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

.dockerignore

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

.github/workflows/test.yml

@@ -17,7 +17,7 @@ jobs:
     - name: build Docker image
       run: docker build -t tuv-x-test .
     - name: run tests in container
-      run: docker run --name test-container -t tuv-x-test bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+      run: docker run --name test-container -t tuv-x-test bash -c 'make test ARGS="--rerun-failed --output-on-failure"'
   build_test_with_mpi_no_memcheck:
     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
@@ -28,7 +28,7 @@ jobs:
     - name: build Docker image for MPI tests
       run: docker build -t tuv-x-mpi-test . -f Dockerfile.mpi
     - name: run MPI tests in container
-      run: docker run -t tuv-x-mpi-test bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+      run: docker run -t tuv-x-mpi-test bash -c 'make test ARGS="--rerun-failed --output-on-failure"'
   build_test_no_mpi_with_memcheck:
     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
@@ -39,24 +39,13 @@ jobs:
     - name: build Docker image
       run: docker build -t tuv-x-test . -f Dockerfile.memcheck
     - name: run tests in container
-      run: docker run --name test-container -t tuv-x-test bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+      run: docker run --name test-container -t tuv-x-test bash -c 'make coverage ARGS="--rerun-failed --output-on-failure"'
     - name: copy coverage from container
       run: docker cp test-container:build/coverage.info .
     - uses: codecov/codecov-action@v2
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: coverage.info
-  build_test_yaml_no_mpi_with_memcheck:
-    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
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-    - name: build Docker image with YAML and memcheck
-      run: docker build -t tuv-x-yaml-test . -f Dockerfile.yaml.memcheck
-    - name: run tests in container
-      run: docker run -t tuv-x-yaml-test bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
   build_test_with_mpi_with_memcheck:
     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
@@ -67,15 +56,4 @@ jobs:
     - name: build Docker image for MPI tests
       run: docker build -t tuv-x-mpi-test . -f Dockerfile.mpi.memcheck
     - name: run MPI tests in container
-      run: docker run -t tuv-x-mpi-test bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
-  build_test_yaml_with_mpi_with_memcheck:
-    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
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-    - name: build Docker image with YAML and memcheck for MPI tests
-      run: docker build -t tuv-x-mpi-yaml-test . -f Dockerfile.yaml.mpi.memcheck
-    - name: run MPI tests in container
-      run: docker run -t tuv-x-mpi-yaml-test bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+      run: docker run -t tuv-x-mpi-test bash -c 'make test ARGS="--rerun-failed --output-on-failure"'

CMakeLists.txt

@@ -34,7 +34,6 @@ option(ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(ENABLE_MEMCHECK "Enable memory checking in tests" ON)
 option(ENABLE_NC_CONFIG "Use nc-config to determine NetCDF libraries" OFF)
 option(BUILD_DOCS "Build the documentation" OFF)
-option(ENABLE_YAML "Uses YAML parser instead of JSON" OFF)
 
 # Set up include and lib directories
 set(TUVX_MOD_DIR "${PROJECT_BINARY_DIR}/include")
@@ -79,11 +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()

Dockerfile

@@ -1,4 +1,4 @@
-FROM fedora:35
+FROM fedora:37
 
 RUN dnf -y update \
     && dnf -y install \
@@ -15,34 +15,17 @@ RUN dnf -y update \
         python3 \
         python3-pip \
         lapack-devel \
+        yaml-cpp-devel \
     && dnf clean all
 
 RUN pip3 install numpy scipy
 
-# install json-fortran
-RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
-    && tar -zxvf 8.2.0.tar.gz \
-    && cd json-fortran-8.2.0 \
-    && export FC=gfortran \
-    && mkdir build \
-    && cd build \
-    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && sudo make install
-
-# add a symlink
-# Create symlinks in the Docker container
-RUN ln -s /usr/local/jsonfortran-gnu-8.2.0/lib/libjsonfortran.a /usr/local/lib64/libjsonfortran.a && \
-    ln -s /usr/local/jsonfortran-gnu-8.2.0/lib/libjsonfortran.so.8.2 /usr/local/lib64/libjsonfortran.so.8.2 && \
-    ln -s /usr/local/jsonfortran-gnu-8.2.0/lib/libjsonfortran.so /usr/local/lib64/libjsonfortran.so && \
-    ln -s /usr/local/jsonfortran-gnu-8.2.0/lib/libjsonfortran.so.8.2.0 /usr/local/lib64/libjsonfortran.so.8.2.0
-
 ENV LD_LIBRARY_PATH=/usr/local/lib64
 
 # build the tuv-x tool
 COPY . /tuv-x/
 RUN mkdir /build \
       && cd /build \
-      && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
       && cmake -D CMAKE_BUILD_TYPE=release \
                -D ENABLE_MEMCHECK=OFF \
                /tuv-x \

Dockerfile.docs

@@ -1,4 +1,4 @@
-FROM fedora:35
+FROM fedora:37
 
 RUN dnf -y update \
     && dnf -y install \
@@ -16,18 +16,9 @@ RUN dnf -y update \
         python3 \
         python3-pip \
         lapack-devel \
+        yaml-cpp-devel \
     && dnf clean all
 
-# install json-fortran
-RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
-    && tar -zxvf 8.2.0.tar.gz \
-    && cd json-fortran-8.2.0 \
-    && export FC=gfortran \
-    && mkdir build \
-    && cd build \
-    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && sudo make install
-
 # build the tuv-x tool
 COPY . /tuv-x/
 
@@ -40,7 +31,6 @@ RUN echo "The suffix is '$SWITCHER_SUFFIX'"
 
 RUN mkdir /build \
       && cd /build \
-      && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
       && cmake -D ENABLE_TESTS=OFF \
                -D BUILD_DOCS=ON \
                /tuv-x \

Dockerfile.memcheck

@@ -1,4 +1,4 @@
-FROM fedora:35
+FROM fedora:37
 
 RUN dnf -y update \
     && dnf -y install \
@@ -15,25 +15,15 @@ RUN dnf -y update \
         python3 \
         python3-pip \
         lapack-devel \
+        yaml-cpp-devel \
     && dnf clean all
 
 RUN pip3 install numpy scipy
 
-# install json-fortran
-RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
-    && tar -zxvf 8.2.0.tar.gz \
-    && cd json-fortran-8.2.0 \
-    && export FC=gfortran \
-    && mkdir build \
-    && cd build \
-    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && sudo make install
-
 # build the tuv-x tool
 COPY . /tuv-x/
 RUN mkdir /build \
       && cd /build \
-      && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
       && cmake -D ENABLE_COVERAGE:BOOL=TRUE \
                -D CMAKE_BUILD_TYPE=COVERAGE \
                /tuv-x \

Dockerfile.mpi

@@ -1,4 +1,4 @@
-FROM fedora:35
+FROM fedora:37
 
 RUN dnf -y update \
     && dnf install -y sudo \
@@ -24,31 +24,22 @@ RUN sudo dnf -y install \
         python3-pip \
         valgrind-openmpi \
         lapack-devel \
+        yaml-cpp-devel \
     && sudo dnf clean all
 
 ENV PATH="${PATH}:/usr/lib64/openmpi/bin/"
 ENV OMP_NUM_THREADS=5
 
 RUN pip3 install numpy scipy
 
-# install json-fortran
-RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
-    && tar -zxvf 8.2.0.tar.gz \
-    && cd json-fortran-8.2.0 \
-    && export FC=gfortran \
-    && mkdir build \
-    && cd build \
-    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && sudo make install
-
-
 # build the tuv-x tool
 COPY . tuv-x/
 RUN mkdir build \
       && cd build \
-      && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
       && cmake -D CMAKE_BUILD_TYPE=release \
                -D CMAKE_Fortran_COMPILER=/usr/lib64/openmpi/bin/mpif90 \
+               -D CMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc \
+               -D CMAKE_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx \
                -D ENABLE_OPENMP:BOOL=TRUE \
                -D ENABLE_MPI:BOOL=TRUE \
                -D ENABLE_MEMCHECK:BOOL=FALSE \

Dockerfile.mpi.memcheck

@@ -1,4 +1,4 @@
-FROM fedora:35
+FROM fedora:37
 
 RUN dnf -y update \
     && dnf install -y sudo \
@@ -24,30 +24,22 @@ RUN sudo dnf -y install \
         python3-pip \
         valgrind-openmpi \
         lapack-devel \
+        yaml-cpp-devel \
     && sudo dnf clean all
 
 ENV PATH="${PATH}:/usr/lib64/openmpi/bin/"
 ENV OMP_NUM_THREADS=5
 
 RUN pip3 install numpy scipy
 
-# install json-fortran
-RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
-    && tar -zxvf 8.2.0.tar.gz \
-    && cd json-fortran-8.2.0 \
-    && export FC=gfortran \
-    && mkdir build \
-    && cd build \
-    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && sudo make install
-
 # build the tuv-x tool
 COPY . tuv-x/
 RUN mkdir build \
       && cd build \
-      && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
       && cmake -D CMAKE_BUILD_TYPE=debug \
                -D CMAKE_Fortran_COMPILER=/usr/lib64/openmpi/bin/mpif90 \
+               -D CMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc \
+               -D CMAKE_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx \
                -D ENABLE_OPENMP:BOOL=TRUE \
                -D ENABLE_MPI:BOOL=TRUE \
                -D ENABLE_MEMCHECK:BOOL=TRUE \

README.md

@@ -10,7 +10,7 @@ Tropospheric ultraviolet-extended (TUV-x): A photolysis rate calculator
 [![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 +22,7 @@ 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. 
@@ -185,4 +185,4 @@ 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