sagemathgh-40435: Add faster implementations of matrix_from_* constructors to GF(2) and  GF(2^e)
    
Dense matrices over GF(2) and GF(2^e) currently have slow performance
for the following methods:
- matrix_from_rows()
- matrix_from_columns()
- matrix_from_rows_and_columns()

They are using the default implementation in matrix1.pyx which involves
conversion of each element every time it is read or written. This PR
puts direct naive implementations for these methods into both classes.

### 📝 Checklist

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- [X] The title is concise and informative.
- [X] The description explains in detail what this PR is about.
- [ ] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [X] I have updated the documentation and checked the documentation
preview.
    
URL: sagemath#40435
Reported by: Biffo89
Reviewer(s): Xavier Caruso

Author: Release Manager

src/sage/matrix/matrix0.pxd

@@ -48,6 +48,7 @@ cdef class Matrix(sage.structure.element.Matrix):
     # Unsafe entry access
     cdef set_unsafe(self, Py_ssize_t i, Py_ssize_t j, object x)
     cdef get_unsafe(self, Py_ssize_t i, Py_ssize_t j)
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc)
     cdef _coerce_element(self, x)
     cdef bint get_is_zero_unsafe(self, Py_ssize_t i, Py_ssize_t j) except -1
 

src/sage/matrix/matrix0.pyx

@@ -556,6 +556,28 @@ cdef class Matrix(sage.structure.element.Matrix):
         """
         raise NotImplementedError("this must be defined in the derived type.")
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        """
+        Copy element (iSrc, jSrc) from ``src`` to position (iDst, jDst) in
+        ``self``. It is assumed ``src`` is the same type of matrix as``self``,
+        with the same base ring.
+
+        This should generally be reimplemented in subclasses to avoid the type
+        conversion that often is necessary in ``get_unsafe`` and
+        ``set_unsafe``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be the same type as
+                    ``self`` with the same base ring.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+        """
+        cdef Matrix _src = <Matrix>src
+        self.set_unsafe(iDst, jDst, _src.get_unsafe(iSrc, jSrc))
+
     cdef bint get_is_zero_unsafe(self, Py_ssize_t i, Py_ssize_t j) except -1:
         """
         Return 1 if the entry ``(i, j)`` is zero, otherwise 0.

src/sage/matrix/matrix1.pyx

@@ -2043,7 +2043,7 @@ cdef class Matrix(Matrix0):
             if col < 0 or col >= self._ncols:
                 raise IndexError("column index out of range")
             for i in range(self._nrows):
-                A.set_unsafe(i, j, self.get_unsafe(i, col))
+                A.copy_from_unsafe(i, j, self, i, col)
         return A
 
     def delete_columns(self, dcols, check=True):
@@ -2141,7 +2141,7 @@ cdef class Matrix(Matrix0):
             if row < 0 or row >= self._nrows:
                 raise IndexError("row index out of range")
             for j in range(self._ncols):
-                A.set_unsafe(i, j, self.get_unsafe(row, j))
+                A.copy_from_unsafe(i, j, self, row, j)
         return A
 
     def delete_rows(self, drows, check=True):
@@ -2268,7 +2268,7 @@ cdef class Matrix(Matrix0):
             if row < 0 or row >= self._nrows:
                 raise IndexError("row index out of range")
             for j, col in enumerate(columns):
-                A.set_unsafe(i, j, self.get_unsafe(row, col))
+                A.copy_from_unsafe(i, j, self, row, col)
         return A
 
     def submatrix(self, Py_ssize_t row=0, Py_ssize_t col=0,

src/sage/matrix/matrix_complex_ball_dense.pyx

@@ -307,6 +307,53 @@ cdef class Matrix_complex_ball_dense(Matrix_dense):
         acb_set(z.value, acb_mat_entry(self.value, i, j))
         return z
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        """
+        Copy the ``(iSrc, jSrc)`` entry of ``src`` into the ``(iDst, jDst)``
+        entry of ``self``.
+
+        .. warning::
+
+           This is very unsafe; it assumes ``iSrc``, ``jSrc``, ``iDst`` and
+           ``jDst`` are in the right range, and that ``src`` is a
+           Matrix_complex_ball_dense with the same base ring as ``self``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be a
+                    Matrix_complex_ball_dense with the same base ring as
+                    ``self``.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+
+        TESTS::
+
+            sage: m = MatrixSpace(CBF,3,4)(range(12))
+            sage: m
+            [                0 1.000000000000000 2.000000000000000 3.000000000000000]
+            [4.000000000000000 5.000000000000000 6.000000000000000 7.000000000000000]
+            [8.000000000000000 9.000000000000000 10.00000000000000 11.00000000000000]
+            sage: m.transpose()
+            [                0 4.000000000000000 8.000000000000000]
+            [1.000000000000000 5.000000000000000 9.000000000000000]
+            [2.000000000000000 6.000000000000000 10.00000000000000]
+            [3.000000000000000 7.000000000000000 11.00000000000000]
+            sage: m.matrix_from_rows([0,2])
+            [                0 1.000000000000000 2.000000000000000 3.000000000000000]
+            [8.000000000000000 9.000000000000000 10.00000000000000 11.00000000000000]
+            sage: m.matrix_from_columns([1,3])
+            [1.000000000000000 3.000000000000000]
+            [5.000000000000000 7.000000000000000]
+            [9.000000000000000 11.00000000000000]
+            sage: m.matrix_from_rows_and_columns([1,2],[0,3])
+            [4.000000000000000 7.000000000000000]
+            [8.000000000000000 11.00000000000000]
+        """
+        cdef Matrix_complex_ball_dense _src = <Matrix_complex_ball_dense> src
+        acb_set(acb_mat_entry(self.value, iDst, jDst), acb_mat_entry(_src.value, iSrc, jSrc))
+
     cpdef _richcmp_(left, right, int op):
         r"""
         EXAMPLES::

src/sage/matrix/matrix_cyclo_dense.pyx

@@ -407,6 +407,53 @@ cdef class Matrix_cyclo_dense(Matrix_dense):
 
         return x
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        """
+        Copy the (iSrc,jSrc)-th entry of ``src`` to the (iDst,jDst)-th entry
+        ``self``.
+
+        WARNING: As the name suggests, expect segfaults if iSrc,jSrc,iDst,jDst
+        are out of bounds!! This is for internal use only. This method assumes
+        ``src`` is a Matrix_cyclo_dense with the same base ring as ``self``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be a Matrix_cyclo_dense
+                    with the same base ring as ``self``.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+
+        TESTS::
+
+            sage: K.<z> = CyclotomicField(3)
+            sage: M = matrix(K,3,4,[i + z/(i+1) for i in range(12)])
+            sage: M
+            [          z   1/2*z + 1   1/3*z + 2   1/4*z + 3]
+            [  1/5*z + 4   1/6*z + 5   1/7*z + 6   1/8*z + 7]
+            [  1/9*z + 8  1/10*z + 9 1/11*z + 10 1/12*z + 11]
+            sage: M.transpose()
+            [          z   1/5*z + 4   1/9*z + 8]
+            [  1/2*z + 1   1/6*z + 5  1/10*z + 9]
+            [  1/3*z + 2   1/7*z + 6 1/11*z + 10]
+            [  1/4*z + 3   1/8*z + 7 1/12*z + 11]
+            sage: M.matrix_from_rows([0,2])
+            [          z   1/2*z + 1   1/3*z + 2   1/4*z + 3]
+            [  1/9*z + 8  1/10*z + 9 1/11*z + 10 1/12*z + 11]
+            sage: M.matrix_from_columns([1,3])
+            [  1/2*z + 1   1/4*z + 3]
+            [  1/6*z + 5   1/8*z + 7]
+            [ 1/10*z + 9 1/12*z + 11]
+            sage: M.matrix_from_rows_and_columns([1,2],[0,3])
+            [  1/5*z + 4   1/8*z + 7]
+            [  1/9*z + 8 1/12*z + 11]
+        """
+        cdef Matrix_cyclo_dense _src = src
+        cdef int a
+        for a in range(self._degree):
+            self._matrix.copy_from_unsafe(a, jDst + iDst*self._ncols, _src._matrix, a, jSrc + iSrc*_src._ncols)
+
     cdef bint get_is_zero_unsafe(self, Py_ssize_t i, Py_ssize_t j) except -1:
         r"""
         Return 1 if the entry ``(i, j)`` is zero, otherwise 0.

src/sage/matrix/matrix_dense.pyx

@@ -138,7 +138,7 @@ cdef class Matrix_dense(matrix.Matrix):
         cdef Py_ssize_t i, j
         for j from 0<= j < nc:
             for i from 0<= i < nr:
-                trans.set_unsafe(j,i,self.get_unsafe(i,j))
+                trans.copy_from_unsafe(j, i, self, i, j)
 
         if self._subdivisions is not None:
             row_divs, col_divs = self.subdivisions()
@@ -183,7 +183,7 @@ cdef class Matrix_dense(matrix.Matrix):
             rj -= 1
             for i from 0 <= i < nr:
                 ri -= 1
-                atrans.set_unsafe(j, i, self.get_unsafe(ri, rj))
+                atrans.copy_from_unsafe(j, i, self, ri, rj)
 
         if self._subdivisions is not None:
             row_divs, col_divs = self.subdivisions()

src/sage/matrix/matrix_gap.pyx

@@ -204,6 +204,46 @@ cdef class Matrix_gap(Matrix_dense):
         """
         self._libgap[i,j] = x
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        r"""
+        Copy the ``(iSrc, jSrc)`` entry of ``src`` into the ``(iDst, jDst)``
+        entry of ``self``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be a Matrix_gap with the
+                    same base ring as ``self``.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+
+        TESTS::
+
+            sage: M = MatrixSpace(ZZ, 3, 4, implementation='gap')(range(12))
+            sage: M
+            [ 0  1  2  3]
+            [ 4  5  6  7]
+            [ 8  9 10 11]
+            sage: M.transpose()
+            [ 0  4  8]
+            [ 1  5  9]
+            [ 2  6 10]
+            [ 3  7 11]
+            sage: M.matrix_from_rows([0,2])
+            [ 0  1  2  3]
+            [ 8  9 10 11]
+            sage: M.matrix_from_columns([1,3])
+            [ 1  3]
+            [ 5  7]
+            [ 9 11]
+            sage: M.matrix_from_rows_and_columns([1,2],[0,3])
+            [ 4  7]
+            [ 8 11]
+        """
+        cdef Matrix_gap _src = <Matrix_gap>src
+        self._libgap[iDst,jDst] = _src._libgap[iSrc,jSrc]
+
     cpdef _richcmp_(self, other, int op):
         r"""
         Compare ``self`` and ``right``.

src/sage/matrix/matrix_generic_dense.pyx

@@ -99,6 +99,47 @@ cdef class Matrix_generic_dense(matrix_dense.Matrix_dense):
     cdef get_unsafe(self, Py_ssize_t i, Py_ssize_t j):
         return self._entries[i*self._ncols + j]
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        r"""
+        Copy the ``(iSrc, jSrc)`` entry of ``src`` into the ``(iDst, jDst)``
+        entry of ``self``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be a Matrix_generic_dense
+                    with the same base ring as ``self``.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+
+        TESTS::
+
+            sage: K.<z> = GF(9)
+            sage: m = matrix(K,3,4,[((i%9)//3)*z + i%3 for i in range(12)])
+            sage: m
+            [      0       1       2       z]
+            [  z + 1   z + 2     2*z 2*z + 1]
+            [2*z + 2       0       1       2]
+            sage: m.transpose()
+            [      0   z + 1 2*z + 2]
+            [      1   z + 2       0]
+            [      2     2*z       1]
+            [      z 2*z + 1       2]
+            sage: m.matrix_from_rows([0,2])
+            [      0       1       2       z]
+            [2*z + 2       0       1       2]
+            sage: m.matrix_from_columns([1,3])
+            [      1       z]
+            [  z + 2 2*z + 1]
+            [      0       2]
+            sage: m.matrix_from_rows_and_columns([1,2],[0,3])
+            [  z + 1 2*z + 1]
+            [2*z + 2       2]
+        """
+        cdef Matrix_generic_dense _src = <Matrix_generic_dense>src
+        self._entries[iDst*self._ncols + jDst] = _src._entries[iSrc*_src._ncols + jSrc]
+
     def _reverse_unsafe(self):
         r"""
         TESTS::

src/sage/matrix/matrix_generic_sparse.pyx

@@ -200,6 +200,50 @@ cdef class Matrix_generic_sparse(matrix_sparse.Matrix_sparse):
     cdef get_unsafe(self, Py_ssize_t i, Py_ssize_t j):
         return self._entries.get((i,j), self._zero)
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        r"""
+        Copy the ``(iSrc, jSrc)`` entry of ``src`` into the ``(iDst, jDst)``
+        entry of ``self``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be a Matrix_generic_sparse
+                    with the same base ring as ``self``.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+
+        TESTS::
+
+            sage: K.<z> = GF(9)
+            sage: m = matrix(K,3,4,[((i%9)//3)*z + i%3 if is_prime(i) else 0 for i in range(12)],sparse=True)
+            sage: m
+            [      0       0       2       z]
+            [      0   z + 2       0 2*z + 1]
+            [      0       0       0       2]
+            sage: m.transpose()
+            [      0       0       0]
+            [      0   z + 2       0]
+            [      2       0       0]
+            [      z 2*z + 1       2]
+            sage: m.matrix_from_rows([0,2])
+            [0 0 2 z]
+            [0 0 0 2]
+            sage: m.matrix_from_columns([1,3])
+            [      0       z]
+            [  z + 2 2*z + 1]
+            [      0       2]
+            sage: m.matrix_from_rows_and_columns([1,2],[0,3])
+            [      0 2*z + 1]
+            [      0       2]
+        """
+        cdef Matrix_generic_sparse _src = <Matrix_generic_sparse>src
+        if (iSrc,jSrc) in _src._entries:
+            self._entries[(iDst,jDst)] = _src._entries.get((iSrc, jSrc), _src._zero)
+        elif (iDst,jDst) in self._entries:
+            del self._entries[(iDst,jDst)]
+
     cdef bint get_is_zero_unsafe(self, Py_ssize_t i, Py_ssize_t j) except -1:
         """
         Return 1 if the entry ``(i, j)`` is zero, otherwise 0.

src/sage/matrix/matrix_gf2e_dense.pyx

@@ -284,6 +284,47 @@ cdef class Matrix_gf2e_dense(matrix_dense.Matrix_dense):
         cdef Cache_base cache = <Cache_base> self._base_ring._cache
         return cache.fetch_int(r)
 
+    cdef copy_from_unsafe(self, Py_ssize_t iDst, Py_ssize_t jDst, src, Py_ssize_t iSrc, Py_ssize_t jSrc):
+        r"""
+        Copy the ``(iSrc, jSrc)`` entry of ``src`` into the ``(iDst, jDst)``
+        entry of ``self``.
+
+        INPUT:
+
+        - ``iDst`` - the row to be copied to in ``self``.
+        - ``jDst`` - the column to be copied to in ``self``.
+        - ``src`` - the matrix to copy from. Should be a Matrix_gf2e_dense with
+                    the same base ring as ``self``.
+        - ``iSrc``  - the row to be copied from in ``src``.
+        - ``jSrc`` - the column to be copied from in ``src``.
+
+        TESTS::
+
+            sage: K.<z> = GF(512)
+            sage: m = matrix(K,3,4,[sum([(i//(2^j))%2 * z^j for j in range(4)]) for i in range(12)])
+            sage: m
+            [          0           1           z       z + 1]
+            [        z^2     z^2 + 1     z^2 + z z^2 + z + 1]
+            [        z^3     z^3 + 1     z^3 + z z^3 + z + 1]
+            sage: m.transpose()
+            [          0         z^2         z^3]
+            [          1     z^2 + 1     z^3 + 1]
+            [          z     z^2 + z     z^3 + z]
+            [      z + 1 z^2 + z + 1 z^3 + z + 1]
+            sage: m.matrix_from_rows([0,2])
+            [          0           1           z       z + 1]
+            [        z^3     z^3 + 1     z^3 + z z^3 + z + 1]
+            sage: m.matrix_from_columns([1,3])
+            [          1       z + 1]
+            [    z^2 + 1 z^2 + z + 1]
+            [    z^3 + 1 z^3 + z + 1]
+            sage: m.matrix_from_rows_and_columns([1,2],[0,3])
+            [        z^2 z^2 + z + 1]
+            [        z^3 z^3 + z + 1]
+        """
+        cdef Matrix_gf2e_dense _src = <Matrix_gf2e_dense>src
+        mzed_write_elem(self._entries, iDst, jDst, mzed_read_elem(_src._entries, iSrc, jSrc))
+
     cdef bint get_is_zero_unsafe(self, Py_ssize_t i, Py_ssize_t j) except -1:
         r"""
         Return 1 if the entry ``(i, j)`` is zero, otherwise 0.