fetch4 · jwallwork23 · Jul 3, 2024 · Jul 8, 2024 · Jul 16, 2024 · Jul 24, 2024
diff --git a/.ci-pipelines/build-matrix.yml b/.ci-pipelines/build-matrix.yml
@@ -46,7 +46,7 @@ container: $[ variables['containerImage'] ]
 # Try building GEOS-Chem (this is run for each "matrix" entry above)
 steps:
 - checkout: self
-  submodules: true
+  submodules: recursive
 - script: |
     . /opt/spack/share/spack/setup-env.sh
     export CC=gcc

diff --git a/.ci-pipelines/quick-build.yml b/.ci-pipelines/quick-build.yml
@@ -31,7 +31,7 @@ container: geoschem/buildmatrix:netcdf-ubuntu
 # Try building GEOS-Chem
 steps:
 - checkout: self
-  submodules: true
+  submodules: recursive
 - script: |
     . /opt/spack/share/spack/setup-env.sh
     export CC=gcc

diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml
@@ -33,6 +33,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+          persist-credentials: false
       - name: Set Initial Variables
         # By default we use 1Hr benchmarks
         run: |
@@ -43,8 +44,8 @@ jobs:
       # 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`" >> $GITHUB_ENV
+          echo "GITHUB_SHA_SHORT=${{ github.event.pull_request.head.sha | substr(0, 7) }}" >> $GITHUB_ENV
+          echo "COMMIT_NAME=${{ github.event.pull_request.head.sha | substr(0, 7) }}" >> $GITHUB_ENV
         if: github.event_name == 'pull_request'
       - name: Reset Variables For Tags
         # We do a 1Month benchmark for tags

diff --git a/.github/workflows/gcclassic-compile-tests.yml b/.github/workflows/gcclassic-compile-tests.yml
@@ -19,6 +19,8 @@ jobs:
 
     steps:
       - name: Checkout code
+        with:
+          persist-credentials: false
         uses: actions/checkout@v4
 
       - name: Install dependencies

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,58 @@
+# Workflow to run linting checks on source
+name: Lint
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pushes to the "main" branch, i.e., PR merges
+  push:
+    branches: [ "main" ]
+
+  # 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
+  workflow_dispatch:
+
+# 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
+    strategy:
+      fail-fast: false
+
+    # 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
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - 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
diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -7,7 +7,7 @@ name: Mark stale issues
 
 on:
   schedule:
-  - cron: '0 0 * * *' # Run every night at midnight
+    - cron: '0 0 * * *'  # Run every night at midnight
 
 jobs:
   stale:
@@ -22,7 +22,7 @@ jobs:
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-label: 'stale'
-        exempt-issue-labels: ['category: Discussion','category: Feature Request','deferred','help needed: Open Research Problem','help needed: Request Input from Community','never stale','TODO: Documentation']
+        exempt-issue-labels: 'category: Discussion,category: Feature Request,deferred,help needed: Open Research Problem,help needed: Request Input from Community,never stale,TODO: Documentation'
         days-before-issue-stale: 30
         days-before-issue-close: 7
         stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.'

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,57 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit
 - src/HEMCO/CHANGELOG.md
 - src/Cloud-J/CHANGELOG.md
 
-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).
+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).
+
+## [14.5.3] - 2025-03-05
+### Added
+- Updated RTD docs to state that users wishing not to open AWS account can use AWS CLI commands with `--no-sign-request1`
+
+### Changed
+- Updated GEOS-Chem submodule to 14.5.3
+- Updated HEMCO submodule to 3.10.2
+
+### Fixed
+- Fixed error with the `rubric` section in the RTD planeflight documentation
+
+## [14.5.2] - 2025-02-12
+### Added
+- Added clarifying text about which types of data can use altitude coordinates for the Planeflight diagnostic in RTD documentation 
+- Added warning for users to preprocess ObsPack GLOBALVIEWplus CH4 data files before reading into GEOS-Chem in RTD documentation
+- Added text to RTD stating that data download from `s3://geos-chem` is and `s3://gcgrid` is free
+
+### Changed
+- Bumped `jinja2` to version 3.1.5 in `docs/requirements.txt` to fix a security issue
+- Changed the build sequence so that the KPP-Standalone is only built when configuring with `-DKPPSA=y`
+- Updated RTD documentation to state that older Intel compilers may cause unexpected results; Also updated to recommend GCC 10 and later.
+- Updated RTD documentation for fullchem rundir creation, which now asks users if they wish to build KPP-Standalone
+
+## [14.5.1] - 2025-01-10
+### Added
+- Added code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected
+- Added ReadTheDocs Supplemental Guide on using the KPP-Standalone Box Model and KPP-Standalone Interface in GEOS-Chem
+
+### Changed
+- Changed `submodules: true` to `submodules: recursive` in `.ci-pipelines/*.yml` files, which will fetch all levels of submodules in Azure CI tests.
+
+### Fixed
+- Fixed logic error in `src/CMakeLists.txt` that attempted to build the KPP standalone for the carbon simulation (see geoschem/GCClassic #78)
+- Fixed broken links in ReadTheDocs documentation
+
+## [14.5.0] - 2024-11-08
+### Changed
+- Updated GEOS-Chem to 14.5.0
+- Updated HEMCO to 3.10.0
+- Updated Cloud-J to 8.0.1
+- Updated `docs/source/geos-chem-shared-docs/spack/packages.yaml` to use GCC 12.2.0 compilers
+- Updated documentation for version 14.5.0
+- Moved several doc files (not supplemental guides) that are used in both GCClassic and GCHP the to `geos-chem-shared-docs/doc` folder
+
+### Fixed
+- Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run
+- Updated to Python package `jinja2==3.1.4` in `docs/requirements.txt` (fixes a security issue)
 
 ## [14.4.3] - 2024-08-13
 ### Changed

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -2,7 +2,7 @@
 
 cmake_minimum_required (VERSION 3.13)
 project (geos-chem-classic
-  VERSION 14.4.3
+  VERSION 14.5.3
   LANGUAGES Fortran
 )
 

diff --git a/CMakeScripts/GC-ConfigureClassic.cmake b/CMakeScripts/GC-ConfigureClassic.cmake
@@ -175,6 +175,14 @@ function(configureGCClassic)
     )
     gc_pretty_print(VARIABLE HCOSA IS_BOOLEAN)
 
+    #-------------------------------------------------------------------------
+    # Build the KPP-Standalone?
+    #-------------------------------------------------------------------------
+    set(KPPSA OFF CACHE BOOL
+      "Switch to build the KPP-Standalone Box Model"
+    )
+    gc_pretty_print(VARIABLE KPPSA IS_BOOLEAN)
+
     #-------------------------------------------------------------------------
     # Build Luo et al wetdep scheme?
     # (Currently a research option... turn OFF by default)
@@ -208,7 +216,7 @@ function(configureGCClassic)
             INTERFACE FASTJX
         )
     endif()
-
+    
     #-------------------------------------------------------------------------
     # Export the following variables to GEOS-Chem directory's scope
     #-------------------------------------------------------------------------

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==3.1.5
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 = '14.5.3'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/gcclassic-user-guide/compile-cmake.rst b/docs/source/gcclassic-user-guide/compile-cmake.rst
@@ -433,17 +433,16 @@ Classic contains code from the various repositories:
 
    .. note::
 
-   If you are cloning GEOS-Chem Classic between official releases, you
-   may the see :code:`Current status` reported like this:
+      If you are cloning GEOS-Chem Classic between official releases, you
+      may the see :code:`Current status` reported like this:
 
-   .. code-block:: console
+      .. code-block:: console
 
-      X.Y.Z-alpha.n-C-gabcd1234.dirty  or
+         X.Y.Z-alpha.n-C-gabcd1234.dirty  or
 
-      X.Y.Z.rc.n-C.gabcd1234.dirty
+         X.Y.Z.rc.n-C.gabcd1234.dirty
 
-   We will explain these formats below. |br|
-   |br|
+      We will explain these formats below.
 
 #. `HEMCO (Harmonized Emissions Component) submodule <https://github.com/geoschem/hemco.git>`_:
 

diff --git a/docs/source/gcclassic-user-guide/config-overview.rst b/docs/source/gcclassic-user-guide/config-overview.rst
@@ -27,9 +27,9 @@ edit most (if not all) of these configuration files:
 .. toctree::
    :maxdepth: 1
 
-   geoschem-config.rst
-   hemco-config.rst
-   hemco-diagn.rst
+   ../geos-chem-shared-docs/doc/geoschem-config.rst
+   ../geos-chem-shared-docs/doc/hemco-config.rst
+   ../geos-chem-shared-docs/doc/hemco-diagn.rst
    history.rst
 
 All of the above-mentioned files are included in your :ref:`GEOS-Chem
@@ -52,5 +52,5 @@ you'll need to edit these configuration files:
 .. toctree::
    :maxdepth: 1
 
-   spec-db.rst
-   phot-chem.rst
+   ../geos-chem-shared-docs/doc/spec-db.rst
+   ../geos-chem-shared-docs/doc/phot-chem.rst
diff --git a/docs/source/gcclassic-user-guide/download-data.rst b/docs/source/gcclassic-user-guide/download-data.rst
@@ -5,7 +5,7 @@ Download input data
 ###################
 
 In the following chapters, you will learn how to download input data
-for your GEOS-Chem simulation:
+for your GEOS-Chem simulation.
 
 .. note::
 
@@ -18,6 +18,7 @@ for your GEOS-Chem simulation:
 .. toctree::
    :maxdepth: 2
 
-   input-overview.rst
+   ../geos-chem-shared-docs/doc/gcid-portal-overview.rst
+   ../geos-chem-shared-docs/doc/gcid-special-portals.rst
    restart-files.rst
    dry-run.rst