libpressio version 0.9.0

Major Features

- New MGARD compressor plugin
- Provided the ability to disable compressor plugins at compile time.
- Breaking Change: the compressor_compress and compressor_decompress and
  implementing functions now accept the input as const instead of
  mutable. This was done to reduce user surprise

Bug Fixes:

- Removed invalid uses of constexpr
- Added Header include guards that were missing
- Corrected naming inconsistency between pressio_data_num_dimensions and
  pressio_data::num_dimensions.  New pressio_data::dimentions function
  returns a copy of the vector of the sizes.

CMakeLists.txt

@@ -1,29 +1,14 @@
 cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
-project(libpressio VERSION "0.8.0" LANGUAGES CXX C)
+project(libpressio VERSION "0.9.0" LANGUAGES CXX C)
 
 enable_testing()
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 option(BUILD_SHARED_LIBS "build libpressio as a shared library" ON)
 
 include(GNUInstallDirs)
-find_package(ZFP REQUIRED)
-find_package(SZ REQUIRED)
-find_package(ZLIB REQUIRED)
-find_package(PkgConfig REQUIRED)
-find_package(Python COMPONENTS Interpreter Development NumPy)
-pkg_search_module(ZSTD IMPORTED_TARGET GLOBAL libzstd)
 
 
-set(LIBPRESSIO_FEATURES "sz zfp")
-configure_file(
-  ${CMAKE_CURRENT_SOURCE_DIR}/include/pressio_version.h.in
-  ${CMAKE_CURRENT_BINARY_DIR}/include/pressio_version.h
-  )
-configure_file(
-  ${CMAKE_CURRENT_SOURCE_DIR}/libpressio.pc.in
-  ${CMAKE_CURRENT_BINARY_DIR}/libpressio.pc
-  @ONLY
-  )
+set(LIBPRESSIO_FEATURES "")
 
 add_library(libpressio
   #core implementation
@@ -38,8 +23,6 @@ add_library(libpressio
 
   #plugins
   ./src/plugins/compressors/compressor_base.cc
-  ./src/plugins/compressors/sz_plugin.cc
-  ./src/plugins/compressors/zfp_plugin.cc
   ./src/plugins/metrics/composite.cc
   ./src/plugins/metrics/metrics_base.cc
   ./src/plugins/metrics/size.cc
@@ -48,8 +31,6 @@ add_library(libpressio
 
   #public headers
   include/libpressio.h
-  include/libpressio_ext/compressors/sz.h
-  include/libpressio_ext/compressors/zfp.h
   include/libpressio_ext/cpp/compressor.h
   include/libpressio_ext/cpp/metrics.h
   include/libpressio_ext/cpp/plugins.h
@@ -74,9 +55,57 @@ target_include_directories(libpressio
   PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/include
   )
 target_compile_options(libpressio PRIVATE $<$<CONFIG:Debug>: -Wall -Werror -Wextra -Wpedantic>)
-target_link_libraries(libpressio PUBLIC zfp::zfp SZ)
 target_compile_features(libpressio PUBLIC cxx_std_17)
 
+option(LIBPRESSIO_HAS_MGARD "build the MGARD plugin" OFF)
+if(LIBPRESSIO_HAS_MGARD)
+  set(LIBPRESSIO_FEATURES "${LIBPRESSIO_FEATURES} mgard")
+  find_package(mgard REQUIRED)
+  target_sources(libpressio
+    PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/plugins/compressors/mgard_plugin.cc
+    ${CMAKE_CURRENT_SOURCE_DIR}/include/libpressio_ext/compressors/mgard.h
+    )
+  target_link_libraries(libpressio PUBLIC mgard::mgard)
+endif()
+
+option(LIBPRESSIO_HAS_ZFP "build the ZFP plugin" ON)
+if(LIBPRESSIO_HAS_ZFP)
+  set(LIBPRESSIO_FEATURES "${LIBPRESSIO_FEATURES} zfp")
+  find_package(ZFP REQUIRED)
+  target_sources(libpressio
+    PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/plugins/compressors/zfp_plugin.cc
+    ${CMAKE_CURRENT_SOURCE_DIR}/include/libpressio_ext/compressors/zfp.h
+    )
+  target_link_libraries(libpressio PUBLIC zfp::zfp)
+endif()
+
+option(LIBPRESSIO_HAS_SZ "build the SZ plugin" ON)
+if(LIBPRESSIO_HAS_SZ)
+  set(LIBPRESSIO_FEATURES "${LIBPRESSIO_FEATURES} sz")
+  find_package(SZ REQUIRED)
+  find_package(ZLIB REQUIRED)
+  find_package(PkgConfig REQUIRED)
+  pkg_search_module(ZSTD IMPORTED_TARGET GLOBAL libzstd)
+  target_sources(libpressio
+    PRIVATE
+      ${CMAKE_CURRENT_SOURCE_DIR}/src/plugins/compressors/sz_plugin.cc
+      ${CMAKE_CURRENT_SOURCE_DIR}/include/libpressio_ext/compressors/sz.h
+    )
+  target_link_libraries(libpressio PUBLIC SZ)
+endif()
+
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/include/pressio_version.h.in
+  ${CMAKE_CURRENT_BINARY_DIR}/include/pressio_version.h
+  )
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/libpressio.pc.in
+  ${CMAKE_CURRENT_BINARY_DIR}/libpressio.pc
+  @ONLY
+  )
+
 export(TARGETS libpressio NAMESPACE LibPressio:: FILE LibPressio.cmake)
 install(TARGETS libpressio EXPORT LibPressioConfig
   ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
@@ -89,7 +118,6 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/pressio_version.h DESTINATION
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpressio.pc DESTINATION ${CMAKE_INSTALL_PREFIX}/share/pkgconfig)
 
 option(BUILD_TESTS "build the test cases and examples" OFF)
-
 if(BUILD_TESTS)
   add_subdirectory(test)
 endif()

COPYRIGHT.txt

@@ -1,6 +1,6 @@
 Copyright © 2019 , UChicago Argonne, LLC
 All Rights Reserved
-[libpressio, Version 0.8.0]
+[libpressio, Version 0.9.0]
 Robert Underwood
 Argonne National Laboratory
 

include/libpressio_ext/compressors/mgard.h

@@ -0,0 +1,5 @@
+/** 
+ * \file
+ * \brief Includes definitions needed to use the MGRAD pressio compressor
+ * */
+#include <mgard_capi.h>

include/libpressio_ext/cpp/compressor.h

@@ -41,11 +41,11 @@ class libpressio_compressor_plugin {
   /** compresses a pressio_data buffer
    * \see pressio_compressor_compress for the semantics this function should obey
    */
-  int compress(struct pressio_data* input, struct pressio_data* output);
+  int compress(const pressio_data *input, struct pressio_data* output);
   /** decompress a pressio_data buffer
    * \see pressio_compressor_decompress for the semantics this function should obey
    */
-  int decompress(struct pressio_data* input, struct pressio_data* output);
+  int decompress(const pressio_data *input, struct pressio_data* output);
   /** get a version string for the compressor
    * \see pressio_compressor_version for the semantics this function should obey
    */
@@ -123,11 +123,11 @@ class libpressio_compressor_plugin {
   /** compresses a pressio_data buffer
    * \see pressio_compressor_compress for the semantics this function should obey
    */
-  virtual int compress_impl(struct pressio_data* input, struct pressio_data* output)=0;
+  virtual int compress_impl(const pressio_data *input, struct pressio_data* output)=0;
   /** decompress a pressio_data buffer
    * \see pressio_compressor_decompress for the semantics this function should obey
    */
-  virtual int decompress_impl(struct pressio_data* input, struct pressio_data* output)=0;
+  virtual int decompress_impl(const pressio_data *input, struct pressio_data* output)=0;
 
   /** checks for extra arguments set for the compressor.
    * Unlike other functions, this option is NOT required

include/libpressio_ext/cpp/data.h

@@ -233,31 +233,38 @@ struct pressio_data {
   /**
    * \returns the number of dimensions
    */
-  size_t dimensions() const {
+  size_t num_dimensions() const {
     return dims.size();
   }
 
+  /**
+   * \returns a copy of the vector of dimensions
+   */
+  std::vector<size_t> dimensions() const {
+    return dims;
+  }
+
   /**
    * \param idx the specific index to query
    * \returns a specific dimension of the buffer of zero if the index exceeds dimensions()
    */
   size_t get_dimension(size_t idx) const {
-    if(idx >= dimensions()) return 0;
+    if(idx >= num_dimensions()) return 0;
     else return dims[idx];
   }
 
   /**
    * \returns the size of the buffer in bytes
    */
   size_t size_in_bytes() const {
-    return data_size_in_bytes(data_dtype, dimensions(), dims.data());
+    return data_size_in_bytes(data_dtype, num_dimensions(), dims.data());
   }
 
   /**
    * \returns the size of the buffer in elements
    */
   size_t num_elements() const {
-    return data_size_in_elements(dimensions(), dims.data());
+    return data_size_in_elements(num_dimensions(), dims.data());
   }
 
   private:

include/libpressio_ext/cpp/options.h

@@ -1,3 +1,6 @@
+#ifndef PRESSIO_OPTIONS_CPP
+#define PRESSIO_OPTIONS_CPP
+
 #include <optional>
 #include <variant>
 #include <string>
@@ -53,11 +56,6 @@ struct pressio_option final {
   template<class T>
   pressio_option(T value): option(std::optional<T>(value)) {}
 
-  /** specialization for option to reset the type to hold no type or value
-   * \param[in] value the monostate singleton
-   * */
-  template<>
-  pressio_option(std::monostate value): option(value) {}
 
   /** returns a pressio option that has the appropriate type if the conversion is allowed for the specified safety
    * \param[in] type the type to convert to
@@ -75,21 +73,21 @@ struct pressio_option final {
    * \returns returns true if the option holds the current type
    */
   template <class T>
-  constexpr bool holds_alternative() const {
+  bool holds_alternative() const {
     return std::holds_alternative<std::optional<T>>(option);
   }
 
   /** Specialization for the std::monostate singleton
    * \returns true if the option has no specified type or value
    */
   template <>
-  constexpr bool holds_alternative<std::monostate>() const;
+  bool holds_alternative<std::monostate>() const;
 
   /** 
    * \returns a std::optional which holds a value if the option has one or an empty optional otherwise
    */
   template <class T>
-  constexpr std::optional<T> const& get() const{
+  std::optional<T> const& get() const{
     return std::get<std::optional<T>>(option);
   }
 
@@ -98,7 +96,7 @@ struct pressio_option final {
    * \returns the value contained by the option
    */
   template <class T>
-  constexpr T const& get_value() const{
+  T const& get_value() const{
     return get<T>().value();
   }
 
@@ -187,14 +185,17 @@ struct pressio_option final {
   option_type option;
 };
 
+/** specialization for option to reset the type to hold no type or value
+ * \param[in] value the monostate singleton
+ * */
+template<>
+pressio_option::pressio_option(std::monostate value);
+
 /** Specialization for the std::monostate singleton
  * \returns true if the option has no specified type or value
  */
 template <>
-constexpr bool pressio_option::holds_alternative<std::monostate>() const {
-  return std::holds_alternative<std::monostate>(option);
-}
-
+bool pressio_option::holds_alternative<std::monostate>() const;
 /**
  * represents a map of dynamically typed objects
  */
@@ -381,3 +382,5 @@ enum pressio_options_key_status pressio_options::get(std::string const& key, con
  */
 template <>
 enum pressio_options_key_status pressio_options::cast(std::string const& key, char** value, enum pressio_conversion_safety safety) const;
+
+#endif

include/libpressio_ext/cpp/plugins.h

@@ -5,12 +5,24 @@
 #define LIBPRESSIO_PLUGINS_PUBLIC
 #include <memory>
 #include <vector>
+#include "pressio_version.h"
 #include "libpressio_ext/cpp/compressor.h"
 #include "libpressio_ext/cpp/metrics.h"
+
+#if LIBPRESSIO_HAS_SZ
 /** construct the sz plugin */
 std::unique_ptr<libpressio_compressor_plugin> make_c_sz();
+#endif
+
+#if LIBPRESSIO_HAS_ZFP
 /** construct the zfp plugin */
 std::unique_ptr<libpressio_compressor_plugin> make_c_zfp();
+#endif
+
+#if LIBPRESSIO_HAS_MGARD
+std::unique_ptr<libpressio_compressor_plugin> make_c_mgard();
+#endif
+
 /** construct the time metrics plugin */
 std::unique_ptr<libpressio_metrics_plugin> make_m_time();
 /** construct the size metrics plugin */

include/libpressio_ext/cpp/printers.h

@@ -1,6 +1,7 @@
 #include <string>
 #include <ostream>
 #include "options.h"
+#include "pressio_dtype.h"
 
 /** \file 
  *  \brief C++ stream compatible IO functions
@@ -82,3 +83,37 @@ operator<<(std::basic_ostream<CharT, Traits>& out, pressio_options const& option
   return out;
 }
 
+/**
+ * human readable debugging IO function for pressio_dtype, the format is unspecified
+ * \param[in] out the stream to write to
+ * \param[in] type the type to print
+ */
+template <class CharT = char, class Traits = std::char_traits<CharT>>
+std::basic_ostream<CharT, Traits>&
+operator<<(std::basic_ostream<CharT, Traits>& out, enum pressio_dtype type)
+{
+  switch (type) {
+    case pressio_double_dtype:
+      return out << "double";
+    case pressio_float_dtype:
+      return out << "float";
+    case pressio_uint8_dtype:
+      return out << "uint8_t";
+    case pressio_uint16_dtype:
+      return out << "uint16_t";
+    case pressio_uint32_dtype:
+      return out << "uint32_t";
+    case pressio_uint64_dtype:
+      return out << "uint64_t";
+    case pressio_int8_dtype:
+      return out << "int8_t";
+    case pressio_int16_dtype:
+      return out << "int16_t";
+    case pressio_int32_dtype:
+      return out << "int32_t";
+    case pressio_int64_dtype:
+      return out << "int64_t";
+    case pressio_byte_dtype:
+      return out << "byte";
+  }
+}

include/pressio_compressor.h

@@ -64,7 +64,7 @@ int pressio_compressor_check_options(struct pressio_compressor* compressor, stru
  *      2. A new owning pressio_data structure with the results of the compression
  * \returns 0 if successful, positive values on errors, negative values on warnings
  */
-int pressio_compressor_compress(struct pressio_compressor* compressor, struct pressio_data * input, struct pressio_data* output);
+int pressio_compressor_compress(struct pressio_compressor* compressor, const struct pressio_data *input, struct pressio_data* output);
 /*!
  * decompresses the compressed data using the specified compressor
  * calling this without calling libpressio_compressor_set_options() has undefined behavior
@@ -80,7 +80,7 @@ int pressio_compressor_compress(struct pressio_compressor* compressor, struct pr
  * \see pressio_data_new_empty often used as the pointer passed into \c output
  * \see pressio_data_new_move often used as the pointer passed out of \c output
  */
-int pressio_compressor_decompress(struct pressio_compressor* compressor, struct pressio_data * input, struct pressio_data* output);
+int pressio_compressor_decompress(struct pressio_compressor* compressor, const struct pressio_data *input, struct pressio_data* output);
 
 /**
  * \param[in] compressor the compressor to get results from

include/pressio_version.h.in

@@ -3,3 +3,5 @@
 #define LIBPRESSIO_MAJOR_VERSION @PROJECT_VERSION_MAJOR@
 #define LIBPRESSIO_MINOR_VERSION @PROJECT_VERSION_MINOR@
 #define LIBPRESSIO_PATCH_VERSION @PROJECT_VERSION_PATCH@
+#cmakedefine01 LIBPRESSIO_HAS_SZ
+#cmakedefine01 LIBPRESSIO_HAS_ZFP

src/plugins/compressors/compressor_base.cc

@@ -87,14 +87,14 @@ int libpressio_compressor_plugin::set_options(struct pressio_options const* opti
   return ret;
 }
 
-int libpressio_compressor_plugin::compress(struct pressio_data* input, struct pressio_data* output) {
+int libpressio_compressor_plugin::compress(const pressio_data *input, struct pressio_data* output) {
   if(metrics_plugin) (*metrics_plugin)->begin_compress(input, output);
   auto ret = compress_impl(input, output);
   if(metrics_plugin) (*metrics_plugin)->end_compress(input, output, ret);
   return ret;
 }
 
-int libpressio_compressor_plugin::decompress(struct pressio_data* input, struct pressio_data* output) {
+int libpressio_compressor_plugin::decompress(const pressio_data *input, struct pressio_data* output) {
   if(metrics_plugin) (*metrics_plugin)->begin_decompress(input, output);
   auto ret = decompress_impl(input, output);
   if(metrics_plugin) (*metrics_plugin)->end_decompress(input, output, ret);