Mailman 3 July 2008 - SciPy-Dev

NumPy 1.2.0 and SciPy 0.7.0 schedule
by Jarrod Millman July 27, 2008

July 27, 2008

Now that NumPy 1.1.1 is almost out, I wanted to remind everyone of the NumPy 1.2.0 schedule: - 8/05/08 tag the 1.2.0rc1 release and prepare packages - 8/12/08 tag the 1.2.0rc2 release and prepare packages - 8/23/08 tag the 1.2.0 release and prepare packages - 8/24/08 announce release Ideally, I would like to release SciPy 0.7.0 at the same time. In order for this to have any chance of success, I will need help keeping an eye on the outstanding tickets and help rallying everyone to fix bugs. In particular, I would appreciate it if you could let me know of any bugs that should be considered release blockers. According to this release schedule, the first release candidate is due in a little less than two weeks with the final release in exactly one month. While this may seem an aggressive release schedule, I believe it is very achievable if everyone pitches in. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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numpy long vs. int
by Damian Eads July 26, 2008

July 26, 2008

Hi there, I had some problems porting some internal extension code I wrote recently. The code worked fine on 32-bit but did not work on 64-bit. When np.int_ is used as the dtype argument to np.zeros or np.asarray, an array results that has typecode NPY_INT on 32-bit and NPY_LONG on 64-bit. This inconsistency is problematic when type checking arrays in C-space prior to passing them to a C function expecting a specific type, like int. Changing dtype=np.int_ to dtype='i' seems to consistently result in an array with typecode NPY_INT on both architectures, which is desired. I didn't think to write about this until I encountered the very same problem today when trying to compile the ANN scikit on 64-bit. All the tests failed because the kd-tree array passed was of type long. ====================================================================== ERROR: test_ann.TestANNWrapper.test_knn_returns_nearest_neighbor(array([[ 0.53209373, 0.2149725 ], ---------------------------------------------------------------------- Traceback (most recent call last): File "/mirror/ssrc/eads/sci-tools/prefix-x86-64/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/case.py", line 182, in runTest self.test(*self.arg) File "/mirror/ssrc/eads/sci-tools-source/x86-64/ann/scikits/ann/tests/test_ann.py", line 49, in checkReturnNN nn,nn_distances = tree.knn(pt,1) File "scikits/ann/__init__.py", line 113, in knn self._knn2(pts, idx, d2, eps) File "scikits/ann/ANN.py", line 45, in _knn2 def _knn2(*args): return _ANN._kdtree__knn2(*args) TypeError: Array of type 'int' required. Array of type 'long' given ================================= Changing line 110 from dtype=np.int_ to dtype='i' fixed the problem. Some people seem insistent on using a type object (e.g. np.int_ or np.float_) instead of a string. In fact, when I checked in my hierarchical clustering code, I noticed someone eventually changed all the dtype's in my code to use the type objects. I had no qualms with this until now. Are there type objects that can be passed to dtype to guarantee consistency in translation to NPY_XXX type codes? We should probably write a caveat in the Numpy C extensions help document explaining this inconsistency. Thanks, Damian

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Ticket 709
by Nils Wagner July 25, 2008

July 25, 2008

Hi all, Can someone reproduce the bug http://scipy.org/scipy/scipy/ticket/709 ? The eigencurves should be smooth. Nils

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Windows binary for openopt ?
by Nils Wagner July 25, 2008

July 25, 2008

Hi all, I am looking for a windows binary of openopt. Is it available somewhere ? Nils

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ERROR: test_sparse_formats (test_mmio.TestMMIOCoordinate)
by Nils Wagner July 24, 2008

July 24, 2008

The error mentioned in the subject happens with >>> scipy.__version__ '0.7.0.dev4559' ====================================================================== ERROR: test_sparse_formats (test_mmio.TestMMIOCoordinate) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/io/tests/test_mmio.py", line 311, in test_sparse_formats mmwrite(fn, mat.asformat(fmt)) File "/usr/local/lib64/python2.5/site-packages/scipy/io/mmio.py", line 67, in mmwrite MMFile().write(target, a, comment, field, precision) File "/usr/local/lib64/python2.5/site-packages/scipy/io/mmio.py", line 284, in write self._write(stream, a, comment, field, precision) File "/usr/local/lib64/python2.5/site-packages/scipy/io/mmio.py", line 564, in _write IJV = vstack((a.row, a.col, a.data)).T File "/usr/local/lib64/python2.5/site-packages/scipy/sparse/csr.py", line 93, in __getattr__ return _cs_matrix.__getattr__(self, attr) File "/usr/local/lib64/python2.5/site-packages/scipy/sparse/base.py", line 393, in __getattr__ raise AttributeError, attr + " not found" AttributeError: row not found Nils

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[Fwd: Re: permission requested]
by Alan G Isaac July 23, 2008

July 23, 2008

For completeness, I did ask them if their code could be included in SciPy under the BSD license. See the attached email response. Alan

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Once more unto the breach
by theodore test July 23, 2008

July 23, 2008

"Middling-to-fair pythonian seeking long walks on an interactive prompt with a triple-quoted beauty." In other words, I'd like to be an editor for the SciPy documentation marathon, please. user_name = theodore_test preferred_num_spaces = 4 sense_of_humor = True Thanks, Theo

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removing lil_eye() and lil_diags()
by Nathan Bell July 23, 2008

July 23, 2008

Is there any objection to removing lil_eye() and lil_diags() from scipy.sparse? I believe these functions were added after the 0.6 release and have now been superceded by sparse.eye(..., format='lil') and sparse.spdiags(..., format='lil'). For reference: http://projects.scipy.org/scipy/scipy/browser/trunk/scipy/sparse/construct.… -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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scipy.test() error
by Nils Wagner July 22, 2008

July 22, 2008

Hi Nathan, I found a new error in scipy.sparse. I have used >>> scipy.__version__ '0.7.0.dev4549' ====================================================================== ERROR: test_sparse_formats (test_mmio.TestMMIOCoordinate) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/io/tests/test_mmio.py", line 311, in test_sparse_formats mmwrite(fn, mat.asformat(fmt)) File "/usr/local/lib64/python2.5/site-packages/scipy/io/mmio.py", line 67, in mmwrite MMFile().write(target, a, comment, field, precision) File "/usr/local/lib64/python2.5/site-packages/scipy/io/mmio.py", line 284, in write self._write(stream, a, comment, field, precision) File "/usr/local/lib64/python2.5/site-packages/scipy/io/mmio.py", line 564, in _write IJV = vstack((a.row, a.col, a.data)).T File "/usr/local/lib64/python2.5/site-packages/scipy/sparse/csr.py", line 93, in __getattr__ return _cs_matrix.__getattr__(self, attr) File "/usr/local/lib64/python2.5/site-packages/scipy/sparse/base.py", line 393, in __getattr__ raise AttributeError, attr + " not found" AttributeError: row not found Nils

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Functions with print statements
by Alan McIntyre July 21, 2008

July 21, 2008

Hi all, There are some functions in SciPy that use print statements to warn the user of various questionable conditions, such as scipy.stats.shapiro, ansari, and wilcoxon. Should these be using warnings.warn instead? Thanks, Alan

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