Squashed 'src/H5Z-ZFP/' changes from 5d9a995..cd5422c

cd5422c Compatibility with Visual Studio 2019 (silx-kit#93)
bcff4d2 CMake: (fix) Missing header file. (silx-kit#90)
59b7f38 updating for 1.0.0 (silx-kit#85)
3802c0f Tests: (fix) Makefile - CFLAGS and clean target (silx-kit#84)
111e5a1 Fix Silo doc section and warnings (silx-kit#83)
9dd4546 Use ZFP's version string (silx-kit#80)
557a4f6 Pin zfp version in windows ci (silx-kit#82)
f51ac59 added parameter to fortran const (silx-kit#76)
35a08e0 [github] add windows build config (silx-kit#72)
1844b5b Fixed detection of CFP availability (silx-kit#74)
c8544d3 [windows] enable compilation in windows with ClangCL (silx-kit#71)
7b34cac Update installation.rst (silx-kit#66)
e153bf9 Feature direct write zfp array (silx-kit#43)
20b0f1f Added missing HDF5 include (CMake) (silx-kit#63)
20b893a Test and fix working with HDF5-1.12 (silx-kit#62)
497e942 CMake: (fix) Autotools build HDF5 (silx-kit#59)
8f63f7d Add missing headers for string functions and fix printfs for cd_nelmts (silx-kit#60)
8de12f7 Added generic interface fortran wrappers with tests (silx-kit#58)
983a187 find zfp and hdf5 in lib64 instead of lib (silx-kit#56)
e6c9c14 Fix typos
f7670c4 Fix second typo in h5repack docs (silx-kit#55)
57a849d handle optional/mandatory flag (silx-kit#54)
48126d3 CMake: (feature) Added CMake build configuration (silx-kit#52)
bee7434 fix link to travis badge (silx-kit#51)
00146c1 update to download from github (silx-kit#49)
259feb8 Remove include for HDF5 header file (silx-kit#48)
3d0b176 adding missing call to h5z_zfp_finaliz() (silx-kit#45)
b642fe8 minor fixes to docs and h5repack utility (silx-kit#42)

git-subtree-dir: src/H5Z-ZFP
git-subtree-split: cd5422c146836e17c7a0380bfb05cf52d0c4467c

.github/workflows/main.yml

@@ -0,0 +1,133 @@
+name: h5z-zfp
+
+# Controls when the action will run. 
+#Triggers the workflow on push or pull requests.
+on: 
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+# A workflow run is made up of one or more jobs that
+# can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  linux-build:
+    strategy:
+      matrix:
+        name: ["Ubuntu Latest GCC"]
+        include:
+          - name: "Ubuntu Latest GCC"
+            artifact: "Linux.tar.xz"
+            os: ubuntu-latest
+
+    name: ${{ matrix.name }}
+    # The type of runner that the job will run on.
+    runs-on: ${{ matrix.os }}
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+
+    # Steps represent a sequence of tasks that will be executed 
+    # as part of the job.
+    steps:
+    - name: Install Dependencies (Linux)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get install -qq libhdf5-dev
+        sudo apt-get install -qq hdf5-tools
+        echo  "HDF5_HOME=/usr/include/hdf5/serial,/usr/lib/x86_64-linux-gnu/hdf5/serial,/usr/bin" >> $GITHUB_ENV
+        # Set env vars
+        echo "CC=gcc" >> $GITHUB_ENV
+        echo "FC=gfortran" >> $GITHUB_ENV
+        echo "CXX=g++"  >> $GITHUB_ENV
+        
+ # Checks-out the repository under $GITHUB_WORKSPACE so the job can access it.
+    - name: Get Sources
+      uses: actions/checkout@v2
+
+##################################
+# INSTALL ZFP
+##################################
+
+    - name: install ZFP
+      run: |
+        git clone https://github.com/LLNL/zfp.git
+        export HOME_DIR=$(echo ~)
+        cd zfp
+        git checkout 1.0.0
+        mkdir build;cd build
+        cmake -D ZFP_BIT_STREAM_WORD_SIZE=8 -D BUILD_CFP=ON -D CMAKE_INSTALL_PREFIX=$PWD/zfp -D BUILD_TESTING=OFF -D BUILD_UTILITIES=OFF ..
+        make install
+        echo "ZFP_HOME=$PWD/zfp" >> $GITHUB_ENV
+        echo "ZFP_DIR=$PWD/zfp" >> $GITHUB_ENV
+      shell: bash
+
+##################################
+# BUILD AND TEST H5Z-ZFP
+##################################
+
+    - name: build (autotools) and check
+      run: |
+        make all
+        make check
+      shell: bash
+
+    - name: build (cmake)
+      run: |
+        mkdir build; cd build
+        cmake -D FORTRAN_INTERFACE=ON -D CMAKE_BUILD_TYPE=Release ..
+        make
+      shell: bash
+
+
+  windows-build:
+    name: 'Windows MSVC/Clang'
+    defaults:
+      run:
+        shell: bash
+    runs-on: windows-2019
+    steps:
+      - name: checkout repository
+        uses: actions/checkout@v2
+      - name: install prerequisites
+        run: |
+          choco install \
+            unzip \
+            wget
+      - name: setup MSVC Tools
+        uses: ilammy/msvc-dev-cmd@v1
+      - name: download HDF5 for Windows
+        run: |
+          wget --quiet \
+            https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/windows/hdf5-1.12.1-Std-win10_64-vs16.zip
+          unzip hdf5-1.12.1-Std-win10_64-vs16.zip
+      - name: Install HDF5 for Windows
+        run: msiexec /i "hdf\HDF5-1.12.1-win64.msi" /qn
+        shell: cmd
+      - name: Download and install ZFP
+        run: |
+          git clone https://github.com/LLNL/zfp.git
+          cd zfp
+          git checkout 1.0.0
+          mkdir -p build
+          cd build
+          cmake .. \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DBUILD_UTILITIES=OFF \
+            -DBUILD_TESTING=OFF \
+            -DBUILD_CFP=ON \
+            -DZFP_BIT_STREAM_WORD_SIZE=8
+          cmake --build . -j 3
+          cmake --build . --target install
+      - name: update PATH
+        run: |
+          echo "C:/Program Files/HDF_Group/HDF5/1.12.1/bin" >> $GITHUB_PATH
+      - name: configure cmake
+        run: |
+          mkdir build
+          cd build
+          cmake .. \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DFORTRAN_INTERFACE=OFF \
+            -TClangCL
+          cmake --build . -j 3
+          cmake --build . --target install

.travis.yml

@@ -7,7 +7,7 @@ before_install:
   - pwd
   - ls
   - pushd /tmp
-  - wget http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.5.tar.gz
+  - wget https://github.com/LLNL/zfp/releases/download/0.5.5/zfp-0.5.5.tar.gz
   - tar -xzf zfp-0.5.5.tar.gz
   - pushd zfp-0.5.5
   - make DEFS=-DBIT_STREAM_WORD_TYPE=uint8

CMakeLists.txt

@@ -0,0 +1,68 @@
+cmake_minimum_required(VERSION 3.9)
+
+# Fail immediately if not using an out-of-source build
+if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
+  message(FATAL_ERROR
+    "In-source builds are not supported.  Please create a build directory "
+    "separate from the source directory")
+endif ()
+
+#------------------------------------------------------------------------------#
+# Parse version number from H5Zzfp_version.h
+#------------------------------------------------------------------------------#
+file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/src/H5Zzfp_version.h" H5Z_ZFP_H REGEX "^\#define H5Z_FILTER_ZFP_VERSION_MAJOR")
+string(REGEX REPLACE "^.*MAJOR " "" H5Z_ZFP_VERSION_MAJOR "${H5Z_ZFP_H}")
+file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/src/H5Zzfp_version.h" H5Z_ZFP_H REGEX "^\#define H5Z_FILTER_ZFP_VERSION_MINOR")
+string(REGEX REPLACE "^.*MINOR " "" H5Z_ZFP_VERSION_MINOR "${H5Z_ZFP_H}")
+file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/src/H5Zzfp_version.h" H5Z_ZFP_H REGEX "^\#define H5Z_FILTER_ZFP_VERSION_PATCH")
+string(REGEX REPLACE "^.*PATCH " "" H5Z_ZFP_VERSION_PATCH "${H5Z_ZFP_H}")
+set(H5Z_ZFP_VERSION "${H5Z_ZFP_VERSION_MAJOR}.${H5Z_ZFP_VERSION_MINOR}.${H5Z_ZFP_VERSION_PATCH}")
+
+project(H5Z_ZFP VERSION ${H5Z_ZFP_VERSION} LANGUAGES C)
+
+#------------------------------------------------------------------------------#
+# Compile options.
+#------------------------------------------------------------------------------#
+option(FORTRAN_INTERFACE "Enable the Fortran interface" ON)
+if (FORTRAN_INTERFACE)
+  enable_language(Fortran)
+endif ()
+
+#------------------------------------------------------------------------------#
+# Some boilerplate to setup nice output directories
+#------------------------------------------------------------------------------#
+set(CMAKE_INSTALL_INCLUDEDIR include)
+set(CMAKE_INSTALL_CMAKEDIR lib/cmake/h5z_zfp)
+
+#------------------------------------------------------------------------------#
+# Required packages
+#------------------------------------------------------------------------------#
+# Find HDF5, relies on HDF5_DIR or HDF5_ROOT being set in environment.
+set(COMPONENTS C)
+if (FORTRAN_INTERFACE)
+  list(APPEND COMPONENTS Fortran)
+endif ()
+find_package(HDF5 REQUIRED COMPONENTS ${COMPONENTS})
+
+# Find ZFP, relies on ZFP_DIR or ZFP_ROOT being set in environment.
+find_package(ZFP REQUIRED CONFIG)
+
+#------------------------------------------------------------------------------#
+# Add source
+#------------------------------------------------------------------------------#
+add_subdirectory(${CMAKE_SOURCE_DIR}/src)
+
+#------------------------------------------------------------------------------#
+# Packaging
+#------------------------------------------------------------------------------#
+# Install h5z_zfp-config.cmake and h5z_zfp-config-version.cmake
+set(H5Z_ZFP_CONFIG_IN  ${CMAKE_CURRENT_SOURCE_DIR}/cmake/h5z_zfp-config.cmake.in)
+set(H5Z_ZFP_CONFIG_OUT ${CMAKE_CURRENT_BINARY_DIR}/cmake/h5z_zfp-config.cmake)
+configure_file(${H5Z_ZFP_CONFIG_IN} ${H5Z_ZFP_CONFIG_OUT} @ONLY)
+set(H5Z_ZFP_CONFIG_VERSION_IN  ${CMAKE_CURRENT_SOURCE_DIR}/cmake/h5z_zfp-config-version.cmake.in)
+set(H5Z_ZFP_CONFIG_VERSION_OUT ${CMAKE_CURRENT_BINARY_DIR}/cmake/h5z_zfp-config-version.cmake)
+configure_file(${H5Z_ZFP_CONFIG_VERSION_IN} ${H5Z_ZFP_CONFIG_VERSION_OUT} @ONLY)
+install(FILES ${H5Z_ZFP_CONFIG_OUT}
+        DESTINATION ${CMAKE_INSTALL_CMAKEDIR})
+install(FILES ${H5Z_ZFP_CONFIG_VERSION_OUT}
+        DESTINATION ${CMAKE_INSTALL_CMAKEDIR})

Makefile

@@ -14,6 +14,8 @@ help:
 	@echo "    make CC=<C-compiler> HDF5_HOME=<path> ZFP_HOME=<path> PREFIX=<path> all"
 	@echo ""
 	@echo "where <path> is a dir whose children are include/lib/bin subdirs."
+	@echo "HDF5_HOME can also be specified by the HDF5 include directory,"
+	@echo "library directory and bin directory separated by commas, i.e. HDF5_HOME=INC,LIB,BIN"
 	@echo "Standard make variables (e.g. CFLAGS, LD, etc.) can be set as usual."
 	@echo "Optionally, add FC=<fortran-compiler> to include Fortran support and tests."
 	@echo ""

README.md

@@ -3,7 +3,7 @@
 A highly flexible floating point and integer
 compression plugin for the HDF5 library using ZFP compression.
 
-[![Build Status](https://travis-ci.org/LLNL/H5Z-ZFP.svg?branch=master)](https://travis-ci.org/LLNL/H5Z-ZFP)
+[![Build Status](https://travis-ci.com/LLNL/H5Z-ZFP.svg?branch=master)](https://travis-ci.com/LLNL/H5Z-ZFP)
 [![Documentation Status](https://readthedocs.org/projects/h5z-zfp/badge/?version=latest)](http://h5z-zfp.readthedocs.io)
 [![codecov](https://codecov.io/gh/LLNL/H5Z-ZFP/branch/master/graph/badge.svg)](https://codecov.io/gh/LLNL/H5Z-ZFP)
 
@@ -28,10 +28,11 @@ package  due  to  the  likely  broad  appeal  and  utility  of the ZFP
 compression library.
 
 This plugin supports all modes of the ZFP compression library, *rate*,
-*accuracy*, *precision* and *expert* and *lossless*. It supports 1, 2 and
-3 dimensional datasets of single and double precision integer and floating
-point data. It can be applied to HDF5 datasets of more than 3 dimensions
-(or 4 dimensions for ZFP versions 0.5.5 and newer) as long as no more than 3
-(or 4) dimensions of the HDF5 dataset chunking are of size greater than 1.
+*accuracy*, *precision*, *expert* and *lossless*. It supports 1, 2, 3 and
+4 dimensional datasets (for ZFP version 0.5.5 and newer) of single and double
+precision integer and floating point data. It can be applied to HDF5 datasets
+of more than 3 dimensions (or 4 dimensions for ZFP versions 0.5.5 and newer)
+as long as no more than 3 (or 4) dimensions of the HDF5 dataset *chunking* are
+of size greater than 1.
 
 [**Full documentation**](http://h5z-zfp.readthedocs.io)

cmake/h5z_zfp-config-version.cmake.in

@@ -0,0 +1,15 @@
+set(PACKAGE_VERSION_MAJOR @PROJECT_VERSION_MAJOR@)
+set(PACKAGE_VERSION_MINOR @PROJECT_VERSION_MINOR@)
+set(PACKAGE_VERSION_PATCH @PROJECT_VERSION_PATCH@)
+set(PACKAGE_VERSION @PROJECT_VERSION@)
+
+# Check whether the requested PACKAGE_FIND_VERSION is compatible
+if(PACKAGE_VERSION VERSION_LESS PACKAGE_FIND_VERSION OR
+   PACKAGE_VERSION_MAJOR GREATER PACKAGE_FIND_VERSION_MAJOR)
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+else()
+  set(PACKAGE_VERSION_COMPATIBLE TRUE)
+  if(PACKAGE_VERSION VERSION_EQUAL PACKAGE_FIND_VERSION)
+    set(PACKAGE_VERSION_EXACT TRUE)
+  endif()
+endif()

cmake/h5z_zfp-config.cmake.in

@@ -0,0 +1,59 @@
+# h5z_zfp-config.cmake
+# --------------------
+#
+# Finds the H5Z_ZFP library, specify the starting search path in H5Z_ZFP_ROOT
+#
+# Static vs. shared
+# ----------------- 
+# To make use of the static library instead of the shared one, one needs
+# to set the variable H5Z_ZFP_USE_STATIC_LIBS to ON before calling find_package.
+# Example:
+#   set(H5Z_ZFP_USE_STATIC_LIBS ON)
+#   find_package(H5Z_ZFP REQUIRED CONFIG)
+#
+# This will define the following variables:
+#
+#   H5Z_ZFP_FOUND       - True if the system has the H5Z_ZFP library.
+#   H5Z_ZFP_WITH_OPENMP - True if the zfp library has been built with OpenMP support.
+#
+# and the following imported targets:
+#
+#   h5z_zfp::h5z_zfp - The H5Z_ZFP library.
+
+find_path(H5Z_ZFP_INCLUDE_DIR NAMES H5Zzfp.h DOC "H5Z_ZFP include directory")
+if(H5Z_ZFP_USE_STATIC_LIBS)
+  find_library(H5Z_ZFP_LIBRARY NAMES libh5zzfp.a DOC "H5Z_ZFP library")
+else()
+  find_library(H5Z_ZFP_LIBRARY NAMES libh5zzfp.so HINTS $ENV{H5Z_ZFP_ROOT}/plugin DOC "H5Z_ZFP library")
+endif()
+
+include(FindPackageHandleStandardArgs)
+set(${CMAKE_FIND_PACKAGE_NAME}_CONFIG "${CMAKE_CURRENT_LIST_FILE}")
+find_package_handle_standard_args(H5Z_ZFP
+  FOUND_VAR H5Z_ZFP_FOUND
+  REQUIRED_VARS H5Z_ZFP_LIBRARY H5Z_ZFP_INCLUDE_DIR
+  CONFIG_MODE
+)
+
+if(H5Z_ZFP_FOUND)
+  set(HDF5_USE_STATIC_LIBRARIES ${H5Z_ZFP_USE_STATIC_LIBS})
+  find_package(HDF5 MODULE REQUIRED COMPONENTS C)
+  find_package(ZFP REQUIRED CONFIG)
+  if(H5Z_ZFP_USE_STATIC_LIBS)
+    add_library(h5z_zfp::h5z_zfp STATIC IMPORTED)
+  else()
+    add_library(h5z_zfp::h5z_zfp SHARED IMPORTED)
+  endif()
+  set_target_properties(h5z_zfp::h5z_zfp PROPERTIES
+    IMPORTED_LOCATION "${H5Z_ZFP_LIBRARY}"
+    INTERFACE_INCLUDE_DIRECTORIES "${H5Z_ZFP_INCLUDE_DIR}"
+    INTERFACE_LINK_LIBRARIES "zfp::zfp;${HDF5_LIBRARIES}"
+    LINK_LIBRARIES "zfp::zfp;${HDF5_LIBRARIES}"
+  )
+  set(H5Z_ZFP_WITH_OPENMP ${ZFP_WITH_OPENMP})
+endif()
+
+mark_as_advanced(
+  H5Z_ZFP_INCLUDE_DIR
+  H5Z_ZFP_LIBRARY
+)