Mdp

2011-10-24: FIX: do not complain when failing to remove temporary directory.
The error warning breaks doctests. On top of that, I do not think
the error message is really useful.

2011-10-22: FIX: fix previous commit (options can not be None)
2011-10-22: FIX: fix bug with pytest when MDP is installed on user
non-writable directory.
2011-10-22: ENH: make NeuralGasNode automatic tests faster
2011-10-22: ENH: call scklearn with its name whenever possible without too
much disruption
2011-10-22: FIX: workaround for debian patch to pp that disables pp's default
password.
2011-10-22: FIX: could not find submodules and classes in old versions of
sklearn the problem was that we build names of sub-modules from
strings, and we need to take into account two possible prefixes
"sklearn" or "scikits.learn"

2011-10-22: FIX: accomodate new name for scikits.learn 0.9 aka sklearn
2011-10-22: RF: extract two methods and simplify logic of metaclass wrapping
2011-10-22: OTH: one more metaclass test also cleand up whitespaces

2011-10-21: FIX/python2.5: forgotten __future__ imports
2011-10-21: ERF: rewrite one format string to make is clearer
2011-10-21: FIX: extend infodict with **kwargs name, to avoid guessing later
2011-10-19: ENH: metaclass: use dict to replace two lists and avoid infodict
No functional changes.

2011-10-21: FIX: finally fig bug in metaclass signature overwriting
2011-10-21: OTH: make test_metaclass more stringent
2011-10-21: OTH: added self contained test for metaclass and extensions
issues.
2011-10-19: OTH: added more detailed failing test for metaclass
2011-10-19: OTH: another bug in signature overwriting. commited a failing
test. Thanks to Alberto Escalante!

2011-10-16: ENH: make tests for NeuralGasNode shorter
2011-10-15: FIX: chmod -x mdp/test/test_NeuralGasNode.py
2011-10-15: DOC: tiny changes in comments
2011-10-15: FIX: tests for neural gas node
2011-10-15: FIX: when start positions for the nodes was set, the number of
nodes default is discarded
2011-10-14: DOC+RF: slight improvements to documentation, comments, and
spacing
2011-10-14: FIX: NeuralGas fixes by Michael Schmucker
2011-08-03: ENH: remove tuple unpacking init: it took twice as much lines
2011-08-03: FIX: NeuralGas fixed by Michael Schmuker
2011-08-03: FIX: remove \ line breaks
2011-07-25: FIX: remove \ line breaks
2011-07-25: NEW, FIX: tests for NeuralGasNode and two fixes
2011-07-25: FIX: _remove_old_edges makes use of its argument
2011-07-25: DOC, FIX: Typos in docstrings and whitespaces
2011-07-25: NEW: NeuralGasNode by Michael Schmuker
2011-10-14: FIX: remove unused variable
2011-10-14: FIX: py3k bytes/str issue in subprocess input
2011-10-14: FIX: remove unused variable
2011-10-14: ENH: use a context manager for sys.stdout stealing
2011-10-14: FIX: add pytest ini file to manifest
2011-10-14: NEW: really check if pp needs monkey-patching
2011-10-14: NEW: be compatible with shogun 1.0. Drop support for older
releases.
2011-10-14: FIX: fix handling of MDP_DISABLE_SHOGUN variable
2011-10-14: Fix KeyError with NSDEBUG=1 Commit 7345d4a changed old-style
formatting to new-style formatting, or at least the format string,
but .format was not replaced with %!

2011-10-13: DOC: make it a bit easier to see that you can use pp on debian too
2011-10-13: FIX: remove (now) useless duplicated test in bimdp
2011-10-13: FIX: windows does not allow me to remove a file
2011-10-13: FIX: no with statement in tests {flow,node}.save Apparently
windows does not allow one process to open a file multiple times.
As {flow,node}.save use internally the with statement to open the
dump file, we can not use the with statement in the test of these
methods: nesting with statement means opening the same file
multiple times.

2011-10-12: NEW: allow for pretty printing of mdp.config. now config.info() is
printed on stdout when you type

>>> print mdp.config

or

>>> mdp.config

don't think about the fact that this is only achievable by a
metaclass ;-)

2011-10-12: ERF: also add mdp.__version__ in config.info
__revision__ is not enough, when mdp is installed and does not
load from a git repository that string is empty (by the way: we
should fix it!)

2011-10-11: FIX: remove forgotten print statement
2011-10-11: NEW: add tempfile test to help diagnose win7 problems
2011-10-11: FIX: make py.test.__version__ check more robust
2011-10-11: Add mdp.__revision__ to mdp.config.info() output This changes the
order of initialization a bit: first mdp.configuration is fully
imported, then mdp.utils. Because of this change,
mdp.utils.repo_revision was renamed to mdp.repo_revision. It is
imported only in mdp.configuration and then deleted from the
visible namespace. get_git_revision was available as
utils.get_git_revision, and now it's gone, but mdp.__revision__
contains the same value, so there little need to export the
function. I hope nobody used it.

>>> print mdp.config.info()
python: 2.7.2.final.0
mdp: MDP-3.1-74-gbaca2a8+
parallel python: 1.6.0
shogun: NOT AVAILABLE: No module named shogun
libsvm: libsvm.so.3
joblib: 0.4.6
scikits: 0.8.1
numx: scipy 0.9.0
symeig: scipy.linalg.eigh

2011-10-11: NEW: append + to mdp.__revision__ in modified repo
2011-10-11: FIX: half of an assert message was lost
2011-10-11: ERF: use py.test 2 ini-file configuration. we can now check for
py.test version, and get finally rid of the redundant conftest.py
files. we now have only one conftest.py file for bimdp and mdp.

2011-10-11: FIX: check if we have ENOENT in TemporaryDir.__del__
2011-10-11: FIX: stop complaining if dir is gone already in TemporaryDirectory
2011-10-11: ERF: get rid of the pp monkey patch dirs the hard way.
TemporaryDirectory does not manage to delete itself when created
in a subprocess

2011-10-11: ERF: make the pp monkeypatch dir prefix more explicit
2011-10-11: ERF: change the interpretation of MDP_MONKEYPATCH_PP now you can
specify a container directory for the patching. it defaults to
tempfile.gettempdir(), i.e. /tmp on unix and something else on
windows
2011-10-11: FIX: only allow py.test version >= 2.1.2 py.test version > 2 are
subtly incompatible with versions < 2. just settle on the new
ones. problem: debian still does not package a reasonably recent
version of py.test. in this case, just use the standalone script.
thanks to 8a5b2e272de4230f15d09f85b7d35b0aeee3078e it's as
flexible as py.test itself.
2011-10-11: ERF: pass options to py.test in mdp.test. this way using the
standalone script run_tests.py is as flexible as using py.test
directly

2011-10-11: ERF: updated standalone py.test script to version 2.1.2
2011-10-11: DOC: added pointer to win64 binaries distributor
2011-10-10: ENH: use with statement for better readability in a couple of
tests No functional changes.

2011-10-10: ENH: make pyflakes happy by not defining unused names No
functional changes.

2011-10-10: FIX: make monkeypatch_pp compatible with both pp 1.6 and 1.6.1
>>> import pp
>>> pp.version
'1.6.0'
>>> pp._Worker.command
'"/usr/bin/python" -u "/usr/lib/pymodules/python2.6/ppworker.py" >
2>/dev/null'

>>> import pp
>>> pp.version
'1.6.1'
>>> pp._Worker.command
['/usr/bin/python2.6', '-u',
'/usr/lib/pymodules/python2.6/ppworker.py', '2>/dev/null']

2011-10-10: FIX: temporary directory for tests was not managed properly sed
's/mdp_toolkit_reporting_configured/mdp_configured/g' because the
existence of this variable guards not only reporting
configuration, but also the temporary directory stuff (and also
the name was kind of long).

sed 's/tempdirname/mdp_tempdirname/' because it goes in the
py.test namespace and should have a prefix like the other
variable.

sed -r 's+bimdp/+TMP\/+g; s+mdp/+bimdp/+g; s+TMP\/+mdp/+g'
<mdp/test/conftest.py >bimdp/test/conftest.py because bimdp should
be kept in sync. In my installation bimdp is actually configured
first, so tests in the temporary directory were failing with
AttributeError on py.test.tempdirname.

2011-10-10: FIX: tempdirs in cacheing tests were shortlived A temporary
directory created with TemporaryDirectory can go at any time, so a
construct like
dirname = TemporaryDirectory().name is broken.

Since the directories are created in the master temporary
directory anyway, they don't have to be deleted separately.

2011-10-10: FIX: do not set the cachedir by default on import mdp.caching
setting it by default was creating a lot of bogus temporary
directories when parallel processes where started using
process_scheduler. I see no side effects for not setting it

2011-10-10: FIX: better name for global temp dir
2011-10-10: FIX: fix pp monkey patching. pp._Worker.command.replace(ppworker,
ppworker3) did not work, as pp._Worker.command is a list and not a
string!

2011-10-10: FIX: put joblib caching stuff in the new global test tempdir
2011-10-10: ERF: added a container directory for temporary test files. the
directory gets deleted (no matter its contents) at the end of the
test run. This should fix stale temp files.

2011-10-05: FIX: partially revert 569cbe7 Changing 'except Exception:' clauses
to bare 'except:' would catch and swallow ^C and the like.

2011-10-02: ENH: revert the condition for pp monkeypatching It's better to
only enable it when explicitely requested. The warning is also
removed, because it doesn't make sense to warn about something
that was explicitely requested. If the option to monkey patch is
not given, check if pp is likely to be broken, and if so, disable
it at configuration time.

2011-10-02: FIX: remove some unused imports and one allocation
2011-10-02: ENH: make temporary directory names more readable tmpxayPZEpp4mdp/
=> pp4mdp.tmpxayPZE/

2011-09-08: FIX: new module structure in scikits.learn 0.8
2011-09-07: BF: Exclude float16 dtypes in numpy.linalg.eigh.
2011-08-24: Fixes to FastICA node Fine tuning and stabilisation are now used
correctly, and the result closely resembles the original matlab
version for the deflation/gaussian case with prewhitened data. The
results are not numerically identical because there are still some
differences in stopping criteria, but it's close. To verify, see
original Matlab implementation.

2011-08-10: DOC: added documentation item to TODO list
2011-06-30: ERF: PEP8 fix (da pignolo)
2011-06-30: ERF: simplify metaclass wrapping code
2011-06-30: FIX: Fixed the node metaclass to correctly handle signatures and
docstrings for inheritance chains.
2011-06-30: ERF: Some small pylint-motivated updates.
2011-06-30: ERF: wrap private methods in meteclass even if no docstring is
defined.
2011-06-30: ERF: Made the _get_required_train_args method more robust.
2011-06-30: OTH: refactored metaclass tests, again.
2011-06-30: OTH: refactored metaclass tests
2011-06-16: DOC: added proper git format for changelog
2011-06-16: OTH: commit failing test for docstring overwriting Thanks to
Alberto Escalante to point this bug out.

2011-04-07: FIX: verbose argument in set_cachedir was ignored.
2011-06-12: FIX: Fixed a regression that broke the DBN example.
2011-06-11: ERF: Major refactoring of the binet inspection code. This follows
the refactoring of the flow-to-HTML conversion. Smaller
refactorings in realted parts (slideshow) were also done.
2011-06-11: ERF: Prepare large refactoring by renaming the files first.
2011-05-31: ERF: Refactored the flow-to-HTML conversion. Threw out useless
code, fixed style issues and now use the proper vocabulary
(visitor pattern). The bimdp inspection has not yet been updated
and is therefore broken in this commit.
2011-04-18: FIX: monkeypatch_pp was broken I made some changes without
actually testing if stuff works...

2011-04-15: FIX: delete main joblib cache directory at mdp exit The directory
is of course only deleted if we created it ourselves, i.e. if it
is a temporary directory.

2011-04-15: FIX: delete joblib cache directory after tests
2011-04-15: DOC: describe MDPNUMX and MDPNSDEBUG env. vars.
2011-04-15: FIX: bump supported scikits-learn version number Setting >=0.6 is
pretty conservative, but Debian's 0.5-1 is bad for sure.

2011-04-14: DOC: document MDP_DISABLE_MONKEYPATCH_PP
2011-04-14: DOC: document MDP_DISABLE_* variables
2011-01-12: DOC: improve rst in mdp/extension.py
2011-03-21: FIX: drop some unused variables & imports Wanted to test pyflakes
on something. This is the result.

2011-04-14: FIX: apply a temporary workaround to the pp import problem For
details see
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=620551.

ppworker.py must be run from some safe place. A temporary dir
seems a good option. Unfortunately a temporary file is not enough,
because parent directory should be empty. TemporaryDirectory is so
complicated, because the code is run during Python shutdown
procedure and some modules are not available.

2011-04-05: FIX: make short description fit within 200 char limit Tiziano
proposed the text, nobody protested... I guess that this signifies
a consensus. :)

Some small formatting fixes in source code and output were
applied.

2011-04-01: OTH: remove unnecessary parentheses around assert
2011-04-04: FIX: restore python2.4, 2.5 support in setup.py Module ast is not
available in python < 2.6.

The format of docstrings is slightly changed: removed empty lines
at the top.

Tested with python 2.4, 2.5, 2.6, 2.7, 3.1, 3.2. Output looks
identical.

2011-04-01: FIX: [pp] Result container was shared between invocations
2011-04-01: ERF: improved scikits.learn detection code.
2011-03-31: ERF: Some small code improvements, no functional changes.
2011-03-31: FIX: Fixed source path handling.

-------------------------------------------------------------------------------

2011-03-29: FIX: fixed shogun version detection code. As I expected, explicit
version checking is bound to fail. I would prefer to just remove
it and rely on functional checks, i.e. is the feature we depend on
present or not?
2011-03-24: ERF: CovarianceMatrix has the option of not centering the data;
SFANode modified accordingly
2011-03-22: FIX: fix wrong normalization in SFANode SFANode was using the
covariance matrix of the derivatives, while the SFA algorithm
requires the non-centered second moment matrix of the derivatives.
This bug is probably irrelevant in most cases, but in some corner
cases the error scales with 1/sqrt(N) where N is the number of
samples. Many thanks to Sven Dähne for fishing this out ;-)
2011-03-22: ERF: added new tests for SFANode Those tests are currently
failing.
2011-03-22: ERF: really use the debug flag in SFANode.stop_training
2011-03-02: FIX: old svm versions would break the import process Bug reported
by Philipp Meier.
2011-03-03: DOC: updated TODO
2011-03-03: DOC: updated TODO
2011-02-23: DOC: updated CHECKLIST and TODO
2011-02-23: ERF: performance and memory improvements for KNNClassifier.
Transform array of n_samples^2 * n_features array into
n_samples^2. Thanks to Fabian Pedregosa!
2011-02-17: FIX: Small cosmetic fix in flow inspection for the case when
stop_training doesn't receive any argument.
2011-02-17: FIX: Do not wrap abstract scikits.learn transformers
2011-02-17: Robustify wrap_scikits_transformer. Fix for the case that a
transform does not implement some of the methods.
2011-01-31: ERF: running self-contained test script is now blocking the prompt
2011-01-27: FIX: Made the target checks more permissive when execution ends or
is aborted.
2011-01-27: ERF: Added additional checks for copy flag in BiLayer.
2011-01-27: FIX: Fixed regression in inspection method output.
2011-01-27: FIX: BiLayer was not compatible with all return value options.
2011-01-27: FIX: Fixed some leftover inconsistencies from BiMDP stop_training
interface changes.
2011-01-26: DOC: with_extension doesn't work for coroutines, tell epydoc about
extension
2011-01-25: ERF: remove unittest-style wrapper class from test_extension.py.
2011-01-25: OTH: use context managers to open/close file for pickling
2011-01-25: ERF: Check for empty slides in execution as well.
2011-01-25: ERF: Improved the behavior of show_training if an already trained
flow is given (a special expection is now raised).
2011-01-17: FIX: add trove classifiers for Python 2 and 3.
2011-01-14: ERF: Updated the Parallel Python support, especially the
NetworkPPScheduler. It now works with pp 1.6, and there are some
refactoring and robustnes improvements as well.
2011-01-13: FIX: really update CHECKLIST
2011-01-13: NEW: mdp descriptions now defined in the module. They new
descriptions are used in the setup.py script and in generating the
web site.
2011-01-13: ERF: get version and description in a robust way.

-------------------------------------------------------------------------------

2011-01-12: FIX: import NormalizeNode in mdp.nodes
2011-01-12: FIX: no return in IdentityNode method
2011-01-12: FIX: test_scikits should be run only if scipy is available
2011-01-12: FIX: tell epydoc that nodes are documented in rst
2011-01-11: NEW: convert scikits docstrings to rst This way I'm only getting
missing target warnings and the text is parse as rst. No monospace
font :)

2011-01-11: FIX: fix some epydoc warnings, add some links and a forgotten
export
2011-01-07: MISC: duplicate some useful code among the three wrappers last
merge from scikits branch.

2011-01-11: ERF: make scikits default docs rst-compatible
2011-01-10: Merge branch 'namespace_fixup' Conflicts:
mdp/__init__.py
mdp/nodes/__init__.py
mdp/utils/__init__.py

Add missing comma in __all__ in mdp/__init__.py.

2011-01-10: OTH: shorten test name
(Looked awkward in py.test output.)

2011-01-10: NEW: introduce MDPNSDEBUG environment variable This variable
controls namespace fixup debugging messages.

Also remove 'advanced string formatting' in favour of printf-style
statements (for python 2.5 compatibility).

2011-01-10: FIX: made the one scikits test a bit more useful
2011-01-10: FIX: there is no problem with output_dim in scikits classifiers
because they are identity nodes

2011-01-10: DOC: documentation of output_dim problem in scikits.learn wrappers
2011-01-10: FIX: check for existence of im_func in classifier wrapper
2011-01-10: FIX: fail meaningfully when trying to set output_dim
2011-01-10: FIX: added docstrings to scikits wrappers
2011-01-10: FIX: Cache mechanism called pre_execution_check with too much
information
2011-01-10: FIX: broken variable for disabling scikits.learn
2011-01-10: FIX: fix wrapper string in scikits nodes
2011-01-10: FIX: fixed hard-coded scikits test.
2011-01-10: FIX: fixed a bit pp_remote support. I commented out the test.
There's no point in having a test that requires a working ssh
setup. we should move that code in the examples. TODO: I still did
not manage to test the remote support properly: it does not work
if ssh spits some session information on startup :-(

2011-01-10: FIX: fix namespace issues with scikits nodes.
2011-01-10: FIX: Made the straight forward fixes for pp 1.6 support, not sure
if this is working now.
2011-01-10: Merge remote branch 'origin/master'
2011-01-10: Merge a branch with some scikits work I'm doing this as a merge
instead of rebasing, because the work was really done in parallel,
and e.g. Tiziano removed the file, which I moved and updated.

2011-01-10: FIX: make scikits support depend on version 0.5 Version 0.4
breaks... Version 0.5 at least does learn & execute.

2011-01-10: FIX: move scikits test into mdp/tests/
2011-01-10: Merge remote branch 'origin/master' Conflicts:
mdp/test/test_pp_local.py

2011-01-10: FIX: Updated local scheduler to work with latest pp version 1.6.
2011-01-10: FIX: fix name leaking in nodes/__init__.py
2011-01-10: FIX: add scikits to list of dependencies in testall.py
2011-01-10: FIX: Fixed local Parallel Python tests.
2011-01-10: FIX: make test_ISFANode more robust.
2011-01-10: FIX: remove stale test_scikits.py file
2011-01-10: NEW: merged constant_expansion_node branch. Adds new
GeneralExpansionNode thanks to Alberto Escalante.

Tests and node had to be adjusted to merge cleanly and to follow
new conventions. TODO: pseudo_inverse method is quite fragile,
why?

2011-01-10: ERF: Added native traceback flag to IDE test run template.
2011-01-09: FIX: remove bitrot in test_pp_*.py. This makes the local tests
pass with parallel python 1.5.4. Remote tests still fail because
amongst other things the server list must be passed explicitely.

The tests fail horribly with newer pp version.

2011-01-09: FIX: kill epydoc warnings
2011-01-09: Revert "DOC: migrated class.__doc__ to rst for nerual_gas_nodes"
This reverts commit 2c2a4cd72ecd7d2dbb2032dd7db4f0754b3ba846.

2011-01-07: FIX: make joblib version checking more robust e.g.
joblib.__version__='1.0.0-gitABCEDFG' should pass.

2011-01-07: FIX: be more tolerant against missing modules in scikits.learn.
depending on the installation procedure, user may or may not have
some of the scikits.learn modules. we just wrap the modules we
find.

2011-01-07: FIX: add wrongly removed 'scikits' namespace from mdp.nodes.
2011-01-07: FIX: wrong version in scikits.learn info item.
2011-01-07: ERF: Merged "scikits" branch into "master". Conflicts:
mdp/__init__.py. Fixed new config syntax and generic_tests.

2011-01-06: FIX: fixed testall script. now it works. the script should be
ported to use subprocess, so that it runs OS agnostic.

2011-01-05: ERF: improved testall.py
2011-01-05: DOC: updated CHECKLIST for release.
2011-01-05: FIX: Slightly changed the include_last_sample argument to fix the
problem with the standard parallel fork implementation.
2011-01-05: FIX: fix test broken due to new keyword in SFANode.
2011-01-05: FIX: added include_last_sample to SFA2Node too.
2011-01-05: ERF: added include_last_sample switch to SFANode. Motivation and
discussion can be found in this thread:
http://sourceforge.net/mailarchive/forum.php?thread_name=20100826183424.GF26995%40tulpenbaum.cognition.tu-berlin.de&forum_name=mdp-toolkit-users

2011-01-05: FIX: clean up __all__ in mdp/__init__.py numx* should not be in
all. Quoting Tiziano:

> numx was not in __all__, and therefore was not documented by
epydoc.
> Once it is added to __all__, indeed things break heavily. well,
I think even it was by mistake, it is a good thing that numx is
not in __all__. mdp.numx is an *internal* thing. people doing from
mdp import * should not get numx. so, leave it like this and we
don't even need a workaround for epydoc.

While at it, remove whitening which was already gone and make the
list alphabetical.

2011-01-04: Merge branch 'cache' Conflicts:
mdp/__init__.py

2011-01-04: FIX: make setup.py run on also on python3 The code must run on all
supported python versions.

try: ... except Type, v: ...

file()

cannot be used.

While at it, I'm changing exec() to re.match. It's simpler.

2011-01-04: FIX: python2.5 has no itertools.product
2011-01-04: ERf: added script to test all python versions and dependencies.
2011-01-04: FIX: fix name error in configuration.py
2011-01-04: ERF: added way of disabling optional dependencies optional
dependencies can be disabled setting the env variable
MDP_DISABLE_DEPNAME

2011-01-04: ERF: remove long deprecated helper functions. pca and fastica
survive because we use them as ad in the the site and because most
probably they are the only one in real use out there.

2011-01-04: FIX: fix test failures due to previous commit.
2011-01-04: ERF: cleaned up mdp/__init__.py. configuration is now a separate
file. the logic of numx loading has been changed (again!).
numpt/scipy can not be treated as an external dependency.

2011-01-04: FIX: fix generic node test failures for
TimeFrameSlidingWindowNode.
2011-01-04: ERF: support iterables in generic node tests.
2011-01-03: FIX: MDP depends on joblib >= 0.4.3
2011-01-03: FIX; fixed git log format in CHECKLIST
2011-01-03: DOC: add __homepage__ variable in __init__.py
2011-01-03: FIX: removed useless file.
2011-01-03: ERF: updated author and maintainers, put version in one single
place.
2011-01-03: DOC: changed reference to installation instructions
2011-01-03: ERF: removed our names from COPYRIGHT. It makes little sense to
keep up-to-date the list of maintainers in this file. we have one
authoritative source: the development.rst page.

2010-12-31: FIX: fixed TimeDelayNode docstring rst formatting
2010-12-31: NEW: new TimeDelay and TimeDelaySlidingWindow nodes. Thanks to
Sebastian Höfer!

2010-12-31: DOC: specify dependency in svm nodes.
2010-12-31: FIX: change order of nodes in nodes/__init__.py __all__ order is
somehow arbitrary, but better than before. it is needed for the
automatic node list generation in the web site.

2010-12-31: DOC: migrated class.__doc__ to rst for svm family
2010-12-31: FIX: logic and wording of the symeig dependency test were wrong. I
don't have a 64bit machine to test that the function in
mdp/utils/routines.py still does the right thing. if it does not,
just change mdp.config.has_symeig == '...' to
mdp.config.has_symeig != '...'
;-)

2010-12-31: DOC: migrated class.__doc__ to rst for misc_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for classifier_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for expansion_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for nerual_gas_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for regression_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for rbm_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for lle_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for em_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for fda_nodes
2010-12-31: DOC: migrated class.__doc__ to rst for sfa family
2010-12-31: DOC: migrated class.__doc__ to rst for ica family
2010-12-31: DOC: migrated class.__doc__ to rst for nipals
2010-12-31: DOC: migrated class.__doc__ to rst for pca_nodes
2010-12-31: DOC: migrate convolution nodes to rst docstring
2010-12-31: DOC: fixed migration to rst docstrings for xsfa_nodes.
2010-12-30: Merge branch 'feature/libsvm_291_support' Conflicts:
mdp/__init__.py
mdp/test/test_contrib.py

2010-12-30: FIX: failing dtype_consistency_tests with numpy as backend The
config.has_symeig logic was that config.has_symeig is False when
using the _fake_symeig compatibility wrapper. Dtypes were selected
based on that.

2010-12-30: FIX: make sure mdp.config.has_{numpy,scipy} are always set, really
2010-12-30: FIX: make sure mdp.config.has_{numpy,scipy} are always set
2010-12-30: FIX: Don’t try to fetch version of numx_version twice.
2010-12-29: ERF: Put SVM tests into a separate file. Also: Fix
skip_on_condition on class.
2010-12-27: DOC: rename ExternalDepFail to -Failed and document stuff
2010-12-27: FIX: test_seed failured when testing running bimdp.test() after
mdp.test() The reason was that when the test functions were
imported from mdp.test into bimdp.test, they still referenced
mdp.test._SEED global variable. But the --seed option in bimdp is
independent, so it was set to a different random seed. By
duplicating test_seed.py, a second independent global is created.

2010-12-27: Add a test for separable data.
2010-12-27: NEW: check if joblib is >= 0.4.6
2010-12-27: ERF: Restructured the libsvm tests.
2010-12-27: OTH: make COPYRIGHT valid rst This makes is easier to include in
the webpage.

2010-12-27: Merge branch 'config_simplification' Conflicts:
mdp/__init__.py

This merge commit contains an adaptation of caching to the new
framework.

2010-12-27: NEW: convert caching_extention.py to rst
2010-12-27: Merge branch 'rst_docstrings' Conflicts:
mdp/signal_node.py

2010-12-27: Merge branch 'cache' Conflicts:
mdp/caching/caching_extension.py

2010-12-27: Merge commit '06007d3e8987a6c8574fd63c7608b37e9e657e66'
2010-12-27: ERF: Added test for execute_method in classifiers.
2010-12-27: ERF: Add validation for libsvm parameters.
2010-12-27: ERF: Get rid of superfluous parameter handling. Use svm_parameter
directly.
2010-12-27: FIX: Get the libsvm tests running for versions >=2.91. TODO: * The
new interface still needs some polishing.
* We need to test the RBF classifier. It won’t work right now.
2010-12-24: FIX: fix test of PCANode for degenerate case, it was failing
occasionally.
2010-12-24: removed now useless copy method overwriting in NoiseNode
2010-12-24: Merge branches 'deepcopy' and 'master'
2010-12-24: ERF: added additional tests for node and flow deepcopy This tests
fail in master branch righ now, because lambdas can not be
pickled!

2010-12-24: ERF: added additional tests for node and flow deepcopy
2010-12-24: Merge branch 'master' of
ssh+git://mdp-toolkit.git.sourceforge.net/gitroot/mdp-toolkit/mdp-toolkit
2010-12-24: FIX: fixex bimdp.test() under windows. The FIX introduced with
dfa8ec5a0d367941e4c297325a43361d579f8bbd was not working on
windows, because git does not support symlinks there. It has been
fixed differently now, and it should work reliably under any
system, I hope.

2010-12-22: ERF: Improved the exception handling for failing training argument
check (user now gets a better error message).
2010-12-22: changed my email address in copyright and setup
2010-12-21: Merge remote branch 'new_guidelines'
2010-12-21: FIX: now bimdp.test() really works as advertised!
2010-12-21: FIX: regenerate run_tests.py script for running tests without
py.test
2010-12-03: OTH: remove uses of deprecated dict.has_key()
2010-12-03: OTH: use with_statement in signal_node
2010-12-18: DOC: improved docs of caching mechanism
2010-12-18: FIX: possible to switch caching path while extension active
2010-12-18: FIX: caching started at second execution because of automatic
setting of dtype, input_dim
2010-12-18: NEW: caching extension can now cache individual classes or
instances
2010-12-18: DOC: a few fixes to the cache extension docs
2010-12-09: NEW: Added parallelization for NearestMean and KNN classifier.
Also updated NearestMeanClassifier attribute names to avoid
confusion.
2010-12-09: DOC: Added explanation in _default_fork docstring.
2010-12-09: DOC: Improved code documentation.
2010-12-03: FIX: copy with deepcopy everywhere, raise DeprecationWarning on
old API Since Node.copy() is a public function, changing the
allowed parameters might be bad. So just ignore the parameter and
raise a DeprecationWarning if the parameter has a non-None value.

>>> import mdp
>>> node = mdp.Node()
>>> node2 = node.copy(protocol=1)
__main__:1: MDPDeprecationWarning: protocol parameter to copy() is
ignored

2010-12-03: FIX: Patch for using deepcopy instead of pickle for Node and Flow
Hi all,

here is a patch and test script for replacing the pickle with
deepcopy in Node.copy() and Flow.copy(). The signature of the copy
function changes (the protocol keyword is no longer necessary), I
don't know what the proper way to handle this is (deprecation
error?), so I'll leave it up to you guys.

Thanks for all the efforts, we get very positive feedback from all
users of mdp and Oger!

David

2010-12-02: OTH: remove redundant shogun version checking
2010-12-02: NEW: add tests for the new config architecture
2010-12-01: OTH: Convert config.has* to an attribute I have suspicions that
using a lambda function was causing problems with the process
scheduler.

git grep -l -E 'config.has_'|xargs sed -r -i
's/(config.has_[a-z_]+)\(\)/\1/g'

2010-12-01: OTH: simplify mdp config discovery Create
ExternalDepFound/ExternalDepFail objects immediately after
attempting import. This way there's no need to reverse engineer
where the symeig implementation comes from.

TODO: test_process_schedule fails!

2010-12-01: OTH: simplify numpy/scipy imports
2010-12-01: OTH: make ExternalDep objects have boolean value
2010-12-02: OTH: replace 'map()' with 'for:' following 2to3's advice
2010-12-02: OTH: remove redundant OrderedDict implementation I'm also moving
the OrderedDict recipe to a separate file, because it's kind of
logically separate and will not be used in newer versions of
Python anyway.

2010-12-01: OTH: mdp.test() should not cause SystemExit Function
py.cmdline.pytest calls py.test.cmdline.main, but also raises
SystemExit. Just call the latter one, so the interactive session
can continue.

2010-12-01: Change __license__ to 'Modified BSD' in source code The license
text was already changed in the documentation, but not in the
source code.

2010-11-30: NEW: Added the execute_method argument and attribute to the
Classifier class. This makes it possible to get the classification
results from a normal flow without resorting to monkey patching
(which makes nodes unpickelable).
2010-11-30: ERF: Improved code readibility.
2010-11-30: NEW: Added iadd method to Flow. Also fixed the error strings.
2010-11-29: NEW: Added parallel version of Gaussian classifier.
2010-11-29: ERF: Added helper function to combine CovarianceMatrix instances.
2010-11-24: NEW: Added KNN classifier.
2010-11-24: FIX: Fixed wrongly created classifier BiNodes.
2010-11-24: NEW: Added nearest-mean classifier node.
2010-11-24: FIX: Updated test name.
2010-11-24: ERF: Some cleanup in the GaussianClassifier. Added an exception if
any class covariance matrix is singular.
2010-11-23: BRK: Renamed GaussianClassifierNode to GaussianClassifier to
follow the general classifier convention (otherwise a special case
would be needed in the BiMDP autogenerated code).
2010-11-23: FIX: Updated BiMDP test for the new siganture of FDANode.
2010-11-23: BRK: Updated FDANode siganture to follow the newer conventions
from ClassifierNode (labels instead of cl) and the PCA/SFANode (n
instead of range).
2010-11-09: OTH: move PROJECT_GUIDELINES and NEW_DEVELOPER_INFO to
development.rst in docs
2010-11-01: NEW: convert neural_gas_nodes.py and rbm_nodes.py docstrings to
rst
2010-11-01: NEW: add reference to JoMLR article
2010-11-01: NEW: convert mdp/nodes/xsfa_nodes.py docstrings to rst
2010-11-01: NEW: convert mdp/__init__.py and mdp/nodes/signal_node.py
docstrings to rst
2010-11-01: Merge commit 'c3bdc14c092b92c214f8bd76002be565706f07ca'
2010-11-01: FIX: Fixed bug in node join, leading to inconsistent state under
certain conditions with FlowNode.
2010-10-31: ERF: Added copy_callable option for thread scheduler.
2010-10-16: FIX: Updated failing unittest.
2010-10-16: FIX: Fixed the parameter names in the switchboard factory.
2010-10-15: BRK: Updated the remaining switchboards.
2010-10-15: BRK: Started to replace the x_ and y_ arguments in 2d switchboards
with a single _xy argument. So far only the
Rectangular2dSwitchboard is done.
2010-09-26: FIX: Correctly distinguish Flow and BiFlow in trace inspection
execute.
2010-09-25: FIX: Fixed bug in ParallelFlowNode and added unittest.
2010-09-14: DOC: Fixed wrong docstring.
2010-09-14: BRK: Improved extension context manager and decorator to only
deactivate extensions that were activated by it. This prevents
unintended side effects. Corresponsing tests were added.
2010-09-14: FIX: Fixed outdated import.
2010-09-14: Merge commit '4671fc2511b3446e57afcc1974d46f15ac92cb5f'
2010-09-14: BRK: Improved the dimension consistency handling in FlowNode, also
making the dimension setting stricter. This is to prevent really
strange errors in some corner cases (e.g. when the output_dim is
automatically set in execute). One generic test had to be dropped,
but explicit test for the dimension setting were added.
2010-09-14: ERF: Streamlined the parallel fork template method.
2010-09-14: FIX: Fixed the test node in the test_execute_fork unittest.
2010-09-14: ERF: Removed the ParallelBiNode, since it is no longer needed.
2010-09-14: Revert "FIX: Fixed small bug in dimension consistency check." This
reverts commit 0b37100894f08faf3653bab09bc4b5fb21705d72.

2010-09-13: ERF: Added more unittests for parallel. One still fails because an
improvement in FlowNode is needed.
2010-09-13: DOC: Added comment on necessary extension context improvement.
2010-09-13: FIX: Fixed small bug in dimension consistency check.
2010-09-13: ERF: Improved the threaded scheduler (better exception handling).
2010-09-13: FIX: Fixed parallel bug, missing argument in callable.
2010-09-13: ERF: Turned the use_execute_fork property into a normal method.
2010-09-12: FIX: Added the missing property decorators (this was dangerous,
since a function attribute is cast as True)..
2010-09-12: FIX: Fixed bug in ParallelNode.
2010-09-12: FIX: Updated ParallelFlow to use correct execution result
container.
2010-09-12: FIX: Updated __all__ list.
2010-09-10: OTH: python2.5: remove PEP 3101 formatting
2010-07-30: OTH: python2.5: 'with' and 'as'
2010-09-09: Remove next-to-last import numpy from mdp codebase numx rules!

2010-09-09: ERF: Changed the node purging mechanism in parallel to no longer
use a special extension method in FlowNode. Also some smaller
comment updates.
2010-09-09: NEW: MDP migrates to BSD license!
2010-09-09: BRK: Clarfied some subtle aspects of the parallel API and updated
the code to improve consistency.
2010-09-09: Make git display python diffs better
2010-09-08: FIX: Some smaller fixes in the updated parallel code.
2010-09-08: FIX: The parallel BiMDP tests are running again. Also some more
cleanup in MDP parallel.
2010-09-08: FIX: The standard MDP tests now all run again after the changes in
parallel.
2010-09-07: BRK: Continued work on the parallelization update, not working
yet.
2010-09-06: BRK: Started to modify the parallel node forking. The
is_bi_training in BiNode is replaced with a use_execute_fork in
the ParallelExtensionNode base class. This is more logical, less
complicated and a first step towards enabling more parallelization
patterns.
2010-09-02: OTH: the caching mechanism could be simplified with the latest
joblib
2010-08-31: DOC: Improve docs of caching mechanism, keywork argument for
verbosity of cache
2010-08-26: FIX: SFANode.train fails with a meaningful error if trained with
x.shape = (1, n)
2010-08-26: Fix --seed option for py.test >= 1.3 Py.test in version 1.3 added
a feature to skip conftest.py files when they are exactly the
same. This helps when a directory is copied to a subdirectory of
itself and the config files are not idempotent. Unfortunately,
this runs afoul of our logic to add the --seed option everywhere,
irrespective of wheter py.test is run implicitely for the whole
mdp-toolkit or for mdp or for bimdp or for both. The solution is
to modify one of the conftest.py files to be unidentical.

Tested with with py.test 1.2.1 and 1.3.3.

2010-08-18: OTH: Simplify docstring formatting.
2010-08-25: NEW: FANode detects singluar matrices
2010-08-24: ERF: fftpack does not support float >64; those types are removed
from the supported list for ConvolutionNode
2010-08-24: FIX: Remove forgotten print statements
2010-08-24: ERF: ISFA supports float>64
2010-08-23: ERF: added python version to mdp.config
2010-08-19: ERF: Add complex256 to list of unsafe dtypes
2010-08-19: FIX: Generic tests failed for MDPNUMX='numpy' When symeig and
scipy.linalg.eigh are not present, MDP falls back into using
numpy.linalg.eig . This does not support large floating point
types, for some reasons, which caused the tests to fail.

2010-08-17: ERF: Updated the classifier nodes that were overlooked in the big
PreserveDimNode cleanup.
2010-08-17: Merge branch 'supporteddtypes' Conflicts:
mdp/nodes/misc_nodes.py

2010-08-17: ERF: Clarify questions about support for float64 only
2010-08-17: FIX: Fixed generic tests, now check that PreserveDimNode raises
right exceptions.
2010-08-17: ERF: Added tests for PreserveDimNode.
2010-08-17: ERF: Wrapped up the PreserveDimNode changes. Unable to fix the
generic unittests, somebody has to fix those.
2010-08-16: ERF: Refined the choice of supported dtypes
2010-08-16: ERF: Redefine default supported dtypes to be 'Floats', and modify
all nodes accordingly
2010-08-16: ERF: Further simplified Cumulator mechanism; added test After
digging into numpy's C code, we decided that at present
numpy.concatenate does the right thing, i.e. it creates a buffer
large enough and uses memcpy to copy the data in each array.

2010-08-16: FIX: py.test failed with an error reporting a duplicated 'seed'
option In py.test 1.3.3 they changed the sequence in which the
conftest.py
files are loaded. In our case, the /mdp/test/conftest.py file
was
laoded before the /conftest.py file, which tried to redefine
the
optione 'seed', causing an error.

2010-08-14: ERF: Simplified concatenation mechanism in Cumulator The new
solution is much faster and still avoids direct calls to
numpy.concatenate, that performs pairwise concatenations and
wastes a lot of memory.

2010-08-14: FIX: Cumulator had no docstring
2010-08-10: FIX: Added missing exit target check in BiFlow. Changed the
unittest to better test this case.
2010-08-10: ERF: Changed BiFlow.execute to always return a tuple (x,msg), even
if the msg is empty. The previous changing return signature was
too likely to cause errors.
2010-08-10: DOC: Small fix in docstring.
2010-08-10: DOC: Small fix in comment.
2010-08-09: ERF: Added check for case when both x and msg are None to produce
better error message.
2010-08-09: ERF: Removed duplicate verbose print.
2010-08-08: FIX: Fixed the missing import for PreserveDimNode and fixed the
broken generic tests for these nodes by excluding them. This is
only a provisional fix.
2010-08-08: ERF: Rewrote the creation of the autogenerated BiNode classes.
Went back to dynamically creating the classes at runtime. Now use
a node blacklist instead of the previous whitelist. These two
changes allow the import of nodes with dependencies, like the SVM
nodes.
2010-08-08: NEW: Added new PreserveDimNode base class for input_dim ==
output_dim. This should avoid duplication of the set_dim methods.
2010-08-05: ERF: Tweaked the hinet CSS.
2010-08-05: DOC: Improved the ParallelFlow docstrings.
2010-07-30: DOC: Small improvements to the corutine decorator docs.
2010-07-30: FIX: Removed some left over stop_message references.
2010-07-29: NEW: extend namespace_fixup to bimdp
2010-07-29: ERF: rework fixup_namespace function and add tests
2010-07-27: FIX: NodeMetaclass and ExtensionException where imported but not
in __all__
2010-07-27: FIX: remove helper_funcs module from mdp namespace, they are
imported into mdp
2010-07-27: NEW: Added a simple run script to run the tests from a .py file
(e.g. to use the Eclipse debugger).
2010-07-27: ERF: Optimized the switchboard gradient implementation (about 10x
faster).
2010-07-27: ERF: Changed one more unittest to use scheduler context manager.
2010-07-27: ERF: Added context manager interface to Scheduler class and added
unittests.
2010-07-27: ERF: Renamed callable_ to task_callable and made some small
docstring updates.
2010-07-27: ERF: Removed unused imprts and updated docs.
2010-07-27: FIX: Fix double delete
2010-07-26: NEW: use sphinx links in mdp.parallel docstring
2010-07-25: FIX: remove del's of nonexistent symbols
2010-07-25: NEW: use fixup_namespace to clean up __import__
2010-07-25: FIX: missing comma in __all__ was concatentating names
2010-07-25: OTH: add import of fixup_namespace without actually using it This
is seperate to check if there are no circular imports

2010-07-24: FIX: remove nonexistent name from __all__
2010-07-23: FIX: remove unused import of hotshot.log
2010-07-23: FIX: fix broken name delete
2010-07-23: FIX: fixed setup.py (remove refs to demo & contrib)
2010-07-23: FIX: convolution nodes are conditional on scipy.signal
2010-07-23: FIX: remove del of nonexistent symbol
2010-07-23: FIX: move pp_simple_slave_test.py to examples
2010-07-23: FIX: regenerate bimdp wrappers for classifiers
2010-07-23: ERF: convert parallel python tests to py.test and disable them
2010-07-23: FIX: TODO had the wrond line ending. Sorry everybody :-(
2010-07-23: FIX: Fix tests in test_nodes_generic with svm classifier nodes.
Add arguments to ShogunSVMClassifier and LibSVMClassifier to
automatically set kernel and classifier on __init__. Add
parameters to test_nodes_generic to use these arguments.

2010-07-23: DOC: updated TODO list
2010-07-23: NEW: Added new tests for Convolution2DNode
2010-07-23: FIX: removed contrib directory
2010-07-23: FIX: duplicate conftest.py twice, so py.test can be run without
options, try 3 Previous version worked only under cygwin when on
windows.

2010-07-23: ERF: PEP8
2010-07-23: DOC: The reason of the strange transformations in CumulatorNode
2010-07-23: FIX: Automatic test now cover everything, fixed a lot of stuff in
the meanwhile!
2010-07-23: FIX: NormalNoise did not function properly
2010-07-23: FIX: KMeansNode failed on some special cases
2010-07-23: FIX: duplicate conftest.py twice, so py.test can be run without
options, try 2 Previous version worked only when PYTHONPATH
included mdp-toolkit/.

2010-07-23: ERF: Migrated the demos to the examples. Removed the tutorial
demo.
2010-07-23: FIX: duplicate conftest.py twice, so py.test can be run without
options Note: bimdp/test/conftest.py is a symbolic link to
bindmp/test/conftest.py.
OTOH, conftest.py in the top directory is a little different.

2010-07-23: ERF: remove old run_coverage script The new way is:
py.test --figleaf and the result go into html/.

2010-07-23: OTH: Renamed NEW_DEVELOPER_INFO.txt → NEW_DEVELOPER_INFO.
2010-07-23: ERF: Made tests for SVM classifiers, Convolution2D conditional on
presence of nodes
2010-07-23: Merge branch 'test_cleanup' Conflicts:
mdp/test/_tools.py

2010-07-23: FIX: fix broken conditional test for caching
2010-07-23: ERF: simplify testing by providing commonly used imports in
test/_tools All testing files can just say
from _tools import * and the get numx, numx_rand, mult, ...

Py.test is not imported into _tools, so that it is easier to
possible to import files which don't actually depend on py.test
when it is not available.

Also includes some tiny naming and space corrections.

2010-07-23: NEW: Conditional tests decorator; decorated test_caching tests
2010-07-23: FIX: use the right TESTDECIMALS in test_utils_generic
2010-07-23: ERF: convert utils tests to py.test
2010-07-23: NEW: add QuadraticFormException for QuadraticForm errors
2010-07-23: ERF: Caching now imported conditional on joblib
2010-07-23: Merge branch 'master' of
ssh+git://mdp-toolkit.git.sourceforge.net/gitroot/mdp-toolkit/mdp-toolkit
2010-07-23: Merge branch 'master' into HEAD Conflicts:
mdp/__init__.py

2010-07-23: ERF: Added *Cumulator and ClassifierNode to __all__
2010-07-23: OTH: Trying to push changes
2010-07-23: ERF: Caching tests moved to own file, updated to py.test style
2010-07-23: ERF: de-obfuscated code in config object
2010-07-23: Merge branch 'sprint_cache' Conflicts:
mdp/__init__.py
mdp/extension.py
mdp/nodes/__init__.py
mdp/nodes/convolution_nodes.py
mdp/test/test_extension.py
mdp/test/test_nodes.py
mdp/utils/__init__.py
mdp/utils/routines.py

2010-07-23: FIX: Windows specific fix.
2010-07-23: OTH: whitespaces
2010-07-23: ERF: make generic_test_factory a public function It is now even
documented.

2010-07-23: OTH: Fixed whitespaces in convolution nodes
2010-07-23: DOC: describe the complicated big_nodes argument of
_generic_test_factory
2010-07-23: NEW: tests can be run within python shell. You can run the tests
with import mdp mdp.test()

you don't need py.test installed!

2010-07-23: Merge branch 'sprint_conv2'
2010-07-23: ERF: Made import of Convolution2DNode conditional on presence of
scipy
2010-07-23: ERF: Added method in config object to check for existence of
arbitrary module by name
2010-07-22: FIX: remove nonexistent import from __all__
2010-07-22: ERF: Adding numpy and scipy to config.
2010-07-22: Merge branch 'sprint_variadic_cumulator'
2010-07-22: FIX: fix broken test_gradient. It was not useing the numx,
numx_rand convention!!!
>:-(

2010-07-22: FIX: Fixing an error in contrib tests.
2010-07-22: ERF: migrated bimdp tests to py.test
2010-07-22: FIX: remove unexistent test name
2010-07-22: NEW: Added convolution class and tests
2010-07-22: ERF: Merged master to convolution branch and removed vestigial
file
2010-07-22: DOC: Update docs
2010-07-22: ERF: Cache extension migrated to own directory, tests updated
2010-07-22: NEW: Init for caching module
2010-07-22: OTH: Attempted refactoring cache extension in own directory, got
metaclass conflict
2010-07-22: ERF: update gitignore for py.test gnerated files
2010-07-22: Merge branch 'test_framework' Conflicts:
bimdp/test/test_binode.py
mdp/nodes/misc_nodes.py

2010-07-22: NEW: Context manager for caching extension
2010-07-22: FIX: Fixed documentation and call with wrong argument
2010-07-22: DOC: Fixed error in documentation of context manager
2010-07-22: ERF: Deleted forgotten print statement
2010-07-22: NEW: activate_caching, deactivate_caching
2010-07-22: ERF: Simplified extension context manager
2010-07-22: ERF: port contrib and hinet to py.test
2010-07-22: ERF: Cache directory can be changed or picked at random (default)
2010-07-22: Merge branch 'sprint_info_refactoring'
2010-07-22: ERF: Renamed ‘Requirements’ → ‘MDPConfiguration’. Changed the API
style a little. Needs more love with version checking.
2010-07-22: ERF: Caching extension moved to own file
2010-07-22: ERF: Tests for cache extension
2010-07-22: DOC: add note about where the links must be changed in sphinx rst
2010-07-22: FIX: Exception missing mdp module.
2010-07-22: ERF: ClassifyCumulator also inherits from VariadicCumulator. A
little bit useless atm, since many methods are overwritten.
2010-07-22: FIX: UTF-8 problem. I want to have Python 3 only…
2010-07-22: FIX: broken linear regression test Use non-random input value, so
that it doesn't fail randomly.

2010-07-22: NEW: added hooks and a command-line option in py.test Use --seed
to set the random seed.

Added report of extended configuration infos before and after
testing reports. Added unit test for random seed [should only
fail in case of a bug in py.test and/or numpy].

2010-07-22: FIX: make generated hinet tests pass
2010-07-22: ERF: Cache extension now based on joblib
2010-07-22: NEW: Added VariadicCumulator with mdp.Cumulator being a special
case of it. VariadicCumulator adds as many automatic fields as are
specified in the initialisation function.
2010-07-22: ERF: use py.test.raises for exception testing
2010-07-22: FIX: correct PCANode generation
2010-07-22: ERF: extract PCANode generation to a helper function
2010-07-22: ERF: migrate tests for hinet to py.test
2010-07-22: FIX: Switchboard.is_invertible() cannot be a staticmethod
2010-07-22: ERF: remove previously converted tests from test_nodes.py
2010-07-22: ERF: migrate tests for CuBICA- and TDSEPNodes to py.test
2010-07-22: ERF: migrate tests for HistParade- and TimeFrameNodes to py.test
2010-07-22: ERF: migrate tests for EtaComputerNode to py.test
2010-07-22: ERF: migrate tests for GrowingNeuralGasNode to py.test
2010-07-22: ERF: migrate tests for NoiseNode to py.test
2010-07-22: ERF: migrate tests for FDANode to py.test
2010-07-22: ERF: migrate tests for GaussianClassifier to py.test
2010-07-22: ERF: migrate tests for FANode to py.test
2010-07-22: ERF: migrate tests for ISFANode to py.test
2010-07-22: ERF: migrate tests for RMB*Node to py.test
2010-07-22: ERF: move spinner to _tools
2010-07-22: ERF: migrate tests for LinearRegressionNode to py.test
2010-07-22: ERF: migrate tests for CutoffNode to py.test
2010-07-22: ERF: migrate tests for HistogramNode to py.test
2010-07-22: ERF: migrate tests for RBFExpansionNode to py.test
2010-07-22: ERF: migrate tests for AdaptiveCutoffNode to py.test
2010-07-22: ERF: migrate tests for SFA2Node to py.test
2010-07-22: ERF: migrate tests for SFANode to py.test
2010-07-22: ERF: migrate tests for WhiteningNode to py.test
2010-07-22: ERF: migrate tests for PCANode to py.test
2010-07-22: ERF: migrate tests for PolynomialExpansionNode to py.test
2010-07-22: ERF: migrate covariance Node tests to py.test
2010-07-22: ERF: add node copying, saving and training tests
2010-07-22: ERF: move BogusNode* to _tools
2010-07-22: FIX: fix python2.5 compatibility
2010-07-21: FIX: Don’t include utils until it is needed.
2010-07-21: ERF: Drop Python 2.4, use built-in all().
2010-07-21: ERF: Fix some of the issues with contrib.__all__ and dependencies.
2010-07-21: FIX: Fixing bugs with scheduling. Avoid printing while mdp is
imported.

Rename _info() to req.info() in MDPVersionCallable. req.info() is
a different object but it’s exact layout is not important for
scheduling.
2010-07-21: ERF: add tests for RBFExpansionNode
2010-07-21: FIX: don't use self in staticmethod
2010-07-21: ERF: add generated tests for FastICA
2010-07-21: ERF: generate tests for reversing
2010-07-21: ERF: use any and all to check conditions
2010-07-21: BRK: make is_trainable staticmethod where possible
2010-07-21: BRK: make is_invertible staticmethod where possible
2010-07-21: ERF: Everybody loves nicer output
2010-07-21: OTH: implemented obvious thing of decorating the execute method
with joblib, it does not work; breaks the caching extension
2010-07-21: ERF: Remove all the cool logic and decorators because __dict__ is
not ordered and all the methods are executed in arbitrary order.
2010-07-21: Merge commit '38664d80675ea7304ee28b460ba88c547b55629e'
2010-07-20: NEW: Added a new Requirements object which checks for available
features. Current version needs some discussion/rework because
class methods are not initialised in order...

2010-07-21: ERF: generate dimdtypeset consistency tests
2010-07-21: FIX: Fixed the remaining broken unittests.
2010-07-21: ERF: generate outputdim_consistency tests
2010-07-21: NEW: Adding the ‘official’ backport for OrderedDict to our
routines.py.
2010-07-21: FIX: Updated the bimdp.hinet package to work with the new
stop_training.
2010-07-21: ERF: world's first automatic test generation
2010-07-21: OTH: Merged cache branch with convolution branch
2010-07-21: FIX: Updated the BiFlowNode to work with new stop_training.
2010-07-21: DOC: Improved documentation for Convolution2DNode
2010-07-21: FIX: Fixed the failing BiFlow unittest.
2010-07-21: ERF: Convolution2DNode now supports FFT convolution, checks for
the validity of all of its argments; the new tests are in a file
outside the repository, waiting for the new test framework
2010-07-21: FIX: Fixed the inspection by removing the stop_message reference.
2010-07-21: BRK: Simplified the coroutine decorator according the stop_message
removal.
2010-07-21: BRK: Updated and simplified BiFlow for the new stop_training
specification. Not tested yet.
2010-07-21: ERF: Added output dimension check to IdentityNode.
2010-07-21: ERF: ported test_flows to py.test
2010-07-21: ERf: ported test_graph.py to py.test
2010-07-21: ERF: ported test_parallelflows to py.test
2010-07-21: ERF: ported test_parallelhinet.py to py.test
2010-07-21: ERF: ported test_parallelnodes.py to py.test
2010-07-21: ERF: ported test_process_schedule to py.test
2010-07-21: ERF: ported test_extension to py.test
2010-07-21: FIX: caching extension now works with non-contiguous arrays
2010-07-21: OTH: Updated bimdp todo list.
2010-07-21: BRK: Started with change of the stop_training signature in bimdp
and removed stop_message. The binode file is basically done.
2010-07-21: NEW: New utility function to generate Gabor wavelets
2010-07-21: ERF: ported test_classifier to py.test
2010-07-21: ERF: added new testing tools file.
2010-07-21: ERF: ported test_schedule to py.test
2010-07-20: FIX: globally remove trailing whitespace Used
http://svn.python.org/projects/python/trunk/Tools/scripts/reindent.py
.

2010-07-20: FIX: broken import
2010-07-20: Merge branch 'py3k', remote branch 'origin/sprint_gradient' into
master Conflicts:
bimdp/inspection/trace_inspection.py

2010-07-20: FIX: Removed use of new.instancemethod from inspection.
2010-07-20: FIX: typo in Flow.__setitem__
2010-07-20: ERF: use context manager for file access
2010-07-20: FIX: don't create a list that is ignored RefactoringTool:
Warnings/messages while refactoring: RefactoringTool: In file
/home/zbyszek/mdp/mdp-toolkit/build/py3k/mdp/linear_flows.py
RefactoringTool: Line 481: You should use a for loop here

2010-07-20: FIX: Fixed the integer division in bimdp.
2010-07-20: FIX: remove bogus import in test/__init__.py
2010-07-20: FIX: get rid of the "callable" variable and fix the scheduler
shutdown An explicit flush was needed.

2010-07-20: NEW convolution2d node
2010-07-20: ERF: esthetic change: activate heart beat spinner
2010-07-20: FIX: another integer division problem
2010-07-20: FIX: don't use None in comparisons
2010-07-20: FIX: integer division again
2010-07-20: FIX: fixed handling of binary mode for stdin and stdout for pickle
2010-07-20: FIX: remove unused import
2010-07-20: FIX: don't compare float with NoneType In Python2.6 None is
smaller than any float, but in Python3 the comparison fails with
TypeError.

2010-07-20: FIX: whitespace
2010-07-20: FIX: correct relative imports in process_schedule.py
2010-07-20: FIX: another integer division problem
2010-07-20: FIX: whitespace
2010-07-20: FIX: add x before range git grep -l 'for.*[^x]range'
mdp/test/|xargs sed -i -r 's/for(.*[^x])in range/for\1in xrange/g'

2010-07-20: FIX: matlab→python and py3k cleanups a = a + 1 becomes a += 1
/ becomes // range() becomes xrange() useless cast removed
exception variable doesn't leak out after the catch block anymore

2010-07-19: FIX: whitespace
2010-07-20: FIX: zip returns a generator in py3k, we need a list
2010-07-19: FIX: fixed integer division
2010-07-19: FIX: fixed calling unbound class methods in extensions. unbound
methods have been removed in python3.
2010-07-19: ERF: refactored py3tool
2010-07-19: FIX: use sets not lists in testing GraphNode
2010-07-19: FIX: open files in binary mode when loading a pickle
2010-07-19: MISC: gitignore build stuff
2010-07-19: ERF: use 'open' function instead of the deprecated 'file' in
mdp/demo
2010-07-19: FIX: missing import in setup.py [2]
2010-07-19: FIX: missing import in setup.py
2010-07-19: NEW: python3 setup logic (from numpy)
2010-07-19: ERF: use 'open' function instead of the deprecated 'file'.
2010-07-20: ERF: Restricted the gradient default implementation to the
IdentityNode, now raise an exception as the default.
2010-07-20: ERF: Removed the explicitly defined IdentityBiNode, use the
autogenerated one instead.
2010-07-20: NEW context manager for extensions
2010-07-20: NEW basic implementation of the cache execute extension
2010-07-19: ERF: Added a gradient unittest with a small network.
2010-07-19: ERF: Improved one layer gradient unittest into a functional test.
Insignificant cleanup in gradient module.
2010-07-19: FIX: Fixed the switchboard gradient and added unittest.
2010-07-19: NEW: Added the switchboard gradient implementation with a test
(more unittests are needed).
2010-07-19: NEW: Added gradient implementation for layer with some unittests
(more are needed). Added check in gradient base node that node has
finished training.
2010-07-19: DOC: Added the new project guidelines.
2010-07-19: ERF: use integer division
2010-07-19: NEW: Added gradient extension with some implementations for simple
nodes (no hinet yet).
2010-07-02: Added kwargs to SenderBiNode init to enable multiple Inheritance.
2010-07-02: Fixed bug in inspection: If nodes were added in later training
phases the clickability broke for all nodes. Again this affected
XSFA. Changed text in inspection from layer to node.
2010-07-02: Updated the inspection example (more training phases for better
illustration). Tiny doc update in SenderBiNode.
2010-07-02: Fixed bug for normal node in BiFlowNode (this broke the XSFA
inspection example).
2010-07-01: Simplified the inspection msg printing.
2010-07-01: Improved the inspection message printing (alphabetic sorting and
highlighted keywords).
2010-06-29: Improved the key order in the inspection msg HTML view.
2010-06-29: Improved the array HTML display in the inspection.
2010-06-29: Fixed one corner case bug in coroutine decorator and added more
unittests. Updated bimdp todo list. Small docstring update in
switchboard.
2010-06-16: Merged the coroutine mixin class into the BiNode base class. Added
_bi_reset hook method that should be overwritten instead of
bi_reset. This is more consistent with the standard MDP design.
The bi_reset template method now clears the coroutine table.
Dervied BiNode classes should rename their bi_reset to _bi_reset,
but unless they use the coroutine decorator there is currently no
negative effect for not doing so. Updated the BiMDP todo list.
2010-06-15: Fixed duplicate classifier nodes in autogenereated code.
2010-06-14: Added check and unittest for corner case of a directly terminating
coroutine.
2010-06-13: Reverted my misguided fixes to the metaclass wrapping helpers.
2010-06-11: Small comments update.
2010-06-11: Updated the codecorator to work with the updated NodeMetaclass
wrapping helper functions. Add new feature to specify argument
default values. Changed the _coroutine_instances to be initially
None for better efficiency.
2010-06-11: Rewrote the NodeMetaclass wrapping helper functions. The old
versions contained a bug (default values would prevent user
defined values from being passed to the function). The new version
is also arguably more elegant and flexible. A unittest was added
for parts of the new functionality.
2010-06-11: Fixed the n argument in PCANode inverse.
2010-06-09: Added new coroutine decorator and mixin for BiMDP, allowing easy
continuations (without boilerplate code or explicit state
machines).
2010-06-09: Fixed bug in SenderBiNode.
2010-06-09: Fixed typo.
2010-06-09: Fixed broken SFA execute range argument and renamed it to n. Added
unittests for PCA and SFA n arguments. Added some missing SFANode
attributes to init.
2010-06-09: Fixed bug in BiFlowNode.
2010-05-31: Added loop check for previous button in slideshow.
2010-05-27: Numpy still uses the deprecated string exceptions, which were
naturally not caught during inspection. I now changed inspection
to catch everything.
2010-05-19: Added check for loop setting in slideshow next().
2010-05-17: Very small cosmetic updates.
2010-05-17: fixed other two python2.4 incompatibilities in demos.
2010-05-15: fixed bug with ProcessScheduler when mdp installed by debian
package. Now it works correctly even when multiple versions of mdp
are installed, for example a system version via debian and a local
git version. A unit test has been added to make sure parent and
child processes are running the very same mdp. Thanks to Yaroslav
Halchenko for pointing out the problem!

-------------------------------------------------------------------------------

2010-05-14: fix spurious shogun warning.
2010-05-14: applied patch from Rike to re-enable some of the working Shogun
tests.
2010-05-14: fixed bug when using most recent numpy (1.4.1). utils.get_dtype
was failing when called with 'All' argument. most of MDP unittests
were failing!
2010-05-14: added stylesheet files to setup script. only *.py files are
installed by default.
2010-05-14: modified mechanism to get git revision in order to properly handle
the case when git fails. added stylesheets to MANIFEST template
2010-05-14: several additions to distribution files
2010-05-14: removed NaiveBayesClassifer from automatically generated nodes in
bimdp. regenerated node wrappers
2010-05-14: fixed bug in GaussianClassifierNode and FDANode when training with
a list of labels. Removed obsolete 'uniq' function in utils. we
can use builtin set instead.
2010-05-14: disabled Shogun tests. they often fail withtou apparent reasons.
try for example: python2.5 -c 'import mdp;
mdp.test(seed=257416710)'
2010-05-14: Added a maximum iteration constraint to the k-means classifier.
2010-05-14: Moved the NaiveBayesClassifier to the demo.
2010-05-14: Fixed a bug where the Classifier rank() method returned items in
the reverse order.
2010-05-13: LLENode was not fixed ;-) disabled 2D test and added reminder to
TODO
2010-05-13: fixed ever failing LLENode test.
2010-05-13: added info about LibSVM and Shogun in mdp.info()
2010-05-13: first take at disabling SVM tests when libraries are not available
2010-05-12: Updated the todo list to reflect the latest developments.
2010-05-12: Adjusted the BiClassifier node according to the renamings.
2010-05-12: Renamings in the classifier nodes (classify->label, cl->labels).
2010-05-11: removed code duplication from test/__init__.py
2010-05-11: added info function to display infos about MDP and dependencies
2010-04-29: Added ability to exit BiFlow with -1 target value, making it
easier to use inverse execution.
2010-04-22: Inserted the new sys.path behavior also in the main clause.
2010-04-22: Changed the sys.path behavior in subprocesses to fix problems with
multiple MDP versions on a system.
2010-04-14: Fall back on default if specified browser is not available.
2010-04-14: Added tracebacks to exception handling during debug inspection.
2010-04-12: Added ability to specify a specific browser for slideshows, also
changed the argument name.
2010-04-09: Rewrote K-Means training to be aligned with the Cumulator
training.
2010-04-09: Adapted the SVM Classifiers to use the new ClassifierCumulator
class.
2010-04-03: Made a Cumulator version for simple Classifiers.
2010-04-06: Made GaussianClassifierNode inherit from ClassifierNode.
2010-04-04: Simplified the inheritance names in classifier nodes’
declarations.
2010-03-29: Patch from Benjamin Schrauwen to fix the method polution issue.
2010-03-29: Fixed the dysfunctional unittest, it now breaks, currently no
solution.
2010-03-29: Added test for pp scheduler with real flow.
2010-03-28: Improved the extension verbose printing.
2010-03-28: Fixed one more issue (method polution) and added a test.
2010-03-28: Added new failing test, caused by polution.
2010-03-28: Added unittest for the special behavior when multiple extensions
extend the same method.
2010-03-28: Patch from Benjamin Schrauwen for extension mechanism.
2010-03-27: Slightly changed the behavior of targeted message keys: They are
now removed even if they are not args of the method. Updated the
unittests accordingly.
2010-03-27: Fixed bug for layer containing a single node.
2010-03-26: Added BiClassifier and automatic creation of BiMDP versions for
MDP classifiers (currently except the SVN based ones).
2010-03-25: Applied patch from Benjamin Schrauwen, the BiMDP tests now all
pass.
2010-03-25: Changed the BiMDP msg key seperator from "=>" to "->" to allow for
more consistent convention in the future, when more options might
be added. Updated the todos accordingly.
2010-03-25: Undid the changes to the extension mechanism, they are now
available in a seperate branch.
2010-03-25: Enable inheritance in extensions. Patch thanks to Benjamin
Schrauwen! (cherry picking from commit
aacbc906be0f79e66124085e1c51c35a0aee731d) Enable inheritance in
extensions. Test thanks to Benjamin Schrauwen! (cherry picking
from commit 89b7facb223aff09d4581ce5aa68d07a8ef47b1b)
2010-03-25: Enable inheritance in extensions. Test thanks to Benjamin
Schrauwen!
2010-03-25: Enable inheritance in extensions. Patch thanks to Benjamin
Schrauwen!
2010-03-24: Python fixes for compatibility with 2.4.
2010-03-24: Reverted some of the Python 2.6 (and Numpy 1.4) only changes.
2010-03-24: Added verbose argument to mdp.activate_extension.
2010-03-23: Added a section about dealing with testing branches.
2010-03-22: Added unittest for bimdp parallel stuff and updated another.
Update the todos.
2010-03-22: Improved the CloneBiLayer message data splitting and added
corresponding unittest.
2010-03-22: Slightly changed the message handing in BiSwitchboard and added
corresponding unittests. Small rename in BiNode. Small todo
update.
2010-03-16: Added a simple k-means clustering classifier.
2010-03-14: Added node_id support to BiFlowNode.
2010-03-13: Added utility function izip_stretched.
2010-03-12: Added test for adding node to flow. Moved one BiNode test to
correct class.
2010-03-11: Fixed bug in flow in-place adding method.
2010-03-11: Added a refcast to classify and prob methods.
2010-03-10: Fixed the remaining failing tests from Tiziano. It was caused by
an ambiguity of the BiFlow.train docstring, so this is now
explained in more detail. An additional check was added to BiFlow
to detect this kind of error.
2010-03-10: Refactored the additional argument check into seperate method, so
that it can be reused by derived flow classes (especially BiFlow).
2010-03-10: Fixed the test for FDA in a biflow.
2010-03-10: Added other failing tests for BiFlow.
2010-03-10: Added failing tests for BiFlows.
2010-03-10: Added special __add__ method to BiNode, creating a BiFlow. Also
added corresponding unittest.
2010-03-09: Fixed an assertion bug in Shogun test.
2010-03-09: Added unittests for recent stop_message magic. Also made some
small improvements and added for documentation for this. Made
small updates to the general bimdp docstring.
2010-03-09: Added a section on using git with Windows or Eclipse. Added a
section on following PEP 8.
2010-03-09: Added checks for input_dim.
2010-03-09: We need to have shogun 0.9 for our SVM Classifier.
2010-03-08: Updated NEW_DEVELOPER_INFO to ‘The git situation’.
2010-03-08: Fixed Py2.6 DeprecationWarning in RBMLearning test.
2010-03-08: Fixed a new bug in BiNode. Moved the SVN nodes to the classifier
part in the autogen module.
2010-03-08: Made a larger set of additions to the SVM tests.
2010-03-08: Updated the docstrings for the SVM classifiers.
2010-03-06: Fix: Forgot to set the classifier_type in libsvm.
2010-03-06: Added simple support for probability estimations in LibSVM through
our _prob() method.
2010-03-04: Renamed SVM_Node -> SVM_Classifier.
2010-03-02: Supplying arguments to the shogun classifier works now. Improved
the test suite.
2010-03-01: Lots of updates and refinements to shogun integration.
2010-02-28: Added some recognition for KernelMachines in shogun.
2010-02-27: Applied some fixes and optimisations to the SVM code.
2010-02-26: Added class _LabelNormalizer to ease the handling of label
mapping.
2010-02-26: ClassifierNode-Migration: Now use ClassifierNode._classify in
SVMNodes.
2010-02-26: Last commit before migration of SVM nodes to ClassifierNode.
2009-09-16: Made some improvements in SVM testing and overall structure.
2010-03-06: Improved the algorithm for _randomly_filled_hyperball(). Scaling
is much better now.
2010-03-06: Fixed a bug in ClassifierNode.rank(). It now expects a list of
feature vectors to function.
2010-03-06: Fixed one potential stop_message issue.
2010-03-06: Added magic in BiNode to call execute or inverse from
stop_message.
2010-02-27: Made the product helper method take advantage of Python 2.6.
2010-03-04: Moved release files in root of master branch.
2010-03-03: Added automatic detection of number of CPU cores. This is used in
the ProcessScheduler and the ThreadScheduler as the default value.
2010-03-02: Fixed bug left over from inspection cleanup.
2010-02-27: get_svn_revision --> get_git_revision
2010-02-25: Made a couple of smaller improvements in the inspections stuff.
Added a nice demo for customized inspections.
2010-02-22: Introducing a node for a simple discrete Hopfield model.
2010-02-22: Stupid bug in bool_to_sign fixed.
2010-02-23: Simplified the improved import precautions.
2010-02-23: Enabled calling bimdp.test(). Removed redundant code from autogen.
2010-02-23: Made the import process in the worker processes more robust, to
fix the problem with calling bimdp.test() from the command line.
2010-02-23: Small updated in the autogen code.
2010-02-23: Changed the automatic creation of BiNode versions for MDP nodes.
Now a module file is used that is created by a special script.
While less elegant than the original dynamic solution this is now
compatible with code checkers and is more transparent for users.
2010-02-23: Added general purpose routines bool_to_sign and sign_to_bool.
2010-02-22: Fixed mdp import bug in process scheduler (caused by the occurance
of mdp in the repo name).
2010-02-19: Delete mdp_dist. All future updates should be made in
release-manager branch.
2010-02-19: Removed remaining binet references. Renamed some inspection
classes to get the MDP out of the name. Updated the todo list.
2010-02-19: Need to check against numpy.all when comparing array elements.
2010-02-18: Corrected the common assert-statement-with-parentheses mistake.
2010-02-18: Restructured bimdp to follow the mdp structure.
2010-02-17: Renamed binet to bimdp.
2009-08-01: Typo fix in progressbar script and clarification for OS X (the
automatic size works there as well).
2010-02-17: Added .gitignore file for .pyc files and some generic patterns.
2010-02-14: Added option to automatically handle the source_paths in the
worker processes.
2010-02-13: Added more unittests for BiFlow. Fixed one bug in inspection.
Moved the JumpBiNode to the tests.
2010-02-11: Updated the parallel demo.
2010-02-11: Added a new thread based scheduler. Some very tiny updates to
ProcessScheduler.
2010-02-09: Added more BiNode unittests. Updated BiNode documentation. Updated
BiFlow unittests (not yet complete).
2010-01-30: Some small fixes in the inspection. Tried to use cgitd to show
nice HTML tracebacks, but so far this failed (FlowExceptionCR only
preserves a traceback string).
2010-01-29: Removed the updown module (this should be no longer needed).
2010-01-26: Added check in get_quadratic_form to make it more flexible (e.g.
when a derived class wants to use it in _stop_training). Also made
some small PEP8 updates.
2010-01-26: Updated the imports for the parallel package. Fixed some other
small issues.
2010-01-22: Fixed one issue in rectangular switchboards (the data in each
patch was transposed). Added corresponding unittests.
2010-01-11: Seriously beefed up the automatic BiNode creation to preserve the
init signature. This makes it compatible with the introspection in
the parallel default fork implementation. Also added a special
ParallelBiNode and made a tiny style improvement in BiNode.
2010-01-11: Added a default implementation for forking nodes.
2010-01-06: Updated the todos. Also one small improvement to the metaclass
modification.
2010-01-05: Some small fixes and cosmetic correction.
2010-01-05: Fixed one bug from hell in FlowNode (copy was broken for nested
FlowNodes when the copy happened after training).
2010-01-05: Fixed a bug in BiFlowNode.
2010-01-04: Modified the automatic node creation, now is compatible with
pickle and should be 100% transparent. Also fixed the switchboard
factory extension support.
2010-01-04: Put the automatic node creation into a function to avoid namespace
polution. Added automatic node creation for switchboards. There is
one remaining issue with pickling.
2010-01-04: Fixed bugs from refactoring.
2010-01-04: Small refactoring in switchboard factory extension (to allow
easier modification by derived classes).
2010-01-04: Added automatic creation of BiNode versions of all nodes in
mdp.nodes.
2010-01-04: Removed leftover code.
2010-01-04: Updated todos and docstring in init. Small cosmetic updates
elsewhere.
2010-01-03: Fixed bug of the new inspection training node highlighting
feature.
2010-01-03: Fixed one issue with stop messages in ParallelBiFlow, added a
related convenience check to CloneBiLayer.
2010-01-03: Small improvements and bugfixes with respect to stop_message.
2010-01-03: Added highlighting of the currently training node in the
inspection.
2010-01-02: Fixed a couple of bugs. The DBN example is now working again.
2010-01-02: Inspection was simplified, parallel did not need any changes. The
binet simplification should now be complete (but I have not run
real-world tests yet).
2010-01-02: Updated bilayer and biswitchboard (with some huge simplifications
in biswitchboard). Now parallel and inspection remain to be
updated.
2010-01-02: Added a new switchboard.
2010-01-01: Fixed some issues in BiFlow after simplification. Updated
BiFlowNode, this is hopefully done.
2009-12-30: Finished simplification of BiFlow. bihinet still needs to be
updated as well.
2009-12-25: Added /usr/share/dict/words to the list of dictionaries.
2009-12-23: Started with the binet simplification. BiNode should be more or
less finished, most of the rest is not yet done. In principle
everything should already work, there is just a large amount of
dead code around.
2009-12-22: Fixed one bug in the trace inspection (added check for msg being
None).
2009-12-22: Slightly modified the BiLayer data splitting behavior.
2009-12-22: Fixed bug in iterator / argument check for train: default argument
values were not considered.
2009-12-16: Renamed the 'html_representation' extension to 'html'.
2009-12-15: Added a copy method to FlowNode to enable delegation to internal
nodes. Added corresponding tests.
2009-12-13: Prettified the argument representations in the slides.
2009-12-12: Small update to SenderBiNode.
2009-12-12: Improved the exception display in the inspection slideshows. Fixed
missing reset in fascade.
2009-12-12: Fixed bug in BiFlow (same bug that was previously fixed in
BiFlowNode, just forgot to commit this).
2009-12-12: Fixed bug in BiFlowNode (relative target index was not translated
to absolute index during training).
2009-12-12: Increased the robustnes of the training inspection in debug mode
(it can now deal with exceptions before the stop training hook is
reached).
2009-12-11: clean up a couple of lines in RBM nodes
2009-12-09: Added a small parallelization demo to demonstrate and explore the
speedup.
2009-12-05: Fixed outdated default value in slideshow (could cause JS error in
special circumstances).
2009-12-04: added documentation about the convention for the train methods of
multiple training phase nodes.
2009-12-04: added Node.has_multiple_training_phases method.
2009-12-03: Modified check for missing argument in node training to also check
for too many arguments. Added a corresponding test.
2009-12-03: Added check for missing training arguments in Flow (which should
be provided by the iterator). Also edited the corresponding
unittest.
2009-12-03: Fixed small error in docstring for slideshow.
2009-12-02: well, NoiseNode *can* be pickled if you use pickle instead of
cPickle. I hope this bug is fixed in python2.6 or python3 ;-)
2009-12-02: raise error if trying to copying or saving the NoiseNode error
(bug in cPickle)
2009-12-02: added failing test for iterables mess in flow.
2009-12-01: Added missing super call.
2009-12-01: Fixed one evil bug: When the last training phase of a node was not
parallelizable in a ParallelCheckpointFlow then the checkpoint
function was not called. The fix required the addition of another
hook method in ParallelFlow, but is overall much cleaner than the
previous solution. Also improved the status messages for local
training phases.
2009-12-01: gaussian classifier still had overwritten train just to offer a
doc-string. putting the doc-string in _train is sufficient.
2009-11-29: Added new version of SenderBiNode (doesn't use branching).
2009-11-26: Fixed one biflow issue when in inverse mode (especially inside a
BiFlowNode).
2009-11-26: Updated some docstrings for the extension mechanism (they were
only refering to methods and not attributes).
2009-11-26: Fixed a bug in the inspection facade.
2009-11-22: Improved the extension unittests (now testing class attributes as
well).
2009-11-21: Improved the slideshow button text hints (they now also contain
the keyboard shortcuts).
2009-11-21: Fixed one embarrassing mistake in the node metaclasses.
2009-11-21: Added support for kwargs in training and execution inspection.
2009-11-16: Added a SimpleMarkovClassifier node. There is duplicated
functionality compared to the NaiveBayesClassifier, so the
NaiveBayesClassifier could be refactored to be based on the
SimpleMarkovClassifier.
2009-11-15: Fixed the signature overwriting in NodeMetaclass. Also renamed
some occurances of "kargs" to "kwargs" in the Node class
(previously both names were used in different methods).
2009-11-15: Fixed a bug in rank().
2009-11-14: Moved ClassifierNode up one directory.
2009-11-14: added file with info for new developers
2009-11-13: Added a ClassifierNode with basic methods classify, rank and prob.
2009-11-13: Fixed one bug in the message container, thanks to Sven Dähne.
2009-11-09: Fixed one small bug in switchboard factory. Added switchboard
factory extension in binet. Updated todos.
2009-11-07: Added new switchboard factory node extension. This has been
factored out of the hinet planer and I will now use it in my
simulation software as well (therefore I wanted to integrate it
into MDP). Unittests and documentation are currently missing
(unittests will be somewhat tricky, not sure how deeply this
should be covered in the tutorial anyway).
2009-11-06: Rewrote some parts of the extension mechanism. It now works for
arbitrary attributes. One nice things is that this actually
reduced the number of lines of code. The tutorial has not yet been
updated. Attribute specific unittests are missing as well.
2009-11-06: Updated the todo list.
2009-11-05: Slightly improved the API for activating multiple extensions.
Discovered that the extension mechanism does not work for
classmethods/staticmethods, since they appear as non-callable
descriptors. I will change the extension mechanism to work for
arbitrary attributes ASAP.
2009-11-04: Small improvements in extension mechanism, added more comments.
Added missing Exception import in hinet init.
2009-11-04: Fixed a small slideshow issue.
2009-11-03: Completed the clickable inspection nodes. One can now click on a
node to jump to the next slide where it is reached. This does not
work in IE yet (the workaround would be simple, but don't want to
clutter the code with IE specific garbage). Also removed the AJAX
storage div (caused trouble due to duplicate ids and is not needed
anyway).
2009-11-03: Added support for active node ids in binet inspection. This will
make it possible to click on a node and directly jump to the next
time it is reached. The JS part of this is not yet implemented.
2009-11-03: Fixed the slideshow image CSS and added IE support.
2009-10-30: Cleaned up the JavaScript code in the binet inspection.
2009-10-27: Added checks in channel switchboard.
2009-10-21: Sorry, forgot to fix the webbrowser.open issue in binet.
2009-10-21: Fixed the webbrowser.open issue on MacOS as suggested by Rike.
2009-10-20: Tweaked hinet css. Extracted slideshow css into speparate file.
2009-10-20: Extracted CSS code into separate file.
2009-10-18: Fixed error in rhombic switchboard, added corresponding unittest.
2009-10-17: Added new features to the ChannelSwitchboard base class to get the
effective receptive fields in hierarchical networks. Also added
corresponding tests. Minor cosmetic updates in hinet translator.
2009-10-16: Added hinet translatation adapter for valid XHTML (instead of
HTML). Also added a corresponding unittest, but this does not test
the validity of the XHTML.
2009-10-16: Fixed two small issues in the hinet HTML representation.
2009-10-14: fixed bug in TimeFramesNode when input_dim was set explicitly.
thanks to anonymous sourceforge user [Bug ID: 2865106]
2009-10-14: Some CSS fixes and a fix in the demo.
2009-10-14: Added slideshow CSS for crisp rescaling, in anticipation of the
Firefox 3.6 beta release.
2009-10-12: Added feature that nicely line wraps the section ids in a
slideshow.
2009-10-07: Added more checks to DoubleRect2dSwitchboard. Some small
improvements. Updated the package init file.
2009-10-07: Reverted output_channels renaming in switchboard, to not create
compatibility issues.
2009-10-07: Many switchboard updates. A new ChannelSwitchbard base class was
introduced, many code improvements, HTML representations were
added for the new switchboard types.
2009-10-06: removed spurious print statement in QuadraticForm tests.
2009-10-04: Added a section on the extension mechanism in the tutorial (note
that this is a first draft). Also added a description of the
slideshow stuff (plus a minor update in the slideshow code).
2009-10-04: Migrated extension stuff to separate module.
2009-10-01: Fixed some issues in the new DoubleRhomb2dSwitchboard, added more
tests.
2009-09-29: Added a new switchboard class, DoubleRhomb2dSwitchboard. The tests
are currently incomplete and there are probably bugs in there.
2009-09-29: Some simplifications in the switchboard classes.
2009-09-29: Added a new switchboard class, DoubleRect2dSwitchboard. This will
probably be complemented in the future by a Rhomb2d switchboard
for multilayer networks.
2009-09-24: Fixed support for multiple slideshows in one file. Added multiple
slideshow demo. Allowed keyboard shortcuts for slideshows to be
turned off.
2009-09-23: Updated todos.
2009-09-23: Fixed the template indentation handling. Updated the binet
inspection to work with the new slideshow. Moved the manual tests
for slideshow and hinet to the demos folder.
2009-09-23: Some more cleanup for the slideshow stuff.
2009-09-23: Small update in binet for moving the hinet basic CSS to utils.
2009-09-23: Cleaned up the slideshow JavaScript code. Most importantly the use
of global variables is now minimized by using an object oriented
design with a closure. Some additional cleanup in the slideshow
classes was done as well. Added one helper function to directly
create an HTML slideshow. Moved the default CSS from hinet to
utils, so it can be used by both slideshow and hinet. Moved the
hinet HTML test/demo to the test folder and added a similar demo
for slideshow (using the MDP logo animation).
2009-09-19: added script to analyze code coverage during tests and output html
report; needs figleaf,
http://darcs.idyll.org/~t/projects/figleaf/doc/; mostly, we don't
test exception, but there are some more worrying parts, like we
don't test for for flow inversion...
2009-09-17: Added new utility function orthogonal_permutations. The function
helps avoiding deeply nested statements when several of several
arguments need to be tested against each other.
2009-09-14: Many thanks to Christian Hinze for pointing out a bug in
QuadraticForm.get_invariances. Removed warning about bug in
linalg.qr in numpy 1.0.1.
2009-09-14: Mainly added basic svm tests and did some cleanup and bug fixes.
Also, the requested comments have been investigated.
2009-09-10: fixed bug in QuadraticForm.get_invariances: second derivative
value was wrong when linear term significantly large; second
derivative directions were ok
2009-08-30: small cleanups of svm_nodes and comments/requests for comments.
rike?
2009-08-30: changed import order in nodes/__init__.py to clean up import in
expansion_nodes.py for GrowingNeuralGasExpansionNode.
2009-08-23: Made extension method attributes public. Improved the extension
unittests.
2009-08-22: Small code improvement in binet inspector. Updated todo for
extensions.
2009-08-22: Modified the NodeMetaclass wrapping procedure to use super instead
of direct method references. Hopefully this has no negative side
effects. The advantage is that it is compatible with runtime
monkey patching, so it enables more extension stuff.
2009-08-21: Extension decorator now preserves function docstring and
signature.
2009-08-17: Fixed extension related bug in ParallelBiFlow. Improved the
related unittests. Added some comments.
2009-08-16: Added little comment.
2009-08-16: Removed use of parallel FlowNodes in parallel flows. Small update
to extensions.
2009-08-12: Added option to extension decorator to specify the method name.
Added extension decorator unittest (now we have 400 unittests,
wheee!).
2009-08-12: Fixed left-over bugs from yesterdays mess, fixed unittests.
2009-08-11: Added more unittests for the extension mechanism. Changes in the
extension documentation and comments, and one small fix.
2009-08-11: Use set for list of active extensions.
2009-08-11: Added safety mechanisms to extensions, added one corresponding
unittest.
2009-08-10: Re-enabled Shogun nodes.
2009-08-10: Added Henning Sprekeler to the list of developers and removed him
from the list of contributors. Updated the various copyright
statements all over the place, and the home page.
2009-08-10: Corrected the docstring of the GrowingNeuralGasExpansionNode to be
more precise on the relation between max_nodes and the dimension
of the expansion.
2009-08-10: added standard tests for GworingNeuralGasExpansionNode and cleaned
up its setting of output_dim.
2009-08-07: Bug removed in GrowingNeuralGasExpansionNode: scipy -> numx
2009-08-07: missing file added; UpDownNode modified so it can pass down the
results of computations at he top
2009-08-07: Added GrowingNeuralGasExpansionNode to expansion_nodes. Tests are
still missing.
2009-08-07: ShogunSVMNode only gets imported when libraries are present.
Stylistic changes (not all done yet). Some parameter issues and
docstring clarified. Non-kernel classification.
self._classification_type added. Parameter mapping for kernels
introduced.
2009-08-06: remove import of svm_nodes in contrib. the automatic shogun import
is not ready for prime-time.
2009-08-02: Initial SVM commit. Using only shogun for now. Still needs a lot
of work and a better API. But it is already working somehow.
2009-08-02: uploaded UpDownBiNode, mother class for DBN, backpropagation;
corrected small bug in binet; I've got loads of questions about
binet
2009-07-31: GaussianClassifierNode has now explicit output_dim method (which
fails).
2009-07-25: Added RBF node, utilities to replicate array on an additional
dimension (rrep, lrep, irep) -> very useful
2009-07-19: Updated BiNet todo list.
2009-07-16: Fixed bug in rectangular switchboard that was introduced in the
previous update.
2009-07-15: Added unused channel information to rectangular switchboard, this
is also shown in the HTML representation. Added comments in
slideshow.

-------------------------------------------------------------------------------

2009-06-30: Added online detection of numerical backend, parallel
python support, symeig backend and numerical backend to the output of
unit tests. Should help in debugging.
2009-06-12: Integration of the cutoff and histogram nodes.
2009-06-12: Fixed bug in parallel flow (exception handling).
2009-06-09: Fixed bug in LLENode when output_dim is a float. Thanks to Konrad
Hinsen.
2009-06-05: Fixed bugs in parallel flow for multiple schedulers.
2009-06-05: Fixed a bug in layer inverse, thanks to Alberto Escalante.
2009-04-29: Added a LinearRegressionNode.
2009-03-31: PCANode does not complain anymore when covariance matrix has negative
eigenvalues iff svd==True or reduce==True. If output_dim has been
specified has a desired variance, negative eigenvalues are ignored.
Improved error message for SFANode in case of negative eigenvalues,
we now suggest to prepend the node with a PCANode(svd=True) or
PCANode(reduce=True).
2009-03-26: Migrated from old thread package to the new threading one.
Added flag to disable caching in process scheduler. There are some
breaking changes for custom schedulers (parallel flow training or
execution is not affected).
2009-03-25: Added svn revision tracking support.
2009-03-25: Removed the copy_callable flag for scheduler, this is now completely
replaced by forking the TaskCallable. This has no effect for the
convenient ParallelFlow interface, but custom schedulers get broken.
2009-03-22: Implemented caching in the ProcessScheduler.
2009-02-22: make_parallel now works completely in-place to save memory.
2009-02-12: Added container methods to FlowNode.
2009-03-03: Added CrossCovarianceMatrix with tests.
2009-02-03: Added IdentityNode.
2009-01-30: Added a helper function in hinet to directly display a flow HTML
representation.
2009-01-22: Allow output_dim in Layer to be set lazily.
2008-12-23: Added total_variance to the nipals node.
2008-12-23: Always set explained_variance and total_variance after training in
PCANode.
2008-12-12: Modified symrand to really return symmetric matrices (and not only
positive definite). Adapted GaussianClassifierNode to account for
that. Adapted symrand to return also complex hermitian matrices.
2008-12-11: Fixed one problem in PCANode (when output_dim was set to input_dim
the total variance was treated as unknown).
Fixed var_part parameter in ParallelPCANode.
2008-12-11: Added var_part feature to PCANode (filter according to variance
relative to absoute variance).
2008-12-04: Fixed missing axis arg in amax call in tutorial.
Thanks to Samuel John!
2008-12-04: Fixed the empty data iterator handling in ParallelFlow.
Also added empty iterator checks in the normal Flow (raise an
exception if the iterator is empty).
2008-11-19: Modified pca and sfa nodes to check for negative eigenvalues
in the cov matrices
2008-11-19: symeig integrated in scipy, mdp can use it from there now.
2008-11-18: Added ParallelFDANode.
2008-11-18: Updated the train callable for ParallelFlow to support additional
arguments.
2008-11-05: Rewrite of the make parallel code, now supports hinet structures.
2008-11-03: Rewrite of the hinet HTML repesentation creator. Unfortunately this
also breaks the public interface, but the changes are pretty simple.
2008-10-29: Shut off warnings coming from remote processes in ProcessScheduler
2008-10-27: Fixed problem with overwriting kwargs in the init method
of ParallelFlow.
2008-10-24: Fixed pretrained nodes bug in hinet.FlowNode.
2008-10-20: Fixed critical import bug in parallel package
when pp (parallel python library) is installed.

-------------------------------------------------------------------------------

2008-10-16: added interface to BLAS's "gemm" matrix multiplication
function.
2008-10-15: removed obsolete helper functions.
2008-10-15: added new feature. Now:
output = XXXNode(output_dim=10)(x)
trains and executes the node. This makes helper_functions obsolete!
It even works for multiple training phases (only if the training
phase has not started yet).
2008-10-15: removed use of deprecated features with python2.6 -3.
2008-10-14: removed dangerous list default argument in rotate and permute
functions. A tuple is now used.
2008-10-13: PEP8 code restyling (pylint).
2008-10-07: Removed workarounds for pickle bug in numpy < 1.1.x (see
numpy ticket 551).
2008-09-24: Implemeted metaclass trick for automatic inheritance of
documentation for private methods. Node's subclass authors
can now directly document "_execute", and let users see those
docs as documenting "execute":

class MyNode(Node):
def _execute(self):
"""blah"""

>>> print MyNode.execute.__doc__
blah.

Just defined set of methods allow overwriting of the docstring.
the current list is:
['_train', '_stop_training', '_execute', '_inverse']
2008-09-22: Added new functionality to nodes and flows.
Node1+Node2 now returns a flow and Flow1+Node1 appends
Node1 to Flow1.
2008-09-07: New node for Locally Linear Embedding
2008-08-28: The docstring of Flow.train now mentions that instead of x the
iterators can also return a tuple of x and additional args.
2008-08-28: Fixed bug in PCANode:
when setting output_dim to a float number after instantiation
but before stop_training, i.e:
pca = PCANode()
pca.train(x)
pca.output_dim = 0.9
pca.stop_training()
an exception was thrown: Output dim are set already (0) (1 given)
2008-08-28: Fixed bug in PCANode:
when setting output_dim to float number, after stop_training
pca.output_dim was a float number instead of integer.
2008-08-21: Added inverse for Switchboard, including unittests.
2008-08-19: Added parallel package.
2008-08-19: Added new NormalNoiseNode (with small unittest),
which can be safely pickled.
2008-08-07: fixed bug in rbm_nodes (TrainingFinishedException).
Thanks to Mathias Franzius!
2008-07-03: Node.__call__ method now takes *args and **kwargs to call
the execute method. Thanks to Jake VanderPlas!
2008-06-30: Fix debian bug 487939:
Modifed the fix for the debian bug so that white_parm defaults to
None instead of {}. With default {} a sublcass updating the
dictionary would have updated it for all instances...
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=487939
Applied patch from Michael Hanke. Thank you!

-------------------------------------------------------------------------------