Hi Chris, I know at Enthought, we considered the benefits of the former PyTables Pro (now v2.3) worth the current beta status. Putting my PyTables hat on, it still is beta so if you include it in your distribution, be prepared to update ;).
[thread hijack] Everyone else, Do we have a timeline for a release? Are we trying to release the Governance or the 2.3 Milestone or both? It would be nice if we could split up the remaining tickets somehow... Be Well Anthony On Sat, Aug 20, 2011 at 8:40 AM, Chris Kees <cek...@gmail.com> wrote: > Hi Antonio, > > Thanks, I'm glad to be able to use the pytables repository. It was > just the cython executable. I hadn't set the path properly in my test > build. I haven't been able to get rid of the warning about the hdf5 > runtime--I appear to only have .a's and .dylib's. For future reference > here is the set of tools that are working and some output. > > Thanks, > Chris > > pytables: > % python > Python 2.7.2 (default, Aug 20 2011, 07:44:38) > [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin > Type "help", "copyright", "credits" or "license" for more information. > >>> import tables > >>> tables.test() > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > PyTables version: 2.3b1.dev > HDF5 version: 1.8.7 > NumPy version: 1.6.2.dev-f21011a > Numexpr version: 1.5.dev (not using Intel's VML/MKL) > Zlib version: 1.2.5 (in Python interpreter) > BZIP2 version: 1.0.5 (10-Dec-2007) > Blosc version: 1.1.2 (2010-11-04) > Cython version: 0.15 > Python version: 2.7.2 (default, Aug 20 2011, 07:44:38) > [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] > Platform: darwin-i386 > Byte-ordering: little > Detected cores: 4 > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > Performing only a light (yet comprehensive) subset of the test suite. > If you want a more complete test, try passing the --heavy flag to this > script > (or set the 'heavy' parameter in case you are using tables.test() call). > The whole suite will take more than 4 hours to complete on a relatively > modern CPU and around 256 MB of main memory. > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > /Users/cekees/src/git-test/proteus/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/filters.py:264: > FiltersWarning: compression library ``lzo`` is not available; using > ``zlib`` instead > % (complib, default_complib), FiltersWarning ) > ...(and so on ...) > Ran 4723 tests in 223.846s > > OK > > Machine: > macbook pro (intel) Mac OS X 10.6.8, using the default compilers > (/usr/bin/gcc, etc.). > > Python 2.7.2: > ./configure --prefix=/Users/cekees/src/git-test/proteus/darwin > > --enable-framework=/Users/cekees/src/git-test/proteus/darwin/Library/Frameworks > --enable-toolbox-glue CC=/usr/bin/gcc CXX=/usr/bin/g++ > CPPFLAGS=-I//Users/cekees/src/git-test/proteus/darwin/include > CXXFLAGS=-I/Users/cekees/src/git-test/proteus/darwin/include > LD=/usr/bin/gcc > LDFLAGS=-L/Users/cekees/src/git-test/proteus/darwin/lib > > HDF5 1.8.7: > SUMMARY OF THE HDF5 CONFIGURATION > ================================= > > General Information: > ------------------- > HDF5 Version: 1.8.7 > Configured on: Sat Aug 20 07:48:53 CDT 2011 > Configured by: cekees@minikees-3.local > Configure mode: production > Host system: i386-apple-darwin10.8.0 > Uname information: Darwin minikees-3.local 10.8.0 Darwin > Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 i386 > Byte sex: little-endian > Libraries: > Installation point: /Users/cekees/src/git-test/proteus/darwin > > Compiling Options: > ------------------ > Compilation Mode: production > C Compiler: /usr/bin/gcc ( (GCC) 4.2.1 (Apple > Inc. build 5666) (dot 3)) > CFLAGS: > -I/Users/cekees/src/git-test/proteus/darwin/include > H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra > -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual > -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return > -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations > -Wredundant-decls -Wnested-externs -Winline -Wno-long-long > -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked > -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels > -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch > -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs > -Wswitch-default -Wswitch-enum -Wunused-macros > -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var > -Wstrict-overflow -O3 -fomit-frame-pointer -finline-functions > AM_CFLAGS: > CPPFLAGS: > H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API > AM_CPPFLAGS: > -I/Users/cekees/src/git-test/proteus/darwin/include > -I/Users/cekees/src/git-test/proteus/darwin/include > Shared C Library: yes > Static C Library: yes > Statically Linked Executables: no > LDFLAGS: > -L/Users/cekees/src/git-test/proteus/darwin/lib > H5_LDFLAGS: > AM_LDFLAGS: > -L/Users/cekees/src/git-test/proteus/darwin/lib > -L/Users/cekees/src/git-test/proteus/darwin/lib > Extra libraries: -lpthread -lsz -lz -lm -lsz -lz > Archiver: ar > Ranlib: ranlib > Debugged Packages: > API Tracing: no > > Languages: > ---------- > Fortran: no > > C++: no > > Features: > --------- > Parallel HDF5: no > High Level library: yes > Threadsafety: yes > Default API Mapping: v18 > With Deprecated Public Symbols: yes > I/O filters (external): deflate(zlib),szip(encoder) > I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset > MPE: no > Direct VFD: no > dmalloc: no > Clear file buffers before write: yes > Using memory checker: no > Function Stack Tracing: no > GPFS: no > Strict File Format Checks: no > Optimization Instrumentation: no > Large File Support (LFS): yes > H5dump Packed Bits: yes > > Contents of lib dir: > % ls $PROTEUS_PREFIX/lib > libdaetk.a libhdf5.settings libmetis.a > libsuperlu.a libsz.dylib libz.a > libhdf5.7.dylib libhdf5_hl.7.dylib libparmetis.a > libsuperlu_dist_2.4.a libsz.la libz.dylib > libhdf5.a libhdf5_hl.a libpetsc.a > libsz.2.0.0.dylib libtri.a pkgconfig > libhdf5.dylib libhdf5_hl.dylib libpetsc.dylib > libsz.2.dylib libz.1.2.5.dylib > libhdf5.la libhdf5_hl.la libpetsc.dylib.dSYM > libsz.a libz.1.dylib > > > > On Sat, Aug 20, 2011 at 3:10 AM, Antonio Valentino > <antonio.valent...@tiscali.it> wrote: > > Hi Chris, > > > > Il giorno 20/ago/2011, alle ore 03.57, Chris Kees ha scritto: > > > >> Hi, > >> > >> We use pytables and numexpr, and I'd like to add them as submodules to > >> our project so that I can easily keep updated with pytables > >> improvements and pass changes back up stream if I can be of any help > >> (we do a lot of HPC work with pytables). Is there a plan to add 2.3 as > >> a release branch fairly soon or some other stable point in the git > >> repository that I could point my submodule to? I could also stick with > >> 2.2 for the time being but noticed below that 2.3beta had been used in > >> EPD so I thought there must be a branch or fork somewhere that is > > > > The master branch should be beta quality at the moment. We plan to pack a > beta release soon. > > If you look at > > > > https://github.com/PyTables/PyTables/issues?milestone=2&state=open > > > > there are still a few bugs to close and they are mainly related to the > setup process which seems to be your problem too. > > > > > > > >> relatively stable. I would just go with the head of the master > >> branch, but compiling with Cython 0.15 and numpy 1.6.1 gave me the > >> error below. > >> > >> Thanks, > >> Chris > > > > Chris, I'm setting up a virtual environment to reproduce your issue. > > Can you confirm that the cython executable is in your path? > > > > Looking at the error message below it seems that the setup script is > unable to find the HDF5 runtime: > > > > ".. WARNING:: Could not find the HDF5 runtime." > > > > Can you please post more detail on your system setup and the exact > command line you used? > > > > > >> * Found numpy 1.6.2.dev-f21011a package installed. > >> * Found numexpr 1.5.dev package installed. > >> * Found Cython 0.15 package installed. > >> * Found HDF5 headers at > >> ``/Users/cekees/src/proteus-git/darwin/include``, library at > >> ``/Users/cekees/src/proteus-git/darwin/lib``. > >> .. WARNING:: Could not find the HDF5 runtime. > >> The HDF5 shared library was *not* found in the default library > >> paths. In case of runtime problems, please remember to install it. > >> * Could not find LZO 2 headers and library; disabling support for it. > >> * Could not find LZO 1 headers and library; disabling support for it. > >> * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``. > >> cythoning tables/utilsExtension.pyx to tables/utilsExtension.c > >> Traceback (most recent call last): > >> File "setup.py", line 464, in <module> > >> cython_extfiles = get_cython_extfiles(cython_extnames) > >> File "setup.py", line 455, in get_cython_extfiles > >> retcode = subprocess.call(["cython", extpfile]) > >> File > "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > >> line 493, in call > >> return Popen(*popenargs, **kwargs).wait() > >> File > "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > >> line 679, in __init__ > >> errread, errwrite) > >> File > "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > >> line 1228, in _execute_child > >> raise child_exception > > > > regards > > > > -- > > Antonio Valentino > > > > > > > ------------------------------------------------------------------------------ > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > > user administration capabilities and model configuration. Take > > the hassle out of deploying and managing Subversion and the > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > > Pytables-users mailing list > > Pytables-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pytables-users > > > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > Pytables-users mailing list > Pytables-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pytables-users >
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