File python-tables.changes of Package python-tables
-------------------------------------------------------------------
Sun Aug 25 20:55:20 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Update to 3.10.1
## Bugfixes
* Fix version constraints for the numpy runtime requirements
* (#1204).
* For a mistake it didn't allow to use PyTables with numpy 2.x.
* Fix compatibility with PyPy (:issue:1205), Thanks to Michał
Górny.
## Improvements
* Upstream: Enforce numpy >= 2 as build constraint (see
discussion in #1200). -- not enforced in openSUSE
* Use tuple of plain ints for chunk info coordinates. Thanks to
Ivan Vilata-i-Balaguer.
* Enable faulthandler in tables.tests.test_all. Thanks to Eric
Larson.
- Release 3.10.0
* New direct chunking API which allows access to raw chunk data
skipping the HDF5 filter pipeline (cutting overhead, see
"Optimization tips" in User's Guide), as well as querying chunk
information (#1187). Thanks to Ivan Vilata and Francesc Alted.
This development was funded by a NumFOCUS grant.
## Improvements
* This release is finally compatible with NumPy 2 with wheels
being built against it so that they are still binary-compatible
with NumPy 1 installations (#1176, #1183, #1184, #1192, #1195,
#1160, #1172, #1185). NumPy >= 1.20 is required now. Thanks to
Antonio Valentino, Maximilian Linhoff and Eric Larson.
* Fix compatibility with Python 3.13 (#1166), Python >= 3.10
required. Cython 3.0.10 is required for building. Thanks to
Antonio Valentino.
* Add type hints to atom.py (#1079). This also narrows some
types, only allowing bytes to be stored in VLStringAtom and
only str in VLUnicodeAtom. Thanks to Nils Carlson.
* Add type hints to (hopefully) the complete PyTables API (#1119,
#1120, #1121, #1123, #1124, #1125, #1125, #1126, #1128, #1129,
#1130, #1131, #1132, #1133, #1135, #1136, #1137, #1138, #1139,
#1140, #1141, #1142, #1143, #1145, #1146, #1147, #1148, #1150,
#1151, #1152). Thanks to Ko Stehner.
* Reduce impact of CPU information gathering by caching in local
file (#1091, #1118, #1081). Thanks to Antti Mäkinen and
Maximilian Linhoff.
## Bugfixes
* Fix typos and may other language errors in docstrings (#1122).
Thanks to Ko Stehner.
* Fix Blosc2 filter not setting dparams.schunk on decompression
(#1110 and #1109). Thanks to Tom Birch.
* Fix using B2ND optimizations when Blosc2 is not the only
enabled filter; move Fletcher32 compression to end of pipeline
when enabled (#1191 and #1162). Thanks to Ivan Vilata and Alex
Laslavic.
* Fix broken internal passing of createparents argument in
Leaf.copy (#1127 and #1125). Thanks to Ko Stehner.
* Re-enable relative paths in ExternalLink class (#1095). Thanks
to erikdl-zeiss.
* Fix using prefix in heavy tests methods of test_queries
(#1169). Thanks to Miro Hrončok.
* Fix TypeError when computing Blosc2 search paths with missing
library (#1188 and #1100). Thanks to martinowitsch, Padraic
Calpin and Eric Larson.
* Avoid overflow RuntimeWarning on NumPy expectedrows value
(#1010). Thanks to wony-zheng and Ivan Vilata.
## Other changes
* Assorted fixes to b2nd benchmark, with new results. Thanks to
Ivan Vilata.
* Point users to example code to handle "Selection lists cannot
have repeated values" exception (#1161 and #1149). Thanks to
Joshua Albert.
* Remove unused getLibrary C code. Thanks to Antonio Valentino.
-------------------------------------------------------------------
Fri Apr 19 12:01:41 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Pin to numpy < 2: gh#PyTables/PyTables#1083
- Clean obsolete python39
-------------------------------------------------------------------
Fri Feb 23 12:25:06 UTC 2024 - Dominique Leuenberger <dimstar@opensuse.org>
- Use newly supported shrink{} on OBS to exclude python flavors
will all python versions skipped.
-------------------------------------------------------------------
Tue Feb 20 15:17:07 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Reenable test flavor for Python 3.9 instead of actually testing
it with every other test flavor. Will now automatically be
excluded when globally dropped and can be removed at a later
time.
- Enable sle15_python_module_pythons for the sake of multiflavor
simplicity (still unresolvable for now)
-------------------------------------------------------------------
Tue Feb 6 09:37:59 UTC 2024 - Dirk Müller <dmueller@suse.com>
- disable testing for 3.9, add 3.12 testing
-------------------------------------------------------------------
Fri Dec 1 02:23:22 UTC 2023 - Steve Kowalik <steven.kowalik@suse.com>
- Update to 3.9.2:
* Minimum supported version for Python is 3.9 (see gh-1062).
* New features
+ Apply optimized slice read to Blosc2-compressed CArray and EArray
+ Add basic API for column-level attributes as Col._v_col_attrs
* Bugfixes
+ Fix the assembly of returned slice data in Blosc2 NDim optimized
slice reads by using Blosc2’s b2nd_copy_buffer
+ Fix crash in Blosc2 optimized path with large tables
+ Fix compatibility with NumExpr v2.8.5
+ Fix ptrepack failures with external links
+ Replace stderr messages with Python warnings
+ Fix Cython slice indexing under Python 3.12
+ Fix unsafe temporary file creation in benchmark
* Improvements
+ PyTables wheels now use a threadsafe build of the HDF5 library
+ Partial support for the future NumPy 2, with some tests still failing
+ Relax the reading of Blosc2 NDim to cope with datasets stored with
other tools
+ Use H5Dchunk_iter (when available) to speed up walking over many chunks
in a very large table, as well as with random reads
+ Improve setup.py (now using pyproject.toml as per PEP 518) and
blosc2 discovery mechanism
+ Enable compatibility with Cython 3
+ Handle py-cpuinfo missing in some platforms
+ Avoid NumPy >= 1.25 deprecations, use numpy.all, numpy.any, etc. instead.
* Other changes
+ Drop compatibility with the obsolete HDF5 1.8 API
+ Require python-blosc2 >= 2.3.0 or c-blosc2 >= 2.11.0
+ Assorted fixes to b2nd slicing optimization tips
+ New benchmark for ERA5 climate data
+ New “100 trillion baby” benchmark
+ New benchmark for querying meteorologic data
- Unpin Cython, Cython 3 is now supported
- Drop patches tables-pr1000-debundled-blosc2.patch and numpy-1.25.patch:
* Both included upstream
-------------------------------------------------------------------
Mon Aug 21 00:59:03 UTC 2023 - Steve Kowalik <steven.kowalik@suse.com>
- Pin Cython to < 3.
-------------------------------------------------------------------
Fri Aug 18 10:11:42 UTC 2023 - Daniel Garcia <daniel.garcia@suse.com>
- Add numpy-1.25.patch upstream patch
gh#PyTables/PyTables@337792561e59
-------------------------------------------------------------------
Tue Apr 11 08:30:57 UTC 2023 - Dominique Leuenberger <dimstar@opensuse.org>
- Remove test-py38 flavor from multibuild: python 3.8 is no longer
supported.
-------------------------------------------------------------------
Sat Feb 25 18:35:30 UTC 2023 - Ben Greiner <code@bnavigator.de>
- Promote tables-debundled-blosc2.patch to
tables-pr1000-debundled-blosc2.patch
* Do not require python-blosc2 for anything
* gh#PyTables/PyTables#1000
- Remove pre-compiled libblosc2.so gh#PyTables/PyTables#1001
- Split out test into multibuilds: Even the "light" test suite
takes more than 1 hour for all 4 python flavors executed
sequentially
-------------------------------------------------------------------
Fri Feb 17 21:15:02 UTC 2023 - Ben Greiner <code@bnavigator.de>
- Use python-blosc2 and c-blosc2
- Drop environement vars which would have only been used with
embedded c-blosc
- Disable building docs (sphinx update broke it)
- Add tables-debundled-blosc2.patch gh#PyTables/PyTables#1000
-------------------------------------------------------------------
Wed Feb 8 18:39:24 UTC 2023 - Arun Persaud <arun@gmx.de>
- specfile:
* update copyright year
* require python >= 3.8
- update to version 3.8.0:
* Improvements
+ Support for Python 3.11 has been added (PR #962).
+ Support for Python 3.6 and Python 3.7 has been dropped (PR
#966).
+ Added a new (registered) HDF5 filter for Blosc2 compressor (PR
#969).
+ Added optimized paths for Blosc2 reading and writing in
tables. This bypasses the HDF5 filter pipeline by building the Blosc2 CFrames
and sending them to the HDF5 direct chunking machinery (PR #969).
+ Internal C-Blosc sources updated to 1.21.2.
+ Thanks to Oscar Guiñon, Francesc Alted for implementing Blosc2
the support and NumFOCUS for providing a grant for that.
* Other changes
+ Starting form this release, C source files generated by Cython
are no longer included in the source distribution package.
+ Pre-built HTML documentation is no longer included in the source
package.
-------------------------------------------------------------------
Tue Mar 29 19:31:32 UTC 2022 - Ben Greiner <code@bnavigator.de>
- Avoid HDF5 library version mismatches -- see boo#1196682
-------------------------------------------------------------------
Sun Jan 16 10:40:28 UTC 2022 - Ben Greiner <code@bnavigator.de>
- Update to 3.7.0
* Compatibility with Python 3.10, numpy 1.21 and HDF5 1.12.
* Support for Python 3.5 has been dropped (#840 and #850).
* Internal C-Blosc sources updated to 1.21.1 (#931). Note that,
starting from C-Blosc 1.19 does not include the Snappy codec
sources anymore, so Snappy will be not available if you compile
from included sources; other packages (like conda or wheels),
may (or may not) include it.
* Switch to git submodule for the management of vendored c-blosc
sources.
* Improved code formatting and notation consistency (#873, #868,
#865 thanks to Miroslav Šedivý).
* Improve the use of modern Python including :mod:pathlib,
f-strings (#859, #855, #839 and #818 thanks to Miroslav
Šedivý).
* Simplified management of version information.
* Drop dependency on the deprecated distutils.
* Modernize the setup script and add support for PEP517 (#907).
* Fix pkg-config (setup.py) for Python 3.9 on Debian. Thanks to
Marco Sulla PR #792.
* Fix ROFileNode fails to return the fileno() (#633).
* Do not flush read only files (#915 thanks to @lrepiton).
* Drop the deprecated hdf5Version and File.open_count.
* the :func:get_tables_version and :func:get_hdf5_version
functions are now deprecated please use the coresponding
:data:tables.__version__ and :data:tables.hdf5_version instead.
- Drop patches fixed upstream
* PyTables-compat-numpy119.patch
* PyTables-pr810-tostring.patch
* PyTables-skip-test_vlarray.patch
* tables-pr862-lowercasefdtype.patch
- Replace Never-use-the-msse2-flag-explicitly.patch by use of
environment variable
-------------------------------------------------------------------
Wed Feb 17 22:16:55 UTC 2021 - Ben Greiner <code@bnavigator.de>
- Skip python36 build: python36-numpy was dropped in Tumbleweed
due to NEP 29
- Add tables-pr862-lowercasefdtype.patch to support NumPy 1.20
gh#PyTables/PyTables#862
-------------------------------------------------------------------
Thu Dec 24 13:47:31 UTC 2020 - Benjamin Greiner <code@bnavigator.de>
- remove mock requirement
- add PyTables-compat-numpy119.patch for compatibility with numpy
1.19
- add PyTables-pr810-tostring.patch in order to avoid numerous
deprecation warnings -- gh#PyTables/PyTables#810
- add PyTables-skip-test_vlarray.patch in order to skip failing
tests -- gh#PyTables/PyTables#845
-------------------------------------------------------------------
Tue May 19 08:03:09 UTC 2020 - Petr Gajdos <pgajdos@suse.com>
- %python3_only -> %python_alternative
-------------------------------------------------------------------
Sat Nov 9 15:08:18 UTC 2019 - Arun Persaud <arun@gmx.de>
- specfile:
* make it python3 only
* remove six
* update required version for numpy and numexpr
- update to version 3.6.1:
* Maintenance release to fix packaging issues. No new features or
bugfixes.
- changes from version 3.6.0:
* PyTables 3.6 no longer supports Python 2.7 see PR #747.
* Improvements
+ Full python 3.8 support.
+ On Windows PyTables wheels on PyPI are linked to
`pytables_hdf5.dll` instead of `hdf5.dll` to prevent collisions
with other packages/wheels that also vendor `hdf5.dll`. This
should prevent problems that arise when a different version of a
dll is imported that the version to which the program was linked
to. This problem is known as "DLL Hell". With the renaming of
the HDF5 DLL to `pytables_hdf5.dll` these problems should be
solved.
* Bugfixes
+ Bugfix for HDF5 files/types with padding. For details see
:issue:`734`.
+ More fixes for python 3.8 compatibility: Replace deprecated
time.clock with time.perf_counter Thanks to Sergio Pascual
(sergiopasra). see :issue:`744` and PR #745.
+ Improvements in tests as well as clean up from dropping Python
2.7 support. Thanks to Seth Troisi (sethtroisi).
-------------------------------------------------------------------
Mon Jul 22 16:58:48 UTC 2019 - Todd R <toddrme2178@gmail.com>
- Update to 3.5.2
* Fixed compatibility with python 3.8: Fixed `Dictonary keys changed during
iteration` RuntimeError while moving/renameing a node.
Thanks to Christoph Gohlke for reporting and Miro Hroncok for help with
building PyTables for python 3.8alpha (cython compatibility).
* Fixed a bug in offset calculations producing floats instead of ints
affecting python 3. See PR #736. Thanks to Brad Montgomery.
- Update to 3.5.1
* Maintenance release to fix how PyPi repo is handling wheel versions.
- Update to 3.5.0
* When copying data from native HDF5 files with padding in compound types,
the padding is not removed now by default. This allows for better
compatibility with existing HDF5 applications that expect the padding
to stay there.
Also, when the `description` is a NumPy struct array with padding, this
is honored now. The previous behaviour (i.e. getting rid of paddings) can
be replicated by passing the new `allow_padding` parameter when opening
a file. For some examples, see the new `examples/tables-with-padding.py`
and `examples/attrs-with-padding.py`. For details on the implementation
* Added a new flag `--dont-allow-padding` in `ptrepack` utility so as to
replicate the previous behaviour of removing padding during file copies.
The default is to honor the original padding in copies.
* Improve compatibility with numpy 1.16.
* Improve detection of the LZO2 library at build time.
* Suppress several warnings.
* Add AVX2 support for Windows.
- Rebase Never-use-the-msse2-flag-explicitly.patch
- Remove upstream-included patches:
* pytables_no_unsafe_write.patch
* pytables_fix_exception_check.patch
-------------------------------------------------------------------
Wed Feb 13 19:21:03 UTC 2019 - Todd R <toddrme2178@gmail.com>
- Add patches for numpy 1.16 compatibility:
* pytables_fix_exception_check.patch
from: https://github.com/PyTables/PyTables/commit/46fa2f07c00613ed6b647b2cf44e388f547fe668
* pytables_no_unsafe_write.patch
from: https://github.com/PyTables/PyTables/commit/f6b64c942fb91e6c261fa455969a38482c22beeb
-------------------------------------------------------------------
Fri Aug 10 11:48:19 UTC 2018 - tchvatal@suse.com
- Drop python-unittest2 dependency it was needed only on py2.6
-------------------------------------------------------------------
Wed Jun 13 17:39:10 UTC 2018 - toddrme2178@gmail.com
- Update to 3.4.4
+ Improvements
* Environment variable to control the use of embedded libraries.
* Include citation in repository.
+ Bugs fixed
* Fixed import error with numexpr 2.6.5.dev0
* Fixed linter warnings.
* Fixed for re.split() is version detection.
* Fixed test failures with Python 2.7 and NumPy 1.14.3
- Remove upstream-included initRecArray_tuples.patch
-------------------------------------------------------------------
Thu May 3 17:06:41 UTC 2018 - toddrme2178@gmail.com
- Add initRecArray_tuples.patch
Upstream bug report: https://github.com/PyTables/PyTables/issues/688
From: https://github.com/PyTables/PyTables/pull/689
Should be in next release
-------------------------------------------------------------------
Wed May 2 10:31:55 UTC 2018 - tchvatal@suse.com
- Version update to 3.4.3:
* On interactive python sessions, group/attribute __dir__() method
autocompletes children that are named as valid python identifiers.
* Implement Group.__getitem__() to have groups act as python-containers,
so code like this works: hfile.root['some child'].
* Enable building with Intel compiler (icc/icpc).
* PEP 519 support, using new os.fspath method.
* Optional disable recording of ctime (metadata creation time) when
creating datasets that makes possible to get bitwise identical output
from repeated runs.
* Prevent from reading all rows for each coord in a VLArray when
indexing using a list .
* Fixed division by zero when using _convert_time64() with an empty
nparr array.
* Fixed deprecation warnings with numpy 1.14.
* Skip DLL check when running from a frozen app.
* Fixed behaviour with slices out of range.
- Drop merged patch fix_numpy_recarray.patch
- Add patch Never-use-the-msse2-flag-explicitly.patch to avoid using
msse2 and avx on buildbots that support it, as we can be on non
avx machines...
-------------------------------------------------------------------
Mon Feb 26 17:31:44 UTC 2018 - toddrme2178@gmail.com
- Add fix_numpy_recarray.patch
Fixes issues with recarrays under numpy 1.14.
Patch accepted upstream. Should be in next release.
From: https://github.com/PyTables/PyTables/pull/664
-------------------------------------------------------------------
Tue Apr 25 19:08:44 UTC 2017 - toddrme2178@gmail.com
- Update to version 3.4.2
+ Improvements
* setup.py detects conda env and uses installed conda
(hdf5, bzip2, lzo and/or blosc) packages when building from
source.
+ Bugs fixed
* Linux wheels now built against built-in blosc.
* Fixed windows absolute paths in ptrepack, ptdump, ptree.
:issue:`616`. Thanks to oscar6echo.
- Update to version 3.4.1
+ Bugs fixed
* Fixed bug in ptrepack
- Switch to hdf5 1.10 series.
- Implement single-spec version.
-------------------------------------------------------------------
Thu Aug 25 17:49:47 UTC 2016 - toddrme2178@gmail.com
- hdf5_18 has been renamed to hdf5-1_8.
-------------------------------------------------------------------
Tue Aug 16 15:37:55 UTC 2016 - toddrme2178@gmail.com
- update to version 3.2.3.1:
* Fixed issues with pip install.
- update to version 3.2.3:
* Improvements
+ It is now possible to use HDF5 with the new shared library
naming scheme (>= 1.8.10, hdf5.dll instead of hdf5dll.dll) on
Windows (gh-540). Thanks to Tadeu Manoel.
+ Now :program: ptdump sorts output by node name and does not
print a backtrace if file cannot be opened. Thanks to Zbigniew
Jędrzejewski-Szmek.
* Bugs fixed
+ Only run tables.tests.test_basics.UnicodeFilename if the
filesystem encoding is utf-8. Closes gh-485.
+ Add lib64 to posix search path. (closes gh-507) Thanks to Mehdi
Sadeghi.
+ Ensure cache entries are removed if fewer than 10 (closes
gh-529). Thanks to Graham Jones.
+ Fix segmentation fault in a number of test cases that use
index.Index (closes gh-532 and gh-533). Thanks to Diane Trout.
+ Fixed the evaluation of transcendental functions when numexpr is
compiled with VML support (closes gh-534, PR #536). Thanks to
Tom Kooij.
+ Make sure that index classes use buffersizes that are a multiple
of chunkshape[0] (closes gh-538, PR #538). Thanks to Tom Kooij.
+ Ensure benchmark paths exist before benchmarks are executed (PR
#544). Thanks to rohitjamuar.
* Other changes
+ Minimum Cython version is now v0.21
- specfile:
* add python-py-cpuinfo to build requirements
* depend on hdf5_18-devel, since pytables is not compatible with
hdf5 >= 1.10
-------------------------------------------------------------------
Mon Aug 15 14:51:56 UTC 2016 - toddrme2178@gmail.com
- Fix update-alternatives implementation.
-------------------------------------------------------------------
Mon Feb 1 11:28:11 UTC 2016 - toddrme2178@gmail.com
- update to version 3.2.2:
* Fix AssertionError in Row.__init_loop. See gh-477.
* Fix issues with Cython 0.23. See gh-481.
* Only run tables.tests.test_basics.UnicodeFilename if the
filesystem encoding is utf-8. Closes gh-485.
* Fix missing missing PyErr_Clear. See gh-#486.
* Fix the C type of some numpy attributes. See gh-494.
* Cast selection indices to integer. See gh-496.
* Fix indexesextension._keysort_string. Closes gh-497 and gh-498.
- changes from version 3.2.1.1:
* Fix permission on distributed source distribution
- update to version 3.2.1:
* Fix indexesextension._keysort. Fixes gh-455. Thanks to Andrew Lin.
- Implement update-alternatives
-------------------------------------------------------------------
Thu May 14 09:07:43 UTC 2015 - benoit.monin@gmx.fr
- update to version 3.2.0:
Improvements
* The nrowsinbuf is better computed now for EArray/CArray having
a small chunkshape in the main dimension. Fixes #285.
* PyTables should be installable very friendly via pip, including
NumPy being installed automatically in the unlikely case it is
not yet installed in the system. Thanks to Andrea Bedini.
* setup.py has been largely simplified and now it requires
setuptools. Although we think this is a good step, please keep
us informed this is breaking some installation in a very bad
manner.
* setup.py now is able to used pkg-config, if available, to
locate required libraries (hdf5, bzip2, etc.). The use of
pkg-config can be controlled via setup.py command line flags or
via environment variables. Please refer to the installation
guide (in the User Manual) for details. Closes gh-442.
* It is now possible to create a new node whose parent is a
softlink to another group (see gh-422). Thanks to Alistair
Muldal.
* link.SoftLink objects no longer need to be explicitly
dereferenced. Methods and attributes of the linked object are
now automatically accessed when the user acts on a soft-link
(see gh-399). Thanks to Alistair Muldal.
* Now ptrepack recognizes hardlinks and replicates them in the
output (repacked) file. This saves disk space and makes
repacked files more conformal to the original one. Closes
gh-380.
* New pttree script for printing HDF5 file contents as a pretty
ASCII tree (closes gh-400). Thanks to Alistair Muldal.
* The internal Blosc library has been downgraded to version
1.4.4. This is in order to still allow using multiple threads
inside Blosc, even on multithreaded applications (see gh-411,
gh-412, gh-437 and gh-448).
* The print_versions() function now also reports the version of
compression libraries used by Blosc.
* Now the setup.py tries to use the ‘-march=native’ C flag by
default. In falls back on ‘-msse2’ if ‘-march=native’ is not
supported by the compiler. Closes gh-379.
* Fixed a spurious unicode comparison warning (closes gh-372 and
gh-373).
* Improved handling of empty string attributes. In previous
versions of PyTables empty string were stored as scalar HDF5
attributes having size 1 and value ‘0’ (an empty null
terminated string). Now empty string are stored as HDF5
attributes having zero size
* Added a new cookbook recipe and a couple of examples for simple
threading with PyTables.
* The redundant utilsextension.get_indices() function has been
eliminated (replaced by slice.indices()). Closes gh-195.
* Allow negative indices in point selection (closes gh-360)
* Index wasn’t being used if it claimed there were no results.
Closes gh-351 (see also gh-353)
* Atoms and Col types are no longer generated dynamically so now
it is easier for IDEs and static analysis tool to handle them
(closes gh-345)
* The keysort functions in idx-opt.c have been cythonised using
fused types. The perfomance is mostly unchanged, but the code
is much more simpler now. Thanks to Andrea Bedini.
* Small unit tests re-factoring
Bugs fixed
* Fixed compatibility problems with numpy 1.9 and 1.10-dev
(closes gh-362 and gh-366)
* Fixed compatibility with Cython >= 0.20 (closes gh-386 and
gh-387)
* Fixed support for unicode node names in LRU cache (only Python
2 was affected). Closes gh-367 and gh-369.
* Fixed support for unicode node titles (only Python 2 was
affected). Closes gh-370 and gh-374.
* Fixed a bug that caused the silent truncation of unicode
attributes containing the ‘0’ character. Closes gh-371.
* Fixed descr_from_dtype() to work as expected with complex
types. Closes gh-381.
* Fixed the tests.test_basics.ThreadingTestCase test case. Closes
gh-359.
* Fix incomplete results when performing the same query twice and
exhausting the second iterator before the first. The first one
writes incomplete results to seqcache (gh-353)
* Fix false results potentially going to seqcache if
tableextension.Row.update() is used during iteration (see
gh-353)
* Fix Column.create_csindex() when there’s NaNs
* Fixed handling of unicode file names on windows (closes gh-389)
* No longer not modify sys.argv at import time (closes gh-405)
* Fixed a performance issue on NFS (closes gh-402)
* Fixed a nasty problem affecting results of indexed queries.
Closes gh-319 and probably gh-419 too.
* Fixed another problem affecting results of indexed queries too.
Closes gh-441.
* Replaced “len(xrange(start, stop, step))” -> “len(xrange(0,
stop - start, step))” to fix issues with large row counts with
Python 2.x. Fixes #447.
Other changes
* Cython is not a hard dependency anymore (although developers
will need it so as to generated the C extension code).
* The number of threads used by default for numexpr and Blosc
operation that was set to the number of available cores have
been reduced to 2. This is a much more reasonable setting for
not creating too much overhead.
- add python-setuptools as a new build dependency
- pass -q to %setup to avoid spamming the build log
- rename README.txt to README.rst: changed upstream
- add new binary pttree to the package
-------------------------------------------------------------------
Thu May 8 11:15:34 UTC 2014 - toddrme2178@gmail.com
- New version 3.1.1
- Fixed a critical bug that caused an exception at import time.
The error was triggered when a bug in long-double detection is detected
in the HDF5 library (see :issue:`275`) and numpy_ does not expose
`float96` or `float128`. Closes :issue:`344`.
- The internal Blosc_ library has been updated to version 1.3.5.
This fixes a false buffer overrun condition that made c-blosc to fail,
even if the problem was not real.
- New version 3.1.0
- New features¶
- Now PyTables is able to save/restore the default value
of EnumAtom types.
- Implemented support for the H5FD_SPLIT driver.
- New quantization filter: the filter truncates floating point
data to a specified precision before writing to disk.
This can significantly improve the performance of compressors.
- Added new VLArray.get_row_size() method to VLArray for querying
the number of atoms of a VLArray row. Closes gh-24 and gh-315.
- The internal Blosc library has been updated to version 1.3.2.
All new features introduced in the Blosc 1.3.x series, and in
particular the ability to leverage different compressors within
Blosc (see the Blosc Release Notes), are now available in
PyTables via the blosc filter.
- Improvements¶
- The node caching mechanism has been completely redesigned to
be simpler and less dependent from specific behaviours of
the __del__ method. Now PyTables is compatible with the
forthcoming Python 3.4. Closes gh-306.
- PyTables no longer uses shared/cached file handlers.
This change somewhat improves support for concurrent reading
allowing the user to safely open the same file in different
threads for reading (requires HDF5 >= 1.8.7). More details
about this change can be found in the Backward incompatible
changes section. See also gh-130, gh-129 gh-292 and gh-216.
- PyTables is now able to detect and use external installations
of the Blosc library (closes gh-104). If Blosc is not found in
the system, and the user do not specify a custom installation
directory, then it is used an internal copy of the Blosc source
code.
- Automatically disable extended float support if a buggy version
of HDF5 is detected (see also Issues with H5T_NATIVE_LDOUBLE).
- Documented an unexpected behaviour with string literals in query
conditions on Python 3 (closes gh-265)
- The deprecated getopt module has been dropped in favour of
argparse in all command line utilities (close gh-251)
- Improved the installation section of the PyTables User’s Guide.
- instructions for installing PyTables via pip have been added.
- added a reference to the Anaconda, Canopy and Christoph
Gohlke suites (closes gh-291)
- Enabled Travis-CI builds for Python 3.3
- Tables.read_coordinates() now also works with boolean indices input.
- Improved compatibility with numpy >= 1.8 (see gh-259)
- The code of the benchmark programs (bench directory) has been updated.
- Fixed some warning related to non-unicode file names
(the Windows bytes API has been deprecated in Python 3.4)
- Bugs fixed¶
- Fixed detection of platforms supporting Blosc
- Fixed a crash that occurred when one attempts to write a numpy array
to an Atom (closes gh-209 and gh-296)
- Prevent creation of a table with no columns.
- Fixed a memory leak that occured when iterating over
CArray/EArray objects.
- Make NaN types sort to the end. Closes gh-282 and gh-313
- Fixed selection on float columns when NaNs are present.
- Fix computation of the buffer size for iterations on rows.
The buffers size was overestimated resulting in a MemoryError
in some cases. Closes gh-316. Thamks to bbudescu.
- Better check of file open mode. Closes gh-318.
- The Blosc filter now works correctly together with fletcher32. Closes gh-21.
- Close the file handle before trying to delete the corresponding file.
Fixes a test failure on Windows.
- Use integer division for computing indices (fixes some warning on Windows)
- Use external python-blosc. The internal one builds a bad version
of zlib.
-------------------------------------------------------------------
Tue Oct 22 13:34:13 UTC 2013 - toddrme2178@gmail.com
- new version 3.0.0
* New features
- Since this release PyTables provides full support to Python_ 3
(closes :issue:`188`).
- The entire code base is now more compliant with coding style guidelines
describe in the PEP8_ (closes :issue:`103` and :issue:`224`).
See `API changes`_ for more details.
- Basic support for HDF5 drivers. Now it is possible to open/create an
HDF5 file using one of the SEC2, DIRECT, LOG, WINDOWS, STDIO or CORE
drivers. Users can also set the main driver parameters (closes
:issue:`166`).
Thanks to Michal Slonina.
- Basic support for in-memory image files. An HDF5 file can be set from or
copied into a memory buffer (thanks to Michal Slonina). This feature is
only available if PyTables is built against HDF5 1.8.9 or newer.
Closes :issue:`165` and :issue:`173`.
- New :meth:`File.get_filesize` method for retrieving the HDF5 file size.
- Implemented methods to get/set the user block size in a HDF5 file
(closes :issue:`123`)
- Improved support for PyInstaller_. Now it is easier to pack frozen
applications that use the PyTables package (closes: :issue:`177`).
Thanks to Stuart Mentzer and Christoph Gohlke.
- All read methods now have an optional *out* argument that allows to pass a
pre-allocated array to store data (closes :issue:`192`)
- Added support for the floating point data types with extended precision
(Float96, Float128, Complex192 and Complex256). This feature is only
available if numpy_ provides it as well.
Closes :issue:`51` and :issue:`214`. Many thanks to Andrea Bedini.
- Consistent ``create_xxx()`` signatures. Now it is possible to create all
data sets :class:`Array`, :class:`CArray`, :class:`EArray`,
:class:`VLArray`, and :class:`Table` from existing Python objects (closes
:issue:`61` and :issue:`249`). See also the `API changes`_ section.
- Complete rewrite of the :mod:`nodes.filenode` module. Now it is fully
compliant with the interfaces defined in the standard :mod:`io` module.
Only non-buffered binary I/O is supported currently.
See also the `API changes`_ section. Closes :issue:`244`.
- New :program:`pt2to3` tool is provided to help users to port their
applications to the new API (see `API changes`_ section).
* Improvements
- Improved runtime checks on dynamic loading of libraries: meaningful error
messages are generated in case of failure.
Also, now PyTables no more alters the system PATH.
Closes :issue:`178` and :issue:`179` (thanks to Christoph Gohlke).
- Improved list of search paths for libraries as suggested by Nicholaus
Halecky (see :issue:`219`).
- Removed deprecated Cython_ include (.pxi) files. Contents of
:file:`convtypetables.pxi` have been moved in :file:`utilsextension.pyx`.
Closes :issue:`217`.
- The internal Blosc_ library has been upgraded to version 1.2.3.
- Pre-load the bzip2_ library on windows (closes :issue:`205`)
- The :meth:`File.get_node` method now accepts unicode paths
(closes :issue:`203`)
- Improved compatibility with Cython_ 0.19 (see :issue:`220` and
:issue:`221`)
- Improved compatibility with numexpr_ 2.1 (see also :issue:`199` and
:issue:`241`)
- Improved compatibility with development versions of numpy_
(see :issue:`193`)
- Packaging: since this release the standard tar-ball package no more includes
the PDF version of the "PyTables User Guide", so it is a little bit smaller
now. The complete and pre-build version of the documentation both in HTML
and PDF format is available on the file `download area`_ on SourceForge.net.
Closes: :issue:`172`.
- Now PyTables also uses `Travis-CI`_ as continuous integration service.
All branches and all pull requests are automatically tested with different
Python_ versions. Closes :issue:`212`.
* Other changes
- PyTables now requires Python 2.6 or newer.
- Minimum supported version of Numexpr_ is now 2.0.
* API changes
The entire PyTables API as been made more PEP8_ compliant (see :issue:`224`).
This means that many methods, attributes, module global variables and also
keyword parameters have been renamed to be compliant with PEP8_ style
guidelines (e.g. the ``tables.hdf5Version`` constant has been renamed into
``tables.hdf5_version``).
We made the best effort to maintain compatibility to the old API for existing
applications. In most cases, the old 2.x API is still available and usable
even if it is now deprecated (see the Deprecations_ section).
The only important backwards incompatible API changes are for names of
function/methods arguments. All uses of keyword arguments should be
checked and fixed to use the new naming convention.
The new :program:`pt2to3` tool can be used to port PyTables based applications
to the new API.
Many deprecated features and support for obsolete modules has been dropped:
- The deprecated :data:`is_pro` module constant has been removed
- The nra module and support for the obsolete numarray module has been removed.
The *numarray* flavor is no more supported as well (closes :issue:`107`).
- Support for the obsolete Numeric module has been removed.
The *numeric* flavor is no longer available (closes :issue:`108`).
- The tables.netcdf3 module has been removed (closes :issue:`68`).
- The deprecated :exc:`exceptions.Incompat16Warning` exception has been
removed
- The :meth:`File.create_external_link` method no longer has a keyword
parameter named *warn16incompat*. It was deprecated in PyTables 2.4.
- The :meth:`File.create_array`, :meth:`File.create_carray`,
:meth:`File.create_earray`, :meth:`File.create_vlarray`, and
:meth:`File.create_table` methods of the :class:`File` objects gained a
new (optional) keyword argument named ``obj``. It can be used to initialize
the newly created dataset with an existing Python object, though normally
these are numpy_ arrays.
The *atom*/*descriptor* and *shape* parameters are now optional if the
*obj* argument is provided.
- The :mod:`nodes.filenode` has been completely rewritten to be fully
compliant with the interfaces defined in the :mod:`io` module.
The FileNode classes currently implemented are intended for binary I/O.
Main changes:
* the FileNode base class is no more available,
* the new version of :class:`nodes.filenode.ROFileNode` and
:class:`nodes.filenode.RAFileNode` objects no more expose the *offset*
attribute (the *seek* and *tell* methods can be used instead),
* the *lineSeparator* property is no more available end the ``\n``
character is always used as line separator.
- The `__version__` module constants has been removed from almost all the
modules (it was not used after the switch to Git). Of course the package
level constant (:data:`tables.__version__`) still remains.
Closes :issue:`112`.
- The :func:`lrange` has been dropped in favor of xrange (:issue:`181`)
- The :data:`parameters.MAX_THREADS` configuration parameter has been dropped
in favor of :data:`parameters.MAX_BLOSC_THREADS` and
:data:`parameters.MAX_NUMEXPR_THREADS` (closes :issue:`147`).
- The :func:`conditions.compile_condition` function no more has a *copycols*
argument, it was no more necessary since Numexpr_ 1.3.1.
Closes :issue:`117`.
- The *expectedsizeinMB* parameter of the :meth:`File.create_vlarray` and of
the :meth:`VLArrsy.__init__` methods has been replaced by *expectedrows*.
See also (:issue:`35`).
- The :meth:`Table.whereAppend` method has been renamed into
:meth:`Table.append_where` (closes :issue:`248`).
* Other possibly incompatible changes
- All methods of the :class:`Table` class that take *start*, *stop* and
*step* parameters (including :meth:`Table.read`, :meth:`Table.where`,
:meth:`Table.iterrows`, etc) have been redesigned to have a consistent
behaviour. The meaning of the *start*, *stop* and *step* and their default
values now always work exactly like in the standard :class:`slice` objects.
Closes :issue:`44` and :issue:`255`.
- Unicode attributes are not stored in the HDF5 file as pickled string.
They are now saved on the HDF5 file as UTF-8 encoded strings.
- System attributes are now stored in the HDF5 file using the character set
that reflects the native string behaviour: ASCII for Python 2 and UTF8 for
Python 3. In any case, system attributes are represented as Python string.
- The :meth:`iterrows` method of :class:`*Array` and :class:`Table` as well
as the :meth:`Table.itersorted` now behave like functions in the standard
:mod:`itertools` module.
If the *start* parameter is provided and *stop* is None then the
array/table is iterated from *start* to the last line.
In PyTables < 3.0 only one element was returned.
* Deprecations
- As described in `API changes`_, all functions, methods and attribute names
that was not compliant with the PEP8_ guidelines have been changed.
Old names are still available but they are deprecated.
- The use of upper-case keyword arguments in the :func:`open_file` function
and the :class:`File` class initializer is now deprecated. All parameters
defined in the :file:`tables/parameters.py` module can still be passed as
keyword argument to the :func:`open_file` function just using a lower-case
version of the parameter name.
-------------------------------------------------------------------
Tue Jul 31 01:11:15 UTC 2012 - toddrme2178@gmail.com
- new version 2.4.0
-------------------------------------------------------------------
Thu Mar 8 12:31:53 UTC 2012 - saschpe@suse.de
- Spec file cleanup
- Only ship HTML docs, not the doc sources
-------------------------------------------------------------------
Sat Feb 25 21:35:21 UTC 2012 - scorot@free.fr
- fix build for SLE-11
-------------------------------------------------------------------
Fri Jan 6 17:28:34 UTC 2012 - toddrme2178@gmail.com
- Clean up spec file
- Fix .changes file
- Update manual
- Removed seperate manual from the sources since it is included in the tarball
-------------------------------------------------------------------
Sun Nov 20 17:56:24 UTC 2011 - werner.ho@gmx.de
- new version 2.3.1
-------------------------------------------------------------------
Sun May 29 00:00:00 UTC 2011 - werner@linux-xl08.site
- fixed hdf5 package change
-------------------------------------------------------------------
Sat Sep 19 00:00:00 UTC 2010 - werner.ho@gmx.de
- new version 2.2 with numexpr support
-------------------------------------------------------------------
Sat Oct 10 00:00:00 UTC 2009 - werner.ho@gmx.de
- new version 2.1.2
-------------------------------------------------------------------
Sun Apr 29 00:00:00 UTC 2009 - werner.ho@gmx.de
- new version 2.1.1
-------------------------------------------------------------------
Thu Dec 21 00:00:00 UTC 2008 werner.ho@gmx.de
- new version 2.1
-------------------------------------------------------------------
Thu Dec 21 00:00:00 UTC 2008 - werner.ho@gmx.de
- new version 2.1
-------------------------------------------------------------------
Thu Dec 19 00:00:00 UTC 2008 - werner.ho@gmx.de
- new version 2.1rc2
-------------------------------------------------------------------
Thu Dec 16 00:00:00 UTC 2008 - werner.ho@gmx.de
- need numpy-devel now
-------------------------------------------------------------------
Sun Jul 27 00:00:00 UTC 2008 - werner.ho@gmx.de
- new version 2.0.4
-------------------------------------------------------------------
Mon Mar 24 00:00:00 UTC 2008 - werner.ho@gmx.de
- new version 2.0.3
-------------------------------------------------------------------
Sat Nov 26 00:00:00 UTC 2007 - werner.ho@gmx.de
- new version 2.0.2
-------------------------------------------------------------------
Sat Sep 08 00:00:00 UTC 2007 - werner.ho@gmx.de
- new version 2.0
-------------------------------------------------------------------
Mon May 29 00:00:00 UTC 2007 - werner.ho@gmx.de
- new version 2.0rc2
-------------------------------------------------------------------
Thu May 24 00:00:00 UTC 2007 - werner.ho@gmx.de
- initial spec file based on a draft provided by
Felix Richter <felix.richter2@uni-rostock.de>
