carray 1.5.2 → 1.5.7

checksums.yaml

@@ -1,7 +1,7 @@
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data/.yardopts

@@ -0,0 +1,32 @@
+--markup markdown
+--markup-provider redcarpet
+--no-private
+--exclude lib/carray/obsolete.rb
+--exclude lib/carray/autoload.rb
+--exclude 'lib/carray/autoload/'
+--readme README.md
+--files NEWS.md,TODO.md 
+lib/carray.rb 
+ext/ruby_carray.c 
+ext/ca_obj_array.c 
+ext/ca_obj_bitarray.c 
+ext/ca_obj_bitfield.c 
+ext/ca_obj_block.c 
+ext/carray_attribute.c 
+ext/carray_call_cfunc.c 
+ext/carray_cast.c 
+ext/carray_class.c 
+ext/carray_conversion.c 
+ext/carray_copy.c 
+ext/carray_core.c 
+ext/carray_data_type.c 
+ext/carray_element.c 
+ext/carray_generate.c 
+ext/carray_loop.c
+ext/carray_mask.c 
+ext/carray_operator.c 
+ext/carray_order.c 
+ext/carray_sort_addr.c 
+ext/carray_test.c 
+ext/carray_utils.c 
+

data/NEWS.md

@@ -1,6 +1,59 @@
 ChangeLog of Ruby/CArray
 ========================
 
+1.5.6 -> 1.5.7
+
+* [Mod] Modify the methods 'CArray#first' and 'CArray#last' to return nil when the number of elements is zero
+* [Fix] Added check of having ArithmeticSeuqence in ruby_carray.c
+
+1.5.5 -> 1.5.6
+
+* [Mod] Modify CArray access methods to accept Enumerator::ArithmeticSequence for index, address
+* [Mod] Remove some gem autoloading (io_csv, io_sqlite3, rmagick, cairo, opencv, ffi)
+* [Mod] Modify 'CArray#valid_index?' and 'CArray#valid_addr?' to accept negative integers
+* [Mod] Modify the methods 'CArray#double' etc not to raise error for invalid string in conversion into float
+
+1.5.4 -> 1.5.5
+
+* [Fix] Fix recognition of "atan2", ... in "math.h"
+* [Fix] Fix serialize.rb of keyword parameters for Ruby2.7
+
+1.5.3 -> 1.5.4
+--------------
+
+* [New] Import method 'CArray#section' from gem 'carray-calculus'
+* [New] Add new method 'CArray#pull', 'CArray#pulled'
+* [New] Add new option 'expand_scalar' to 'CArray.broadcast'
+* [Mod] Modify the method 'CArray.broadcast' to accept block.
+* [Mod] Modify the method 'CArray.meshgrid' to accept block.
+* [Mod] Modify 'CScalar#broadcast_to' to return CArray
+* [Mod] Modify 'CScalar#is_masked' and 'CScalar#is_masked' to return CScalar
+* [Fix] Fix order of repetitive dimensions in 'CArray#meshgrid'
+* [Fix] Fix errors in installing on MinGW+msys2
+
+1.5.2 -> 1.5.3
+--------------
+
+* [New] Add new method 'CArray#exp2'
+* [New] Add new method 'CArray#log2'
+* [New] Add new method 'CArray#logb'
+* [New] Add new method 'CArray#remainder'
+* [New] Add new method 'CArray.guard_undef'
+* [New] Add new method 'CArray#data_class='
+* [New] Add new method 'CArray.data_class?'
+* [Mod] Modify 'CArray#pmax' to use 'fmax' for float type
+* [Mod] Modify 'CArray#pmin' to use 'fmin' for float type
+* [Mod] Remove method 'Object#undef?'
+* [Mod] Remove method '::nan', '::inf'
+* [Mod] Remove method 'TrueClass#*', 'FalseClass#*' (unknown origin)
+* [Fix] Fix invalid access for CAUnboundRepeat using index
+* [Fix] Fix treatment of extra :* in operation between CAUnboundRepeat objects
+* [Fix] Fix to accept Symbol for the name of data_class member
+* [Fix] Fix 'CArray#uniq' to accept the array with the dimension more than 2.
+* [Fix] Fix for CArray serialization to include data_class
+* [Fix] Fix data_class inheritance in some methods in which new CArray is created.
+* [Fix] Fix 'CArray#broadcast_to' to accept the case of dimension extension.
+
 1.5.1 -> 1.5.2
 --------------
 
@@ -13,8 +66,8 @@ ChangeLog of Ruby/CArray
 * [New] Add new API function `rb_ca_wrap_new`
 * [Mod] Modify 'CArray#linspace' to return float64 array for integer arguments
 * [Mod] Modify CAUnboundRepeat to have `ndim` same as the bounded array (before `ndim` same as parent array)
-* [Mod] Depret the obsolete mothod 'CArray#dump'.
-* [Mod] Depret the obsolete mothod 'CArray#load'.
+* [Mod] Remove the obsolete mothod 'CArray#dump'.
+* [Mod] Remove the obsolete mothod 'CArray#load'.
 * [Mod] Modify CArray.wrap_readonly to wrap string as array.
 * [Fix] Add support for Integer (same as for Fixnum, Bignum)
 
@@ -23,12 +76,12 @@ ChangeLog of Ruby/CArray
 
 * [New] Add data type classes like 'Float64' ... to provide the methods like 'CArray::Float64.linspace'
 * [Mod] Modify 'CArray.float64' ... without aruguments to return the corresponding data type class 
+* [Mod] Set obsolete flag to 'CAIterator#sort_with'
 * [Fix] Move C extension files into 'ext/'
 * [Fix] Rename member 'rank' to 'ndim' in struct CArray in C extension
 * [Fix] Remove 'CArray#shuffle' (gone to 'carray-random' gem)
 * [Fix] Remove dependencies on 'rb_secure()' and 'rb_safe_level()'
 * [Fix] Modify 'CArray#span' to handle fractional step for integer array
-* [Obsolete] Set obsolete flag to 'CAIterator#sort_with'
 
 1.4.0 -> 1.5.0
 --------------

data/README.md

@@ -6,16 +6,16 @@ Ruby/CArray is an extension library for the multi-dimensional array class.
 Features
 --------
 
-* Multidimensional array for storing uniform data
-* Various ways to access data elements
-* Masks for each element to handle missing values
-* Element-wise operations and mathematical functions
-* Statistical functions for the elements
-* Indirect data manipulation for original array by virtual array 
+* Collection class for multidimensional array storing the value with uniform data type
+* Element-wise mathematical operations and functions
+* Statistical operation for the elements
+* Various methods for referencing data elements
+* Internally included element-wise mask to handle missing values
+* Indirect data manipulation to referent by virtual array 
 * Special iterators (dimension, block, window, categorical)
-* User-defined array
-* Storing fixed length data with data_class
-* Memory sharing with other objects (Experimental)
+* User-defined array class with same multi-dimensional interfaces as CArray
+* Accessing the partial data in fixed length data via data_class interface
+* Wrapping the memory block owned by the other object (such as NArray).
 
 Requirements
 ------------
@@ -25,16 +25,32 @@ Requirements
   + IEEE754 floating point number
   + C99 complex number
 
-Directories
------------
+What is Ruby/CArray 
+------------------
 
-    lib       - Ruby sorce codes
-    ext       - C extension source codes
-    utils     - support tools for development
-    spec      - rspec files
-    misc      - misc files
+Ruby/CArray is an extension library for the multi-dimensional numerical array class. The name "CArray" comes from a wrapper's meaning to a numerical array handled by the C language. CArray stores integers or floating-point numbers in memory block and treats them collectively to ensure efficient performance. Therefore, Ruby/CArray is suitable for numerical computation and data analysis. 
 
-Licenses
---------
+#### Multi-dimensional uniform array ####
+
+CArray is a collection class that can store the array of values with a uniform data type of one of fixed-width integer (8,16,32,64bits), floating-point number (32,64bits), complex number (64,128bits), fixed-length string, ruby object. These values are stored in memory block as binary data. CArray has multi-dimensional interfaces for the array to access their values. The multi-dimensional array has the attributes of the dimension size (1,2,3,...) and the shape of dimension ([dim0], [dim0,dim1], [dim0,dim1,dim2],...) which define the size of array. 
+
+#### Collective mathematical operations ####
+
+CArray supports the collective calculation for the element-wise arithmetic operations and elementary mathematical functions. Additionally, some basic statistical summarization along specific dimensions are also provided.
+
+#### Referencing data and virtual arrays ####
+
+CArray provides various methods for referencing data, such as addressing, slicing, selection by condition, address mapping, grid reference, transposing, shifting, rolling, data type conversion, reshaping, and so on. These data referencing are realized by the creation of virtual arrays, so-called 'view'. The virtual array doesn't have its data and retrieves the data from the referent only on-demand, including dereferencing, copying, or calculation. Since virtual array classes are sub-class of CArray, it has the same interfaces to access data as CArray. The changes in a virtual array by storing data are also reflected in the referent (if not a read_only array). Multiple heterogeneous chains of reference are also allowed, although the trade-offs with performance must be carefully considered.
+
+#### Built-in element-wise mask handling ####
+
+CArray possesses masked states about each element (so-called "element-wise mask"). By referring the element-wise mask, CArray can perform mathematical and statistical calculations on the data with missing values by appropriate handling of masked elements. , which include the propagation of mask state to result in element-wise arithmetics and ignoring the masked elements in a statistical calculation, and so on.
+
+#### User-defined array ####
+
+Users can define a new virtual array class in Ruby level or C-extension level with TemplateMethod pattern. They are defined as a subclass of CAObject in Ruby level and as a subclass of CAVirtual in C-extension level. In particular, at the Ruby level, you can easily define a CArray-like class by implementing just a few template methods.
+
+License
+-------
 
 MIT (after version 1.5.0)

data/Rakefile

@@ -15,7 +15,7 @@ task :install do
     exit(1)
   end
   system %{
-    gem build #{GEMSPEC}; gem install #{spec.full_name}.gem
+    gem build #{GEMSPEC}; gem install #{spec.full_name}.gem --no-document
   }
 end
 

data/TODO.md

@@ -3,13 +3,14 @@ ToDo List
 
 ToDo
 -------
-
+ * Implement CArray.broadcast in C
+ * Implement Integer#{|,&,^,<<,>>} with Refinement (remove monkey patch)
+ * Remove RSTRUCT hack in carray_access.c for handling of Range object.
+ * Solve abs probrems
  * Create spec
    - str_format (cyclic format)
    - CA_SIZE
- * Remove RSTRUCT hack in carray_access.c for handling of Range object.
- * Implement CArray.broadcast in C
- * Solve abs probrems
+   - serialization of carray which has data_class
 
 Done
 -------

data/carray.gemspec

@@ -1,32 +1,31 @@
 Gem::Specification::new do |s|
 
-  version = "1.5.2"
+  version = "1.5.7"
 
-  files = Dir.glob("**/*") - [ 
+  files = Dir.glob("**/*") + [".yardopts"] -
+                             [ 
                                Dir.glob("carray-*.gem"), 
                                Dir.glob("ext/**/{Makefile,mkmf.log}"),
                                Dir.glob("**/*.{o,so,bundle}"),
                                Dir.glob("**/*~"),
                                Dir.glob("doc/**/*"),
+                               Dir.glob("test/**/*"),
                              ].flatten
 
   s.platform    = Gem::Platform::RUBY
   s.name        = "carray"
   s.summary     = "Multi-dimesional array class for Ruby"
   s.description = <<-HERE
-    Ruby/CArray is an extension library for the multi-dimensional array class.
-    CArray can store integers and floating point numbers to perform calculations
-    efficiently. Therefore, Ruby/CArray is suitable for numerical computation and data
-    analysis. Ruby/CArray has different features from other multidimensional array
-    libraries (narray, numo-narray, nmatrix), such as element-specific masks, 
-    creation of reference arrays that can reflect changes to the referent, 
-    the ability to access memory pointers of other objects, user-defined arrays,
-    and so on.
+    Ruby/CArray is an extension library for the multi-dimensional numerical array
+    class. The name "CArray" comes from the meaning of a wrapper to a numerical array
+    handled by the C language. CArray stores integers or floating-point numbers in
+    memory block and treats them collectively to ensure efficient performance.
+    Therefore, Ruby/CArray is suitable for numerical computation and data analysis.
   HERE
   s.version     = version
   s.author      = "Hiroki Motoyoshi"
   s.email       = ""
-  s.licenses    = ['MIT']
+  s.license     = 'MIT'
   s.homepage    = 'https://github.com/himotoyoshi/carray'
   s.files       = files
   s.extensions  = [ "ext/extconf.rb" ] 

data/ext/ca_obj_bitarray.c

@@ -462,12 +462,9 @@ rb_ca_bitarray_new (VALUE cary)
   return obj;
 }
 
-/* yard:
-  class CArray
-    def bits
-    end
-    alias bitarray bits
-  end
+/* @overload bitarray
+
+[TBD]
 */
 
 VALUE
@@ -511,8 +508,8 @@ Init_ca_obj_bitarray ()
   CA_OBJ_BITARRAY = ca_install_obj_type(rb_cCABitarray, ca_bitarray_func);
   rb_define_const(rb_cObject, "CA_OBJ_BITARRAY", INT2NUM(CA_OBJ_BITARRAY));
 
-  rb_define_method(rb_cCArray, "bits", rb_ca_bitarray, 0);
   rb_define_method(rb_cCArray, "bitarray", rb_ca_bitarray, 0);
+  rb_define_alias(rb_cCArray, "bits", "bitarray");
 
   rb_define_alloc_func(rb_cCABitarray, rb_ca_bitarray_s_allocate);
   rb_define_method(rb_cCABitarray, "initialize_copy",

data/ext/ca_obj_bitfield.c

@@ -557,11 +557,9 @@ rb_ca_bitfield_new (VALUE cary, ca_size_t offset, ca_size_t bitlen)
   return obj;
 }
 
-/* yard:
-  class CArray
-    def bitfield (range, type)
-    end
-  end
+/* @overload bitfield (range, type)
+
+[TBD]
 */
 
 VALUE

data/ext/ca_obj_block.c

@@ -12,11 +12,6 @@
 
 VALUE rb_cCABlock;
 
-/* yard:
-  class CABlock < CAVirtual # :nodoc:
-  end
-*/
-
 static int
 ca_block_setup (CABlock *ca, CArray *parent, int8_t ndim, ca_size_t *dim,
                ca_size_t *start, ca_size_t *step, ca_size_t *count, ca_size_t offset)
@@ -733,7 +728,7 @@ rb_cb_initialize_copy (VALUE self, VALUE other)
     return ary;                                     \
 }
 
-/* yard:
+/* @overload size0:
   class CABlock
     def size0
     end

data/ext/ca_obj_refer.c

@@ -32,11 +32,11 @@ ca_refer_setup (CARefer *ca, CArray *parent,
   CA_CHECK_BYTES(data_type, bytes);
 
   if ( ca_is_object_type(parent) && data_type != CA_OBJECT ) {
-    rb_raise(rb_eRuntimeError, "object carray can't be referred by other type");
+    rb_raise(rb_eRuntimeError, "object array can't be referred by other data type");
   }
 
   if ( parent->elements && bytes > parent->bytes * parent->elements ) {
-    rb_raise(rb_eRuntimeError, "byte size mismatch");
+    rb_raise(rb_eRuntimeError, "bytes exceeds the data size of referent");
   }
 
   /* calc datanum and check deformation */
@@ -51,27 +51,25 @@ ca_refer_setup (CARefer *ca, CArray *parent,
   }
   if ( bytes < parent->bytes ) {
     if ( parent->bytes % bytes != 0 ) {
-      rb_raise(rb_eArgError, "invalid bytes");
+      rb_raise(rb_eRuntimeError, "bytes of reference array must be a multiple of that of referent");
     }
     is_deformed = -2;
     ratio = parent->bytes / bytes;
   }
   else if ( bytes > parent->bytes ) {
     if ( bytes % parent->bytes != 0 ) {
-      rb_raise(rb_eArgError, "invalid bytes");
+      rb_raise(rb_eRuntimeError, "bytes of reference array must be a multiple of that of referent");
     }
     is_deformed = 2;
     ratio = bytes / parent->bytes;
   }
-
   if ( offset < 0 ) {
-    rb_raise(rb_eRuntimeError, 
-             "negative offset for CARefer");
+    rb_raise(rb_eRuntimeError, "negative offset is not permitted for CARefer");
   }
 
   if ( ( bytes * elements + parent->bytes * offset ) >
                                      ( parent->bytes * parent->elements ) ) {
-    rb_raise(rb_eRuntimeError, "data size too large for CARefer");
+    rb_raise(rb_eRuntimeError, "data size of reference array must not exceed that of referent");
   }
 
   ca->obj_type  = CA_OBJ_REFER;

data/ext/ca_obj_unbound_repeat.c

@@ -50,15 +50,9 @@ ca_ubrep_setup (CAUnboundRepeat *ca, CArray *parent,
   ca->rep_ndim  = rep_ndim;
   ca->rep_dim   = ALLOC_N(ca_size_t, rep_ndim);
 
-  memcpy(ca->rep_dim, rep_dim, rep_ndim * sizeof(ca_size_t));
-
-  for (i=0; i<ca->ndim; i++) {
-    if ( ca->rep_dim[i] ) {
-      ca->dim[i] = ca->rep_dim[i];      
-    }
-    else {
-      ca->dim[i] = 1;
-    }
+  for (i=0; i<rep_ndim; i++) {
+    ca->rep_dim[i] = rep_dim[i];
+    ca->dim[i] = ( rep_dim[i] ) ? rep_dim[i] : 1;      
   }
 
   if ( ca_has_mask(parent) ) {
@@ -104,13 +98,6 @@ ca_ubrep_func_ptr_at_addr (void *ap, ca_size_t addr)
   return ca_ptr_at_addr(ca->parent, addr);
 }
 
-static char *
-ca_ubrep_func_ptr_at_index (void *ap, ca_size_t *idx)
-{
-  CAUnboundRepeat *ca = (CAUnboundRepeat *) ap;
-  return ca_ptr_at_index(ca->parent, idx);
-}
-
 static void
 ca_ubrep_func_fetch_addr (void *ap, ca_size_t addr, void *ptr)
 {
@@ -118,13 +105,6 @@ ca_ubrep_func_fetch_addr (void *ap, ca_size_t addr, void *ptr)
   ca_fetch_addr(ca->parent, addr, ptr);
 }
 
-static void
-ca_ubrep_func_fetch_index (void *ap, ca_size_t *idx, void *ptr)
-{
-  CAUnboundRepeat *ca = (CAUnboundRepeat *) ap;
-  ca_fetch_index(ca->parent, idx, ptr);
-}
-
 static void
 ca_ubrep_func_store_addr (void *ap, ca_size_t addr, void *ptr)
 {
@@ -132,13 +112,6 @@ ca_ubrep_func_store_addr (void *ap, ca_size_t addr, void *ptr)
   ca_store_addr(ca->parent, addr, ptr);
 }
 
-static void
-ca_ubrep_func_store_index (void *ap, ca_size_t *idx, void *ptr)
-{
-  CAUnboundRepeat *ca = (CAUnboundRepeat *) ap;
-  ca_store_index(ca->parent, idx, ptr);
-}
-
 static void
 ca_ubrep_func_allocate (void *ap)
 {
@@ -227,11 +200,11 @@ ca_operation_function_t ca_ubrep_func = {
   free_ca_ubrep,
   ca_ubrep_func_clone,
   ca_ubrep_func_ptr_at_addr,
-  ca_ubrep_func_ptr_at_index,
+  NULL, 
   ca_ubrep_func_fetch_addr,
-  ca_ubrep_func_fetch_index,
+  NULL, 
   ca_ubrep_func_store_addr,
-  ca_ubrep_func_store_index,
+  NULL, 
   ca_ubrep_func_allocate,
   ca_ubrep_func_attach,
   ca_ubrep_func_sync,
@@ -304,11 +277,10 @@ rb_ca_unbound_repeat (int argc, VALUE *argv, VALUE self)
   rep_ndim = argc;
 
   count = 0;
-  ndim = 0;
-
+  ndim  = 0;
   elements = 1;
   for (i=0; i<rep_ndim; i++) {
-    if ( rb_obj_is_kind_of(argv[i], rb_cSymbol) ) {
+    if ( TYPE(argv[i]) == T_SYMBOL ) {
       if ( argv[i] == ID2SYM(rb_intern("*")) ) {
         rep_dim[i] = 0;
       }
@@ -321,8 +293,8 @@ rb_ca_unbound_repeat (int argc, VALUE *argv, VALUE self)
         rb_raise(rb_eArgError, "invalid argument");
       }
       rep_dim[i] = ca->dim[count];
-      dim[ndim] = ca->dim[count];
-      elements *= ca->dim[count];
+      dim[ndim]  = ca->dim[count];
+      elements  *= ca->dim[count];
       count++; ndim++;
     }
   }
@@ -334,9 +306,8 @@ rb_ca_unbound_repeat (int argc, VALUE *argv, VALUE self)
   if ( ndim != ca->ndim ) {
     rb_raise(rb_eArgError, "invalid number of nil's (%i for %i)", ndim, ca->ndim);
   }
-  else {
-    return rb_ca_ubrep_new(self, rep_ndim, rep_dim);
-  }
+
+  return rb_ca_ubrep_new(self, rep_ndim, rep_dim);
 }
 
 static VALUE
@@ -388,6 +359,7 @@ ca_ubrep_bind2 (VALUE self, int32_t new_ndim, ca_size_t *new_dim)
   ca_size_t upr_spec[CA_RANK_MAX];
   ca_size_t srp_spec[CA_RANK_MAX];
   int uprep = 0, srp_ndim;
+  int ndim_real;
   int i;
 
   Data_Get_Struct(self, CAUnboundRepeat, ca);
@@ -398,6 +370,7 @@ ca_ubrep_bind2 (VALUE self, int32_t new_ndim, ca_size_t *new_dim)
   }
 
   srp_ndim = 0;
+  ndim_real = 0;
   for (i=0; i<new_ndim; i++) {
     if ( ca->rep_dim[i] == 0 ) {
       if ( new_dim[i] == 0 ) {
@@ -410,14 +383,16 @@ ca_ubrep_bind2 (VALUE self, int32_t new_ndim, ca_size_t *new_dim)
       upr_spec[i] = new_dim[i];
     }
     else {
+      ndim_real++;
       rep_spec[i] = 0;
       srp_spec[srp_ndim++] = 0;
       upr_spec[i] = ca->rep_dim[i];
     }
   }
+  
   if ( uprep ) {
     volatile VALUE rep;
-    if ( srp_ndim >= ca->ndim ) {
+    if ( srp_ndim >= ndim_real ) {
       rep = rb_ca_repeat_new(rb_ca_parent(self), srp_ndim, srp_spec);
     }
     else {
@@ -430,11 +405,8 @@ ca_ubrep_bind2 (VALUE self, int32_t new_ndim, ca_size_t *new_dim)
   }
 }
 
-/* yard:
-  class CAUnboundRepeat
-    def bind_with(other)
-    end
-  end
+/* @overload bind_with (other)
+
 */
 
 VALUE
@@ -460,11 +432,8 @@ ca_ubrep_bind_with (VALUE self, VALUE other)
   }
 }
 
-/* yard:
-  class CAUnboundRepeat
-    def bind(*index)
-    end
-  end
+/* @overload bind (*index)
+
 */
 
 static VALUE