Squashed 'src/SPERR/' changes from d766b3b97..16fa20741

16fa20741 minor changes, preparing for v0.8.2 release (#244)
e9c9e1743 Revert "provide a no output file warning message"
32ac9b4a2 Revert "bump version to 0.8.2"
f3e7ac0fd bump version to 0.8.2
b25ef3ba1 provide a no output file warning message
bd7c72653 remove the NewlySig enum item, and also provide the C++ standard to use as a CMake option
76cf82608 simplify a bit
b0495d143 Update README.md (#241)
aee3236fa minor
015e791e2 minor
c12f5e038 remove clang-tidy badge
724dee7d6 clang-format-14
3d54dc5e2 clang-format
1cc239569 clang-tidy
791d5565b add tail ellison code to code_S() (#240)
ef135ee9d minor
59aa63c3d update CLI11 version
fe9df24e0 Use __cplusplus version check, and minor improve on the bitmask. (#239)
ddb02cdee clang-format
14075a017 minor
47519acb2 remove an unused include
5c3b3cfb6 use countr_zero (#238)
fe698e1ea minor
414efdf41 link Fortran wrapper
f6ddfa742 Division (#236)
d87bdd051 add CMAKE_INSTALL_PREFIX in README
f05b93c87 finish improved has_true() function (#235)
9695e7a0c Revert "use a width parameter in Bitmask"
09db8b5df Revert "change function names"
04a3eb1ce change function names
524761981 use a width parameter in Bitmask
d53dfb077 minor
4ba73ac24 add exhaustive Bitmask::has_true() test
0d659895a add Bitmask::has_true() function
07ee5c7c9 Minor work on README (#232)
f7f2031f9 add examples in PDF format (#231)
08bc43f2a misc (#230)
c1a5e155d bump cli11 version

git-subtree-dir: src/SPERR
git-subtree-split: 16fa20741e5f5ad19127470c93d61d28cc980fae

.github/workflows/clang-format.yml

@@ -22,9 +22,9 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Run clang-format style check for C/C++ programs.
-      uses: jidicula/clang-format-action@v4.8.0
+      uses: jidicula/clang-format-action@v4.13.0
       with:
-        clang-format-version: '13'
+        clang-format-version: '18'
         check-path: ${{ matrix.path['check'] }}
         exclude-regex: ${{ matrix.path['exclude'] }}
         fallback-style: 'Chromium' # optional

.github/workflows/clang-tidy.yml → .github/workflows/clang-tidy.yml.bkp

@@ -22,4 +22,4 @@ jobs:
         builddir: 'build'
         excludedirs: ''
         extensions: 'c,h,C,H,cpp,hpp,cc,hh,c++,h++,cxx,hxx'
-        cmakeoptions: '-DBUILD_CLI_UTILITIES=OFF -DBUILD_UNIT_TESTS=OFF -DUSE_ZSTD=OFF'
+        cmakeoptions: '-DBUILD_CLI_UTILITIES=OFF -DBUILD_UNIT_TESTS=OFF'

CMakeLists.txt

@@ -2,14 +2,13 @@
 
 cmake_minimum_required(VERSION 3.14)
 
-project(SPERR VERSION 0.8.1 LANGUAGES CXX DESCRIPTION "Lossy Scientific Compression with SPERR")
+project(SPERR VERSION 0.8.2 LANGUAGES CXX DESCRIPTION "Lossy Scientific Compression with SPERR")
+
+if(NOT CMAKE_CXX_STANDARD)
+    set(CMAKE_CXX_STANDARD "20" CACHE STRING "Choose the C++ Standard to use." FORCE)
+    set_property(CACHE CMAKE_CXX_STANDARD PROPERTY STRINGS "20" "17")
+endif()
 
-#
-# specify the C++ standard
-# CMake will try to add a -std=c++20 flag if the compiler supports, but if it doesn't,
-# CMake will `decay` to a previous supported flag, e.g. -std=c++11.
-#
-set(CMAKE_CXX_STANDARD 20)
 if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build." FORCE)
     set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "RelWithDebInfo")
@@ -32,7 +31,7 @@ endif()
 option( BUILD_SHARED_LIBS "Build shared SPERR library" ON )
 option( BUILD_UNIT_TESTS "Build unit tests using GoogleTest" ON )
 option( BUILD_CLI_UTILITIES "Build a set of command line utilities" ON )
-option( USE_OMP "Use OpenMP parallelization on 3D volumes" ON )
+option( USE_OMP "Use OpenMP parallelization on 3D volumes" OFF )
 option( SPERR_PREFER_RPATH "Set RPATH; this can fight with package managers so turn off when building for them" ON )
 mark_as_advanced(FORCE SPERR_PREFER_RPATH)
 
@@ -109,8 +108,7 @@ if( BUILD_CLI_UTILITIES )
   set( CLI11_SINGLE_FILE OFF CACHE INTERNAL "Don't use single file CLI11")
   FetchContent_Declare( cli11
     GIT_REPOSITORY https://github.com/CLIUtils/CLI11
-    GIT_TAG        291c58789c031208f08f4f261a858b5b7083e8e2 # v2.3.2
-    PATCH_COMMAND patch -N CMakeLists.txt < ${CMAKE_SOURCE_DIR}/cli11.patch || true
+    GIT_TAG        6c7b07a878ad834957b98d0f9ce1dbe0cb204fc9 # v2.4.2
   )
   FetchContent_MakeAvailable(cli11)
 

README.md

@@ -1,9 +1,6 @@
 [![clang-format](https://github.com/NCAR/SPERR/actions/workflows/clang-format.yml/badge.svg)](https://github.com/NCAR/SPERR/actions/workflows/clang-format.yml)
-[![clang-tidy](https://github.com/NCAR/SPERR/actions/workflows/clang-tidy.yml/badge.svg)](https://github.com/NCAR/SPERR/actions/workflows/clang-tidy.yml)
 [![unit-test](https://github.com/NCAR/SPERR/actions/workflows/unit-test.yml/badge.svg)](https://github.com/NCAR/SPERR/actions/workflows/unit-test.yml)
 [![CodeQL](https://github.com/NCAR/SPERR/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/NCAR/SPERR/actions/workflows/codeql-analysis.yml)
-
-
 [![DOI](https://zenodo.org/badge/225491235.svg)](https://zenodo.org/badge/latestdoi/225491235)
 
 
@@ -20,6 +17,31 @@ This combination gives SPERR flexibility to compress targetting different qualit
 2) peak signal-to-noise ratio (PSNR), and 3) point-wise error (PWE).
 The name of SPERR stands for **SP**eck with **ERR**or bounding.
 
+## Quick Build
+SPERR requires 1) a working C++ compiler and 2) CMake tools to build. On a Unix-like system,
+the build steps are the following:
+
+```bash
+git clone https://github.com/NCAR/SPERR.git     # clone the repo
+mkdir SPERR/build                               # create the build directory
+cd SPERR/build                                  # enter the build directory
+cmake ..                                        # use cmake to configure the project
+cmake -DUSE_OMP=ON ..                           # Optional: enable OpenMP on 3D volumes.
+cmake -DCMAKE_INSTALL_PREFIX=/my/install/dir .. # Optional: specify a directory to install SPERR. The default is /usr/local .
+cmake -DCMAKE_CXX_STANDARD=17 ..                # Optional: use C++17 rather than C++20. The code is slightly faster with C++20.
+make -j 8                                       # build the project
+ctest .                                         # run unit tests, which should have 100% tests passed
+make install                                    # install the library and CLI tools to a specified directory.
+```
+
+## Plugin for HDF5
+SPERR is available as a *dynamically loaded plugin* for HDF5 with a registered ID of `32028`.
+This plugin is available at this [repo](https://github.com/NCAR/H5Z-SPERR).
+
+## Wrapper for Fortran
+A Fortran wrapper for SPERR has also been created by [ofmla](https://github.com/ofmla) 
+at this [repo](https://github.com/ofmla/fortran-sperr).
+
 ## Documentation
 
 SPERR documentation is hosted on Github [Wiki](https://github.com/NCAR/SPERR/wiki) pages. To get started, one might want to
@@ -45,5 +67,6 @@ If SPERR benefits your work, please kindly cite [this publication](https://ieeex
 (Author's copy is available [here](https://vast.ucar.edu/pdfs/SPERR_IPDPS.pdf).)
 
 ## Presentations
+- FZ Workshop Hands-on: Feb 15 2024, Sarasota, FL. ([handout and examples](https://vast.ucar.edu/pdfs/Li_FZ2024.pdf))
 - SC'23 Tutorial on lossy scientific data compression: Nov 13 2023, Denver CO. ([slides](https://vast.ucar.edu/pdfs/Li_SC23_Slides.pdf))
 - IPDPS'23 Lossy Scientific Data Compression With SPERR: May 18 2023, St. Petersburg, FL. ([slides](https://vast.ucar.edu/pdfs/Li_IPDPS23_Slides.pdf))

handout/compile.txt

@@ -0,0 +1 @@
+xelatex -shell-escape main.tex