From noreply at github.com Tue Jun 5 15:45:24 2012 From: noreply at github.com (GitHub) Date: Tue, 05 Jun 2012 12:45:24 -0700 Subject: [Numpy-svn] [numpy/numpy] dabe9a: ENH: Make internal per-op nditer flags type a type... Message-ID: <4fce61d4c191d_450a146cae885980@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: dabe9ab064ae32bfd7cee8c0dc58b175a6955e49 https://github.com/numpy/numpy/commit/dabe9ab064ae32bfd7cee8c0dc58b175a6955e49 Author: Mark Wiebe Date: 2012-05-28 (Mon, 28 May 2012) Changed paths: M numpy/core/src/multiarray/nditer_api.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/nditer_impl.h Log Message: ----------- ENH: Make internal per-op nditer flags type a typedef There are 8 flags now, so to add another one requires bumping up the size. This change makes that easy. Also, because the internal structure of nditer is not exposed to the ABI, we can change it at will. Commit: 4542c43b567af9064f36759afe6064bbb3315728 https://github.com/numpy/numpy/commit/4542c43b567af9064f36759afe6064bbb3315728 Author: Mark Wiebe Date: 2012-05-28 (Mon, 28 May 2012) Changed paths: M numpy/core/src/multiarray/nditer_api.c M numpy/core/src/multiarray/nditer_impl.h Log Message: ----------- BUG: Add a new flag to nditer to indicate when op uses buffering Thouis tracked down an intermittently occurring bug in ticket #2144, where a reduction under certain situations would produce wrong results. This occurs when the array data and the nditer's buffer happen to be adjacent in memory. This fixes it by replacing the "clever" trick of checking if the iterator's pointer is in the buffer with an explicit flag to signal buffer usage. The reason this can't be reliably handled via the pointer/buffer check is that the pointer updates are handled by the consumer of the iterator, who may update them in place or may use local variables instead. Thus, the pointer could still point to the beginning of the buffer, or could point at the byte immediately after the buffer. Using a flag avoids all of this and should be reliable. Commit: de8c536813472be29a6292721df83d73dbf7016e https://github.com/numpy/numpy/commit/de8c536813472be29a6292721df83d73dbf7016e Author: Nathaniel J. Smith Date: 2012-06-05 (Tue, 05 Jun 2012) Changed paths: M numpy/core/src/multiarray/nditer_api.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/nditer_impl.h Log Message: ----------- Merge remote-tracking branch 'mwiebe/nditer_buffer_flag' into merge-293 Compare: https://github.com/numpy/numpy/compare/fd78546...de8c536 From noreply at github.com Wed Jun 6 14:53:09 2012 From: noreply at github.com (GitHub) Date: Wed, 06 Jun 2012 11:53:09 -0700 Subject: [Numpy-svn] [numpy/numpy] cbce4e: Consolidate all array writeability checking in new... Message-ID: <4fcfa71522c97_3b981700ae81537bf@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: cbce4e6565e7a7fbe065502b264622ce7d64740a https://github.com/numpy/numpy/commit/cbce4e6565e7a7fbe065502b264622ce7d64740a Author: Nathaniel J. Smith Date: 2012-05-15 (Tue, 15 May 2012) Changed paths: M doc/release/2.0.0-notes.rst M numpy/core/code_generators/numpy_api.py M numpy/core/src/multiarray/array_assign_array.c M numpy/core/src/multiarray/array_assign_scalar.c M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/mapping.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/sequence.c M numpy/core/src/umath/ufunc_object.c M numpy/core/tests/test_multiarray.py M numpy/numarray/_capi.c Log Message: ----------- Consolidate all array writeability checking in new PyArray_RequireWriteable This is mostly a code cleanup, but it does have a user-visible effect in that attempting to write to a unwriteable array now consistently raises ValueError. (It used to randomly raise either ValueError or RuntimeError.) Passes numpy.test("full"). Commit: 6a90adaea6ba4330e8da4db546425d9cdcc5a940 https://github.com/numpy/numpy/commit/6a90adaea6ba4330e8da4db546425d9cdcc5a940 Author: Nathaniel J. Smith Date: 2012-05-15 (Tue, 15 May 2012) Changed paths: M numpy/core/code_generators/cversions.txt M numpy/core/code_generators/numpy_api.py M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/getset.c M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/tests/test_nditer.py M numpy/numarray/_capi.c Log Message: ----------- Funnel all assignments to PyArrayObject->base through a single point This patch removes all direct assignments of non-NULL values to the 'base' field on PyArrayObjects. A new utility function was created to set up UPDATEIFCOPY arrays, and all assignments to 'base' were adjusted to use either PyArray_SetBaseObject or the new PyArray_SetUpdateIfCopyBase. One advantage of this is that it produces more consistent error handling. This error handling revealed a bug in the nditer code, which this patch does *not* yet fix. The bug is that npyiter_new_temp_array sometimes (when dealing with reversed axes) creates an array and then returns a view onto it. But, npyiter_allocate_arrays assumes that the array returned by npyiter_new_temp_array can have UPDATEIFCOPY set, which requires reassigning its 'base' field. Previously, this meant that the temporary array leaked. Now, it produces a ValueError. This code path doesn't seem to actually be hit very often; only one of the nditer tests fails because of the change. See numpy/core/tests/test_nditer.py:test_iter_array_cast_buggy Commit: d403fed2423caec4149937fe48781ac68b21fddb https://github.com/numpy/numpy/commit/d403fed2423caec4149937fe48781ac68b21fddb Author: Nathaniel J. Smith Date: 2012-05-16 (Wed, 16 May 2012) Changed paths: M numpy/core/tests/test_multiarray.py Log Message: ----------- Add a test for ndarray.diagonal() All 'expected' values were computed using numpy 1.5.1, so we can be pretty sure that the recent rewrite didn't change any results. Commit: bea52bf307782b2a211b7fcfa6696fad45dae275 https://github.com/numpy/numpy/commit/bea52bf307782b2a211b7fcfa6696fad45dae275 Author: Nathaniel J. Smith Date: 2012-05-16 (Wed, 16 May 2012) Changed paths: M numpy/core/include/numpy/ndarraytypes.h M numpy/core/numeric.py M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/arrayobject.h M numpy/core/src/multiarray/arraytypes.c.src M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/getset.c M numpy/core/src/multiarray/item_selection.c M numpy/core/tests/test_maskna.py M numpy/core/tests/test_multiarray.py M numpy/lib/twodim_base.py Log Message: ----------- Transition scheme for allowing PyArray_Diagonal to return a view PyArray_Diagonal is changed to return a copy of the diagonal (as in numpy 1.6 and earlier), but with a new (hidden) WARN_ON_WRITE flag set. Writes to this array (or views thereof) will continue to work as normal, but the first write will trigger a DeprecationWarning. We also issue this warning if someone extracts a non-numpy writeable view of the array (e.g., by accessing the Python-level .data attribute). There are likely still places where the data buffer is exposed that I've missed -- review welcome! New known-fail test: eye() for maskna arrays was only implemented by exploiting ndarray.diagonal's view-ness, so it is now unimplemented again, and the corresponding test is marked known-fail. Commit: 0812564322e1cd282cff489c46a8ce51f7fc2a89 https://github.com/numpy/numpy/commit/0812564322e1cd282cff489c46a8ce51f7fc2a89 Author: Nathaniel J. Smith Date: 2012-05-16 (Wed, 16 May 2012) Changed paths: M doc/release/2.0.0-notes.rst M numpy/core/fromnumeric.py M numpy/lib/twodim_base.py Log Message: ----------- Document the PyArray_Diagonal transition scheme. Commit: c247305a75a20e4e5d421e691d931d6cc98c39ce https://github.com/numpy/numpy/commit/c247305a75a20e4e5d421e691d931d6cc98c39ce Author: Nathaniel J. Smith Date: 2012-05-17 (Thu, 17 May 2012) Changed paths: M doc/release/2.0.0-notes.rst Log Message: ----------- Typo fix Thanks to Travis for catching it. Commit: 412c8a6ad055b7809e5a77e8d5f257c33e102284 https://github.com/numpy/numpy/commit/412c8a6ad055b7809e5a77e8d5f257c33e102284 Author: Nathaniel J. Smith Date: 2012-05-19 (Sat, 19 May 2012) Changed paths: M bscript M doc/source/reference/c-api.array.rst M numpy/core/bscript M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/tests/test_maskna.py M numpy/core/tests/test_multiarray.py M numpy/core/tests/test_nditer.py Log Message: ----------- Merge branch 'master' into clean-up-diagonal Commit: 83f6abe7ab0ccea0a03e97f03606f237a7b563a6 https://github.com/numpy/numpy/commit/83f6abe7ab0ccea0a03e97f03606f237a7b563a6 Author: Nathaniel J. Smith Date: 2012-05-19 (Sat, 19 May 2012) Changed paths: M numpy/core/tests/test_nditer.py Log Message: ----------- Un-KNOWNFAIL the nditer test after merging Mark's fix from master Commit: da9bf058341b7569ed26953fc25564a98ab33578 https://github.com/numpy/numpy/commit/da9bf058341b7569ed26953fc25564a98ab33578 Author: Nathaniel J. Smith Date: 2012-05-19 (Sat, 19 May 2012) Changed paths: M numpy/core/src/multiarray/arrayobject.c Log Message: ----------- Fix a C90 compatibility error Commit: 53d99f2de4be22ca4aff01d5527ff8c8e0455ae9 https://github.com/numpy/numpy/commit/53d99f2de4be22ca4aff01d5527ff8c8e0455ae9 Author: Nathaniel J. Smith Date: 2012-05-19 (Sat, 19 May 2012) Changed paths: M numpy/core/tests/test_multiarray.py Log Message: ----------- Add a missing guard for Python versions <2.6 Commit: 6d361274491df708393dbd8aa8a3431f3f743748 https://github.com/numpy/numpy/commit/6d361274491df708393dbd8aa8a3431f3f743748 Author: Nathaniel J. Smith Date: 2012-05-21 (Mon, 21 May 2012) Changed paths: M numpy/core/include/numpy/ndarraytypes.h M numpy/core/src/multiarray/arrayobject.c Log Message: ----------- Clean up PyArray_Diagonal changes based on Chuck's feedback - NPY_ARRAY_WARN_ON_WRITE flag definition is protected by #ifdef _MULTIARRAYMODULE, to make totally sure that we can recycle the flag bit later. - Improve docs for PyArray_SetUpdateIfCopyBase. - Make the deprecation warning for writes to the diagonal array somewhat more terse. - Use DEPRECATE macro instead of calling PyErr_Warn/PyErr_WarnEx directly. - Comment formatting fixed. Commit: 58392b0ec64b58f1c178f2f88328e864db59b39d https://github.com/numpy/numpy/commit/58392b0ec64b58f1c178f2f88328e864db59b39d Author: Nathaniel J. Smith Date: 2012-05-21 (Mon, 21 May 2012) Changed paths: M numpy/core/tests/test_multiarray.py Log Message: ----------- Don't assume ctypes is available, it's not true on Python 2.4 Commit: ac4ce7b5284c8d1fbda734149121dd1eff52155a https://github.com/numpy/numpy/commit/ac4ce7b5284c8d1fbda734149121dd1eff52155a Author: Nathaniel J. Smith Date: 2012-05-21 (Mon, 21 May 2012) Changed paths: M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/getset.c M numpy/core/tests/test_multiarray.py Log Message: ----------- Fix diagonal-related warnings and tests on Python 3 Commit: baaf1819e3e9319c58269a7a06eb4b20e0a08eec https://github.com/numpy/numpy/commit/baaf1819e3e9319c58269a7a06eb4b20e0a08eec Author: Nathaniel J. Smith Date: 2012-05-22 (Tue, 22 May 2012) Changed paths: M numpy/core/include/numpy/ndarraytypes.h M numpy/core/src/multiarray/arrayobject.h Log Message: ----------- Move internal NPY_ARRAY_WARN_ON_WRITE flag into an internal header. Commit: 51616c9265155f75e536ba19c32f9f91337243af https://github.com/numpy/numpy/commit/51616c9265155f75e536ba19c32f9f91337243af Author: Nathaniel J. Smith Date: 2012-05-22 (Tue, 22 May 2012) Changed paths: M numpy/core/code_generators/cversions.txt M numpy/core/code_generators/numpy_api.py M numpy/core/src/multiarray/array_assign_array.c M numpy/core/src/multiarray/array_assign_scalar.c M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/mapping.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/sequence.c M numpy/core/src/umath/ufunc_object.c M numpy/numarray/_capi.c Log Message: ----------- Rename PyArray_RequireWriteable to PyArray_FailUnlessWriteable Also clean up its API slightly so that the caller passes in a name describing the array being checked which is used to generate an error message, rather than writing an error message from scratch. Commit: 85b682893f1d38cbb3b31f827889e1d54edbc95e https://github.com/numpy/numpy/commit/85b682893f1d38cbb3b31f827889e1d54edbc95e Author: Nathaniel J. Smith Date: 2012-06-06 (Wed, 06 Jun 2012) Changed paths: M .gitignore M bento.info M bscript M doc/HOWTO_DOCUMENT.rst.txt A doc/release/1.6.1-notes.rst A doc/release/1.6.2-notes.rst M doc/source/release.rst M numpy/core/__init__.py M numpy/core/bento.info M numpy/core/bscript M numpy/core/src/multiarray/nditer_api.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/nditer_impl.h M numpy/core/tests/test_numeric.py M numpy/distutils/fcompiler/intel.py M numpy/distutils/system_info.py M numpy/fft/bscript M numpy/lib/bscript M numpy/lib/financial.py M numpy/lib/tests/test_financial.py M numpy/random/bscript M release.sh A tools/test-installed-numpy.py A tox.ini Log Message: ----------- Merge branch 'master' into clean-up-diagonal Compare: https://github.com/numpy/numpy/compare/de8c536...85b6828 From noreply at github.com Fri Jun 8 06:06:22 2012 From: noreply at github.com (GitHub) Date: Fri, 08 Jun 2012 03:06:22 -0700 Subject: [Numpy-svn] [numpy/numpy] adddbc: sphinxext: some cleanup in setup.py Message-ID: <4fd1ce9e441f4_42f6eabaf01515b7@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: adddbc72a7aa9faeb61c708f1c2c0568d0398303 https://github.com/numpy/numpy/commit/adddbc72a7aa9faeb61c708f1c2c0568d0398303 Author: Denis Laxalde Date: 2012-06-07 (Thu, 07 Jun 2012) Changed paths: M doc/sphinxext/setup.py Log Message: ----------- sphinxext: some cleanup in setup.py - remove obsolete entry_points (the corresponding code was removed in 08e85c1820f8502e2a5009da4d3d89c6462a911b). - drop setuptools import - adjust setup() argument to conform with distutils format Commit: 263c877e4f0835c2a7f4ceb6cac5f41ac7a825a6 https://github.com/numpy/numpy/commit/263c877e4f0835c2a7f4ceb6cac5f41ac7a825a6 Author: Denis Laxalde Date: 2012-06-07 (Thu, 07 Jun 2012) Changed paths: M doc/sphinxext/LICENSE.txt Log Message: ----------- sphinxext: remove mention of old files in LICENSE.txt Commit: ac9477775a39449b6a13c7538cf576a9d511919b https://github.com/numpy/numpy/commit/ac9477775a39449b6a13c7538cf576a9d511919b Author: Travis E. Oliphant Date: 2012-06-08 (Fri, 08 Jun 2012) Changed paths: M doc/sphinxext/LICENSE.txt M doc/sphinxext/setup.py Log Message: ----------- Merge pull request #298 from dlaxalde/sphinxext/cleanup sphinxext cleanup Compare: https://github.com/numpy/numpy/compare/85b6828...ac94777 From noreply at github.com Fri Jun 8 07:33:13 2012 From: noreply at github.com (GitHub) Date: Fri, 08 Jun 2012 04:33:13 -0700 Subject: [Numpy-svn] [numpy/numpy] 87a445: BUG: Disallow writing to flat iterators for readon... Message-ID: <4fd1e2f995b73_5210f9faec123011@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 87a445e461fdc25fc682130e0c058e5dd022695f https://github.com/numpy/numpy/commit/87a445e461fdc25fc682130e0c058e5dd022695f Author: Travis E. Oliphant Date: 2012-06-08 (Fri, 08 Jun 2012) Changed paths: M numpy/core/src/multiarray/getset.c M numpy/core/src/multiarray/iterators.c M numpy/core/tests/test_multiarray.py Log Message: ----------- BUG: Disallow writing to flat iterators for readonly arrays. Ensure __array__ does not create UPDATEIFCOPY if underlying array on iterator is readonly. Plus some tests. Commit: 501309341f3cb54c7fbcdeffb342ee217cfa5ade https://github.com/numpy/numpy/commit/501309341f3cb54c7fbcdeffb342ee217cfa5ade Author: Travis E. Oliphant Date: 2012-06-08 (Fri, 08 Jun 2012) Changed paths: M numpy/core/src/multiarray/getset.c M numpy/core/src/multiarray/iterators.c M numpy/core/tests/test_multiarray.py Log Message: ----------- Merge pull request #299 from teoliphant/fixup_flat Fix flat arrays so they cannot be used to write to read-only memory. Compare: https://github.com/numpy/numpy/compare/ac94777...5013093 From noreply at github.com Fri Jun 8 15:34:58 2012 From: noreply at github.com (GitHub) Date: Fri, 08 Jun 2012 12:34:58 -0700 Subject: [Numpy-svn] [numpy/numpy] 7953c0: BUG: missing incref for metadata of datetime dtype... Message-ID: <4fd253e25a755_efa136dae81527ec@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 7953c010971fc091230833355d930ec4ebdd29a0 https://github.com/numpy/numpy/commit/7953c010971fc091230833355d930ec4ebdd29a0 Author: Thouis (Ray) Jones Date: 2012-06-08 (Fri, 08 Jun 2012) Changed paths: M numpy/core/src/multiarray/descriptor.c Log Message: ----------- BUG: missing incref for metadata of datetime dtypes. Commit: db50690809bebb4e66375b6c0a34e9637e68dde9 https://github.com/numpy/numpy/commit/db50690809bebb4e66375b6c0a34e9637e68dde9 Author: Thouis (Ray) Jones Date: 2012-06-08 (Fri, 08 Jun 2012) Changed paths: M numpy/core/src/multiarray/descriptor.c M numpy/core/tests/test_datetime.py Log Message: ----------- More careful checking of datetime metadata in dtype __setstate__() Commit: d0f520a30990c018114672f24197866452a2d088 https://github.com/numpy/numpy/commit/d0f520a30990c018114672f24197866452a2d088 Author: Thouis (Ray) Jones Date: 2012-06-08 (Fri, 08 Jun 2012) Changed paths: M numpy/core/src/multiarray/descriptor.c Log Message: ----------- make sure self->metadata is valid before calling DECREF Compare: https://github.com/numpy/numpy/compare/5013093...d0f520a From noreply at github.com Sun Jun 10 07:33:28 2012 From: noreply at github.com (GitHub) Date: Sun, 10 Jun 2012 04:33:28 -0700 Subject: [Numpy-svn] [numpy/numpy] 3dbfaa: fix previous patch: c_metdata should match metadat... Message-ID: <4fd486081b436_113d1334af4932eb@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 3dbfaa06b45b89b6163574e5349526032920e11b https://github.com/numpy/numpy/commit/3dbfaa06b45b89b6163574e5349526032920e11b Author: Thouis (Ray) Jones Date: 2012-06-10 (Sun, 10 Jun 2012) Changed paths: M numpy/core/src/multiarray/descriptor.c Log Message: ----------- fix previous patch: c_metdata should match metadata before DECREF Commit: a0d1a961a9e3428d378e2189b8c337cc629a2fae https://github.com/numpy/numpy/commit/a0d1a961a9e3428d378e2189b8c337cc629a2fae Author: njsmith Date: 2012-06-10 (Sun, 10 Jun 2012) Changed paths: M numpy/core/src/multiarray/descriptor.c Log Message: ----------- Merge pull request #304 from thouis/datetime_refcnt fix previous patch: c_metadata should match metadata before DECREF Compare: https://github.com/numpy/numpy/compare/d0f520a...a0d1a96 From noreply at github.com Tue Jun 12 03:38:51 2012 From: noreply at github.com (GitHub) Date: Tue, 12 Jun 2012 00:38:51 -0700 Subject: [Numpy-svn] [numpy/numpy] 6cb026: remove unused variables from histogramdd Message-ID: <4fd6f20b5d45d_67591817ae41712c9@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 6cb02660163c107e2cf407c1483bad485fa5fd95 https://github.com/numpy/numpy/commit/6cb02660163c107e2cf407c1483bad485fa5fd95 Author: Jake Vanderplas Date: 2012-06-11 (Mon, 11 Jun 2012) Changed paths: M numpy/lib/function_base.py Log Message: ----------- remove unused variables from histogramdd Commit: 637fa6233b4e5af81e0c8e629adcbee1918b4ebd https://github.com/numpy/numpy/commit/637fa6233b4e5af81e0c8e629adcbee1918b4ebd Author: Travis E. Oliphant Date: 2012-06-12 (Tue, 12 Jun 2012) Changed paths: M numpy/lib/function_base.py Log Message: ----------- Merge pull request #308 from jakevdp/histogram_fix Remove unused declarations Compare: https://github.com/numpy/numpy/compare/a0d1a961a9e3...637fa6233b4e From noreply at github.com Tue Jun 12 03:39:42 2012 From: noreply at github.com (GitHub) Date: Tue, 12 Jun 2012 00:39:42 -0700 Subject: [Numpy-svn] [numpy/numpy] 69c33b: fix the wrapping problem of fill_diagonal with tal... Message-ID: <4fd6f23e3a41f_482312e1ae8137128@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 69c33bf74bcdc1d9781bd5db27f942f6d676c032 https://github.com/numpy/numpy/commit/69c33bf74bcdc1d9781bd5db27f942f6d676c032 Author: Frederic Date: 2012-06-11 (Mon, 11 Jun 2012) Changed paths: M numpy/lib/index_tricks.py M numpy/lib/tests/test_index_tricks.py Log Message: ----------- fix the wrapping problem of fill_diagonal with tall matrix. Commit: e909e4eafba23b6dd6391c8ea6aeb003c6192ef4 https://github.com/numpy/numpy/commit/e909e4eafba23b6dd6391c8ea6aeb003c6192ef4 Author: Frederic Date: 2012-06-11 (Mon, 11 Jun 2012) Changed paths: M numpy/lib/index_tricks.py M numpy/lib/tests/test_index_tricks.py Log Message: ----------- add the warp parameter to fill_diagonal for people that could want the old behavior. Commit: a8f1612c75cc120b6d22896c36a68fea330f5fbe https://github.com/numpy/numpy/commit/a8f1612c75cc120b6d22896c36a68fea330f5fbe Author: Travis E. Oliphant Date: 2012-06-12 (Tue, 12 Jun 2012) Changed paths: M numpy/lib/index_tricks.py M numpy/lib/tests/test_index_tricks.py Log Message: ----------- Merge pull request #306 from nouiz/fill_diagonal fix the wrapping problem of fill_diagonal with tall matrix. Compare: https://github.com/numpy/numpy/compare/637fa6233b4e...a8f1612c75cc From noreply at github.com Tue Jun 12 03:40:20 2012 From: noreply at github.com (GitHub) Date: Tue, 12 Jun 2012 00:40:20 -0700 Subject: [Numpy-svn] [numpy/numpy] e2ec1e: TST: pickling MaskedConstant Message-ID: <4fd6f264ebd93_50ec1a36af0101333@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: e2ec1eaa235dd60ecf768b89d22aa5a35395882a https://github.com/numpy/numpy/commit/e2ec1eaa235dd60ecf768b89d22aa5a35395882a Author: Robert Kende Date: 2012-06-11 (Mon, 11 Jun 2012) Changed paths: M numpy/ma/tests/test_core.py Log Message: ----------- TST: pickling MaskedConstant Commit: a11aab3960005e89f812c59731099de981d73784 https://github.com/numpy/numpy/commit/a11aab3960005e89f812c59731099de981d73784 Author: Robert Kende Date: 2012-06-11 (Mon, 11 Jun 2012) Changed paths: M numpy/ma/core.py Log Message: ----------- BUG: fix pickling MaskedConstant Commit: db5168b157444af0a2da3fc02135d0f0871d92ba https://github.com/numpy/numpy/commit/db5168b157444af0a2da3fc02135d0f0871d92ba Author: Travis E. Oliphant Date: 2012-06-12 (Tue, 12 Jun 2012) Changed paths: M numpy/ma/core.py M numpy/ma/tests/test_core.py Log Message: ----------- Merge pull request #305 from r0k3/picklemaskedconstant Fix for the error while pickling MaskedConstant. Compare: https://github.com/numpy/numpy/compare/a8f1612c75cc...db5168b15744 From noreply at github.com Tue Jun 12 03:51:24 2012 From: noreply at github.com (GitHub) Date: Tue, 12 Jun 2012 00:51:24 -0700 Subject: [Numpy-svn] [numpy/numpy] ee6071: BUG: Add a gap in NPY_DATETIMEUNIT enum where 1.6 ... Message-ID: <4fd6f4fc523dd_1e401a67aec1426fa@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: ee607114d440023d5c717faecaa1368ea0ffa137 https://github.com/numpy/numpy/commit/ee607114d440023d5c717faecaa1368ea0ffa137 Author: Mark Wiebe Date: 2012-06-05 (Tue, 05 Jun 2012) Changed paths: M numpy/core/include/numpy/ndarraytypes.h M numpy/core/src/multiarray/datetime.c M numpy/core/src/multiarray/scalartypes.c.src Log Message: ----------- BUG: Add a gap in NPY_DATETIMEUNIT enum where 1.6 had the busday unit 1.7 doesn't have the business day unit, but instead provides a separate business day API. For binary compatibility, as experienced in Pandas use of datetime64, it's a good idea for the numbers to stay the same. Commit: f2a7464e3b879f2d43709da5f2e456285d107f30 https://github.com/numpy/numpy/commit/f2a7464e3b879f2d43709da5f2e456285d107f30 Author: Travis E. Oliphant Date: 2012-06-12 (Tue, 12 Jun 2012) Changed paths: M numpy/core/include/numpy/ndarraytypes.h M numpy/core/src/multiarray/datetime.c M numpy/core/src/multiarray/scalartypes.c.src Log Message: ----------- Merge pull request #295 from mwiebe/datetime_unit_16compat BUG: Add a gap in NPY_DATETIMEUNIT enum where 1.6 had the busday unit Compare: https://github.com/numpy/numpy/compare/db5168b15744...f2a7464e3b87 From noreply at github.com Tue Jun 12 03:58:32 2012 From: noreply at github.com (GitHub) Date: Tue, 12 Jun 2012 00:58:32 -0700 Subject: [Numpy-svn] [numpy/numpy] 127ae2: ENH: Add kwarg support for vectorize (tickets #210... Message-ID: <4fd6f6a810743_abc1993ae490472@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 127ae2f54d2c96fc7318fe12a3e2009e517828d1 https://github.com/numpy/numpy/commit/127ae2f54d2c96fc7318fe12a3e2009e517828d1 Author: Michael McNeil Forbes Date: 2012-05-31 (Thu, 31 May 2012) Changed paths: M numpy/lib/function_base.py M numpy/lib/tests/test_function_base.py Log Message: ----------- ENH: Add kwarg support for vectorize (tickets #2100, #1156, and #1487) This is a substantial rewrite of vectorize to remove all introspection and caching behaviour. This greatly simplifies the logic of the code, and allows for much more generalized behaviour, simultaneously fixing tickets #1156, #1487, and #2100. There will probably be a performance hit because caching is no longer used (but should be able to be reinstated if needed). As vectorize is a convenience function with poor performance in general, perhaps this is okay. Rather than trying to inspect the function to determine the number of arguments, defaults, and argument names, we just use the arguments passed on the call to determine the behaviour on each call. All tests pass and code is fully covered Fixes: Ticket #2100: kwarg support for vectorize - API: Optional excluded argument to exclude some args from vectorization. - Added documentation, examples, and coverage tests - Added additional coverage test and base case for functions with no args - Factored original behaviour into _vectorize_call - Some minor documentation and error message corrections Ticket #1156: Support vectorizing over instance methods - No longer an issue since everything is determined by the call. Ticket: #1487: result depends on execution order - No longer caching, so the behaviour is as was expected. ENH: Simple cache for vectorize - Added simple cache to prevent vectorize from calling pyfunc twice on the first argument when determining the output types and added regression test. - Added documentation for excluded positional arguments. - Documentation cleanups. - Cleaned up variable names. ENH: Performance improvements for backward compatibility of vectorize. After some simple profiling, I found that the wrapping used to support the caching of the previous commit wasted more time than it saved, so I added a flag to allow the user to toggle. Moral: caching makes sense only if the function is expensive and is off by default. I also compared performance with the original vectorize and opted for keeping a cache of _ufunc if otypes is specified and there are no kwargs/excluded vars. This case is easy to implement, and allows users to reproduce (almost) the old performance characteristics if needed. (The new version is about 5% slower in this case). It would be much more complicated to add a similar cache in the case where kwargs are used, and since a wrapper is used here, the performance gain would be negligible (profiling showed that wrapping was a more significant slowdown than the extra call to frompyfunc). - API: Added cache kwarg which allows the user to toggle caching of the first result. - DOC: Added Notes section with a discussion of performance and a warning that vectorize should not be used for performance. - Added private _ufunc member to implement old-style of cache for special case with no kwargs, excluded, and with otypes specified. - Modified test case. Partially address ticket #1982 - I tried to use hasattr(outputs, '__len__') rather than isinstance(outputs, tuple) in order to allow for functions to return lists. This, however, means that strings will get vectorized over each character which breaks previous behaviour. Keeping old behaviour for now. Commit: c8beafda2251693396794a23601acf167a0e61d5 https://github.com/numpy/numpy/commit/c8beafda2251693396794a23601acf167a0e61d5 Author: Travis E. Oliphant Date: 2012-06-12 (Tue, 12 Jun 2012) Changed paths: M numpy/lib/function_base.py M numpy/lib/tests/test_function_base.py Log Message: ----------- Merge pull request #290 from mforbes/new-vectorize-clean ENH: Add kwarg support for vectorize (tickets #2100, #1156, and #1487) (clean) Compare: https://github.com/numpy/numpy/compare/f2a7464e3b87...c8beafda2251 From noreply at github.com Tue Jun 12 04:00:02 2012 From: noreply at github.com (GitHub) Date: Tue, 12 Jun 2012 01:00:02 -0700 Subject: [Numpy-svn] [numpy/numpy] e3862f: Fix dirty handling of internal compiler variable =0D Message-ID: <4fd6f702ea1bc_61ff1061ae81914ab@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: e3862feeba9d7909ae500d0c08d2234a7c221c47 https://github.com/numpy/numpy/commit/e3862feeba9d7909ae500d0c08d2234a7c221c47 Author: ahmadia Date: 2012-05-24 (Thu, 24 May 2012) Changed paths: M numpy/core/src/npymath/ieee754.c.src Log Message: ----------- Fix dirty handling of internal compiler variable __LDBL_DENORM_MIN__ with C11 LDBL_TRUE_MIN (with help from @jedbrown) Commit: f2f306d55ead9a052dea0b1bc7e4a24a2e8916c8 https://github.com/numpy/numpy/commit/f2f306d55ead9a052dea0b1bc7e4a24a2e8916c8 Author: Aron Ahmadia Date: 2012-05-28 (Mon, 28 May 2012) Changed paths: M numpy/core/src/npymath/ieee754.c.src Log Message: ----------- LDBL_TRUE_MIN falls back to __LDBL_DENORM_MIN__ if not defined Commit: cf72f825c30d4f651bd23814420c9c8f2405581d https://github.com/numpy/numpy/commit/cf72f825c30d4f651bd23814420c9c8f2405581d Author: Travis E. Oliphant Date: 2012-06-12 (Tue, 12 Jun 2012) Changed paths: M numpy/core/src/npymath/ieee754.c.src Log Message: ----------- Merge pull request #287 from ahmadia/patch-1 Fix dirty handling of internal compiler variable Compare: https://github.com/numpy/numpy/compare/c8beafda2251...cf72f825c30d From noreply at github.com Wed Jun 13 04:19:44 2012 From: noreply at github.com (GitHub) Date: Wed, 13 Jun 2012 01:19:44 -0700 Subject: [Numpy-svn] [numpy/numpy] 53e49d: REF: remove unused import. Message-ID: <4fd84d2067b40_18d91a9faf0518ba@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 53e49df035a1eea97ac7291638696d9098d9143c https://github.com/numpy/numpy/commit/53e49df035a1eea97ac7291638696d9098d9143c Author: David Cournapeau Date: 2012-06-13 (Wed, 13 Jun 2012) Changed paths: M bscript Log Message: ----------- REF: remove unused import. Commit: 6fe584f1d2775d96fa68ccb4707ba0f658e85376 https://github.com/numpy/numpy/commit/6fe584f1d2775d96fa68ccb4707ba0f658e85376 Author: David Cournapeau Date: 2012-06-13 (Wed, 13 Jun 2012) Changed paths: M bento.info M bscript A numpy/__config__.py.in M numpy/version.py.in Log Message: ----------- ENH: use new metadata registration for version and config. Compare: https://github.com/numpy/numpy/compare/cf72f825c30d...6fe584f1d277 From noreply at github.com Fri Jun 15 07:06:53 2012 From: noreply at github.com (GitHub) Date: Fri, 15 Jun 2012 04:06:53 -0700 Subject: [Numpy-svn] [numpy/numpy] 4c68a3: ENH: report bad value and dimenion to IndexError e... Message-ID: <4fdb174d8aa93_74651d2bae41285b9@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 4c68a33a5b75cbfed1aa0b3b23e947563b9a513a https://github.com/numpy/numpy/commit/4c68a33a5b75cbfed1aa0b3b23e947563b9a513a Author: Thouis (Ray) Jones Date: 2012-06-06 (Wed, 06 Jun 2012) Changed paths: M numpy/core/src/multiarray/arraytypes.c.src M numpy/core/src/multiarray/common.c M numpy/core/src/multiarray/descriptor.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/mapping.c Log Message: ----------- ENH: report bad value and dimenion to IndexError exceptions Commit: 56f865980447b2fc5475b1b71ef7347383660782 https://github.com/numpy/numpy/commit/56f865980447b2fc5475b1b71ef7347383660782 Author: Thouis (Ray) Jones Date: 2012-06-06 (Wed, 06 Jun 2012) Changed paths: M numpy/core/src/multiarray/arraytypes.c.src M numpy/core/src/multiarray/common.c M numpy/core/src/multiarray/common.h M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/descriptor.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/mapping.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/multiarraymodule.c Log Message: ----------- Add check_and_adjust_index(), and replace most index checks with it. This commit adds a check_and_adjust_index(npy_intp *index, npy_intp max, int axis) function which checks index against max, setting an IndexError and returning -1 if it's not valid, and otherwise adjusting index in-place to handle Python's negative indexing, and returning 0. It also changes most places in the code where indexes were being checked and adjusted with a call to this function. Commit: 330468f751410f56eeacb29cb26320faeaec5135 https://github.com/numpy/numpy/commit/330468f751410f56eeacb29cb26320faeaec5135 Author: Thouis (Ray) Jones Date: 2012-06-06 (Wed, 06 Jun 2012) Changed paths: M numpy/core/src/multiarray/arraytypes.c.src M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/mapping.c A numpy/core/tests/test_indexerrors.py Log Message: ----------- Add coverage tests for IndexErrors, fix one bug, clean up two checks Adds numpy/core/tests/test_indexerrors.py with tests to cover failure cases in indexing not covered by other tests. Added a missing check for invalid index in multiarray/iterators.c:iter_ass_sub_int(). Used the new checking code in multiarray/iterators.c:iter_ass_subscript(). Changed a ValueError to an IndexError in multiarray/mapping.c:PyArray_MapIterBind(). Commit: a83e212d40ea4ccb49ab75a60fd5d7afa9307c2a https://github.com/numpy/numpy/commit/a83e212d40ea4ccb49ab75a60fd5d7afa9307c2a Author: Thouis (Ray) Jones Date: 2012-06-15 (Fri, 15 Jun 2012) Changed paths: M numpy/core/src/multiarray/mapping.c Log Message: ----------- Work around Python 2.4's Py_ssize_t not being the same as npyint_p Commit: 004082c59c102e2f458a595db8adecd21c18793f https://github.com/numpy/numpy/commit/004082c59c102e2f458a595db8adecd21c18793f Author: Nathaniel J. Smith Date: 2012-06-15 (Fri, 15 Jun 2012) Changed paths: M numpy/core/src/multiarray/common.c M numpy/core/src/multiarray/common.h Log Message: ----------- Tweak out-of-bounds exception message based on list feedback Commit: 1b6582d98c58afd977a69ac49f7e8e0d08a800b8 https://github.com/numpy/numpy/commit/1b6582d98c58afd977a69ac49f7e8e0d08a800b8 Author: Nathaniel J. Smith Date: 2012-06-15 (Fri, 15 Jun 2012) Changed paths: M numpy/core/src/multiarray/arraytypes.c.src M numpy/core/src/multiarray/common.c M numpy/core/src/multiarray/common.h M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/descriptor.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/mapping.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/multiarraymodule.c A numpy/core/tests/test_indexerrors.py Log Message: ----------- Merge branch 'index_error_info' Compare: https://github.com/numpy/numpy/compare/6fe584f1d277...1b6582d98c58 From noreply at github.com Sat Jun 16 06:54:39 2012 From: noreply at github.com (GitHub) Date: Sat, 16 Jun 2012 03:54:39 -0700 Subject: [Numpy-svn] [numpy/numpy] 5dbd76: [enh] Remove a print statement in datetime.c Message-ID: <4fdc65ef67a1a_733f1918aec40498@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 5dbd76a482ccca278c2882318bc44f6da9f7d45b https://github.com/numpy/numpy/commit/5dbd76a482ccca278c2882318bc44f6da9f7d45b Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: M numpy/core/src/multiarray/datetime.c Log Message: ----------- [enh] Remove a print statement in datetime.c This removes a distracting "'xxx'" printed while running the test suite. Commit: 7d841f3923c7db63f5ac0f27417a7b026aa90118 https://github.com/numpy/numpy/commit/7d841f3923c7db63f5ac0f27417a7b026aa90118 Author: njsmith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: M numpy/core/src/multiarray/datetime.c Log Message: ----------- Merge pull request #310 from njsmith/remove-print-statement [enh] Remove a print statement in datetime.c Compare: https://github.com/numpy/numpy/compare/1b6582d98c58...7d841f3923c7 From noreply at github.com Sat Jun 16 12:34:45 2012 From: noreply at github.com (GitHub) Date: Sat, 16 Jun 2012 09:34:45 -0700 Subject: [Numpy-svn] [numpy/numpy] 1a050b: Add .travis.yml for Travis CI (http://travis-ci.or... Message-ID: <4fdcb5a53e0b9_670d1785af434474b@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 1a050bb5de62dc15c9edf8c7625e71cb8abe4b1b https://github.com/numpy/numpy/commit/1a050bb5de62dc15c9edf8c7625e71cb8abe4b1b Author: Marc Abramowitz Date: 2012-06-05 (Tue, 05 Jun 2012) Changed paths: A .travis-make-py24-virtualenv.sh A .travis.yml Log Message: ----------- Add .travis.yml for Travis CI (http://travis-ci.org/) Commit: 9e2c5af6cac932bd9f8415ea0af72b2e30d196de https://github.com/numpy/numpy/commit/9e2c5af6cac932bd9f8415ea0af72b2e30d196de Author: Marc Abramowitz Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: M .travis.yml Log Message: ----------- Simpler .travis.yml to test everything from py2.4 to py3.2 Uses Travis's new "matrix: include:" feature which makes "the 2.4 hack" more straightforward. Commit: 27c7526c05ce50db2c56f53522051274ea390d07 https://github.com/numpy/numpy/commit/27c7526c05ce50db2c56f53522051274ea390d07 Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: A .travis-make-py24-virtualenv.sh A .travis.yml Log Message: ----------- Merge remote-tracking branch 'msabramo/travis' Commit: d129a54335eb7186a408404ad93b7fd63c6ea919 https://github.com/numpy/numpy/commit/d129a54335eb7186a408404ad93b7fd63c6ea919 Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: M .travis.yml Log Message: ----------- Disable email notifications from travis-ci for now Compare: https://github.com/numpy/numpy/compare/7d841f3923c7...d129a54335eb From noreply at github.com Sat Jun 16 13:09:35 2012 From: noreply at github.com (GitHub) Date: Sat, 16 Jun 2012 10:09:35 -0700 Subject: [Numpy-svn] [numpy/numpy] 36681e: travis-ci: add python 3.1 to the list of tested ve... Message-ID: <4fdcbdcfbde6b_5fd21b7caf452919@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 36681eb2c4b731d5f8e639607aff41404aa8fc45 https://github.com/numpy/numpy/commit/36681eb2c4b731d5f8e639607aff41404aa8fc45 Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: M .travis.yml Log Message: ----------- travis-ci: add python 3.1 to the list of tested versions. From noreply at github.com Wed Jun 20 11:45:11 2012 From: noreply at github.com (GitHub) Date: Wed, 20 Jun 2012 08:45:11 -0700 Subject: [Numpy-svn] [numpy/numpy] 493f23: fix typos Message-ID: <4fe1f0072d130_7fb71d42af02654d3@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 493f23d4a7215b14af62b64f6fc7f9f524099795 https://github.com/numpy/numpy/commit/493f23d4a7215b14af62b64f6fc7f9f524099795 Author: endolith Date: 2012-06-20 (Wed, 20 Jun 2012) Changed paths: M numpy/core/function_base.py Log Message: ----------- fix typos Commit: 651ef74c4ebe7d24e727fd444b1985117ef16fae https://github.com/numpy/numpy/commit/651ef74c4ebe7d24e727fd444b1985117ef16fae Author: njsmith Date: 2012-06-20 (Wed, 20 Jun 2012) Changed paths: M numpy/core/function_base.py Log Message: ----------- Merge pull request #313 from endolith/patch-1 fix typos Compare: https://github.com/numpy/numpy/compare/36681eb2c4b7...651ef74c4ebe From noreply at github.com Thu Jun 21 04:37:05 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 01:37:05 -0700 Subject: [Numpy-svn] [numpy/numpy] b272bc: Remove maskna API from ndarray, and all (and only)... Message-ID: <4fe2dd311bb67_738d10ffaf4121197@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: b272bc605ce7784be5b3edb13ad7afe22b04e71f https://github.com/numpy/numpy/commit/b272bc605ce7784be5b3edb13ad7afe22b04e71f Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: R doc/source/reference/arrays.maskna.rst M doc/source/reference/arrays.rst M doc/source/reference/c-api.array.rst R doc/source/reference/c-api.maskna.rst M doc/source/reference/c-api.rst M doc/source/reference/routines.polynomials.classes.rst M doc/source/reference/routines.rst M numpy/add_newdocs.py M numpy/core/_methods.py M numpy/core/arrayprint.py M numpy/core/code_generators/genapi.py M numpy/core/code_generators/numpy_api.py M numpy/core/fromnumeric.py M numpy/core/function_base.py M numpy/core/include/numpy/ndarraytypes.h M numpy/core/include/numpy/ufuncobject.h M numpy/core/numeric.py M numpy/core/numerictypes.py M numpy/core/setup.py M numpy/core/src/multiarray/array_assign.h M numpy/core/src/multiarray/array_assign_array.c M numpy/core/src/multiarray/array_assign_scalar.c M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/arraytypes.c.src R numpy/core/src/multiarray/boolean_ops.c.src R numpy/core/src/multiarray/boolean_ops.h M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/calculation.c M numpy/core/src/multiarray/common.c M numpy/core/src/multiarray/common.h M numpy/core/src/multiarray/conversion_utils.c M numpy/core/src/multiarray/convert.c M numpy/core/src/multiarray/convert_datatype.c M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/ctors.h M numpy/core/src/multiarray/datetime.c M numpy/core/src/multiarray/dtype_transfer.c M numpy/core/src/multiarray/einsum.c.src M numpy/core/src/multiarray/flagsobject.c M numpy/core/src/multiarray/getset.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/item_selection.h M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/iterators.h M numpy/core/src/multiarray/mapping.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/multiarraymodule.c M numpy/core/src/multiarray/multiarraymodule_onefile.c R numpy/core/src/multiarray/na_mask.c R numpy/core/src/multiarray/na_mask.h R numpy/core/src/multiarray/na_object.c R numpy/core/src/multiarray/na_object.h M numpy/core/src/multiarray/nditer_api.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/nditer_impl.h M numpy/core/src/multiarray/nditer_pywrap.c M numpy/core/src/multiarray/reduction.c M numpy/core/src/multiarray/reduction.h M numpy/core/src/multiarray/scalarapi.c M numpy/core/src/multiarray/sequence.c M numpy/core/src/multiarray/shape.c M numpy/core/src/private/lowlevel_strided_loops.h M numpy/core/src/umath/ufunc_object.c M numpy/core/src/umath/ufunc_type_resolution.c M numpy/core/tests/test_api.py M numpy/core/tests/test_indexerrors.py R numpy/core/tests/test_maskna.py M numpy/core/tests/test_multiarray.py R numpy/core/tests/test_na.py M numpy/core/tests/test_nditer.py M numpy/core/tests/test_numeric.py M numpy/core/tests/test_regression.py M numpy/lib/function_base.py M numpy/lib/twodim_base.py M numpy/polynomial/chebyshev.py M numpy/polynomial/hermite.py M numpy/polynomial/hermite_e.py M numpy/polynomial/laguerre.py M numpy/polynomial/legendre.py M numpy/polynomial/polynomial.py M numpy/polynomial/tests/test_chebyshev.py M numpy/polynomial/tests/test_hermite.py M numpy/polynomial/tests/test_hermite_e.py M numpy/polynomial/tests/test_laguerre.py M numpy/polynomial/tests/test_legendre.py M numpy/polynomial/tests/test_polynomial.py M numpy/testing/utils.py Log Message: ----------- Remove maskna API from ndarray, and all (and only) the code supporting it The original masked-NA-NEP branch contained a large number of changes in addition to the core NA support. For example: - ufunc.__call__ support for where= argument - nditer support for arbitrary masks (in support of where=) - ufunc.reduce support for simultaneous reduction over multiple axes - a new "array assignment API" - ndarray.diagonal() returning a view in all cases - bug-fixes in __array_priority__ handling - datetime test changes etc. There's no consensus yet on what should be done with the maskna-related part of this branch, but the rest is generally useful and uncontroversial, so the goal of this branch is to identify exactly which code changes are involved in maskna support. The basic strategy used to create this patch was: - Remove the new masking-related fields from ndarray, so no arrays are masked - Go through and remove all the code that this makes dead/inaccessible/irrelevant, in a largely mechanical fashion. So for example, if I saw 'if (PyArray_HASMASK(a)) { ... }' then that whole block was obviously just dead code if no arrays have masks, and I removed it. Likewise for function arguments like skipna that are useless if there aren't any NAs to skip. This changed the signature of a number of functions that were newly exposed in the numpy public API. I've removed all such functions from the public API, since releasing them with the NA-less signature in 1.7 would create pointless compatibility hassles later if and when we add back the NA-related functionality. Most such functions are removed by this commit; the exception is PyArray_ReduceWrapper, which requires more extensive surgery, and will be handled in followup commits. I also removed the new ndarray.setasflat method. Reason: a comment noted that the only reason this was added was to allow easier testing of one branch of PyArray_CopyAsFlat. That branch is now the main branch, so that isn't an issue. Nonetheless this function is arguably useful, so perhaps it should have remained, but I judged that since numpy's API is already hairier than we would like, it's not a good idea to add extra hair "just in case". (Also AFAICT the test for this method in test_maskna was actually incorrect, as noted here: https://github.com/njsmith/numpyNEP/blob/master/numpyNEP.py so I'm not confident that it ever worked in master, though I haven't had a chance to follow-up on this.) I also removed numpy.count_reduce_items, since without skipna it became trivial. I believe that these are the only exceptions to the "remove dead code" strategy. Commit: 605c2b45caa8838716b736e322f9e1b5d347daba https://github.com/numpy/numpy/commit/605c2b45caa8838716b736e322f9e1b5d347daba Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: R numpy/core/src/multiarray/reduction.c R numpy/core/src/multiarray/reduction.h A numpy/core/src/umath/reduction.c A numpy/core/src/umath/reduction.h Log Message: ----------- Move reduction.{c,h} from multiarray/ to umath/ This is done as a separate commit to make sure git can track the change. This commit will not build. See next commit for actual changes and rationale. Commit: 3626d0c4fe510d615ef3e5ef3cf4ed2bfb52b53e https://github.com/numpy/numpy/commit/3626d0c4fe510d615ef3e5ef3cf4ed2bfb52b53e Author: Nathaniel J. Smith Date: 2012-06-16 (Sat, 16 Jun 2012) Changed paths: M numpy/add_newdocs.py M numpy/core/SConscript M numpy/core/code_generators/cversions.txt M numpy/core/code_generators/genapi.py M numpy/core/code_generators/numpy_api.py M numpy/core/include/numpy/ndarraytypes.h M numpy/core/setup.py M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/item_selection.h M numpy/core/src/multiarray/multiarraymodule.c M numpy/core/src/multiarray/multiarraymodule_onefile.c M numpy/core/src/umath/reduction.c M numpy/core/src/umath/reduction.h M numpy/core/src/umath/ufunc_object.c M numpy/core/src/umath/umathmodule_onefile.c M numpy/core/tests/test_numeric.py Log Message: ----------- Remove PyArray_ReduceWrapper from public API There are two reasons to want to keep PyArray_ReduceWrapper out of the public multiarray API: - Its signature is likely to change if/when masked arrays are added - It is essentially a wrapper for array->scalar transformations (*not* just reductions as its name implies -- the whole reason it is in multiarray.so in the first place is to support count_nonzero, which is not actually a reduction!). It provides some nice conveniences (like making it easy to apply such functions to multiple axes simultaneously), but, we already have a general mechanism for writing array->scalar transformations -- generalized ufuncs. We do not want to have two independent, redundant implementations of this functionality, one in multiarray and one in umath! So in the long run we should add these nice features to the generalized ufunc machinery. And in the short run, we shouldn't add it to the public API and commit ourselves to supporting it. However, simply removing it from numpy_api.py is not easy, because this code was used in both multiarray and umath. This commit: - Moves ReduceWrapper and supporting code to umath/, and makes appropriate changes (e.g. renaming it to PyUFunc_ReduceWrapper and cleaning up the header files). - Reverts numpy.count_nonzero to its previous implementation, so that it loses the new axis= and keepdims= arguments. This is unfortunate, but this change isn't so urgent that it's worth tying our APIs in knots forever. (Perhaps in the future it can become a generalized ufunc.) Commit: 134174c9265dd87ea802c89cac7a89478e3184f4 https://github.com/numpy/numpy/commit/134174c9265dd87ea802c89cac7a89478e3184f4 Author: Travis E. Oliphant Date: 2012-06-21 (Thu, 21 Jun 2012) Changed paths: R doc/source/reference/arrays.maskna.rst M doc/source/reference/arrays.rst M doc/source/reference/c-api.array.rst R doc/source/reference/c-api.maskna.rst M doc/source/reference/c-api.rst M doc/source/reference/routines.polynomials.classes.rst M doc/source/reference/routines.rst M numpy/add_newdocs.py M numpy/core/SConscript M numpy/core/_methods.py M numpy/core/arrayprint.py M numpy/core/code_generators/cversions.txt M numpy/core/code_generators/genapi.py M numpy/core/code_generators/numpy_api.py M numpy/core/fromnumeric.py M numpy/core/function_base.py M numpy/core/include/numpy/ndarraytypes.h M numpy/core/include/numpy/ufuncobject.h M numpy/core/numeric.py M numpy/core/numerictypes.py M numpy/core/setup.py M numpy/core/src/multiarray/array_assign.h M numpy/core/src/multiarray/array_assign_array.c M numpy/core/src/multiarray/array_assign_scalar.c M numpy/core/src/multiarray/arrayobject.c M numpy/core/src/multiarray/arraytypes.c.src R numpy/core/src/multiarray/boolean_ops.c.src R numpy/core/src/multiarray/boolean_ops.h M numpy/core/src/multiarray/buffer.c M numpy/core/src/multiarray/calculation.c M numpy/core/src/multiarray/common.c M numpy/core/src/multiarray/common.h M numpy/core/src/multiarray/conversion_utils.c M numpy/core/src/multiarray/convert.c M numpy/core/src/multiarray/convert_datatype.c M numpy/core/src/multiarray/ctors.c M numpy/core/src/multiarray/ctors.h M numpy/core/src/multiarray/datetime.c M numpy/core/src/multiarray/dtype_transfer.c M numpy/core/src/multiarray/einsum.c.src M numpy/core/src/multiarray/flagsobject.c M numpy/core/src/multiarray/getset.c M numpy/core/src/multiarray/item_selection.c M numpy/core/src/multiarray/item_selection.h M numpy/core/src/multiarray/iterators.c M numpy/core/src/multiarray/iterators.h M numpy/core/src/multiarray/mapping.c M numpy/core/src/multiarray/methods.c M numpy/core/src/multiarray/multiarraymodule.c M numpy/core/src/multiarray/multiarraymodule_onefile.c R numpy/core/src/multiarray/na_mask.c R numpy/core/src/multiarray/na_mask.h R numpy/core/src/multiarray/na_object.c R numpy/core/src/multiarray/na_object.h M numpy/core/src/multiarray/nditer_api.c M numpy/core/src/multiarray/nditer_constr.c M numpy/core/src/multiarray/nditer_impl.h M numpy/core/src/multiarray/nditer_pywrap.c R numpy/core/src/multiarray/reduction.c R numpy/core/src/multiarray/reduction.h M numpy/core/src/multiarray/scalarapi.c M numpy/core/src/multiarray/sequence.c M numpy/core/src/multiarray/shape.c M numpy/core/src/private/lowlevel_strided_loops.h A numpy/core/src/umath/reduction.c A numpy/core/src/umath/reduction.h M numpy/core/src/umath/ufunc_object.c M numpy/core/src/umath/ufunc_type_resolution.c M numpy/core/src/umath/umathmodule_onefile.c M numpy/core/tests/test_api.py M numpy/core/tests/test_indexerrors.py R numpy/core/tests/test_maskna.py M numpy/core/tests/test_multiarray.py R numpy/core/tests/test_na.py M numpy/core/tests/test_nditer.py M numpy/core/tests/test_numeric.py M numpy/core/tests/test_regression.py M numpy/lib/function_base.py M numpy/lib/twodim_base.py M numpy/polynomial/chebyshev.py M numpy/polynomial/hermite.py M numpy/polynomial/hermite_e.py M numpy/polynomial/laguerre.py M numpy/polynomial/legendre.py M numpy/polynomial/polynomial.py M numpy/polynomial/tests/test_chebyshev.py M numpy/polynomial/tests/test_hermite.py M numpy/polynomial/tests/test_hermite_e.py M numpy/polynomial/tests/test_laguerre.py M numpy/polynomial/tests/test_legendre.py M numpy/polynomial/tests/test_polynomial.py M numpy/testing/utils.py Log Message: ----------- Merge pull request #297 from njsmith/separate-maskna Split maskna support out of mainline into a branch Compare: https://github.com/numpy/numpy/compare/651ef74c4ebe...134174c9265d From noreply at github.com Thu Jun 21 04:42:24 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 01:42:24 -0700 Subject: [Numpy-svn] [numpy/numpy] Message-ID: <4fe2de70e4a51_79141659af4140959@sh3.rs.github.com.mail> Branch: refs/heads/with_maskna Home: https://github.com/numpy/numpy From noreply at github.com Thu Jun 21 05:57:14 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 02:57:14 -0700 Subject: [Numpy-svn] [numpy/numpy] db1701: BUG: Fix boolean indexing to previous behavior by ... Message-ID: <4fe2effa3ddcc_4cac1b4daec1762c8@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: db1701baf57965e8533293426a0c3b403e81f39a https://github.com/numpy/numpy/commit/db1701baf57965e8533293426a0c3b403e81f39a Author: Travis E. Oliphant Date: 2012-06-21 (Thu, 21 Jun 2012) Changed paths: M doc/release/2.0.0-notes.rst M numpy/core/src/multiarray/mapping.c M numpy/core/tests/test_multiarray.py Log Message: ----------- BUG: Fix boolean indexing to previous behavior by adding an additional check before using the new code path. Add tests. From noreply at github.com Thu Jun 21 05:58:55 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 02:58:55 -0700 Subject: [Numpy-svn] [numpy/numpy] Message-ID: <4fe2f05f7d4cd_278b1b5aae41586a@sh2.rs.github.com.mail> Branch: refs/heads/maintenance/1.7.x Home: https://github.com/numpy/numpy From noreply at github.com Thu Jun 21 06:10:34 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 03:10:34 -0700 Subject: [Numpy-svn] [numpy/numpy] eee465: Change version number on master to 1.8 Message-ID: <4fe2f31a2fe24_4cac1b4daec179551@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: eee46518b869ae05490c085783fd5b09a40b2273 https://github.com/numpy/numpy/commit/eee46518b869ae05490c085783fd5b09a40b2273 Author: Travis E. Oliphant Date: 2012-06-21 (Thu, 21 Jun 2012) Changed paths: M setup.py Log Message: ----------- Change version number on master to 1.8 From noreply at github.com Thu Jun 21 15:54:15 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 12:54:15 -0700 Subject: [Numpy-svn] [numpy/numpy] 699c2f: BLD: fix Bento and Numscons builds, that were brok... Message-ID: <4fe37be7e59ac_7c1bf92af41078c1@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 699c2f3cca63966bf086c58a59e1b6ee6fa7e090 https://github.com/numpy/numpy/commit/699c2f3cca63966bf086c58a59e1b6ee6fa7e090 Author: Ralf Gommers Date: 2012-06-21 (Thu, 21 Jun 2012) Changed paths: M numpy/core/SConscript M numpy/core/bscript Log Message: ----------- BLD: fix Bento and Numscons builds, that were broken in b272bc60. From noreply at github.com Thu Jun 21 15:57:02 2012 From: noreply at github.com (GitHub) Date: Thu, 21 Jun 2012 12:57:02 -0700 Subject: [Numpy-svn] [numpy/numpy] 66bd39: BLD: fix Bento and Numscons builds, that were brok... Message-ID: <4fe37c8e96d5e_67021633ae81358c9@sh2.rs.github.com.mail> Branch: refs/heads/maintenance/1.7.x Home: https://github.com/numpy/numpy Commit: 66bd39f021007cbade675cb6944441bcb5737ea5 https://github.com/numpy/numpy/commit/66bd39f021007cbade675cb6944441bcb5737ea5 Author: Ralf Gommers Date: 2012-06-21 (Thu, 21 Jun 2012) Changed paths: M numpy/core/SConscript M numpy/core/bscript Log Message: ----------- BLD: fix Bento and Numscons builds, that were broken in b272bc60. (backported from 699c2f3) From noreply at github.com Mon Jun 25 05:22:40 2012 From: noreply at github.com (GitHub) Date: Mon, 25 Jun 2012 02:22:40 -0700 Subject: [Numpy-svn] [numpy/numpy] 998283: ENH: allow NPY_SEPARATE_COMPILATION to be set to 0... Message-ID: <4fe82de0c0303_63f31058aec1832cf@sh2.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 9982831d955bfd87ead42704c76992c3633f4664 https://github.com/numpy/numpy/commit/9982831d955bfd87ead42704c76992c3633f4664 Author: David Cournapeau Date: 2012-06-24 (Sun, 24 Jun 2012) Changed paths: M numpy/core/setup.py Log Message: ----------- ENH: allow NPY_SEPARATE_COMPILATION to be set to 0 to disallow separate build. Commit: 6e1e61da848e8d538d4a0482f4cc9cdcf87aad54 https://github.com/numpy/numpy/commit/6e1e61da848e8d538d4a0482f4cc9cdcf87aad54 Author: David Cournapeau Date: 2012-06-24 (Sun, 24 Jun 2012) Changed paths: M .travis.yml Log Message: ----------- TST: add separate compilation to travis-ci matrix. We only test 2.7 and 3.2 for now. If NumFocus does a donation, maybe we can reasonably expand to all the versions we care about. Commit: e29dc430bd4d55650ec8996ee58feca126c433ea https://github.com/numpy/numpy/commit/e29dc430bd4d55650ec8996ee58feca126c433ea Author: David Cournapeau Date: 2012-06-24 (Sun, 24 Jun 2012) Changed paths: M numpy/core/bscript Log Message: ----------- ENH: handle separate compilation in bento as in setup.py. Commit: e57266c9c738d5823f1eb3e8df846a4df5092179 https://github.com/numpy/numpy/commit/e57266c9c738d5823f1eb3e8df846a4df5092179 Author: David Cournapeau Date: 2012-06-24 (Sun, 24 Jun 2012) Changed paths: M .travis.yml Log Message: ----------- TST: fix matrix def in travis to avoid unwanted builds. Commit: 6bb3ef6b9737f9aae021f8905170eeb160f67d6f https://github.com/numpy/numpy/commit/6bb3ef6b9737f9aae021f8905170eeb160f67d6f Author: David Cournapeau Date: 2012-06-24 (Sun, 24 Jun 2012) Changed paths: M .travis.yml Log Message: ----------- TST: fix .travis.yml to re-enable python 2.4 builds. Commit: 465c2f44f0c19d2abe7b5d060c447f69526ca14c https://github.com/numpy/numpy/commit/465c2f44f0c19d2abe7b5d060c447f69526ca14c Author: David Cournapeau Date: 2012-06-24 (Sun, 24 Jun 2012) Changed paths: M numpy/core/src/multiarray/_datetime.h M numpy/core/src/multiarray/datetime_busdaycal.h M numpy/core/src/umath/reduction.c Log Message: ----------- BUG: fix separate compilation (with distutils only for now). Commit: 6a06466c5970e4f1cd5ba5ba5457eeb41d9a7280 https://github.com/numpy/numpy/commit/6a06466c5970e4f1cd5ba5ba5457eeb41d9a7280 Author: njsmith Date: 2012-06-25 (Mon, 25 Jun 2012) Changed paths: M .travis.yml M numpy/core/bscript M numpy/core/setup.py M numpy/core/src/multiarray/_datetime.h M numpy/core/src/multiarray/datetime_busdaycal.h M numpy/core/src/umath/reduction.c Log Message: ----------- Merge pull request #317 from cournape/travis_ci_separate_compilation Travis ci separate compilation Compare: https://github.com/numpy/numpy/compare/699c2f3cca63...6a06466c5970 From noreply at github.com Tue Jun 26 18:53:03 2012 From: noreply at github.com (GitHub) Date: Tue, 26 Jun 2012 15:53:03 -0700 Subject: [Numpy-svn] [numpy/numpy] 563941: DOC: update HOWTO_RELEASE document. Message-ID: <4fea3d4f23c5f_574a1648aec129474@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 5639414be0869a2e53a62ffeeffb838ddcf9df60 https://github.com/numpy/numpy/commit/5639414be0869a2e53a62ffeeffb838ddcf9df60 Author: Ralf Gommers Date: 2012-06-26 (Tue, 26 Jun 2012) Changed paths: M doc/HOWTO_RELEASE.rst.txt Log Message: ----------- DOC: update HOWTO_RELEASE document. Commit: da3da3d1887d60720e1a2d160d654624ed03421d https://github.com/numpy/numpy/commit/da3da3d1887d60720e1a2d160d654624ed03421d Author: Stefan van der Walt Date: 2012-06-26 (Tue, 26 Jun 2012) Changed paths: M doc/HOWTO_RELEASE.rst.txt Log Message: ----------- Merge pull request #321 from rgommers/update-howto-release DOC: update HOWTO_RELEASE document. Compare: https://github.com/numpy/numpy/compare/6a06466c5970...da3da3d1887d From noreply at github.com Tue Jun 26 22:59:11 2012 From: noreply at github.com (GitHub) Date: Tue, 26 Jun 2012 19:59:11 -0700 Subject: [Numpy-svn] [numpy/numpy] 56183d: PKG: Fix numpy core bscript. Message-ID: <4fea76ff95a19_67a61d3daf036468@sh3.rs.github.com.mail> Branch: refs/heads/master Home: https://github.com/numpy/numpy Commit: 56183d7d4d36e099c6e81ece3bc9ad5a957207b3 https://github.com/numpy/numpy/commit/56183d7d4d36e099c6e81ece3bc9ad5a957207b3 Author: Stefan van der Walt Date: 2012-06-26 (Tue, 26 Jun 2012) Changed paths: M numpy/core/bscript Log Message: ----------- PKG: Fix numpy core bscript. Commit: e15d0bdd3cc0bc0928e1f4d0b419a2fb3de02af9 https://github.com/numpy/numpy/commit/e15d0bdd3cc0bc0928e1f4d0b419a2fb3de02af9 Author: Travis E. Oliphant Date: 2012-06-26 (Tue, 26 Jun 2012) Changed paths: M numpy/core/bscript Log Message: ----------- Merge pull request #322 from stefanv/fix_np_core_bscript PKG: Fix numpy core bscript. Compare: https://github.com/numpy/numpy/compare/da3da3d1887d...e15d0bdd3cc0 From noreply at github.com Fri Jun 29 10:13:57 2012 From: noreply at github.com (GitHub) Date: Fri, 29 Jun 2012 07:13:57 -0700 Subject: [Numpy-svn] [numpy/numpy] 684751: DOC: Rename the release notes to 1.7.0-notes.rst Message-ID: <4fedb82524a5f_39181163af42189fe@sh2.rs.github.com.mail> Branch: refs/heads/maintenance/1.7.x Home: https://github.com/numpy/numpy Commit: 684751304f4d8bec77c705a0f30489e33a55b3e6 https://github.com/numpy/numpy/commit/684751304f4d8bec77c705a0f30489e33a55b3e6 Author: Ondrej Certik Date: 2012-06-28 (Thu, 28 Jun 2012) Changed paths: A doc/release/1.7.0-notes.rst R doc/release/2.0.0-notes.rst Log Message: ----------- DOC: Rename the release notes to 1.7.0-notes.rst Commit: 3a56f5c59759423ca7e9f8b3d3150932009934f6 https://github.com/numpy/numpy/commit/3a56f5c59759423ca7e9f8b3d3150932009934f6 Author: Ondrej Certik Date: 2012-06-28 (Thu, 28 Jun 2012) Changed paths: M doc/release/1.7.0-notes.rst Log Message: ----------- DOC: Improve the release notes for 1.7.0 Besides a few fixes here and there, the following changes were done: * Add a note about C_STYLE_GUIDE.rst.txt * Add a link to arrays.datetime.rst for now * Add more highlights (thanks to @rgommers) * Mention the 'formatter' argument * Mention business day functionality * Improve and merge the two datetime sections Commit: 95c84bfce5610b4cc122541f7cb155a56cf321f9 https://github.com/numpy/numpy/commit/95c84bfce5610b4cc122541f7cb155a56cf321f9 Author: Charles Harris Date: 2012-06-29 (Fri, 29 Jun 2012) Changed paths: A doc/release/1.7.0-notes.rst R doc/release/2.0.0-notes.rst Log Message: ----------- Merge pull request #318 from certik/ondrej1 Release notes Compare: https://github.com/numpy/numpy/compare/66bd39f02100...95c84bfce561