Merge sp into ip (#210)

* ***Merge sp into ip***: main code; tests; spack recipe; update VERSION to 5.0.0 * update cmake option descriptions * u * Update docs (incl. incorporate sp docs) * Doc updates; fix doc build of sp routines * Update docs/layout * cmake description tweak * update docs * Fix parallel test exe builds * remove layout.xml * simplify spack CI * fix some type mismatches in fftpack.F * test allowing arg mismatch * clean up linux CI * move arg mismatch flag * update flags from sp * Revert "fix some type mismatches in fftpack.F" This reverts commit 7f9f5bf. * remove layout.xml from docs/CMakeLists.txt * move bigendian setting to sp tests only * fix tests/CMakeLists.txt typo * fix spack CI * update CI for sp merge * set -fno-bounds-check * whitelist TEST_TIME_LIMIT in recipe check CI * update macos ci * remove noboundcheck flag * disable asan for fftpack.F * Revert "disable asan for fftpack.F" This reverts commit 64f4a9a. * disable bounds checks for specific sp files * remove ip2 references * rename test coverage artifact * update license * update README.md * Update package.py * Update Intel.yml
NOAA-EMC · Jan 23, 2024 · cfbcd25 · cfbcd25
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diff --git a/.github/workflows/Intel.yml b/.github/workflows/Intel.yml
@@ -37,33 +37,8 @@ jobs:
         rm 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 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+        sudo apt-get install 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
-      
-    - name: cache-sp
-      id: cache-sp
-      uses: actions/cache@v2
-      with:
-        path: ~/sp
-        key: sp-${{ runner.os }}-Intel-${{ matrix.compilers }}-${{ matrix.openmp }}
-
-    - name: checkout-sp
-      if: steps.cache-sp.outputs.cache-hit != 'true'
-      uses: actions/checkout@v2
-      with:
-        repository: NOAA-EMC/NCEPLIBS-sp
-        path: sp
-        ref: develop
-
-    - name: build-sp
-      if: steps.cache-sp.outputs.cache-hit != 'true'
-      run: |
-        cd sp
-        mkdir build
-        cd build
-        ${{ matrix.compilers }} cmake -DCMAKE_INSTALL_PREFIX=~/sp -DOPENMP=${{ matrix.openmp}} -DBUILD_8=ON ..
-        make -j2
-        make install
 
     - name: checkout
       uses: actions/checkout@v2
@@ -75,7 +50,7 @@ jobs:
         cd ip
         mkdir build 
         cd build
-        ${{ matrix.compilers }} cmake -DOPENMP=${{ matrix.openmp }} -DBUILD_SHARED_LIBS=OFF -DCMAKE_PREFIX_PATH="~/sp" -DBUILD_8=ON ..
+        ${{ matrix.compilers }} cmake -DOPENMP=${{ matrix.openmp }} -DBUILD_SHARED_LIBS=OFF -DBUILD_8=ON ..
         make -j2 VERBOSE=1
     
     - name: test

diff --git a/.github/workflows/Linux.yml b/.github/workflows/Linux.yml
@@ -26,47 +26,20 @@ jobs:
 
     steps:
 
-    - name: cache-sp
-      id: cache-sp
-      uses: actions/cache@v2
-      with:
-        path: ~/sp
-        key: sp-${{ runner.os }}-Linux-${{ matrix.openmp }}-2.3.3-1
-
-    - name: checkout-sp
-      if: steps.cache-sp.outputs.cache-hit != 'true'
-      uses: actions/checkout@v2
-      with:
-        repository: NOAA-EMC/NCEPLIBS-sp
-        path: sp
-        ref: v2.3.3
-
-    - name: build-sp
-      if: steps.cache-sp.outputs.cache-hit != 'true'
-      run: |
-        cd sp
-        mkdir build
-        cd build
-        cmake -DCMAKE_INSTALL_PREFIX=~/sp -DOPENMP=${{ matrix.openmp }} ${{ matrix.options }} ..
-        make -j2
-        make install
-
     - name: checkout
       uses: actions/checkout@v2
       with: 
         path: ip
-        submodules: true
 
     - name: build
       run: |
         cd ip
         mkdir build 
         cd build
         cmake -DCMAKE_PREFIX_PATH="~/" -DOPENMP=${{ matrix.openmp }} ${{ matrix.options }} ..
-        make -j2
+        make -j2 VERBOSE=1
     
     - name: test
       run: |
         cd $GITHUB_WORKSPACE/ip/build
         ctest --verbose --output-on-failure --rerun-failed
-
diff --git a/.github/workflows/MacOS.yml b/.github/workflows/MacOS.yml
@@ -25,33 +25,6 @@ jobs:
 
     steps:
 
-    - name: cache-sp
-      id: cache-sp
-      uses: actions/cache@v2
-      with:
-        path: ~/sp
-        key: sp-${{ matrix.openmp }}-MacOS-2.3.3-1
-
-    - name: checkout-sp
-      if: steps.cache-sp.outputs.cache-hit != 'true'
-      uses: actions/checkout@v2
-      with:
-        repository: NOAA-EMC/NCEPLIBS-sp
-        path: sp
-        ref: v2.3.3
-
-    - name: build-sp
-      if: steps.cache-sp.outputs.cache-hit != 'true'
-      run: |
-        cd sp
-        mkdir build
-        cd build
-        cmake -DOPENMP=${{ matrix.openmp }} -DCMAKE_INSTALL_PREFIX=~/sp -DBUILD_SHARED_LIBS=${{ matrix.sharedlibs }} -DBUILD_8=ON ..
-        make -j2
-        make install
-        ls -l ~/sp
-        ls -l ~/sp/lib
-
     - name: checkout
       uses: actions/checkout@v2
       with: 
@@ -62,7 +35,7 @@ jobs:
         cd ip
         mkdir build 
         cd build
-        cmake -DOPENMP=${{ matrix.openmp }}  -DCMAKE_PREFIX_PATH="~/sp" -DBUILD_SHARED_LIBS=${{ matrix.sharedlibs }} -DCMAKE_INSTALL_PREFIX=~/install -DBUILD_8=ON ..
+        cmake -DOPENMP=${{ matrix.openmp }} -DBUILD_SHARED_LIBS=${{ matrix.sharedlibs }} -DCMAKE_INSTALL_PREFIX=~/install -DBUILD_8=ON ..
         make -j2 VERBOSE=2
         make install
         ls -l ~/install

diff --git a/.github/workflows/Spack.yml b/.github/workflows/Spack.yml
@@ -21,10 +21,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        openmp: ["+openmp", "~openmp"]
-        sharedlibs: ["+shared", "~shared"]
-        pic: ["+pic", "~pic"]
-        precision: ["d", "4", "8"]
+        variants: ["+openmp +shared +pic precision=d", "+openmp ~shared ~pic precision=4", "~openmp ~shared +pic precision=8"]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -42,16 +39,18 @@ jobs:
         spack env activate ip-env
         cp $GITHUB_WORKSPACE/ip/spack/package.py $SPACK_ROOT/var/spack/repos/builtin/packages/ip/package.py
         spack develop --no-clone --path $GITHUB_WORKSPACE/ip ip@develop
-        spack add ip@develop%gcc@11 ${{ matrix.openmp }} ${{ matrix.sharedlibs }} ${{ matrix.pic }} precision=${{ matrix.precision }} target=x86_64
-        if [ ${{ matrix.precision }} == "d" ]; then spack add grib-util@develop ; fi
+        spack add ip@develop%gcc@11 ${{ matrix.variants }} target=x86_64
+        precision=$(echo ${{ matrix.variants }} | grep -oP " precision=\K[4d8]")
+        if [ "$precision" == "d" ]; then spack add grib-util@develop ; fi
         spack external find cmake gmake
         spack concretize
         # Run installation and run CTest suite
         spack install --verbose --fail-fast --test root
         # Run 'spack load' and check that key build options were respected
         spack load ip
-        if [ ${{ matrix.sharedlibs }} == "+shared" ]; then suffix="so" ; else suffix="a"; fi
-        ls ${IP_LIB${{ matrix.precision }}} | grep -cE '/libip_${{ matrix.precision }}\.'$suffix'$'
+        if [[ "${{ matrix.variants }}" =~ "+shared" ]]; then suffix="so" ; else suffix="a"; fi
+        libvar=IP_LIB${precision}
+        ls ${!libvar} | grep -cE "/libip_${precision}\."$suffix'$'
 
   # This job validates the Spack recipe by making sure each cmake build option is represented
   recipe-check:
@@ -67,7 +66,7 @@ jobs:
     - name: recipe-check
       run: |
         echo "If this jobs fails, look at the most recently output CMake option below and make sure that option appears in spack/package.py"
-        for opt in $(grep -ioP '^option\(\K(?!(ENABLE_DOCS))[^ ]+' $GITHUB_WORKSPACE/ip/CMakeLists.txt) ; do
+        for opt in $(grep -ioP '^option\(\K(?!(ENABLE_DOCS|TEST_TIME_LIMIT))[^ ]+' $GITHUB_WORKSPACE/ip/CMakeLists.txt) ; do
           echo "Checking for presence of '$opt' CMake option in package.py"
           grep -cP "define.+\b${opt}\b" $GITHUB_WORKSPACE/ip/spack/package.py
         done
diff --git a/.github/workflows/developer.yml b/.github/workflows/developer.yml
@@ -28,21 +28,6 @@ jobs:
         sudo apt-get install doxygen
         python3 -m pip install gcovr
 
-    - name: checkout-sp
-      uses: actions/checkout@v2
-      with:
-        repository: NOAA-EMC/NCEPLIBS-sp
-        path: sp
-
-    - name: build-sp
-      run: |
-        cd sp
-        mkdir build
-        cd build
-        cmake -DOPENMP=ON -DCMAKE_INSTALL_PREFIX=~/sp -DBUILD_8=ON ..
-        make -j2
-        make install
-
     - name: checkout
       uses: actions/checkout@v2
       with: 
@@ -53,7 +38,7 @@ jobs:
         cd ip
         mkdir build 
         cd build
-        cmake -DENABLE_DOCS=YES -DCMAKE_PREFIX_PATH="~/" -DOPENMP=ON -DCMAKE_Fortran_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -fsanitize=address" -DCMAKE_C_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -fsanitize=address" -DCMAKE_BUILD_TYPE=Debug -DBUILD_SHARED_LIBS=ON -DBUILD_8=ON ..
+        cmake -DENABLE_DOCS=YES -DOPENMP=ON -DCMAKE_Fortran_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -fsanitize=address" -DCMAKE_C_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -fsanitize=address" -DCMAKE_BUILD_TYPE=Debug -DBUILD_SHARED_LIBS=ON -DBUILD_8=ON ..
         make -j2 VERBOSE=1
     
     - name: test
@@ -69,7 +54,7 @@ jobs:
     - name: upload-test-coverage
       uses: actions/upload-artifact@v2
       with:
-        name: test-coverage
+        name: ip-test-coverage
         path: |
               ip/build/*.html 
               ip/build/*.css

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -13,12 +13,14 @@ project(ip VERSION ${pVersion} LANGUAGES C Fortran)
 include(GNUInstallDirs)
 
 # Handle user options.
-option(ENABLE_DOCS "Enable generation of doxygen-based documentation." OFF)
+option(ENABLE_DOCS "Enable generation of Doxygen-based documentation" OFF)
 option(OPENMP "Use OpenMP threading" OFF)
 option(BUILD_SHARED_LIBS "Build shared libraries" OFF)
-option(BUILD_4 "Build the 4-byte real version of the library, libip_4.a" ON)
-option(BUILD_D "Build the 8-byte real version of the library, libip_d.a" ON)
-option(BUILD_8 "Build the 8-byte integer version of the library, libsp_8.a" OFF)
+option(BUILD_4 "Build the 4-byte real version of the library, libip_4.{a,so}" ON)
+option(BUILD_D "Build the 8-byte real version of the library, libip_d.{a,so}" ON)
+option(BUILD_8 "Build the 8-byte integer & real version of the library, libip_8.{a,so}" OFF)
+option(BUILD_DEPRECATED "Build deprecated spectral processing functions" OFF)
+option(TEST_TIME_LIMIT "Set timeout for tests" OFF)
 
 # Figure whether user wants a _4, a _d, and/or _8.
 if(BUILD_4)
@@ -47,9 +49,6 @@ if(OPENMP)
   find_package(OpenMP REQUIRED COMPONENTS Fortran)
 endif()
 
-# We need the NCEPLIBS-sp library.
-find_package(sp 2.3.0 REQUIRED)
-
 # Set compiler flags.
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel|IntelLLVM)$")
   set(CMAKE_Fortran_FLAGS "-g -traceback -assume byterecl -fp-model strict -fpp -auto ${CMAKE_Fortran_FLAGS}")
@@ -61,10 +60,13 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel|IntelLLVM)$")
   set(fortran_d_flags "-r8")
   set(fortran_8_flags "-i8 -r8")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
-  set(CMAKE_Fortran_FLAGS "-g -fbacktrace -cpp -fimplicit-none ${CMAKE_Fortran_FLAGS}")
+  set(CMAKE_Fortran_FLAGS "-g -fbacktrace -cpp ${CMAKE_Fortran_FLAGS}")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -Wall -Wno-unused-dummy-argument -Wsurprising -Wextra -fcheck=all")
   set(fortran_d_flags "-fdefault-real-8")
   set(fortran_8_flags "-fdefault-integer-8 -fdefault-real-8")
+  if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
+    set(CMAKE_Fortran_FLAGS "-w -fallow-argument-mismatch -fallow-invalid-boz ${CMAKE_Fortran_FLAGS}")
+  endif()
 endif()
 
 # This is the source code directiroy.

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
-Copyright 2020 National Oceanic and Atmospheric Administration (by assignment from I. M. Systems Group)
+Copyright 2020 National Oceanic and Atmospheric Administration
 
-The [NCEPLIBS-ip2] code incorporated in the Unified Forecast System (UFS) was jointly developed by the National Oceanic and Atmospheric Administration and the I. M. Systems Group. The gold standard copy of the Code will be maintained by NOAA at [https://github.com/NOAA-EMC/NCEPLIBS-ip2].
+The [NCEPLIBS-ip] repository is maintained by NOAA at [https://github.com/NOAA-EMC/NCEPLIBS-ip].
 
 The National Oceanic and Atmospheric Administration is releasing this code under the GNU Lesser General Public License v3.0 (the "License"); you may not use this code except in compliance with the License.
 

diff --git a/README.md b/README.md
@@ -2,16 +2,16 @@
 
 # Interpolation Library
 
-The NCEP general interpolation library contains Fortran 90
-subprograms to be used for interpolating between nearly all grids used
-at NCEP. The library is particularly efficient when interpolating many
-fields at one time.
+The NCEP general interpolation library contains Fortran 90 subprograms to be
+used for interpolating between nearly all grids used at NCEP. The library is
+particularly efficient when interpolating many fields at one time. It also
+contains routines for spectral transforms and other processing, including those
+previously contained in the NCEPLIBS-sp library.
 
 This is part of the [NCEPLIBS](https://github.com/NOAA-EMC/NCEPLIBS)
 project.
 
-There are currently six interpolation methods available in the
-library:
+There are currently six interpolation methods available in the library:
 - bilinear
 - bicubic
 - neighbor
@@ -27,40 +27,42 @@ To submit bug reports, feature requests, or other code-related issues including
 
 * NCEP/EMC Developers
 
-Code Manager: [George Gayno](mailto:george.gayno@noaa.gov)
+Code Manager: [Alex Richert](mailto:alexander.richert@noaa.gov)
 
 ### Prerequisites
 
-This package requires the [NCEPLIBS-sp](https://github.com/NOAA-EMC/NCEPLIBS-sp) library.
+This package does not link to any other libraries, but requires CMake (version
+3.15+) to build.
 
 ### Installing
 
 ```
 mkdir build
 cd build
-cmake -DCMAKE_INSTALL_PREFIX=/path/to/install /path/to/NCEPLIBS-ip2
+cmake -DCMAKE_INSTALL_PREFIX=/path/to/install /path/to/NCEPLIBS-ip
 make -j2
-make test (or ctest --verbose)
+make test # (or ctest --verbose)
 make install
 ```
 
 ### Usage
 
-To use the ip library add `use ip_mod` to your Fortran code. It contains all the necessary public interfaces.
+Most routines and any public interfaces required can be accessed by adding `use
+ip_mod` to your Fortran code. Most spectral transform and processing subroutines
+can be accessed by calling them in your code (no `use` statement) and linking
+to the ip library at build time.
 
 ## Disclaimer
 
-The United States Department of Commerce (DOC) GitHub project code is
-provided on an "as is" basis and the user assumes responsibility for
-its use. DOC has relinquished control of the information and no longer
-has responsibility to protect the integrity, confidentiality, or
-availability of the information. Any claims against the Department of
-Commerce stemming from the use of its GitHub project will be governed
-by all applicable Federal law. Any reference to specific commercial
-products, processes, or services by service mark, trademark,
-manufacturer, or otherwise, does not constitute or imply their
-endorsement, recommendation or favoring by the Department of
-Commerce. The Department of Commerce seal and logo, or the seal and
-logo of a DOC bureau, shall not be used in any manner to imply
-endorsement of any commercial product or activity by DOC or the United
-States Government.
+The United States Department of Commerce (DOC) GitHub project code is provided
+on an "as is" basis and the user assumes responsibility for its use. DOC has
+relinquished control of the information and no longer has responsibility to
+protect the integrity, confidentiality, or availability of the information. Any
+claims against the Department of Commerce stemming from the use of its GitHub
+project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark, trademark,
+manufacturer, or otherwise, does not constitute or imply their endorsement,
+recommendation or favoring by the Department of Commerce. The Department of
+Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used
+in any manner to imply endorsement of any commercial product or activity by DOC
+or the United States Government.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-4.4.0
+5.0.0
diff --git a/cmake/PackageConfig.cmake.in b/cmake/PackageConfig.cmake.in
@@ -9,8 +9,6 @@ include("${CMAKE_CURRENT_LIST_DIR}/@[email protected]")
 
 include(CMakeFindDependencyMacro)
 
-find_dependency(sp CONFIG)
-
 if(@OPENMP@)
   find_dependency(OpenMP COMPONENTS Fortran)
 endif()

diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -763,7 +763,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =
+LAYOUT_FILE            = 
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -886,6 +886,8 @@ INPUT_ENCODING         = UTF-8
 
 FILE_PATTERNS          = *.f90 \
                          *.F90 \
+                         *.f \
+                         *.F \
                          *.c \
                          *.h
 
@@ -1011,7 +1013,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/sp_user_guide.md
+USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/user_guide.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing