Merge branch 'prot' into paul

fpm.toml

@@ -16,8 +16,12 @@ source-dir="src"
 [dependencies]
 #Pull from github
 #testify = { git = "git@github.com:nakib/testify.git" }
+#Use local copy
 testify = {path = "thirdparty/testify"}
-fhash = { git = "https://github.com/LKedward/fhash.git" }
+#Pull from github
+#fhash = {git = "https://github.com/LKedward/fhash.git"}
+#Use local copy
+fhash = {path = "thirdparty/fhash"}
 
 #Use local copy from thirdparty directory
 spglib = {path = "thirdparty/spglib"}

thirdparty/fhash/.github/workflows/deploy_api_docs.yml

@@ -0,0 +1,31 @@
+name: Build FORD docs & deploy to gh-pages
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:   
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip ford
+
+      - name: Checkout master
+        uses: actions/checkout@v1
+
+      - name: Build docs
+        run: ford ford.md
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@releases/v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages
+          FOLDER: api-doc

thirdparty/fhash/.github/workflows/test.yml

@@ -0,0 +1,84 @@
+name: fpm test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        toolchain:
+          - {compiler: gcc, version: 10}
+        include:
+          - os: ubuntu-latest
+            toolchain: {compiler: intel, version: '2023.1'}
+          - os: ubuntu-latest
+            toolchain: {compiler: gcc, version: 12}
+
+    steps:
+      - uses: awvwgk/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: ${{ matrix.toolchain.compiler }}
+          version: ${{ matrix.toolchain.version }}
+
+      - run: ${{ env.FC }} --version
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+
+      - name: Install fpm
+        uses: fortran-lang/setup-fpm@v5
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Checkout code
+        uses: actions/checkout@v1
+
+      - name: Run tests and demo programs (debug)
+        run: |
+          fpm test
+          fpm run *-demo
+
+      - name: Run tests and demo programs (release)
+        run: |
+          fpm test --profile release
+          fpm run *-demo --profile release
+
+
+  gfortran-windows-msys2-mingw64:
+    runs-on: windows-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v1
+
+    - name: Setup MinGW (MSYS2)
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: MINGW64
+        update: false
+        install: >-
+          git
+          wget
+          mingw-w64-x86_64-gcc-fortran
+
+    - name: Install fpm
+      shell: msys2 {0}
+      run: |
+        wget https://github.com/awvwgk/mingw-w64-fpm-pkgbuild/releases/download/current/mingw-w64-x86_64-fpm-0.2.0-1-any.pkg.tar.zst
+        pacman -U --noconfirm mingw-w64-x86_64-fpm-*-any.pkg.tar.zst
+
+    - name: Run tests and demo programs (debug)
+      shell: msys2 {0}
+      run: |
+        gfortran --version
+        fpm test
+        fpm run *-demo
+
+    - name: Run tests and demo programs (release)
+      shell: msys2 {0}
+      run: |
+        gfortran --version
+        fpm test --profile release
+        fpm run *-demo --profile release

thirdparty/fhash/.gitignore

@@ -0,0 +1,5 @@
+build*
+api-doc*
+*~
+.\#*
+\#*\#

thirdparty/fhash/CMakeLists.txt

@@ -0,0 +1,138 @@
+cmake_minimum_required(VERSION 3.0.2)
+
+project(fhash Fortran)
+
+if(DEFINED CMAKE_Fortran_COMPILER_VERSION)
+  set(Fortran_MODULE_DIRECTORY include/fortran_modules/${CMAKE_Fortran_COMPILER_ID}/${CMAKE_Fortran_COMPILER_VERSION})
+else()
+  set(Fortran_MODULE_DIRECTORY include/fortran_modules/${CMAKE_Fortran_COMPILER_ID})
+endif()
+
+set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${Fortran_MODULE_DIRECTORY})
+
+add_subdirectory(src)
+
+include(CMakePackageConfigHelpers)
+
+# Add all targets to the build-tree export set
+export(TARGETS fhash
+  FILE "${PROJECT_BINARY_DIR}/fhashTargets.cmake")
+
+# Export the package for use from the build-tree
+# (this registers the build-tree with a global CMake-registry)
+export(PACKAGE fhash)
+
+configure_package_config_file(${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
+  "${CMAKE_CURRENT_BINARY_DIR}/fhashConfig.cmake"
+  INSTALL_DESTINATION lib/cmake/fhash
+  )
+
+install(FILES
+          "${CMAKE_CURRENT_BINARY_DIR}/fhashConfig.cmake"
+        DESTINATION lib/cmake/fhash
+)
+
+install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}/ DESTINATION ${Fortran_MODULE_DIRECTORY})
+
+install(EXPORT fhash
+  FILE fhashTargets.cmake
+  DESTINATION lib/cmake/fhash
+)
+
+# -------------------
+# Build documentation
+# -------------------
+
+set ( SKIP_DOC_GEN FALSE CACHE BOOL
+  "Disable building the API documentation with FORD" )
+if ( NOT SKIP_DOC_GEN )
+  find_program(FORD ford)
+
+  find_package(PythonInterp)
+
+  if(NOT PYTHON_VERSION_STRING VERSION_LESS 3.5)
+    set(MARKDOWN_SUPPORTED_PYTHON true)
+  endif()
+
+  if(NOT MARKDOWN_SUPPORTED_PYTHON)
+    message(WARNING "Python version ${PYTHON_VERSION_STRING} is not supported by Python-Markdown, not attempting to build documentation.")
+  endif()
+
+  if(FORD AND MARKDOWN_SUPPORTED_PYTHON)
+
+    set(DOC_ROOT "${PROJECT_BINARY_DIR}/doc")
+    set(DOC_DIR "${DOC_ROOT}/fhash")
+    set(PROJ_DIR "${PROJECT_SOURCE_DIR}")
+    set(FORD_PROJECT_FILE "${CMAKE_CURRENT_SOURCE_DIR}/ford.md")
+    set(FORD_PROJECT_EXCLUDE_DIRS "${MPI_Fortran_INCLUDE_DIRS};${PROJECT_BINARY_DIR};${PROJ_DIR}/build;${PROJ_DIR}/tests;${PROJ_DIR}/sphinx")
+    set(FORD_PROJECT_EXCLUDE_FILES "random.f90;random_integer.f90")
+    set(MACRO_FLAG "")
+    string(REPLACE ";" "\ninclude:" FORD_PROJECT_INCLUDES "${PROJ_DIR}/src")
+    string(REPLACE ";" "\nexclude_dir:" FORD_PROJECT_EXCLUDE_DIRS "${FORD_PROJECT_EXCLUDE_DIRS}")
+    string(REPLACE ";" "\nexclude:" FORD_PROJECT_EXCLUDE_FILES "${FORD_PROJECT_EXCLUDE_FILES}")
+
+    # Pick the preprocessor to use based on the Fortran compiler
+    if ( "${CMAKE_Fortran_COMPILER_ID}" MATCHES "Intel" )
+      set ( FPP "fpp\n" )
+    else ()
+      set ( FPP "gfortran -E\n" ) # default to gfortran -E for gfortran and unsupported compilers
+    endif ()
+    file ( WRITE "${PROJECT_BINARY_DIR}/.PREPROCESSOR" "${FPP}" )
+
+    # Dynamically generate the FORD outputs list
+    message ( STATUS "Dynamically computing FORD output information..." )
+    if ( NOT (DEFINED FORD_OUTPUTS_CACHED) )
+      message ( STATUS "Running FORD to dynamically compute documentation outputs, this could take a while..." )
+      execute_process ( COMMAND ${CMAKE_COMMAND} -E remove_directory ${DOC_DIR}
+	COMMAND ${CMAKE_COMMAND} -E make_directory ${DOC_DIR}
+	COMMAND "${FORD}" --debug -q ${MACRO_FLAG} -d "${PROJ_DIR}" -o "${DOC_DIR}" -p "${PAGE_DIR}" "${FORD_PROJECT_FILE}" OUTPUT_QUIET )
+    else ()
+      message ( STATUS "Re-using cached FORD outputs, rather than regenerating them" )
+    endif()
+
+    # Compile a list of FORD output files
+    file ( GLOB_RECURSE FORD_OUTPUTS
+      "${DOC_DIR}/*.*" )
+    file ( GLOB_RECURSE FORD_CLEAN_OUTPUTS
+      "${DOC_DIR}/*.*" )
+
+    # Cache FORD outputs
+    if ( (DEFINED FORD_OUTPUTS) AND ( NOT ( "${FORD_OUTPUTS}" STREQUAL "" ) ) )
+      message ( STATUS "Caching FORD outputs" )
+      set ( FORD_OUTPUTS_CACHED "${FORD_OUTPUTS}"
+	CACHE STRING "variable containing FORD outputs to prevent rebuilding FORD docs" FORCE )
+    endif ()
+    message ( STATUS "Done dynamically computing FORD outputs." )
+
+    foreach ( DOC_SRC_FILE ${PROJECT_SOURCE_DIR}/ford.md ${FHASH_SOURCES} )
+      list ( APPEND FORD_DEPENDS "${DOC_SRC_FILE}" )
+    endforeach ()
+
+    # Re-build FORD output if needed
+    add_custom_command ( OUTPUT ${FORD_OUTPUTS_CACHED}
+      COMMAND "${FORD}" --debug ${MACRO_FLAG} -d "${PROJ_DIR}" -o "${DOC_DIR}" "${FORD_PROJECT_FILE}"
+      MAIN_DEPENDENCY "${FORD_PROJECT_FILE}"
+      DEPENDS ${FORD_DEPENDS}
+      COMMENT "Building HTML documentation for ${PROJECT_NAME} using FORD" )
+
+    add_custom_target ( documentation ALL
+      DEPENDS ${FORD_OUTPUTS_CACHED} )
+
+    # Install documentation
+    set ( INSTALL_API_DOCUMENTATION TRUE
+      CACHE BOOL "Install FORD generated documentation?" )
+    if ( INSTALL_API_DOCUMENTATION )
+      install ( DIRECTORY "${DOC_ROOT}/" DESTINATION share/doc )
+    else ()
+
+      # FORD Not found
+      message ( WARNING
+	"FORD not found. Please set the CMake cache variable FORD to point to the installed FORD executable, and reconfigure or disable building the documentation. FORD can be installed from PYPI with `sudo pip install FORD` or from <https://github.com/cmacmackin/ford> If you do not wish to install FORD and build the JSON-Fortran documentation, then please set the CMake cache variable SKIP_DOC_GEN to TRUE." )
+
+    endif ()
+  endif ()
+
+endif()
+
+enable_testing()
+add_subdirectory(test)

thirdparty/fhash/Config.cmake.in

@@ -0,0 +1,9 @@
+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/fhashTargets.cmake")
+
+include(CMakeFindDependencyMacro)
+
+check_required_components(fhash)
+
+set(fhash_DOCDIR @CMAKE_INSTALL_PREFIX@/share/doc/fhash)

thirdparty/fhash/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Laurence Kedward
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

thirdparty/fhash/README.md

@@ -0,0 +1,52 @@
+# fhash
+__[fpm](https://github.com/fortran-lang/fpm) package implementing a hash table with support for generic keys and values.__
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![fpm test](https://github.com/LKedward/fhash/workflows/fpm%20test/badge.svg?branch=master&event=push)](https://github.com/LKedward/fhash/actions)
+[![ford docs](https://img.shields.io/badge/FORD%20API%20Docs-Deployed-green)](https://lkedward.github.io/fhash/)
+
+
+
+## fpm usage
+
+To use *fhash* within your *fpm* project, add the following to your package manifest file (`fpm.toml`):
+
+```toml
+[dependencies]
+fhash = { git = "https://github.com/LKedward/fhash.git" }
+```
+
+
+## Simple example: scalar intrinsics
+
+The package provides a `fhash_tbl_t` type with `set` and `get` methods for storing and retrieving key-value pairs.
+The `fhash_key` interface (aliased to `key` below) is used to define a valid key from different inputs.
+
+```fortran
+program fhash_demo1
+  use fhash, only: fhash_tbl_t, key=>fhash_key
+  implicit none
+  type(fhash_tbl_t) :: tbl
+  integer :: val
+  
+  call tbl%set(key('my_key_1'), value=10)
+  call tbl%set(key('my_key_2'), value=1.0)
+  call tbl%set(key(123456), value='a string value')
+  call tbl%set(key([1,2,3,4,5]), value=.false.)
+  
+  call tbl%get(key('my_key_1'),val)
+  
+end program fhash_demo1
+```
+
+See the [Quickstart Guide](https://lkedward.github.io/fhash/page/index.html) for an explanation of this example and the API methods used.
+
+
+## Advanced usage
+
+- [More table methods](https://lkedward.github.io/fhash/page/1-methods-demo/index.html)
+- [Storing custom derived types as values](https://lkedward.github.io/fhash/page/2-derived-type-demo/index.html)
+- [Using custom derived types as keys](https://lkedward.github.io/fhash/page/3-custom-key-demo/index.html)
+
+
+See <https://lkedward.github.io/fhash/> for the full API documentation.

thirdparty/fhash/app/0-simple-demo/main.f90

@@ -0,0 +1,31 @@
+!> Example program demonstrating basic set/get usage
+!>  for different key/value types
+program fhash_demo
+  use fhash, only: fhash_tbl_t, key=>fhash_key
+  implicit none
+
+  type(fhash_tbl_t) :: tbl
+  integer :: i
+  real :: r
+  character(:), allocatable :: char
+  logical :: bool
+
+  print *, '# fhash demo program: simple-demo'
+
+  call tbl%set(key('my_key_1'), value=10)
+  call tbl%set(key('my_key_2'), value=1.0)
+  call tbl%set(key(123456), value='a string value')
+  call tbl%set(key([1,2,3,4,5]), value=.false.)
+
+  call tbl%get(key('my_key_1'),i)
+  call tbl%get(key('my_key_2'),r)
+  call tbl%get(key(123456),char)
+  call tbl%get(key([1,2,3,4,5]),bool)
+
+  print *, 'Key = "my_key_1"     Value = ',i
+  print *, 'Key = "my_key_2"     Value = ',r
+  print *, 'Key = 123456         Value = "',char,'"'
+  print *, 'Key = [1,2,3,4,5]    Value = ', bool
+  print *
+
+end program fhash_demo