prepare version 0.8.0 (#57)

* add TS1 and TSMLT configuration to examples

* add new data sets for WACCM

* fix memory leak in tests

* add updated CFC cross section datasets

* run example test in sub folders

* copy data into example test folders

* reorganize temperature based cross section

* draft taylor series temperature parameterization

* add taylor series param test

* adjust grid merging logic

* finish BRONO2 config and tests

* fix MPI code

* draft burkholder parameterization and tests

* add range override to quantum yields

* finish HO2NO2 config and tests

* update TSMLT config example

* fix example configurations

* fix ch4 example config

* add ch3cl data set and configuration

* add SO2 data set

* Updates and tests for O2 photolysis (#38)

* stub test of LUT LA-SRB calcs

* update lasrb test conditions

* add od and xs calcs to LUT LA-SRB test

* fix memory issues in tests

* finish LA-SRB LUT comparison test

* Add H2SO4 and NO datasets, configurations, and algorithms for WACCM (#41)

* draft h2so4 quantum yield and test

* add h2so4 qy test

* add data and config for H2SO4 and NO

* Add N2O5 algorithms and data sets for WACCM/TSMLT (#43)

* fix bad jo2 config in ts1 example

* add N2O5 algorithms and datasets for WACCM

* fix pack/unpack for temperature based cross section

* add acetone calcs for WACCM (#45)

* add acetone calcs for WACCM

* fix uninitialized variable and air density in tests

* add branch options to acetone quantum yields

* Add YAML option for configuration files (#48)

* add YAML config option

* add yaml to json run comparison tests

* update to new musica-core release

* Add ability to calculate heating rates for photolysis reactions (#50)

* draft heating rates class and tests

* finish heating rate tests

* add heating rate output to driver, and include in TS example

* Remove musica-core dependency (#51)

* merge in musica-core dependencies

* don't run tests in parallel

* remove unneeded utility modules

* remove io functions from string_t

* remove debug output from tests to reduce log file size

* update valgrind suppressions for MPI

* update valgrind suppressions

* fix valgrind suppression format error

* remove wildcards from valgrind supresssion error types

* add valgrind suppression

* compile for gcc-13 (#53)

* compile for gcc-13

* excluding oldtuv when using gcc 13.2

* removing cmake debug message

* trying to add a gcc action

* syntax error

* isntalling netcdff

* trying to test multiple gcc versions

* installing numpy

* scipy

* using better thing

* separating build into docker and gcc (#54)

* separating build into docker and gcc

* fixing pages build

* run tests in serial

* not running tests in parallel for focker

* making sure memcheck happens

* adding ctiation file (#55)

* adding ctiation file

* only adding software citation

* syntax

* more syntax

* maybe now?

* correcting authors

* ...

* or now

* duplicate key

* *marge noise*

* trying to update url

* Fix bug in map test with OpenMP (#56)

* fix openmp bug in map test

* fix map test for non-openmp builds

* prepare for 0.8.0 release

---------

Co-authored-by: Kyle Shores <[email protected]>

.dockerignore

@@ -3,6 +3,7 @@
 
 # include things to copy
 !src/
+!include/
 !etc/
 !data/
 !cmake/

.github/workflows/docker.yml

@@ -0,0 +1,50 @@
+name: Docker
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.coverage
+          - Dockerfile.memcheck
+          - Dockerfile.mpi
+          - Dockerfile.mpi.memcheck
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Build Docker image
+        run: docker build -t tuvx -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make test ARGS="--rerun-failed --output-on-failure"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make coverage ARGS="--rerun-failed --output-on-failure"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info

.github/workflows/gh-pages.yml

@@ -54,7 +54,7 @@ jobs:
 
           # create two copies of the documentaiton
           # 1. the frozen version, represented as vX.X in the version switcher
-          docker build -t tuvx -f Dockerfile.docs .
+          docker build -t tuvx -f docker/Dockerfile.docs .
           id=$(docker create tuvx)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
@@ -63,7 +63,7 @@ jobs:
 
           # 2. stable, represented as vX.X (stable) in the version switcher
           # edit conf.py to produce a version string that looks like vX.X (stable)
-          docker build -t tuvx -f Dockerfile.docs --build-arg SUFFIX=" (stable)" .
+          docker build -t tuvx -f docker/Dockerfile.docs --build-arg SUFFIX=" (stable)" .
           id=$(docker create tuvx)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
@@ -84,7 +84,7 @@ jobs:
           !contains(github.ref, env.DEFAULT_BRANCH)
         run: |
           set -x
-          docker build -t tuvx -f Dockerfile.docs .
+          docker build -t tuvx -f docker/Dockerfile.docs .
           id=$(docker create tuvx)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id

.github/workflows/ubuntu.yml

@@ -0,0 +1,35 @@
+name: Ubuntu
+
+on: [ push, pull_request ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  gcc:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev
+    - name: Install python dependencies
+      run: pip install numpy scipy
+    - name: Run Cmake 
+      run: cmake -S . -B build 
+    - name: Build
+      run: cmake --build build --parallel
+    - name: Run tests
+      run: |
+        cd build
+        ctest --rerun-failed --output-on-failure . --verbose

CITATION.cff

@@ -0,0 +1,15 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Dawson
+    given-names: Matt
+  - family-names: Shores
+    given-names: Kyle
+  - family-names: Walters
+    given-names: Stacy
+title: "NCAR/tuv-x: Version 0.8.0"
+version: 0.8.0
+doi: 10.5281/zenodo.7126039
+url: "https://github.com/NCAR/tuv-x"
+year: 2024
+publisher: Zenodo

CMakeLists.txt

@@ -6,8 +6,8 @@ set(CMAKE_USER_MAKE_RULES_OVERRIDE "cmake/set_defaults.cmake")
 
 project(
   tuv-x
-  VERSION 0.7.0
-  LANGUAGES Fortran
+  VERSION 0.8.0
+  LANGUAGES Fortran CXX C
 )
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
@@ -31,7 +31,7 @@ option(ENABLE_MPI "Enable MPI parallel support" OFF)
 cmake_dependent_option(ENABLE_OPENMP "Enable OpenMP support" OFF "ENABLE_MPI" OFF)
 option(ENABLE_TESTS "Build tests" ON)
 option(ENABLE_COVERAGE "Enable code coverage output" OFF)
-option(ENABLE_MEMCHECK "Enable memory checking in tests" ON)
+option(ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
 option(ENABLE_NC_CONFIG "Use nc-config to determine NetCDF libraries" OFF)
 option(BUILD_DOCS "Build the documentation" OFF)
 
@@ -78,11 +78,16 @@ add_executable(tuv-x src/tuvx.F90 version.F90)
 target_link_libraries(tuv-x 
   PUBLIC 
     musica::tuvx
-    musica::musicacore
+    yaml-cpp::yaml-cpp
     ${BLAS_LIBRARIES}
     ${LAPACK_LIBRARIES}
 )
 
+target_include_directories(tuv-x
+  PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>
+    $<INSTALL_INTERFACE:${INSTALL_INCLUDE_DIR}>)
+
 if(ENABLE_OPENMP)
   target_link_libraries(tuv-x PUBLIC OpenMP::OpenMP_Fortran)
 endif()

README.md

@@ -5,12 +5,13 @@
 Tropospheric ultraviolet-extended (TUV-x): A photolysis rate calculator
 
 [![License](https://img.shields.io/github/license/NCAR/tuv-x.svg)](https://github.com/NCAR/tuv-x/blob/main/LICENSE)
-[![CI Status](https://github.com/NCAR/tuv-x/actions/workflows/test.yml/badge.svg)](https://github.com/NCAR/tuv-x/actions/workflows/test.yml)
+[![Ubuntu](https://github.com/NCAR/tuv-x/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/NCAR/tuv-x/actions/workflows/ubuntu.yml)
+[![Docker](https://github.com/NCAR/tuv-x/actions/workflows/docker.yml/badge.svg)](https://github.com/NCAR/tuv-x/actions/workflows/docker.yml)
 [![codecov](https://codecov.io/gh/NCAR/tuv-x/branch/main/graph/badge.svg?token=H46AAEAQF9)](https://codecov.io/gh/NCAR/tuv-x)
 [![DOI](https://zenodo.org/badge/396946468.svg)](https://zenodo.org/badge/latestdoi/396946468)
 [![](https://img.shields.io/badge/Contribute%20with-Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/NCAR/tuv-x)
 
-Copyright (C) 2020 National Center for Atmospheric Research
+Copyright (C) 2020-4 National Center for Atmospheric Research
 
 # Try it out!
 
@@ -22,7 +23,7 @@ a tutorial on how to use TUV-x.
 # Building and installing
 To build and install TUV-x locally, you must have the following libraries installed:
 
-- [json-fortran](https://github.com/jacobwilliams/json-fortran)
+- [yaml-cpp](https://github.com/jbeder/yaml-cpp/)
 - [NetCDF](https://www.unidata.ucar.edu/software/netcdf/) (both C and Fortran libraries)
 
 You must also have CMake installed on your machine. 
@@ -143,13 +144,13 @@ The TUV-x software can be cited with
   author       = {Matt Dawson and
                   Kyle Shores and
                   Stacy Walters},
-  title        = {NCAR/tuv-x: Version 0.2.0},
-  month        = sep,
-  year         = 2022,
+  title        = {NCAR/tuv-x: Version 0.5.0},
+  month        = dec,
+  year         = 2023,
   publisher    = {Zenodo},
   version      = {v0.2.0},
-  doi          = {10.5281/zenodo.7126040},
-  url          = {https://doi.org/10.5281/zenodo.7126040}
+  doi          = {10.5281/zenodo.8110063},
+  url          = {https://doi.org/10.5281/zenodo.8110063}
 }
 ```
 
@@ -185,4 +186,4 @@ installation and usage instructions.
 # License
 
 - [Apache 2.0](/LICENSE)
-- Copyright (C) 2022 National Center for Atmospheric Research
+- Copyright (C) 2020-4 National Center for Atmospheric Research