sync with the develop branch

.gitattributes

@@ -0,0 +1 @@
+parm/gefs/postcntrl_gefs.xml text eol=lf

.github/CODEOWNERS

@@ -0,0 +1,14 @@
+# This is a comment.
+# Each line is a file pattern followed by one or more owners.
+
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# @global-owner1 and @global-owner2 will be requested for
+# review when someone opens a pull request.
+*       @WenMeng-NOAA @BenjaminBlake-NOAA 
+
+
+# Support for public releases and documentation 
+docs/*  @gspetro-NOAA
+scripts/run_upp @FernandoAndrade-NOAA @gspetro-NOAA
+

.github/workflows/developer.yml

@@ -0,0 +1,92 @@
+# This is a GitHub Actions workflow for building and testing UPP on the develop branch.
+#
+# Alyson Stahl, 10/2025
+name: developer
+on:
+  push:
+    branches:
+    - develop
+  pull_request:
+    branches:
+    - develop
+
+# Cancel in-progress workflows when pushing to a branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  developer:
+    runs-on: ubuntu-latest 
+    env:
+      CC: gcc
+      FC: gfortran
+      CXX: g++
+
+    steps:
+      - name: install-dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmpich-dev libnetcdf-dev libnetcdff-dev netcdf-bin pkg-config 
+          sudo apt-get install libopenblas-dev libpng-dev autotools-dev libaec-dev autoconf gcovr doxygen
+
+      - name: build-crtm
+        uses: NOAA-EMC/ci-build-cmake-code@develop
+        with:
+          package-name: EMC_crtm
+          package-org: NOAA-EMC
+          git-ref: v2.3.0
+
+      - name: build-g2tmpl
+        uses: NOAA-EMC/ci-build-cmake-code@develop
+        with:
+          package-name: NCEPLIBS-g2tmpl
+          package-org: NOAA-EMC
+
+      - name: build-sigio
+        uses: NOAA-EMC/ci-build-cmake-code@develop
+        with:
+          package-name: NCEPLIBS-sigio
+          package-org: NOAA-EMC
+
+      - name: build-wrf-io
+        uses: NOAA-EMC/ci-build-cmake-code@develop
+        with:
+          package-name: NCEPLIBS-wrf_io
+          package-org: NOAA-EMC
+
+      - name: build-dependencies
+        uses: NOAA-EMC/ci-build-nceplibs@develop
+        with:
+          jasper-version: version-4.0.0
+          bacio-version: develop
+          w3emc-version: develop
+          w3emc-cmake-args: -DBUILD_WITH_BUFR=OFF
+          g2-version: v3.5.1
+          ip-version: develop
+          nemsio-version: develop
+
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          path: UPP
+
+      - name: build
+        run: |
+          set -x
+          cd UPP
+          mkdir build && cd build
+          cmake .. -DBUILD_WITH_WRFIO=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=../install -DCMAKE_C_FLAGS='-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0' -DCMAKE_Fortran_FLAGS='-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -fno-lto'   -DCMAKE_Fortran_COMPILER=gfortran \
+            -DCMAKE_PREFIX_PATH="$GITHUB_WORKSPACE/nceplibs/jasper;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-bacio;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-w3emc;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-ip;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-g2;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-g2tmpl;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-sigio;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-nemsio;$GITHUB_WORKSPACE/nceplibs/NCEPLIBS-wrf_io;$GITHUB_WORKSPACE/nceplibs/EMC_crtm" 
+          make VERBOSE=1
+          make install
+          ctest --verbose --output-on-failure --rerun-failed
+          gcovr --root .. -v --html-details --exclude ../unit_tests --exclude CMakeFiles --print-summary -o test-coverage.html &> /dev/null
+
+      - name: upload-test-coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: UPP-test-coverage
+          path: |
+            UPP/build/*.html
+            UPP/build/*.css

.github/workflows/gcc.yml

@@ -0,0 +1,97 @@
+name: GCC Linux Build
+on: [push, pull_request, workflow_dispatch]
+
+
+# Use custom shell with -l so .bash_profile is sourced
+# without having to do it in manually every step
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+env:
+  cache_key: gcc3  # The number (#) following the cache_key "gcc" is to flush Action cache.
+  CC: gcc-10
+  FC: gfortran-10
+  CXX: g++-10
+
+# A note on flushing Action cache and relevance to "cache_key" above.
+# There is no way to flush the Action cache, and hence a number (#) is appended
+# to the "cache_key" (gcc).
+# If the dependencies change, increment this number and a new cache will be
+# generated by the dependency build step "setup"
+# There is a Github issue to force clear the cache.
+# See discussion on:
+# https://stackoverflow.com/questions/63521430/clear-cache-in-github-actions
+
+# The jobs are split into:
+# 1. a dependency build step (setup), and
+# 2. a UPP build step (build)
+# The setup is run once and the environment is cached,
+# so each build of UPP can reuse the cached dependencies to save time (and compute).
+
+jobs:
+  setup:
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: checkout-upp  # This is for getting spack.yaml
+        uses: actions/checkout@v4
+        with:
+            path: UPP
+
+      # Cache spack, compiler and dependencies
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v4
+        with:
+          path: |
+            spack
+            ~/.spack
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
+
+      # Install dependencies using Spack
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create upp-env UPP/ci/spack.yaml
+          spack env activate upp-env
+          sudo apt install cmake
+          spack external find
+          spack add [email protected]
+          spack add doxygen
+          spack concretize
+          spack install -v --fail-fast --dirty
+          spack clean --all
+
+  build:
+    needs: setup
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: checkout-upp
+        uses: actions/checkout@v4
+        with:
+            path: UPP
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v4
+        with:
+          path: |
+            spack
+            ~/.spack
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
+
+      - name: build-upp
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate upp-env
+          export CC=mpicc
+          export FC=mpif90
+          cd UPP
+          mkdir -p build && cd build
+          cmake -DENABLE_DOCS=ON -DCMAKE_INSTALL_PREFIX=../install ..
+          make -j2 VERBOSE=1
+          make install

.github/workflows/intel.yml

@@ -0,0 +1,115 @@
+name: Intel Linux Build
+on: [push, pull_request, workflow_dispatch]
+
+# Use custom shell with -l so .bash_profile is sourced which loads intel/oneapi/setvars.sh
+# without having to do it in manually every step
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+# Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
+env:
+  cache_key: intel3  # The number (#) following the cache_key "intel" is to flush Action cache.
+  CC: icc
+  FC: ifort
+  CXX: icpc
+  I_MPI_CC: icc
+  I_MPI_F90: ifort
+
+# A note on flushing Action cache and relevance to "cache_key" above.
+# There is no way to flush the Action cache, and hence a number (#) is appended
+# to the "cache_key" (intel).
+# If the dependencies change, increment this number and a new cache will be
+# generated by the dependency build step "setup"
+# There is a Github issue to force clear the cache.
+# See discussion on:
+# https://stackoverflow.com/questions/63521430/clear-cache-in-github-actions
+
+# The jobs are split into:
+# 1. a dependency build step (setup), and
+# 2. a UPP build step (build)
+# The setup is run once and the environment is cached,
+# so each build of UPP can reuse the cached dependencies to save time (and compute).
+
+jobs:
+  setup:
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: checkout-upp  # This is for getting spack.yaml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
+        with:
+            path: UPP
+
+      # Cache spack, compiler and dependencies
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v4
+        with:
+          path: |
+            spack
+            ~/.spack
+            /opt/intel
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
+
+      - name: install-intel-compilers
+        run: |
+          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+          echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+          sudo apt-get update
+          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran-2023.2.1 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.1
+          echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
+
+      # Install dependencies using Spack
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create upp-env UPP/ci/spack.yaml
+          spack env activate upp-env
+          spack compiler find
+          sudo apt install cmake
+          spack external find
+          spack add intel-oneapi-mpi
+          spack concretize
+          spack install --dirty -v --fail-fast
+          spack clean --all
+
+  build:
+    needs: setup
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: checkout-upp
+        uses: actions/checkout@v4
+        with:
+            path: UPP
+
+      - name: install-intel
+        run: |
+          echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v4
+        with:
+          path: |
+            spack
+            ~/.spack
+            /opt/intel
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
+
+      - name: build-upp
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate upp-env
+          export CC=mpiicc
+          export FC=mpiifort
+          cd UPP
+          mkdir -p build && cd build
+          cmake -DENABLE_DOCS=ON -DCMAKE_INSTALL_PREFIX=../install ..
+          make -j2 VERBOSE=1
+          make install