What’s new in PyTables 0.9

On this release you will find a series of quite exciting new features, being the most important the indexing capabilities, in-kernel selections, support for complex datatypes and the possibility to modify values in both tables and arrays (yeah, finally :).

New features:

  • Indexing of columns in tables. That allow to make data selections on tables up to 500 times faster than standard selections (for ex. doing a selection along an indexed column of 100 milion of rows takes less than 1 second on a modern CPU). Perhaps the most interesting thing about the indexing algorithm implemented by PyTables is that the time taken to index grows lineraly with the length of the data, so, making the indexation process to be scalable (quite differently to many relational databases). This means that it can index, in a relatively quick way, arbitrarily large table columns (for ex. indexing a column of 100 milion of rows takes just 100 seconds, i.e. at a rate of 1 Mrow/sec). See more detailed info about that in http://www.pytables.org/docs/SciPy04.pdf.
  • In-kernel selections. This feature allow to make data selections on tables up to 5 times faster than standard selections (i.e. pre-0.9 selections), without a need to create an index. As a hint of how fast these selections can be, they are up to 10 times faster than a traditional relational database. Again, see http://www.pytables.org/docs/SciPy04.pdf for some experiments on that matter.
  • Support of complex datatypes for all the data objects (i.e. Table, Array, EArray and VLArray). With that, the complete set of datatypes of Numeric and numarray packages are supported. Thanks to Tom Hedley for providing the patches for Array, EArray and VLArray objects, as well as updating the User’s Manual and adding unit tests for the new functionality.
  • Modification of values. You can modifiy Table, Array, EArray and VLArray values. See Table.modifyRows, Table.modifyColumns() and the newly introduced __setitem__() method for Table, Array, EArray and VLArray entities in the Library Reference of User’s Manual.
  • A new sub-package called “nodes” is there. On it, there will be included different modules to make more easy working with different entities (like images, files, …). The first module that has been added to this sub-package is “FileNode”, whose mission is to enable the creation of a database of nodes which can be used like regular opened files in Python. In other words, you can store a set of files in a PyTables database, and read and write it as you would do with any other file in Python. Thanks to Ivan Vilata i Balaguer for contributing this.

Improvements:

  • New __len__(self) methods added in Arrays, Tables and Columns. This, in combination with __getitem__(self,key) allows to better emulate sequences.
  • Better capabilities to import generic HDF5 files. In particular, Table objects (in the HDF5_HL naming schema) with “holes” in their compound type definition are supported. That allows to read certain files produced by NASA (thanks to Stephen Walton for reporting this).
  • Much improved test units. More than 2000 different tests has been implemented which accounts for more than 13000 loc (this represents twice of the PyTables library code itself (!)).

Backward-incompatible API changes:

  • The __call__ special method has been removed from objects File, Group, Table, Array, EArray and VLArray. Now, you should use walkNodes() in File and Group and iterrows in Table, Array, EArray and VLArray to get the same functionality. This would provide better compatibility with IPython as well.

‘nctoh5’, a new importing utility:

  • Jeff Whitaker has contributed a script to easily convert NetCDF files into HDF5 files using Scientific Python and PyTables. It has been included and documented as a new utility.

Bug fixes:

  • A call to File.flush() now invoke a call to H5Fflush() so to effectively flushing all the file contents to disk. Thanks to Shack Toms for reporting this and providing a patch.
  • SF #1054683: Security hole in utils.checkNameValidity(). Reported in 2004-10-26 by ivilata
  • SF #1049297: Suggestion: new method File.delAttrNode(). Reported in 2004-10-18 by ivilata
  • SF #1049285: Leak in AttributeSet.__delattr__(). Reported in 2004-10-18 by ivilata
  • SF #1014298: Wrong method call in examples/tutorial1-2.py. Reported in 2004-08-23 by ivilata
  • SF #1013202: Cryptic error appending to EArray on RO file. Reported in 2004-08-21 by ivilata
  • SF #991715: Table.read(field=”var1”, flavor=”List”) fails. Reported in 2004-07-15 by falted
  • SF #988547: Wrong file type assumption in File.__new__. Reported in 2004-07-10 by ivilata

Bon profit!,

– Francesc Altet falted@pytables.org