Merge pull request #544 from LBL-EESA/develop

4.0.0 release

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,20 @@
+Please fill the following sections in as completely as possible. Please include all CMake output under `Additional information` when reporting build issues.
+
+**Description of the issue**
+...
+
+**Platform**
+| Field         | Value               |
+| ------------: | :------------------ |
+| HPC Center:   |                     |
+| System name:  |                     |
+| OS name/ver:  |                     |
+| Compiler ver: |                     |
+| CMake ver:    |                     |
+
+
+**Steps to Reproduce**
+...
+
+**Additional information**
+...

.gitignore

@@ -1,3 +1,4 @@
 *.sw[a-z]
 *.patch
 _build
+*.pt

.readthedocs.yml

@@ -0,0 +1,13 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+sphinx:
+  configuration: doc/rtd/conf.py
+
+python:
+  version: 3.7
+  install:
+    - requirements: doc/rtd/requirements.txt

.travis.yml

@@ -9,23 +9,32 @@ os:
   - linux
   - osx
 
+osx_image:
+  - xcode12.2
+
 env:
   global:
     - BUILD_TYPE=Debug
     - TECA_DIR=/travis_teca_dir
     - TECA_PYTHON_VERSION=3
-    - TECA_DATA_REVISION=49
-  matrix:
-    - DOCKER_IMAGE=ubuntu IMAGE_VERSION=18.04 IMAGE_NAME=ubuntu_18_04
-    - DOCKER_IMAGE=fedora IMAGE_VERSION=28 IMAGE_NAME=fedora_28
+    - TECA_DATA_REVISION=101
+  jobs:
+    - DOCKER_IMAGE=ubuntu IMAGE_VERSION=20.04 IMAGE_NAME=ubuntu_20_04 REQUIRE_NETCDF_MPI=TRUE
+    - DOCKER_IMAGE=ubuntu IMAGE_VERSION=20.04 IMAGE_NAME=ubuntu_20_04 REQUIRE_NETCDF_MPI=FALSE
+    - DOCKER_IMAGE=fedora IMAGE_VERSION=32 IMAGE_NAME=fedora_32 REQUIRE_NETCDF_MPI=TRUE
+    - DOCKER_IMAGE=fedora IMAGE_VERSION=32 IMAGE_NAME=fedora_32 REQUIRE_NETCDF_MPI=FALSE
     - NO_DOCKER=TRUE
 
-matrix:
+jobs:
   exclude:
     - os: osx
-      env: DOCKER_IMAGE=ubuntu IMAGE_VERSION=18.04 IMAGE_NAME=ubuntu_18_04
+      env: DOCKER_IMAGE=ubuntu IMAGE_VERSION=20.04 IMAGE_NAME=ubuntu_20_04 REQUIRE_NETCDF_MPI=TRUE
+    - os: osx
+      env: DOCKER_IMAGE=ubuntu IMAGE_VERSION=20.04 IMAGE_NAME=ubuntu_20_04 REQUIRE_NETCDF_MPI=FALSE
+    - os: osx
+      env: DOCKER_IMAGE=fedora IMAGE_VERSION=32 IMAGE_NAME=fedora_32 REQUIRE_NETCDF_MPI=TRUE
     - os: osx
-      env: DOCKER_IMAGE=fedora IMAGE_VERSION=28 IMAGE_NAME=fedora_28
+      env: DOCKER_IMAGE=fedora IMAGE_VERSION=32 IMAGE_NAME=fedora_32 REQUIRE_NETCDF_MPI=FALSE
     - os: linux
       env: NO_DOCKER=TRUE
 
@@ -48,6 +57,7 @@ install:
     docker exec teca_${DOCKER_IMAGE}_${IMAGE_VERSION} /bin/bash -c
     "export TECA_PYTHON_VERSION=${TECA_PYTHON_VERSION} &&
     export TECA_DATA_REVISION=${TECA_DATA_REVISION} &&
+    export REQUIRE_NETCDF_MPI=${REQUIRE_NETCDF_MPI} &&
     ${TECA_DIR}/test/travis_ci/install_${IMAGE_NAME}.sh";
     fi
 
@@ -64,5 +74,6 @@ script:
     export BUILD_TYPE=${BUILD_TYPE} &&
     export DOCKER_IMAGE=${DOCKER_IMAGE} &&
     export IMAGE_VERSION=${IMAGE_VERSION} &&
+    export REQUIRE_NETCDF_MPI=${REQUIRE_NETCDF_MPI} &&
     ${TECA_DIR}/test/travis_ci/ctest_linux.sh";
     fi

CMake/FindMPI4Py.cmake

@@ -4,22 +4,22 @@
 # Check if mpi4py is installed and configure c-api includes
 #
 # This module defines
-#  MPI4PY_FOUND, set TRUE if mpi4py and c-api are available
-#  MPI4PY_INCLUDE_DIR, where to find c-api headers
-#  MPI4PY_VERSION, mpi4py release version
+#  MPI4Py_FOUND, set TRUE if mpi4py and c-api are available
+#  MPI4Py_INCLUDE_DIR, where to find c-api headers
+#  MPI4Py_VERSION, mpi4py release version
 set(_TMP_PY_OUTPUT)
 set(_TMP_PY_RETURN)
 exec_program("${PYTHON_EXECUTABLE}"
   ARGS "-c 'import mpi4py; print(mpi4py.get_include())'"
   OUTPUT_VARIABLE _TMP_PY_OUTPUT
   RETURN_VALUE _TMP_PY_RETURN)
-set(MPI4PY_INCLUDE_FOUND FALSE)
+set(MPI4Py_INCLUDE_FOUND FALSE)
 if(NOT _TMP_PY_RETURN AND EXISTS "${_TMP_PY_OUTPUT}")
-  set(MPI4PY_INCLUDE_FOUND TRUE)
+  set(MPI4Py_INCLUDE_FOUND TRUE)
 else()
   set(_TMP_PY_OUTPUT)
 endif()
-set(MPI4PY_INCLUDE_DIR "${_TMP_PY_OUTPUT}" CACHE PATH
+set(MPI4Py_INCLUDE_DIR "${_TMP_PY_OUTPUT}" CACHE PATH
   "mpi4py include directories")
 
 set(_TMP_PY_OUTPUT)
@@ -28,22 +28,22 @@ exec_program("${PYTHON_EXECUTABLE}"
   ARGS "-c 'import mpi4py; print(mpi4py.__version__)'"
   OUTPUT_VARIABLE _TMP_PY_OUTPUT
   RETURN_VALUE _TMP_PY_RETURN)
-set(MPI4PY_VERSION_FOUND FALSE)
+set(MPI4Py_VERSION_FOUND FALSE)
 if(NOT _TMP_PY_RETURN)
-  set(MPI4PY_VERSION_FOUND TRUE)
+  set(MPI4Py_VERSION_FOUND TRUE)
 else()
   set(_TMP_PY_OUTPUT)
 endif()
-set(MPI4PY_VERSION "${_TMP_PY_OUTPUT}" CACHE STRING
+set(MPI4Py_VERSION "${_TMP_PY_OUTPUT}" CACHE STRING
   "mpi4py version string")
 
 if (NOT ${QUIET})
-  message(STATUS "MPI4PY_INCLUDE_DIR=${MPI4PY_INCLUDE_DIR}")
-  message(STATUS "MPI4PY_VERSION=${MPI4PY_VERSION}")
+  message(STATUS "MPI4Py_INCLUDE_DIR=${MPI4Py_INCLUDE_DIR}")
+  message(STATUS "MPI4Py_VERSION=${MPI4Py_VERSION}")
 endif()
 
-mark_as_advanced(MPI4PY_INCLUDE_DIR MPI4PY_VERSION)
+mark_as_advanced(MPI4Py_INCLUDE_DIR MPI4Py_VERSION)
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(MPI4PY DEFAULT_MSG
-  MPI4PY_INCLUDE_FOUND MPI4PY_VERSION_FOUND)
+find_package_handle_standard_args(MPI4Py DEFAULT_MSG
+  MPI4Py_INCLUDE_FOUND MPI4Py_VERSION_FOUND)

CMake/FindMatplotlib.cmake

@@ -0,0 +1,25 @@
+#*****************************************************************************
+# FindMatplotlib
+#
+# Check if matplotlib is installed and configure c-api includes
+#
+# This module defines
+#  Matplotlib_FOUND, set TRUE if matplotlib and c-api are available
+#  Matplotlib_VERSION, matplotlib release version
+
+set(_TMP_PY_OUTPUT)
+set(_TMP_PY_RETURN)
+exec_program("${PYTHON_EXECUTABLE}"
+  ARGS "-c 'import matplotlib; print(matplotlib.__version__)'"
+  OUTPUT_VARIABLE _TMP_PY_OUTPUT
+  RETURN_VALUE _TMP_PY_RETURN)
+set(Matplotlib_VERSION_FOUND FALSE)
+if(NOT _TMP_PY_RETURN)
+  set(Matplotlib_VERSION_FOUND TRUE)
+else()
+  set(_TMP_PY_OUTPUT)
+endif()
+set(Matplotlib_VERSION "${_TMP_PY_OUTPUT}")
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Matplotlib DEFAULT_MSG Matplotlib_VERSION_FOUND)

CMake/FindNetCDF.cmake

@@ -32,133 +32,96 @@
 #  target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
 #  target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
 
+
 #search starting from user editable cache var
 if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
   # Already in cache, be silent
   set (NETCDF_FIND_QUIETLY TRUE)
-endif ()
-
-# find the library
-# first look where the user told us
-if (NETCDF_DIR)
-  find_library (NETCDF_LIBRARY NAMES netcdf
-    PATHS "${NETCDF_DIR}/lib" "${NETCDF_DIR}/lib64"
-    NO_DEFAULT_PATH)
-endif()
-
-# next look in LD_LIBRARY_PATH for libraries
-find_library (NETCDF_LIBRARY NAMES netcdf
-  PATHS ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-
-# finally CMake can look
-find_library (NETCDF_LIBRARY NAMES netcdf)
-
-mark_as_advanced (NETCDF_LIBRARY)
-set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
-
-# find the header
-# first look where the user told us
-if (NETCDF_DIR)
-  find_path (NETCDF_INCLUDE_DIR netcdf.h
-    PATHS "${NETCDF_DIR}/include" NO_DEFAULT_PATH)
 endif()
 
-# then look relative to library dir
-get_filename_component(NETCDF_LIBRARY_DIR
-  ${NETCDF_LIBRARY} DIRECTORY)
-
-find_path (NETCDF_INCLUDE_DIR netcdf.h
-  PATHS "${NETCDF_LIBRARY_DIR}/../include"
-  NO_DEFAULT_PATH)
-
-# finally CMake can look
-find_path (NETCDF_INCLUDE_DIR netcdf.h)
-
-mark_as_advanced (NETCDF_INCLUDE_DIR)
-set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
-
-
-#start finding requested language components
-set (NetCDF_libs "")
-set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
-
-get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
-set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
-
-macro (NetCDF_check_interface lang header libs)
-  if (NETCDF_${lang})
-    # find the library
+# find the library
+# use package config, this works well on systems that make
+# use of modules to manage installs not in the standard
+# locations that cmake knows about
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(NC_TMP netcdf QUIET)
+if (NC_TMP_FOUND AND NC_TMP_LINK_LIBRARIES AND NC_TMP_LIBRARY_DIRS AND NC_TMP_INCLUDE_DIRS)
+    set(NETCDF_LIBRARY_DIR ${NC_TMP_LIBRARY_DIRS})
+    set(NETCDF_LIBRARY ${NC_TMP_LINK_LIBRARIES})
+    set(NETCDF_INCLUDE_DIR ${NC_TMP_INCLUDE_DIRS})
+else()
+    # package config failed, use cmake
     # first look where the user told us
     if (NETCDF_DIR)
-      find_library (NETCDF_${lang}_LIBRARY NAMES netcdf
+      find_library(NETCDF_LIBRARY NAMES netcdf
         PATHS "${NETCDF_DIR}/lib" "${NETCDF_DIR}/lib64"
         NO_DEFAULT_PATH)
     endif()
 
     # next look in LD_LIBRARY_PATH for libraries
-    find_library (NETCDF_${lang}_LIBRARY NAMES netcdf
+    find_library(NETCDF_LIBRARY NAMES netcdf
       PATHS ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
 
     # finally CMake can look
-    find_library (NETCDF_${lang}_LIBRARY NAMES netcdf)
+    find_library(NETCDF_LIBRARY NAMES netcdf)
+
+    message(STATUS ${NETCDF_LIBRARY})
+endif()
 
-    # find the header
+# if we can find the library it is found now
+# record what we have
+mark_as_advanced (NETCDF_LIBRARY)
+set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
+
+# find the header
+# package config failed, use cmake
+if (NOT NC_TMP_FOUND OR NOT NC_TMP_LINK_LIBRARIES OR NOT NC_TMP_LIBRARY_DIRS OR NOT NC_TMP_INCLUDE_DIRS)
     # first look where the user told us
     if (NETCDF_DIR)
-      find_path (NETCDF_${lang}_INCLUDE_DIR netcdf.h
+      find_path (NETCDF_INCLUDE_DIR netcdf.h
         PATHS "${NETCDF_DIR}/include" NO_DEFAULT_PATH)
     endif()
 
     # then look relative to library dir
-    get_filename_component(NETCDF_${lang}_LIBRARY_DIR
-      ${NETCDF_${lang}_LIBRARY} DIRECTORY CACHE)
+    get_filename_component(NETCDF_LIBRARY_DIR
+      ${NETCDF_LIBRARY} DIRECTORY)
 
-    find_path (NETCDF_${lang}_INCLUDE_DIR netcdf.h
-      PATHS "${NETCDF_${lang}_LIBRARY_DIR}/../include"
+    find_path (NETCDF_INCLUDE_DIR netcdf.h
+      PATHS "${NETCDF_LIBRARY_DIR}/../include"
       NO_DEFAULT_PATH)
 
-    # finally CMake can look
-    find_path (NETCDF_${lang}_INCLUDE_DIR netcdf.h)
-
-    #export to internal varS that rest of project can use directly
-    mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
-
-    set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
-    set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
-
-    if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
-      list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
-      list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
-    else ()
-      set (NETCDF_HAS_INTERFACES "NO")
-      message (STATUS "Failed to find NetCDF interface for ${lang}")
-    endif ()
-  endif ()
-endmacro (NetCDF_check_interface)
-
-list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
-if (_nextcomp GREATER -1)
-  set (NETCDF_CXX 1)
-endif ()
-list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
-if (_nextcomp GREATER -1)
-  set (NETCDF_F77 1)
-endif ()
-list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
-if (_nextcomp GREATER -1)
-  set (NETCDF_F90 1)
-endif ()
-NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
-NetCDF_check_interface (F77 netcdf.inc  netcdff)
-NetCDF_check_interface (F90 netcdf.mod  netcdff)
+    # CMake can look
+    find_path(NETCDF_INCLUDE_DIR netcdf.h)
+endif()
+
+# look for header file that indicates MPI support
+set(NETCDF_IS_PARALLEL FALSE)
+find_file(NETCDF_PAR_INCLUDE_DIR netcdf_par.h
+    PATHS ${NETCDF_INCLUDE_DIR} NO_DEFAULT_PATH)
+if (NETCDF_PAR_INCLUDE_DIR)
+    set(NETCDF_IS_PARALLEL TRUE)
+endif()
+
+# if we can find the headers they are found now
+# record what we have
+mark_as_advanced(NETCDF_INCLUDE_DIR)
+mark_as_advanced(NETCDF_IS_PARALLEL)
+mark_as_advanced(NETCDF_PAR_INCLUDE_DIR)
+set(NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
+
+#start finding requested language components
+set (NetCDF_libs "")
+set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
+
+get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
 
 #export accumulated results to internal varS that rest of project can depend on
-list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
-set (NETCDF_LIBRARIES ${NetCDF_libs})
-set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
+list(APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
+set(NETCDF_LIBRARIES ${NetCDF_libs})
+set(NETCDF_INCLUDE_DIRS ${NetCDF_includes})
 
 # handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
 # all listed variables are TRUE
 include (FindPackageHandleStandardArgs)
 find_package_handle_standard_args (NetCDF
-  DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)
+  DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS)