libpressio version 0.34.0

Major Changes:

+ Added support for PETSC format to generic IO
+ Added support for CSV format to generic IO
+ Added support to clone compressors/io/metrics modules

Bug fixes

+ Various bug fixes to POSIX IO that prevented it from working correctly
  in C++11

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.13 FATAL_ERROR)
-project(libpressio VERSION "0.33.0" LANGUAGES CXX C)
+project(libpressio VERSION "0.34.0" LANGUAGES CXX C)
 
 #correct was to set a default build type
 # https://blog.kitware.com/cmake-and-the-default-build-type/
@@ -87,6 +87,7 @@ add_library(libpressio
   ./src/plugins/metrics/pearsons.cc
   ./src/plugins/io/posix.cc
   ./src/plugins/io/noop.cc
+  ./src/plugins/io/csv.cc
   ./src/plugins/io/io.cc
 
   #public headers
@@ -237,6 +238,16 @@ if(LIBPRESSIO_HAS_FPZIP)
 
 endif()
 
+option(LIBPRESSIO_HAS_PETSC "build the petsc io plugin" OFF)
+if(LIBPRESSIO_HAS_PETSC)
+  pkg_search_module(PETSc IMPORTED_TARGET PETSc)
+  target_sources(libpressio
+    PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/plugins/io/petsc.cc
+    )
+  target_link_libraries(libpressio PRIVATE PkgConfig::PETSc)
+endif()
+
 configure_file(
   ${CMAKE_CURRENT_SOURCE_DIR}/src/pressio_version.h.in
   ${CMAKE_CURRENT_BINARY_DIR}/include/pressio_version.h

include/libpressio_ext/cpp/compressor.h

@@ -117,6 +117,15 @@ class libpressio_compressor_plugin {
    * */
   int check_options(struct pressio_options const&);
 
+  /**
+   * \returns a copy of each a compressor and its configuration.  If the
+   * compressor is not thread-safe and indicates such via its configuration, it
+   * may return a new shared pointer to the same object.  For this reason, this
+   * function may not be const.
+   */
+  virtual std::shared_ptr<libpressio_compressor_plugin> clone()=0;
+
+
   protected:
   /**
    * Should be used by implementing plug-ins to provide error codes

include/libpressio_ext/cpp/io.h

@@ -85,6 +85,12 @@ struct libpressio_io_plugin {
    * \returns an implementation specific integer error code for the last error, 0 is reserved for no error
    */
   int error_code() const;
+
+  /**
+   * clones an io module 
+   * \returns a new reference to an io plugin.
+   */
+  virtual std::shared_ptr<libpressio_io_plugin> clone()=0;
   protected:
   /**
    * Should be used by implementing plug-ins to provide error codes
@@ -134,6 +140,7 @@ struct libpressio_io_plugin {
    */
   virtual struct pressio_options get_options_impl() const=0;
 
+
   private:
   struct {
     int code;

include/libpressio_ext/cpp/metrics.h

@@ -103,6 +103,11 @@ class libpressio_metrics_plugin {
    * \param[in] options a pressio_options structure containing the options for the provided metrics plugin
    */
   virtual int set_metrics_options(struct pressio_options const& options);
+
+  /**
+   * \returns a clone of the metric
+   */
+  virtual std::unique_ptr<libpressio_metrics_plugin> clone()=0;
 };
 
 /**

include/libpressio_ext/io/pressio_io.h

@@ -121,6 +121,14 @@ int pressio_io_minor_version(struct pressio_io const* io);
  */
 int pressio_io_patch_version(struct pressio_io const* io);
 
+/**
+ * Creates a new reference to an io module with the same configuration
+ *
+ * \param[in] io the io module to clone
+ * \returns a new reference to an io module
+ */
+struct presio_io* pressio_io_clone(struct pressio_io* io);
+
 #endif /* end of include guard: PRESSIO_IO_H */
 
 #ifdef __cplusplus

include/pressio_compressor.h

@@ -162,6 +162,18 @@ int pressio_compressor_minor_version(struct pressio_compressor const* compressor
  */
 int pressio_compressor_patch_version(struct pressio_compressor const* compressor);
 
+/**
+ * Clones a compressor and its configuration including metrics information
+ *
+ * \param[in] compressor the compressor to clone. It will not be modified
+ *                       except to modify a reference count as needed.
+ * \returns a pointer to a new compressor plugin reference which is equivalent
+ *          to the compressor cloned.  It the compressor is not thread safe, it may
+ *          return a new reference to the same object.
+ *                
+ */
+struct pressio_compressor* pressio_compressor_clone(struct pressio_compressor* compressor);
+
 /**
  * reports the level of thread safety supported by the compressor.
  *

include/pressio_metrics.h

@@ -43,6 +43,13 @@ struct pressio_options* pressio_metrics_get_options(struct pressio_metrics const
  */
 int pressio_metrics_set_options(struct pressio_metrics const* metrics, struct pressio_options const* options);
 
+/**
+ * Clones a pressio_metrics object and its configuration
+ * \param[in] metrics the metrics object to clone
+ * \returns a new reference to a pressio metrics object
+ */
+struct pressio_metrics* pressio_metrics_clone(struct pressio_metrics* metrics);
+
 
 #endif
 

src/plugins/compressors/blosc_plugin.cc

@@ -120,6 +120,10 @@ class blosc_plugin: public libpressio_compressor_plugin {
       return "blosc";
     }
 
+    std::shared_ptr<libpressio_compressor_plugin> clone() override {
+      return compat::make_unique<blosc_plugin>(*this);
+    }
+
 
   private:
     int internal_error(int rc) { std::stringstream ss; ss << "interal error " << rc; return set_error(1, ss.str()); }

src/plugins/compressors/fpzip_plugin.cc

@@ -129,6 +129,9 @@ class fpzip_plugin: public libpressio_compressor_plugin {
   const char* prefix() const noexcept override {
     return "fpzip";
   }
+  std::shared_ptr<libpressio_compressor_plugin> clone() override {
+    return compat::make_unique<fpzip_plugin>(*this);
+  }
 
   private:
   std::string version_str;

src/plugins/compressors/magick++.cc

@@ -211,6 +211,10 @@ class magick_plugin: public libpressio_compressor_plugin {
     return "magick";
   }
 
+  std::shared_ptr<libpressio_compressor_plugin> clone() override {
+    return compat::make_unique<magick_plugin>(*this);
+  }
+
   private:
 
   int invalid_dimensions(size_t n_dims) {

src/plugins/compressors/mgard_plugin.cc

@@ -156,6 +156,10 @@ class mgard_plugin: public libpressio_compressor_plugin {
     return "mgard";
   }
 
+  std::shared_ptr<libpressio_compressor_plugin> clone() override {
+    return std::make_unique<mgard_plugin>(*this);
+  }
+
 
   private:
 

src/plugins/compressors/noop.cc

@@ -50,6 +50,9 @@ class noop_compressor_plugin: public libpressio_compressor_plugin {
   const char* prefix() const override {
     return "noop";
   }
+  std::shared_ptr<libpressio_compressor_plugin> clone() override{
+    return std::make_unique<noop_compressor_plugin>(*this);
+  }
 };
 
 static pressio_register X(compressor_plugins(), "noop", [](){ return compat::make_unique<noop_compressor_plugin>();});

src/plugins/compressors/sz_plugin.cc

@@ -15,7 +15,7 @@
 #include "pressio_option.h"
 
 
-class sz_plugin: public libpressio_compressor_plugin {
+class sz_plugin: public libpressio_compressor_plugin, std::enable_shared_from_this<sz_plugin> {
   public:
   sz_plugin() {
     std::stringstream ss;
@@ -178,6 +178,10 @@ class sz_plugin: public libpressio_compressor_plugin {
     return "sz";
   }
 
+  std::shared_ptr<libpressio_compressor_plugin> clone() override {
+    return this->shared_from_this();
+  }
+
 
   private:
   static int libpressio_type_to_sz_type(pressio_dtype type) {

src/plugins/compressors/zfp_plugin.cc

@@ -180,6 +180,10 @@ class zfp_plugin: public libpressio_compressor_plugin {
       return "zfp";
     }
 
+    std::shared_ptr<libpressio_compressor_plugin> clone() override{
+      return compat::make_unique<zfp_plugin>(*this);
+    }
+
 
   private:
     int invalid_type() { return set_error(1, "invalid_type");}