatibility with CPUs returning processor description INTEL
+- Updated `geos-chem-shared-docs/editing_these_docs.rst` with instructions for using a Conda environment to build RTD doc
+- Updated the ESMF version used in ReadTheDocs installation instructions from 8.4.2 to 8.6.1
+- Updated GEOS-Chem submodule to version 14.7.0
+- Updated HEMCO submodule to version 3.12.0
+- Updated ESMA_cmake submodule to commit 01bbf2f (Merge PR #9)
+- Updated geos-chem-shared-docs submodule to commit 03078d4
+
+### Fixed
+- Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail
+- Fixed vertical flipping bug in GCHPctmEnv when using C720 fields with GEOS-FP processed data
+
+### Removed
+- Removed individual submodules for yafYaml, pFlogger, and gFTL-shared since now located in new submodule GFE
+
 ## [14.6.3] - 2025-07-28
 ### Added
 - Added `-DSANITIZE` option for use with GNU Fortran compiler to check for memory leaks

CMakeLists.txt

@@ -1,6 +1,6 @@
-cmake_minimum_required (VERSION 3.13)
+cmake_minimum_required (VERSION 3.24)
 project (gchp_ctm
-  VERSION 14.6.3
+  VERSION 14.7.0
   LANGUAGES Fortran CXX C
 )
 

README.md

@@ -1,14 +1,10 @@
 <img src="https://geoschem.github.io/img/GEOS-Chem_Logo_Light_Background.png" height="60%" width="60%" alt="GEOS-Chem Logo">
 
 <p>
-  <a href="https://github.com/geoschem/GCHP/releases"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?include_prereleases&label=Latest%20Pre-Release"></a>
-  <a href="https://github.com/geoschem/GCHP/releases/"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?label=Latest%20Stable%20Release"></a>
-  <a href="https://github.com/geoschem/GCHP/"><img src="https://img.shields.io/github/release-date/geoschem/GCHP"></a>
-  <a href="https://github.com/geoschem/GCHP/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
-  <br />
-  <a href="https://spack.readthedocs.io/en/latest/package_list.html#gchp"><img src="https://img.shields.io/badge/Install%20with-Spack-ff69b4"></a>
-  <a href="https://hub.docker.com/r/geoschem/gchp"><img src="https://img.shields.io/docker/v/geoschem/gchp?color=blue&label=Docker%2FSingularity"></a>
+  <a href="https://github.com/geoschem/GCHP/releases/"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?label=Latest%20Stable%20Release" alt="Latest release"></a>
+  <a href="https://github.com/geoschem/GCHP/"><img src="https://img.shields.io/github/release-date/geoschem/GCHP" alt="Release date"></a><br/>
   <a href="https://doi.org/10.5281/zenodo.4428926"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4428926.svg" alt="DOI"></a>
+  <a href="https://github.com/geoschem/GCHP/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
   <a href="https://gchp.readthedocs.io"><img src="https://img.shields.io/readthedocs/gchp?label=ReadTheDocs"></a>
 </p>
 

docs/read_the_docs_environment.yml

@@ -0,0 +1,24 @@
+---
+# ======================================================================
+# ReadTheDocs environment file
+#
+# If you wish to build a Mamba/Conda environment with the dependencies
+# needed for building the ReadTheDocs documentation, use:
+#
+# $ mamba env create -n rtd_env --file=read_the_docs_environment.yml
+# ======================================================================
+name: rtd_env
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - python==3.12.0
+  - sphinx==7.2.6
+  - sphinx_rtd_theme==2.0.0
+  - sphinxcontrib-bibtex==2.6.2
+  - sphinx-autobuild==2021.3.14
+  - recommonmark==0.7.1
+  - docutils==0.20.1
+  - jinja2==3.1.6
+
+

docs/source/conf.py

@@ -23,7 +23,7 @@
 author = 'GEOS-Chem Support Team'
 
 # The full version, including alpha/beta/rc tags
-release = '14.6.3'
+release = '14.7.0'
 
 
 # -- General configuration ---------------------------------------------------