Applied changes to numpy for update from 1.3.x to 1.5.0:
Three packages need to be updated - Numpy, SciPy and scipy_sandbox.
Changed doctests:
Some of the doctest have changed due to output changes in numpy (for examples new warnings etc.)
The following files have changed:
- devel/sage/doc/en/faq/faq-usage.rst: deprication warning was removed from numpy.
- devel/sage/sage/matrix/matrix_double_dense.pyx: A complex warning was added in matrix exponential function.
- devel/sage/sage/symbolic/function.pyx: "Inf" changed to "inf"
- devel/sage-numpy/sage/functions/hyperbolic.py: ""Inf" changed to "inf"
Outdated patches:
The following patches were outdated and were removed:
- __init__.py
- cygwin-core-setup.py
- gnu.py
Added patches:
The following patches had to be added:
- buffer.c Memory errors accoured in numpy 1.5.0, these were solved after a bug report on the numpy trac
(see http://projects.scipy.org/numpy/ticket/1605 for details)
This will be obsolte in version 1.5.1
- src/numpy/core/setup.py and src/numpy/distutils/command/config.py :
Fix a bug when building on Solaris: numpy was not built with c99,
but used isfinite, which is only defined in c99 on Solaris. See
Sage trac ticket #9808 and numpy trac ticket #1625
(http://projects.scipy.org/numpy/ticket/1625). To fix, apply
the patch from numpy trac ticket #1625, patching
src/numpy/core/setup.py and src/numpy/distutils/command/config.py.
When numpy 1.5.1 is released, check to see if these patches are
still necessary.
Changes to install-spkg:
- The gcc_fake hack has been removed from the install. (see the 9808-remove-gcc_fake.patch for details)
- The fortran compiler was set to sage_fortran, because especially
g95 on OS X made problems. Also fortran options had to be
added to the numpy install (see the numpy-spkg-install.diff for more details)
Other problems which required no changes:
- networkx-1.0.x versions are incompatible to numpy-1.4.1 or greater
because numpy.core.defmatrix moved to numpy.matrixlib.defmatrix
This is obsolute since networkx-1.1 or higher support this
- runtime warnings appeared after upgrading from numpy-1.3.x to
higher versions, becuase the size of "flatiter" has changed in the
.c files. Recompilation of the .pyx files with sage -ba or
apply little changes to numpy.pxd in cython and apply sage -b
solved this issues.
Applied changes to scipy-0.8 from scipy-1.7.x:
-All patches were outdated and therefore removed
-Changes to the spkg-install are found in scipy-spkg-install.diff
- Exported F77, F90 and F95 in addition to FC, as the above failed to
- to work on a Solaris system with compilers f77 and f90.
- Improved SPKG.txt
Necessary changes to scipy_sandbox
It is essentail that #10092 is applied to update scpipy_sandbox, which
exports FC, F77, F90 and F95, otherwise the wrong compilers may be used
in some cases.