Update to recent R package Matrix.

doc/conf.py

@@ -22,7 +22,7 @@
 author = '---'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.0'
+release = '0.0.3'
 
 
 # -- General configuration ---------------------------------------------------

rpy2_Matrix/Matrix.py

@@ -16,7 +16,7 @@
     warnings.simplefilter("ignore")
     Matrix_pack = importr('Matrix', on_conflict="warn")
 
-TARGET_VERSION = '1.4-'
+TARGET_VERSION = '1.6-'
 
 if not Matrix_pack.__version__.startswith(TARGET_VERSION):
     warnings.warn(
@@ -50,20 +50,13 @@ def _setExtractDelegators(self):
     self.rx2 = vectors.DoubleExtractDelegator(self)
 
 
-class mMatrix(metaclass=rpy2.robjects.methods.RS4Auto_Type):
-    """Mapping for the RS4 class Matrix::mMatrix."""
-    __rname__ = 'mMatrix'
-    __rpackagename__ = 'Matrix'
-
-
 class replValueSp(metaclass=rpy2.robjects.methods.RS4Auto_Type):
     """Mapping for the RS4 class Matrix::replValueSp."""
     __rname__ = 'replValueSp'
     __rpackagename__ = 'Matrix'
 
 
-class Matrix(mMatrix, replValueSp):
-    """Mapping for the RS4 class Matrix::Matrix."""
+class Matrix(replValueSp):
     __rname__ = 'Matrix'
     __rpackagename__ = 'Matrix'
 
@@ -159,7 +152,7 @@ def new(i=vectors.MissingArg, j=vectors.MissingArg,
         unclassed_obj = Matrix_pack.sparseMatrix(
             i=i, j=j, p=p, x=x, dims=dims, dimnames=dimnames,
             symmetric=symmetric, triangular=triangular, index1=index1,
-            giveCsparse=giveCsparse, check=check, use_last_ij=use_last_ij)
+            repr=repr, check=check, use_last_ij=use_last_ij)
         wrapcls = _classmap.get(unclassed_obj.rclass[0])
         if wrapcls is None:
             # TODO: issue a warning if no class map ?
@@ -216,24 +209,46 @@ class CsparseMatrix(sparseMatrix):
     __rname__ = 'CsparseMatrix'
 
 
+class ddenseMatrix(dMatrix, denseMatrix):
+    __rname__ = 'ddenseMatrix'
+
+
+class unpackedMatrix(denseMatrix):
+    __rname__ = 'denseMatrix'
+
+
+class dgeMatrix(unpackedMatrix, ddenseMatrix, generalMatrix):
+    __rname__ = 'dgeMatrix'
+
+
 class dsparseMatrix(dMatrix, sparseMatrix):
     """Mapping for the RS4 class Matrix::dsparseMatrix."""
     __rname__ = 'dsparseMatrix'
 
 
+class dsyMatrix(symmetricMatrix, ddenseMatrix):
+    __rname__ = 'dsyMatrix'
+
+
+class dpoMatrix(dsyMatrix):
+    __rname__ = 'dpoMatrix'
+
+
+class corMatrix(dpoMatrix):
+    __rname__ = 'corMatrix'
+
+
 class dgCMatrix(dsparseMatrix, generalMatrix,
                 RS4Vector):
     """Mapping for the RS4 class Matrix::dcgMatrix."""
     __rname__ = 'dgCMatrix'
 
 
-class dCsparseMatrix(sparseMatrix):
-    """Mapping for the RS4 class Matrix::dCsparseMatrix."""
-    __rname__ = 'dCsparseMatrix'
-
+class CsparseMatrix(sparseMatrix):
+    __rname__ = 'CsparseMatrix'
 
+
 class dsCMatrix(CsparseMatrix, dsparseMatrix, symmetricMatrix,
-                dCsparseMatrix,
                 RS4Vector):
     """Mapping for the RS4 class Matrix::dsCMatrix."""
     __rname__ = 'dsCMatrix'
@@ -280,6 +295,10 @@ class dgTMatrix(TsparseMatrix, dsparseMatrix, generalMatrix,
     'lgCMatrix': lgCMatrix,
     'ngCMatrix': ngCMatrix,
     'dgTMatrix': dgTMatrix,
+    'dgTMatrix': dgTMatrix,
+    'dsyMatrix': dsyMatrix,
+    'dpoMatrix': dpoMatrix,
+    'corMatrix': corMatrix,
 }
 
 nameclassmap = (rpy2.robjects

rpy2_Matrix/__init__.py

@@ -1 +1 @@
-__version__ = '0.0.2'
+__version__ = '0.0.3'

rpy2_Matrix/test_Matrix.py

@@ -8,18 +8,26 @@
 
 @pytest.mark.parametrize(
     'args,expected_cls',
+<<<<<<< Updated upstream
     [((0, 2, 3), Matrix.generalMatrix),
      ((0, 2, 2), Matrix.ddiMatrix),
      ((IntVector([0, 1, 2, 3]), 2, 2), Matrix.dgeMatrix)]
+=======
+    [(((0, ), 2, 3), Matrix.generalMatrix),
+     (((0, 1, 1, 0), 2, 2), Matrix.symmetricMatrix)]
+>>>>>>> Stashed changes
 )
 def test_Matrix(args, expected_cls):
-    m = Matrix.Matrix.new(*args)
+    final_args = (robjects.baseenv['c'](*(args[0])),
+                  args[1], args[2])
+    m = Matrix.Matrix.new(*final_args)
     assert isinstance(m, expected_cls)
 
 
 @pytest.mark.parametrize(
     'args,kwargs,expected_cls',
     [((IntVector([1, 3, 4]), IntVector([2, 3, 5])),
+<<<<<<< Updated upstream
       {'x': IntVector([3, 9, 21])},
       Matrix.dgCMatrix),
      ((IntVector([1, 2, 3]), IntVector([2, 3, 4])),
@@ -29,6 +37,13 @@ def test_Matrix(args, expected_cls):
        IntVector([7, 6, 5, 4, 3, 2])),
       {},
       Matrix.ngCMatrix)]
+=======
+      {'x': IntVector([3, 9, 21]), 'repr': 'C'},
+      Matrix.sparseMatrix),
+     ((IntVector([1, 3, 4]), IntVector([2, 3, 5])),
+      {'x': IntVector([3, 9, 21]), 'repr': 'T'},
+      Matrix.sparseMatrix)]
+>>>>>>> Stashed changes
 )
 def test_sparseMatrix(args, kwargs, expected_cls):
     m = Matrix.sparseMatrix.new(*args, **kwargs)