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<section id="migrating-from-pytables-1-x-to-2-x">
<h1>Migrating from PyTables 1.x to 2.x<a class="headerlink" href="#migrating-from-pytables-1-x-to-2-x" title="Link to this heading"></a></h1>
<dl class="field-list simple">
<dt class="field-odd">Author<span class="colon">:</span></dt>
<dd class="field-odd"><p>Francesc Alted i Abad</p>
</dd>
<dt class="field-even">Contact<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference external" href="mailto:faltet%40pytables.com">faltet<span>@</span>pytables<span>.</span>com</a></p>
</dd>
<dt class="field-odd">Author<span class="colon">:</span></dt>
<dd class="field-odd"><p>Ivan Vilata i Balaguer</p>
</dd>
<dt class="field-even">Contact<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference external" href="mailto:ivan%40selidor.net">ivan<span>@</span>selidor<span>.</span>net</a></p>
</dd>
</dl>
<p>Next are described a series of issues that you must have in mind when
migrating from PyTables 1.x to PyTables 2.x series.</p>
<section id="new-type-system">
<h2>New type system<a class="headerlink" href="#new-type-system" title="Link to this heading"></a></h2>
<p>In PyTables 2.x all the data types for leaves are described through a couple
of classes:</p>
<ul class="simple">
<li><dl class="simple">
<dt><code class="docutils literal notranslate"><span class="pre">Atom</span></code>: Describes homogeneous types of the atomic components in <code class="docutils literal notranslate"><span class="pre">*Array</span></code></dt><dd><p>objects (<code class="docutils literal notranslate"><span class="pre">Array</span></code>, <code class="docutils literal notranslate"><span class="pre">CArray</span></code>, <code class="docutils literal notranslate"><span class="pre">EArray</span></code> and <code class="docutils literal notranslate"><span class="pre">VLArray</span></code>).</p>
</dd>
</dl>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">Description</span></code>: Describes (possibly nested) heterogeneous types in
<code class="docutils literal notranslate"><span class="pre">Table</span></code> objects.</p></li>
</ul>
<p>So, in order to upgrade to the new type system, you must perform the next
replacements:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">*Array.stype</span></code> –> <code class="docutils literal notranslate"><span class="pre">*Array.atom.type</span></code> (PyTables type)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">*Array.type</span></code> –> <code class="docutils literal notranslate"><span class="pre">*Array.atom.dtype</span></code> (NumPy type)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">*Array.itemsize</span></code> –> <code class="docutils literal notranslate"><span class="pre">*Array.atom.itemsize</span></code> (the size of the item)</p></li>
</ul>
<p>Furthermore, the PyTables types (previously called “string types”) have
changed to better adapt to NumPy conventions. The next changes have been
applied:</p>
<ul class="simple">
<li><p>PyTables types are now written in lower case, so ‘Type’ becomes ‘type’. For
example, ‘Int64’ becomes now ‘int64’.</p></li>
<li><p>‘CharType’ –> ‘string’</p></li>
<li><p>‘Complex32’, ‘Complex64’ –> ‘complex64’, ‘complex128’. Note that the
numeric part of a ‘complex’ type refers now to the <em>size in bits</em> of the
type and not to the precision, as before.</p></li>
</ul>
<p>See Appendix I of the Users’ Manual on supported data types for more
information on the new PyTables types.</p>
</section>
<section id="important-changes-in-atom-specification">
<h2>Important changes in <code class="docutils literal notranslate"><span class="pre">Atom</span></code> specification<a class="headerlink" href="#important-changes-in-atom-specification" title="Link to this heading"></a></h2>
<ul>
<li><p>The <code class="docutils literal notranslate"><span class="pre">dtype</span></code> argument of <code class="docutils literal notranslate"><span class="pre">EnumAtom</span></code> and <code class="docutils literal notranslate"><span class="pre">EnumCol</span></code> constructors
has been replaced by the <code class="docutils literal notranslate"><span class="pre">base</span></code> argument, which can take a
full-blown atom, although it accepts bare PyTables types as well.
This is a <em>mandatory</em> argument now.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">vlstring</span></code> pseudo-atoms used in <code class="docutils literal notranslate"><span class="pre">VLArray</span></code> nodes do no longer imply UTF-8
(nor any other) encoding, they only store and load <em>raw strings of bytes</em>.
All encoding and decoding is left to the user. Be warned that reading old
files may yield raw UTF-8 encoded strings, which may be converted back to
Unicode in this way:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">unistr</span> <span class="o">=</span> <span class="n">vlarray</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">'utf-8'</span><span class="p">)</span>
</pre></div>
</div>
<p>If you need to work with variable-length Unicode strings, you may want to
use the new <code class="docutils literal notranslate"><span class="pre">vlunicode</span></code> pseudo-atom, which fully supports Unicode strings
with no encoding hassles.</p>
</li>
<li><p>Finally, <code class="docutils literal notranslate"><span class="pre">Atom</span></code> and <code class="docutils literal notranslate"><span class="pre">Col</span></code> are now abstract classes, so you can’t use
them to create atoms or column definitions of an arbitrary type. If you
know the particular type you need, use the proper subclass; otherwise, use
the <code class="docutils literal notranslate"><span class="pre">Atom.from_*()</span></code> or <code class="docutils literal notranslate"><span class="pre">Col.from_*()</span></code> factory methods. See the section
on declarative classes in the reference.</p>
<p>You are also advised to avoid using the inheritance of atoms to check for
their kind or type; for that purpose, use their <code class="docutils literal notranslate"><span class="pre">kind</span></code> and <code class="docutils literal notranslate"><span class="pre">type</span></code>
attributes.</p>
</li>
</ul>
</section>
<section id="new-query-system">
<h2>New query system<a class="headerlink" href="#new-query-system" title="Link to this heading"></a></h2>
<ul>
<li><p>In-kernel conditions, since they are based now in Numexpr, must be written
<em>as strings</em>. For example, a condition that in 1.x was stated as:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">result</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s1">'col2'</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">table</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">table</span><span class="o">.</span><span class="n">cols</span><span class="o">.</span><span class="n">col1</span> <span class="o">==</span> <span class="mi">1</span><span class="p">)]</span>
</pre></div>
</div>
<p>now should read:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">result</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s1">'col2'</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">table</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="s1">'col1 == 1'</span><span class="p">)]</span>
</pre></div>
</div>
<p>That means that complex selections are possible now:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">result</span> <span class="o">=</span> <span class="p">[</span> <span class="n">row</span><span class="p">[</span><span class="s1">'col2'</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span>
<span class="n">table</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="s1">'(col1 == 1) & (col3**4 > 1)'</span><span class="p">)</span> <span class="p">]</span>
</pre></div>
</div>
</li>
<li><p>For the same reason, conditions for indexed columns must be written as
strings as well.</p></li>
</ul>
</section>
<section id="new-indexing-system">
<h2>New indexing system<a class="headerlink" href="#new-indexing-system" title="Link to this heading"></a></h2>
<p>The indexing system has been totally rewritten from scratch for PyTables 2.0
Pro Edition. The new indexing system has been included into PyTables with
release 2.3. Due to this, your existing indexes created with PyTables 1.x
will be useless, and although you will be able to continue using the actual
data in files, you won’t be able to take advantage of any improvement in
speed.</p>
<p>You will be offered the possibility to automatically re-create the indexes
in PyTables 1.x format to the new 2.0 format by using the <code class="docutils literal notranslate"><span class="pre">ptrepack</span></code>
utility.</p>
</section>
<section id="new-meanings-for-atom-shape-and-array-shape-argument">
<h2>New meanings for atom shape and <code class="docutils literal notranslate"><span class="pre">*Array</span></code> shape argument<a class="headerlink" href="#new-meanings-for-atom-shape-and-array-shape-argument" title="Link to this heading"></a></h2>
<p>With PyTables 1.x, the atom shape was used for different goals depending on
the context it was used. For example, in <code class="docutils literal notranslate"><span class="pre">createEArray()</span></code>, the shape of the
atom was used to specify the <em>dataset shape</em> of the object on disk, while in
<code class="docutils literal notranslate"><span class="pre">CArray</span></code> the same atom shape was used to specify the <em>chunk shape</em> of the
dataset on disk. Moreover, for <code class="docutils literal notranslate"><span class="pre">VLArray</span></code> objects, the very same atom shape
specified the <em>type shape</em> of the data type. As you see, all of these was
quite a mess.</p>
<p>Starting with PyTables 2.x, an <code class="docutils literal notranslate"><span class="pre">Atom</span></code> only specifies properties of the data
type (à la <code class="docutils literal notranslate"><span class="pre">VLArray</span></code> in 1.x). This lets the door open for specifying
multidimensional data types (that can be part of another layer of
multidimensional datasets) in a consistent way along all the <code class="docutils literal notranslate"><span class="pre">*Array</span></code>
objects in PyTables.</p>
<p>As a consequence of this, <code class="docutils literal notranslate"><span class="pre">File.createCArray()</span></code> and <code class="docutils literal notranslate"><span class="pre">File.createVLArray()</span></code>
methods have received new parameters in order to make possible to specify the
shapes of the datasets as well as chunk sizes (in fact, it is possible now to
specify the latter for all the chunked leaves, see below). Please have this
in mind during the migration process.</p>
<p>Another consequence is that, now that the meaning of the atom shape is clearly
defined, it has been chosen as the main object to describe homogeneous data
types in PyTables. See the Users’ Manual for more info on this.</p>
</section>
<section id="new-argument-chunkshape-of-chunked-leaves">
<h2>New argument <code class="docutils literal notranslate"><span class="pre">chunkshape</span></code> of chunked leaves<a class="headerlink" href="#new-argument-chunkshape-of-chunked-leaves" title="Link to this heading"></a></h2>
<p>It is possible now to specify the chunk shape for all the chunked leaves in
PyTables (all except <code class="docutils literal notranslate"><span class="pre">Array</span></code>). With PyTables 1.x this value was
automatically calculated so as to achieve decent results in most of the
situations. However, the user may be interested in specifying its own chunk
shape based on her own needs (although this should be done only by advanced
users).</p>
<p>Of course, if this parameter is not specified, a sensible default is
calculated for the size of the leave (which is recommended).</p>
<p>A new attribute called <code class="docutils literal notranslate"><span class="pre">chunkshape</span></code> has been added to all leaves. It is
read-only (you can’t change the size of chunks once you have created a leaf),
but it can be useful for inspection by advanced users.</p>
</section>
<section id="new-flavor-specification">
<h2>New flavor specification<a class="headerlink" href="#new-flavor-specification" title="Link to this heading"></a></h2>
<p>As of 2.x, flavors can <em>only</em> be set through the <code class="docutils literal notranslate"><span class="pre">flavor</span></code> attribute of
leaves, and they are <em>persistent</em>, so changing a flavor requires that the file
be writable.</p>
<p>Flavors can no longer be set through <code class="docutils literal notranslate"><span class="pre">File.create*()</span></code> methods, nor the
<code class="docutils literal notranslate"><span class="pre">flavor</span></code> argument previously found in some <code class="docutils literal notranslate"><span class="pre">Table</span></code> methods, nor through
<code class="docutils literal notranslate"><span class="pre">Atom</span></code> constructors or the <code class="docutils literal notranslate"><span class="pre">_v_flavor</span></code> attribute of descriptions.</p>
</section>
<section id="system-attributes-can-be-deleted-now">
<h2>System attributes can be deleted now<a class="headerlink" href="#system-attributes-can-be-deleted-now" title="Link to this heading"></a></h2>
<p>The protection against removing system attributes (like <code class="docutils literal notranslate"><span class="pre">FILTERS</span></code>,
<code class="docutils literal notranslate"><span class="pre">FLAVOR</span></code> or <code class="docutils literal notranslate"><span class="pre">CLASS</span></code>, to name only a few) has been completely removed. It
is now the responsibility of the user to make a proper use of this freedom.
With this, users can get rid of all proprietary PyTables attributes if they
want to (for example, for making a file to look more like an HDF5 native one).</p>
</section>
<section id="byteorder-issues">
<h2>Byteorder issues<a class="headerlink" href="#byteorder-issues" title="Link to this heading"></a></h2>
<p>Now, all the data coming from reads and internal buffers is always converted
on-the-fly, if needed, to the <em>native</em> byteorder. This represents a big
advantage in terms of speed when operating with objects coming from files that
have been created in machines with a byte ordering different from native.</p>
<p>Besides, all leaf constructors have received a new <code class="docutils literal notranslate"><span class="pre">byteorder</span></code> parameter
that allows specifying the byteorder of data on disk. In particular, a
<code class="docutils literal notranslate"><span class="pre">_v_byteorder</span></code> entry in a Table description is no longer honored and you
should use the aforementioned <code class="docutils literal notranslate"><span class="pre">byteorder</span></code> parameter.</p>
</section>
<section id="tunable-internal-buffer-sizes">
<h2>Tunable internal buffer sizes<a class="headerlink" href="#tunable-internal-buffer-sizes" title="Link to this heading"></a></h2>
<p>You can change the size of the internal buffers for I/O purposes of PyTables
by changing the value of the new public attribute <code class="docutils literal notranslate"><span class="pre">nrowsinbuf</span></code> that is
present in all leaves. By default, this contains a sensible value so as to
achieve a good balance between speed and memory consumption. Be careful when
changing it, if you don’t want to get unwanted results (very slow I/O, huge
memory consumption…).</p>
</section>
<section id="changes-to-module-names">
<h2>Changes to module names<a class="headerlink" href="#changes-to-module-names" title="Link to this heading"></a></h2>
<p>If your application is directly accessing modules under the <code class="docutils literal notranslate"><span class="pre">tables</span></code>
package, you need to know that <em>the names of all modules are now all in
lowercase</em>. This allows one to tell apart the <code class="docutils literal notranslate"><span class="pre">tables.Array</span></code> <em>class</em> from
the <code class="docutils literal notranslate"><span class="pre">tables.array</span></code> <em>module</em> (which was also called <code class="docutils literal notranslate"><span class="pre">tables.Array</span></code> before).
This includes subpackages like <code class="docutils literal notranslate"><span class="pre">tables.nodes.FileNode</span></code>.</p>
<p>On top of that, more-or-less independent modules have also been renamed and
some of them grouped into subpackages. The most important are:</p>
<ul class="simple">
<li><p>The <code class="docutils literal notranslate"><span class="pre">tables.netcdf3</span></code> subpackage replaces the old <code class="docutils literal notranslate"><span class="pre">tables.NetCDF</span></code> module.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">tables.nra</span></code> subpackage replaces the old <code class="docutils literal notranslate"><span class="pre">nestedrecords.py</span></code> with the
implementation of the <code class="docutils literal notranslate"><span class="pre">NestedRecArray</span></code> class.</p></li>
</ul>
<p>Also, the <code class="docutils literal notranslate"><span class="pre">tables.misc</span></code> package includes utility modules which do not depend
on PyTables.</p>
</section>
<section id="other-changes">
<h2>Other changes<a class="headerlink" href="#other-changes" title="Link to this heading"></a></h2>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">Filters.complib</span></code> is <code class="docutils literal notranslate"><span class="pre">None</span></code> for filter properties created with
<code class="docutils literal notranslate"><span class="pre">complevel=0</span></code> (i.e. disabled compression, which is the default).</p></li>
<li><p>‘non-relevant’ –> ‘irrelevant’ (applied to byteorders)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Table.colstypes</span></code> –> <code class="docutils literal notranslate"><span class="pre">Table.coltypes</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Table.coltypes</span></code> –> <code class="docutils literal notranslate"><span class="pre">Table.coldtypes</span></code></p></li>
<li><p>Added <code class="docutils literal notranslate"><span class="pre">Table.coldescr</span></code>, dictionary of the <code class="docutils literal notranslate"><span class="pre">Col</span></code> descriptions.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Table.colshapes</span></code> has disappeared. You can get it this way:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">colshapes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">col</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="k">for</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">col</span><span class="p">)</span> <span class="ow">in</span> <span class="n">table</span><span class="o">.</span><span class="n">coldescr</span><span class="o">.</span><span class="n">iteritems</span><span class="p">()</span> <span class="p">)</span>
</pre></div>
</div>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">Table.colitemsizes</span></code> has disappeared. You can get it this way:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">colitemsizes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">col</span><span class="o">.</span><span class="n">itemsize</span><span class="p">)</span>
<span class="k">for</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">col</span><span class="p">)</span> <span class="ow">in</span> <span class="n">table</span><span class="o">.</span><span class="n">coldescr</span><span class="o">.</span><span class="n">iteritems</span><span class="p">()</span> <span class="p">)</span>
</pre></div>
</div>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">Description._v_totalsize</span></code> –> <code class="docutils literal notranslate"><span class="pre">Description._v_itemsize</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Description._v_itemsizes</span></code> and <code class="docutils literal notranslate"><span class="pre">Description._v_totalsizes</span></code> have
disappeared.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Leaf._v_chunksize</span></code> –> <code class="docutils literal notranslate"><span class="pre">Leaf.chunkshape</span></code></p></li>
</ul>
<hr class="docutils" />
<blockquote>
<div><p><strong>Enjoy data!</strong></p>
<p class="attribution">—The PyTables Team</p>
</div></blockquote>
</section>
</section>
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