upgrade mir-algorithm version (#400)

.gitignore

@@ -52,3 +52,4 @@ examples/lda_hoffman_sparse
 benchmarks/ndslice/binarization
 benchmarks/ndslice/convolution
 benchmarks/ndslice/euclidean_distance
+mir-test-unittest.exe

circle.yml

@@ -17,16 +17,11 @@ dependencies:
     - ldmd2 --version
     - curl -fsSL --retry 3 http://code.dlang.org/files/dub-${DUB}-linux-x86_64.tar.gz | tar -C ~/ldc2-$LDC-linux-x86_64/bin -zxf -
     - dub --version
-    # - wget -q -O dscanner "http://releases.dlang.io/dscanner/0.3.0-git/dscanner"
-    # - chmod +x dscanner
-    # - wget "https://raw.githubusercontent.com/dlang/dmd/master/src/checkwhitespace.d"
 test:
   override:
-    # - dscanResult=$(./dscanner --config .dscanner.ini --styleCheck source 2> /dev/null ) ; if [ -z "${dscanResult}" ] ; then echo "No warnings found" ; else echo $dscanResult && $(exit 1); fi
-    - grep -nE "(for|foreach|foreach_reverse|if|while)\(" $(find source -name '*.d'); test $? -eq 1
-    # - ldmd2 -O -release -run ./checkwhitespace.d $(find source -name '*.d')
     - dub test --compiler=ldmd2
     - dub test --compiler=ldmd2 --build=unittest-release
+    - git clone https://github.com/libmir/mir-core
     - git clone https://github.com/libmir/mir-random
     - git clone https://github.com/libmir/mir-algorithm
     - make -f doc/Makefile html

doc/Makefile

@@ -16,7 +16,8 @@ DOC_SOURCE_DIR=doc
 GENERATED=.generated
 MIR_DIR=source
 RANDOM_DIR=mir-random/source
-ALOGORITHM_DIR=mir-algorithm/source
+ALGORITHM_DIR=mir-algorithm/source
+CORE_DIR=mir-core/source
 DLANGORG_DIR=$(DOC_SOURCE_DIR)/dlang.org
 ARTWORK_DIR=$(DOC_SOURCE_DIR)/artwork
 
@@ -83,7 +84,7 @@ ADDSOURCE=$(if $(subst index.d,,$1),$(MIR_DIR)/$1,$1)
 # ../web/phobos/std_conv.html : std/conv.d $(STDDOC) ; ...
 $(foreach p,$(SRC_DOCUMENTABLES),$(eval \
 $(DOC_OUTPUT_DIR)/$(call D2HTML,$p) : $(call ADDSOURCE,$p) $(STDDOC) ;\
-  $(DDOC) $(STDDOC) -I$(MIR_DIR) -I$(RANDOM_DIR) -I$(ALOGORITHM_DIR) -Df$$@ $$<))
+  $(DDOC) $(STDDOC) -I$(MIR_DIR) -I$(RANDOM_DIR) -I$(CORE_DIR) -I$(ALGORITHM_DIR) -Df$$@ $$<))
 
 ###########################################################
 # Setup all other resources needed by dlang.org

dub.json

@@ -13,23 +13,22 @@
     "configurations": [
         {
             "name": "source",
-            "targetType": "sourceLibrary",
+            "targetType": "sourceLibrary"
         },
         {
             "name": "static",
-            "targetType": "staticLibrary",
+            "targetType": "staticLibrary"
         },
         {
             "name": "dynamic",
-            "targetType": "dynamicLibrary",
+            "targetType": "dynamicLibrary"
         },
         {
             "name": "unittest",
-            "versions": ["to_be_filled"],
+            "versions": ["to_be_filled"]
         }
     ],
     "dependencies": {
-        "mir-random": ">=1.0.0 <2.0.0",
-        "mir-algorithm": ">=2.0.1 <2.5.0"
+        "mir-random": "~>2.0.0"
     }
 }

examples/means_of_columns.d

@@ -29,8 +29,8 @@
 */
 
 import std.datetime.stopwatch;
-import std.conv : to;
 import std.stdio;
+import mir.conv : to;
 import mir.ndslice;
 
 enum testCount = 10_000;
@@ -41,7 +41,6 @@ void main() {
     sl = iota!int(100, 1000).slice;
     auto r = benchmark!({
     	means = sl
-        .universal
         .transposed
         .pack!1
         .map!(col => reduce!"a + b"(0L, col) / double(col.length))

source/mir/model/lda/hoffman.d

@@ -135,14 +135,15 @@ struct LdaHoffman(F)
 
     Params:
         n = mini-batch, a collection of compressed documents.
-        maxIterations = maximal number of iterations for single document in a batch for E-step.
+        maxIterations = maximal number of iterations for s    This implementation is optimized for sparse documents,
+ingle document in a batch for E-step.
     +/
-    size_t putBatch(SliceKind kind, C, I, J)(Slice!(FieldIterator!(CompressedField!(C, I, J)), 1, kind) n, size_t maxIterations)
+    size_t putBatch(SliceKind kind, C, I, J)(Slice!(ChopIterator!(J*, Series!(I*, C*)), 1, kind) n, size_t maxIterations)
     {
         return putBatchImpl(n.recompress!F, maxIterations);
     }
 
-    private size_t putBatchImpl(CompressedTensor!(F, 2) n, size_t maxIterations)
+    private size_t putBatchImpl(Slice!(ChopIterator!(size_t*, Series!(uint*, F*))) n, size_t maxIterations)
     {
         import std.math: isFinite;
         import mir.sparse.blas.dot;
@@ -191,7 +192,7 @@ struct LdaHoffman(F)
                 }
                 if (c < maxIterations && sum > eps * K)
                 {
-                    nd.values[] = nsave[d].values;
+                    nd.value[] = nsave[d].value;
                     continue;
                 }
                 import core.atomic;
@@ -212,16 +213,13 @@ struct LdaHoffman(F)
         return ret;
     }
 
-    private auto saveN(CompressedTensor!(F, 2) n)
+    private auto saveN(Slice!(ChopIterator!(size_t*, Series!(uint*, F*))) n)
     {
-        import mir.ndslice.topology: universal;
-        return
-            CompressedField!(F)(
-                n.iterator._field.compressedLength,
-                n.iterator._field.values.dup,
-                n.iterator._field.indexes,
-                n.iterator._field.pointers)
-            .slicedField(n.length).universal;
+        import mir.series: series;
+        import mir.ndslice.topology: chopped, universal;
+        return n.iterator._sliceable.index
+            .series(n.iterator._sliceable.value.dup)
+            .chopped(n.iterator._iterator.sliced(n.length + 1));
     }
 
     private static void unparameterize(Vector param, Vector posterior)

source/mir/sparse/blas/axpy.d

@@ -8,6 +8,7 @@ module mir.sparse.blas.axpy;
 import std.traits;
 import mir.ndslice.slice;
 import mir.sparse;
+import mir.series;
 
 /++
 Constant times a vector plus a vector.
@@ -21,47 +22,46 @@ Returns:
 +/
 void axpy(
     CR,
-    V1 : CompressedArray!(T1, I1),
-    T1, I1, V2)
+    V1 : Series!(I1, T1),
+    I1, T1, V2)
 (in CR alpha, V1 x, V2 y)
     if (isDynamicArray!V2 || isSlice!V2)
 in
 {
-    if (x.indexes.length)
-        assert(x.indexes[$-1] < y.length);
+    if (x.index.length)
+        assert(x.index[$-1] < y.length);
 }
 body
 {
     import mir.internal.utility;
 
-    foreach (size_t i; 0 .. x.indexes.length)
+    foreach (size_t i; 0 .. x.index.length)
     {
-        auto j = x.indexes[i];
-        y[j] = alpha * x.values[i] + y[j];
+        auto j = x.index[i];
+        y[j] = alpha * x.value[i] + y[j];
     }
 }
 
 ///
 unittest
 {
-    auto x = CompressedArray!(double, uint)([1.0, 3, 4, 9, 13], [0, 3, 5, 9, 10]);
+    auto x = series([0, 3, 5, 9, 10], [1.0, 3, 4, 9, 13]);
     auto y = [0.0, 1.0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12];
     axpy(2.0, x, y);
     assert(y == [2.0, 1.0, 2, 9, 4, 13, 6, 7, 8, 27, 36, 11, 12]);
 }
 
 unittest
 {
-    auto x = CompressedArray!(double, uint)([1.0, 3, 4, 9, 13], [0, 3, 5, 9, 10]);
+    auto x = series([0, 3, 5, 9, 10], [1.0, 3, 4, 9, 13]);
     auto y = [0.0, 1.0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12];
     axpy(2.0, x, y.sliced);
     assert(y == [2.0, 1.0, 2, 9, 4, 13, 6, 7, 8, 27, 36, 11, 12]);
 }
 
 unittest
 {
-    import std.typecons: No;
-    auto x = CompressedArray!(double, uint)([1.0, 3, 4, 9, 13], [0, 3, 5, 9, 10]);
+    auto x = series([0, 3, 5, 9, 10], [1.0, 3, 4, 9, 13]);
     auto y = [0.0, 1.0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12];
     axpy(2.0, x, y.slicedField);
     assert(y == [2.0, 1.0, 2, 9, 4, 13, 6, 7, 8, 27, 36, 11, 12]);

source/mir/sparse/blas/dot.d

@@ -8,6 +8,7 @@ module mir.sparse.blas.dot;
 import std.traits;
 import mir.ndslice.slice;
 import mir.sparse;
+import mir.series;
 
 /++
 Dot product of two vectors
@@ -19,8 +20,8 @@ Returns:
     scalar `xᵀ × y`
 +/
 Unqual!(CommonType!(T1, T2)) dot(
-    V1 : CompressedArray!(T1, I1),
-    V2 : CompressedArray!(T2, I2),
+    V1 : Series!(I1*, T1*),
+    V2 : Series!(I2*, T2*),
     T1, T2, I1, I2)
 (V1 x, V2 y)
 {
@@ -30,8 +31,8 @@ Unqual!(CommonType!(T1, T2)) dot(
 /// ditto
 D dot(
     D,
-    V1 : CompressedArray!(T1, I1),
-    V2 : CompressedArray!(T2, I2),
+    V1 : Series!(I1*, T1*),
+    V2 : Series!(I2*, T2*),
     T1, T2, I1, I2)
 (V1 x, V2 y)
 {
@@ -42,40 +43,38 @@ D dot(
     Unqual!I1 ai0 = void;
     Unqual!I2 bi0 = void;
 
-    if (x.indexes.length && y.indexes.length) for (;;)
+    if (x.length && y.length) for (;;)
     {
-        bi0 = y.indexes[0];
-        if (x.indexes[0] < bi0)
+        bi0 = y.index[0];
+        if (x.index[0] < bi0)
         {
             do
             {
-                x.values = x.values[1 .. $];
-                x.indexes = x.indexes[1 .. $];
-                if (x.indexes.length == 0)
+                x.popFront;
+                if (x.length == 0)
                 {
                     break;
                 }
             }
-            while (x.indexes[0] < bi0);
+            while (x.index[0] < bi0);
             done = 2;
         }
         if (--done == 0)
         {
             goto L;
         }
-        ai0 = x.indexes[0];
-        if (y.indexes[0] < ai0)
+        ai0 = x.index[0];
+        if (y.index[0] < ai0)
         {
             do
             {
-                y.values = y.values[1 .. $];
-                y.indexes = y.indexes[1 .. $];
-                if (y.indexes.length == 0)
+                y.popFront;
+                if (y.length == 0)
                 {
                     break;
                 }
             }
-            while (y.indexes[0] < ai0);
+            while (y.index[0] < ai0);
             done = 2;
         }
         if (--done == 0)
@@ -84,19 +83,17 @@ D dot(
         }
         continue;
         L:
-        s = x.values[0] * y.values[0] + s;
-        x.indexes = x.indexes[1 .. $];
-        if (x.indexes.length == 0)
+        s = x.value[0] * y.value[0] + s;
+        x.popFront;
+        if (x.length == 0)
         {
             break;
         }
-        y.indexes = y.indexes[1 .. $];
-        if (y.indexes.length == 0)
+        y.popFront;
+        if (y.length == 0)
         {
             break;
         }
-        x.values = x.values[1 .. $];
-        y.values = y.values[1 .. $];
     }
 
     return s;
@@ -105,8 +102,8 @@ D dot(
 ///
 unittest
 {
-    auto x = CompressedArray!(int, uint)([1, 3, 4, 9, 10], [0, 3, 5, 9, 100]);
-    auto y = CompressedArray!(int, uint)([1, 10, 100, 1000], [1, 3, 4, 9]);
+    auto x = series([0u, 3, 5, 9, 100], [1, 3, 4, 9, 10]);
+    auto y = series([1u, 3, 4, 9], [1, 10, 100, 1000]);
     // x = [1, 0, 0,  3, 0, 4, 0, 0, 0, 9, ... ,10]
     // y = [0, 1, 0, 10, 0, 0, 0, 0, 0, 1000]
     assert(dot(x, y) == 9030);
@@ -122,7 +119,7 @@ Returns:
     scalar `x × y`
 +/
 Unqual!(CommonType!(T1, ForeachType!V2)) dot(
-    V1 : CompressedArray!(T1, I1),
+    V1 : Series!(I1*, T1*),
     T1, I1, V2)
 (V1 x, V2 y)
     if (isDynamicArray!V2 || isSlice!V2)
@@ -133,14 +130,14 @@ Unqual!(CommonType!(T1, ForeachType!V2)) dot(
 ///ditto
 D dot(
     D,
-    V1 : CompressedArray!(T1, I1),
+    V1 : Series!(I1*, T1*),
     T1, I1, V2)
 (V1 x, V2 y)
     if (isDynamicArray!V2 || isSlice!V2)
 in
 {
-    if (x.indexes.length)
-        assert(x.indexes[$-1] < y.length);
+    if (x.length)
+        assert(x.index[$-1] < y.length);
 }
 body
 {
@@ -151,9 +148,9 @@ body
 
     alias F = Unqual!(CommonType!(T1, T2));
     F s = 0;
-    foreach (size_t i; 0 .. x.indexes.length)
+    foreach (size_t i; 0 .. x.index.length)
     {
-        s = y[x.indexes[i]] * x.values[i] + s;
+        s = y[x.index[i]] * x.value[i] + s;
     }
 
     return s;
@@ -163,7 +160,7 @@ body
 unittest
 {
     import std.typecons: No;
-    auto x = CompressedArray!(double, uint)([1.0, 3, 4, 9, 13], [0, 3, 5, 9, 10]);
+    auto x = [0u, 3, 5, 9, 10].series([1.0, 3, 4, 9, 13]);
     auto y = [0.0, 1.0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12];
     // x: [1, 0, 0, 3, 0, 4, 0, 0, 0, 9, 13,  0,  0,  0]
     // y: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]