-NOTES.txt
Best regards,
Gilles, on behalf of the Apache Commons community
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-NOTES.txt
Best regards,
Gilles, on behalf of the Apache Commons community
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-trivial enough that I might propose a patch? I wanted to
ask users first.
Patch certainly welcome!
Also, please open a ticket on the bug-tracking system.
Thanks,
Gilles
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that...
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Gilles
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the caveat indicated there (which might require that you use
a custom convergence checker).]
HTH,
Gilles
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, and I am
wondering if I should add slf4j or log4j2 instead?
I think that slf4j is the current de-facto standard.
Regards,
Gilles
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heavy-weight components.
Debug logging is different, but should not be enabled by default.
With slf4j, that is the user's choice.
Gilles
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,
* dependencies allowed (jCuda).
What do you think?
Best regards,
Gilles
[1] Also, we would gradually move there the algorithms that would
obviously
benefit from a multi-thread implementation (e.g Fourier transform,
genetic algorithms, etc.)
[2] This project would also be a place where
, there is this one:
https://issues.apache.org/jira/browse/CLI-219
No idea why its fix version is set to 1.4.
Gilles
* no findbugs checkstyle warnings anymore
* trunk contains lots of fixes and new features
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On Wed, 06 Feb 2013 17:32:06 +0100, Thomas Neidhart wrote:
On 02/06/2013 05:28 PM, Gilles wrote:
On Wed, 06 Feb 2013 15:48:43 +0100, Thomas Neidhart wrote:
Hi,
well, I did not work much on cli, but lately I have cleanup up
together
with sebb the trunk, and I think it is in a state that could
On Wed, 06 Feb 2013 07:19:47 -0800, Phil Steitz wrote:
On 2/5/13 6:08 AM, Gilles wrote:
Hi.
In the thread about static import, Stephen noted that decisions
on a
component's evolution are dependent on whether the future of the
Java
language is taken into account, or not.
A question
On Wed, 06 Feb 2013 09:46:55 -0800, Phil Steitz wrote:
On 2/6/13 9:03 AM, Gilles wrote:
On Wed, 06 Feb 2013 07:19:47 -0800, Phil Steitz wrote:
On 2/5/13 6:08 AM, Gilles wrote:
Hi.
In the thread about static import, Stephen noted that decisions
on a
component's evolution are dependent
On Thu, 07 Feb 2013 08:32:46 -0800, Phil Steitz wrote:
On 2/7/13 8:04 AM, Gilles wrote:
On Thu, 07 Feb 2013 07:01:42 -0800, Phil Steitz wrote:
On 2/7/13 4:58 AM, Gilles wrote:
On Wed, 06 Feb 2013 09:46:55 -0800, Phil Steitz wrote:
On 2/6/13 9:03 AM, Gilles wrote:
On Wed, 06 Feb 2013 07:19
be fine anyway, but maybe name it 3.1.2?
Regards,
Gilles
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be an abstract class.
Regards,
Gilles
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.
Instead of adding synchronized keywords, it is rather all the others
that must
be removed (but we decided no to do it before 4.0 in order to not break
user code
that potentially rely on the existing, but broken, synchronization).
Best regards,
Gilles
Modified:
commons/proper/math/trunk/src
/test/java/org/apache/commons/math3/optimization/general/LevenbergMarquardtOptimizerTest.java-
public void testMath199() {
We can forget about tests that relate to a deprecated package.
Gilles
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() {
Those two uses a RNG with no fixed seed.
I guess they were failing... randomly.
Gilles
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testParseSimpleWithClosingRowSeparator() {
This one is broken:
testParseSimpleWithClosingRowSeparator(org.apache.commons.math3.linear.RealMatrixFormatTest)
Time elapsed: 0.004 sec FAILURE!
java.lang.AssertionError:
expected:Array2DRowRealMatrix{{1.0,1.0,1.0},{1.0,1.0,1.0}} but
was:null
Gilles
).
* The class PollardRho (o.a.c.m.primes) is untested and unused.
Best regards,
Gilles
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On Tue, 02 Apr 2013 14:59:22 +0200, Luc Maisonobe wrote:
Le 02/04/2013 12:37, Gilles a écrit :
Hi.
Hi.
Votes, please.
This vote will close in 72 hours: 2013-04-02T23:00:00 UTC
[ ] +1 Release these artifacts
[X] +0 OK, but...
[ ] -0 OK, but really should fix...
[ ] -1 I oppose
not mean it to be a blocker.]
Thanks a lot.
You're welcome.
Gilles
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lose the -SNAPSHOT suffix.
Checkout trunk, update the workspace, and create the tag from the
workspace.
That's how the release plugin ought to work.
So at the end, there was an authorization failure in a deploy stage.
Best regards,
Gilles
On Wed, 3 Apr 2013 11:00:55 +0100, sebb wrote:
On 3 April 2013 10:23, Gilles gil...@harfang.homelinux.org wrote:
Changed: luc @ Tue 2 Apr 2013 19:17:20 +
Comment: Preparing RC5 for release 3.2.
Files changed:
/commons/proper/math/trunk/**pom.xml ( 1463703 )
It seems continuum tried
On Wed, 03 Apr 2013 12:37:21 +0200, Gilles wrote:
On Wed, 3 Apr 2013 11:00:55 +0100, sebb wrote:
On 3 April 2013 10:23, Gilles gil...@harfang.homelinux.org wrote:
Changed: luc @ Tue 2 Apr 2013 19:17:20 +
Comment: Preparing RC5 for release 3.2.
Files changed:
/commons/proper/math
[X] +1 Release these artifacts
[ ] +0 OK, but...
[ ] -0 OK, but really should fix...
[ ] -1 I oppose this release because...
Gilles
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For additional
/GTest.javaViolationMessageLine[image:
Errors]File does not end with a newline.0 Gary
Those two files do end with a newline.
Gilles
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{execution: default-compile}]
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 788 source files to
/home/gilles/devel/SVN/commons-math/trunk/target/classes
---CUT---
[I.e. it's done even when re-running the test target several times in
a row.]
So, it seems that something is changed
On Fri, 5 Apr 2013 15:19:29 +0100, sebb wrote:
On 5 April 2013 15:17, Gilles gil...@harfang.homelinux.org wrote:
Hi.
At some recent point, maven started to recompile all the source
files
every time,
even when no modification was done in the src directory.
Somewhere in the console output
?
[To be really helpful, such a recipe should be as short as
possible (but no shorter...), and kept up-to-date.]
Thanks,
Gilles
[1] No need to ask questions, figure out between alternatives,
or guessing about missing or outdated bits; just type the
commands in the suggested order and it must
for conservative users.
Regards,
Gilles
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On Mon, 8 Apr 2013 17:33:11 +0100, sebb wrote:
On 8 April 2013 13:22, Gilles gil...@harfang.homelinux.org wrote:
On Mon, 8 Apr 2013 11:52:25 +0100, sebb wrote:
On 8 April 2013 08:14, Luc Maisonobe luc.maison...@free.fr wrote:
Hi Gary (and Sebb who had similar concerns),
Le 08/04/2013 00
must not contain Inf or NaN);
}
}
-
JIRA + diff???
A bug report mentioning the inconsistency is welcome.
A diff is not necessary until we agree on the way to go.
Thanks,
Gilles
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On Thu, 11 Apr 2013 16:45:42 +0200, Arne Ploese wrote:
Am Donnerstag, den 11.04.2013, 16:08 +0200 schrieb Gilles:
Hello.
in class org.apache.commons.math3.linear.RealVector there is the
embedded class Entry which is protected, but it is exposed by
method
public IteratorEntry iterator
to mention them in a JIRA so interested parties
can
test if a bug has been fixed, but not on the user list nor on
download
pages.
The main contribution which users can offer is to test snapshots and
provide
feedback on regressions in their applications.
Regards,
Gilles
be in the details, as usual...]
While doing this, I would also move the non-linear least-squares
solvers
(Gauss-Newton, Levenberg-Marquardt) over to the fitting package.
Regards,
Gilles
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On Mon, 29 Apr 2013 22:47:15 +0100, sebb wrote:
On 29 April 2013 21:49, Gilles gil...@harfang.homelinux.org wrote:
On Mon, 29 Apr 2013 16:56:02 +0100, sebb wrote:
On 29 April 2013 15:51, Phil Steitz phil.ste...@gmail.com wrote:
On 4/29/13 5:39 AM, Jochen Wiedmann wrote:
On Mon, Apr 29
On Tue, 30 Apr 2013 07:36:10 -0700, Phil Steitz wrote:
On 4/29/13 11:49 PM, Thomas Vandahl wrote:
On 30.04.2013 00:01, Gilles wrote:
If someone doesn't develop a Commons component, he is not in the
developer
category for that component.
If his app _uses_ a Commons component, he is a user
subclasses to set the state implemented in the base classes.
Is there something wrong with that approach?
Gilles
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_actually_ use the
proposed
code; we should not accept them as a mere coding exercises that will
potentially increase the burden on regular contributors.
Gilles
Modified:
commons/proper/math/trunk/src/changes/changes.xml
commons/proper/math/trunk/src/main/java/org/apache/commons/math3/util
On Tue, 28 May 2013 20:47:30 +0200, Thomas Neidhart wrote:
On 05/28/2013 08:20 PM, Gilles wrote:
On Tue, 28 May 2013 16:04:32 -, t...@apache.org wrote:
Author: tn
Date: Tue May 28 16:04:32 2013
New Revision: 1486982
URL: http://svn.apache.org/r1486982
Log:
[MATH-851] Added method
Hello.
On Mon, 03 Jun 2013 09:04:40 -, l...@apache.org wrote:
Author: luc
Date: Mon Jun 3 09:04:40 2013
New Revision: 1488914
URL: http://svn.apache.org/r1488914
Log:
Added midpoint integration method.
Patch contributed by Oleksandr Kornieiev.
JIRA: MATH-967
[...]
+private
On Wed, 12 Jun 2013 15:54:49 -0500, Becksfort, Jared wrote:
Hello,
I am wondering if something will replace the deprecated CurveFitter
classes?
Perhaps you are looking in the deprecated o.a.c.m.optimization
package.
Curve fitting is now in o.a.c.m.fitting.
Regards,
Gilles
, Ajo. As Gilles
said on the ticket, its a little easier to have a discussion here
than on JIRA tickets, so We usually start the discussion here about
whether or not a new feature makes sense and, if so, how to
implement it.
I am +1 for adding support for improper integrals. I am not a
numerical
to
CM?
As I tried to explain above, in order to be useful to a wide range of
users, CM must provide code that is flexible. We all have to try hard
not
to consider a general purpose library as a repository for disparate
ad-hoc
code snippets.
Best regards,
Gilles
the interval and terminate the algorithm.
As I explained in the other post we must aim at flexibility. In this
case, that would indeed imply a clean separation, as outlined in the
article referred to above. [This is obviously not the case in your
AdaptiveQuadrature class.]
Best regards,
Gilles
[1
On Fri, 28 Jun 2013 08:32:49 -0700, Ted Dunning wrote:
On Fri, Jun 28, 2013 at 8:14 AM, Gilles
gil...@harfang.homelinux.orgwrote:
Hello.
The existing LegendreGaussQuadrature class incorrectly assumes that
it has
converged for functions where the polynomial approximation fails in
a
small
effort than
the latter.
Gilles
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and
InfiniteIntegral is not legitimate (if that's the case).
Regards,
Gilles
[1] Cf. also my latest comment on the MATH-995 page.
Cheers,
Ajo.
On Fri, Jun 28, 2013 at 11:07 AM, Ajo Fod ajo@gmail.com wrote:
BTW, it is possible that I'm not using LGQ correctly. If so, please
show
how to pass
evaluations.
and providing
you with an alternative that is more accurate.
Cf. above (and my previous post), about how to contribute to
Commons Math.
Please open a new feature request.
Regards,
Gilles
On Mon, Jul 1, 2013 at 8:22 AM, Gilles gil...@harfang.homelinux.org
wrote:
Hi.
I
request; again we
need numbers to back it up. [There is a benchmarking utility in the
test
part of the code repository (class PerfTestUtils).]
Please let me know if this doesn't answer your question about the
discussion:
In essence Gilles thinks there is no problem with LGQ because
of
problems.
Patches welcome.
Gilles
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.]
Gilles
Cheers,
Ajo
On Tue, Jul 2, 2013 at 2:09 PM, Gilles gil...@harfang.homelinux.org
wrote:
On Tue, 2 Jul 2013 12:54:12 -0400, Konstantin Berlin wrote:
IterateiveLegendreGaussIntegra**tor should be replaced by adaptive
guass-kronrod. The simpson and trapezoidal methods should be
replaced
probably only use
a few.
3. Insert links to Commons projects in the External links section of
related Wikipedia articles.
Regards,
Gilles
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(the remaining problem is a missing method
in class Frequency).
Gilles
[...]
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{
...
This class impement the gradient and hessian matrix based on finite
differences
If it can be of any use
The features certainly look interesting.
yours truly
François Laferriere
P.S. I previously submitted this stuff to user list and Gilles
suggested to push it on the dev list
Next step would
= ct.getTrajectory() ;
The same wrapper principle may be applied to count the number of time
the objective function value is invoqued during the optimisation
process.
You can already get it with getEvaluations(). :-)
Regards,
Gilles
fields are basically impossible to test
fully in a multi-threaded environment, and not always easy in a
single-threaded environment.
+1
Gilles
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(and let the fitting be transparently performed with an
instance
of LevenbergMarquardtOptimizer).
Any objection?
Regards,
Gilles
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(e.g. [Math] for the Commons Math
project).]
Then you'd probably want to download the source code and get
acquainted with the coding style(s). Eventually, you can have
a look at the issues posted on the bug tracking system.
Thanks for your interest,
Gilles
understand what this means.
Gilles
On Jul 17, 2013, at 11:16 AM, Gilles gil...@harfang.homelinux.org
wrote:
Hello.
Constructors of classes in the o.a.c.m.fitting are instantiated
using
an (abstract) MultivariateVectorOptimizer. The only concrete
implementations of this class
algorithms aimed at solving a (non-linear)
leastsquares problem:[2]
http://markmail.org/message/nkceta2cskpgbkug
raises unsubstantiated criticism that never[3] translated into
_practical_ advice[4] on how to improve the code.
Gilles
[1] What _I_ observed and used led me to try out what I think
without much
thinking involved. We had the discuss previously, with Gilles
unilaterally deciding on the current tree, which he now wants to
change again.
As I said,
as Luc said,
as Phil said,
again and again and again,
we are not optimization (as a scientific field) experts here,
but we do use
) check?
Introducing the overloads above just to suppress warnings about
valid uses of a Java feature does not seem right.
Regards,
Gilles
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it possible to tell Junit to not run some tests (i.e. the
opposite of -Dtest=SomeTest)?
Regards,
Gilles
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smelled a little to me :)
Indeed; I think it causes more trouble than it is worth.
What I meant is that it's a pity that valid uses must be suppressed
in order to detect invalid code (which will then be suppressed, of
course)...
Gilles
On Thu, 18 Jul 2013 20:35:53 +0100, sebb wrote:
On 18 July 2013 20:06, Gilles gil...@harfang.homelinux.org wrote:
On Thu, 18 Jul 2013 16:19:10 +0100, sebb wrote:
Some MATH unit tests take a long time to run.
One example is CMAESOptimizerTest, which is run twice - once for
the
deprecated
, then everything
is fine!
Gilles
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to best
integrate the new features into the existing code. Just as you
did.
Regards,
Gilles
[1] http://markmail.org/message/erqohcragbxmm4xa
[2] I explained the reasons for not accepting the patch as it was.
It's all on the ML and yet another installment will not provide
more light
,
Gilles
[1] Phil's too, probably, because code reuse places a big part of the
burden (e.g. of numerical analysis in this instance) on the reused
building blocks!
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everyone's opinion on how to
break
the functionality of your patch into its various constituents (so that
they
become independant, manageable, reusable components).
Each of these concepts should then have their own thread for discussing
the
details of implementation.
Regards,
Gilles
On Sat
]
Hermite is defined in [-Inf,+Inf]
I have two issues with the above:
1: Cant imagine how someone would use AQ. Which means as Gilles
noticed,
you can't focus on the hard to converge sections of the integral.
2: If you use the integration without AQ. Any function that has a
high
frequency region
On Sun, 21 Jul 2013 08:04:05 -0700, Ajo Fod wrote:
[...]
Here is some numerical analysis on the issue:
Laguerre is defined only in [0,+ve Inf]
Hermite is defined in [-Inf,+Inf]
I have two issues with the above:
1: Cant imagine how someone would use AQ. Which means as Gilles
noticed,
you
, MathArrays.Position.TAIL, end,
getRandomGenerator());
}
---CUT---
Regards,
Gilles
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with
it.
We already know one, don't we?
[Hint: the plots in https://issues.apache.org/jira/browse/MATH-995
I mean that this function could serve as a validation test and
benchmark (since we know that the answer is 1).]
[...]
Gilles
the test without a change of variables?
The test would consist in assessing how different adaptive strategies
perform
when integrating the transformed Gaussian over [-1, 1].
Gilles
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Hi.
The classes
RandomDataGenerator
and
UniformIntegerDistribution
use different codes for providing random integers in a range.
Shouldn't the same code be used in both?
Are both equally valid on the whole integer range?
Regards,
Gilles
[1] Or better (IMO) shouldn't RandomDataGenerator
) (probably parameterized with mu and sigma) without any
reference to a change of variable.
HTH,
Gilles
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be added to
o.a.c.m.stat.descriptive.DescriptiveStatistics.
Is there a function that would compute min and max on an comparable
collection?
http://docs.oracle.com/javase/7/docs/api/java/util/Collections.html#max(java.util.Collection)
Gilles
On Tue, Jul 23, 2013 at 1:25 PM, Phil Steitz
Hi.
Please have a look at
https://issues.apache.org/jira/browse/MATH-1012
Regards,
Gilles
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= fitter.fit();
[HarmonicFitter and PolynomialFitter would have their new API
counterparts in a similar way.
This would allow to deprecate MultivariateVectorOptimizer whose
only uses are by the classes in o.a.c.m.fitting package.]
Regards,
Gilles
On Mon, 05 Aug 2013 04:27:11 +0200, Gilles wrote:
Hi.
Please have a look at
https://issues.apache.org/jira/browse/MATH-1014
In summary, this is an API change (in line with the fluent API
proposed for the optimizers); but usage is simplified:
[...]
As a further simplification, I also
are invalid/missing for
'jacoco:check'
[0] Inside the definition for plugin 'jacoco-maven-plugin' specify the
following:
configuration
...
rulesVALUE/rules
/configuration.
---CUT---
It seems that in later versions, the check tag must be replaced
by rules.
Regards,
Gilles
be retained by unit tests
that check the contract of copy)
If I'm missing something obvious, please let me know!
Gilles
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in o.a.c.m.fitting.leastsquares.
I strongly suspect that a lot of the code dedicated to the fluent API
could be removed if immutability is dropped.
Gilles
On Wed, Aug 7, 2013 at 11:23 AM, Gilles
gil...@harfang.homelinux.orgwrote:
Hi.
It seems that each two of those concepts are at odds with
the third one.
E.g. you
that the base class Parent is assumed to
have complete knowledge of all its subclass Child: the signature of
create must contain the arguments for fields declared in Child?
Gilles
The create method forces the implementing class to have an
appropriate
constructor. The withXxx methods
Hi.
On Thu, 08 Aug 2013 10:03:36 +0200, Luc Maisonobe wrote:
Le 08/08/2013 01:13, Gilles a écrit :
On Wed, 7 Aug 2013 18:04:39 -0400, Evan Ward wrote:
Hi,
As a grateful user of the library, I would prefer the Fluent API
and
immutability. I have implemented this pattern in some of my own
was thinking something like:
https://gist.github.com/anonymous/6184665
Thanks for the effort of writing the example in more details.
To address a few concerns I saw,
Gilles wrote:
In this way, it does not; what I inferred from the partial code
above was
that there would only be _one_ create
applications should not be utterly annoyed by having
to instantiate several optimizer objects...
[...]
Best,
Gilles
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On Mon, 05 Aug 2013 04:27:11 +0200, Gilles wrote:
Hi.
Please have a look at
https://issues.apache.org/jira/browse/MATH-1014
[...]
In addition to the changes contained in the patch attached
to that issue, I would consider removing the data point
book-keeping from the fitter classes, i.e
spend (a
lot of) time designing complex schemes which are not required by
common use-cases.
In addition to stat, a few other CM areas where MT is of direct
application are: FFT, Genetic Algorithms, Machine-learning, ...
Regards,
Gilles
[...]
[1] Cf. diff (in recent commits of optimizer classes
the
data to another object, as you suggested.
If it's better design and leads to simpler code, there shouldn't be
any problem in applying it for the next release.
Thanks,
Gilles
[...]
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clear. Also, I agree that the Javadoc
should indicate
code does, but I don't think that it should be required to prove that
what it does
yields the expected result (that's for the references to provide).
Rather, the unit
tests would ideally spot that the algorithm is wrong or buggy.]
Gilles
it is a copy.
It also explicitly makes no promise about user-supplied fields.
Would that cover most needs, or did I overlook something?
Best regards,
Gilles
[...]
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On Tue, 13 Aug 2013 17:47:18 -0400, Evan Ward wrote:
On 08/13/2013 08:17 AM, Gilles wrote:
(I.e. GN would
not need 5 superclasses and fields for storing upper and lower
bounds.)
Be careful: GaussNewtonOptimizer does _not_ support bounds!
That is my point! Because of it's complex
of the
implementation could even be removed if it is deemed that we lose more time
doing the check than we gain when the user asks the value of points below
1e-9.]
Also, there probably should not be a ; after the statements.
Regards,
Gilles
-NOTES.txt
Best regards,
Gilles
on behalf of the Apache Commons community
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the convergence
checker) that would allow to e.g. track the optimizer's search path,
...
Regards,
Gilles
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On Wed, 14 Aug 2013 23:40:58 +0100, sebb wrote:
On 14 August 2013 23:34, Gilles gil...@harfang.homelinux.org wrote:
At this point, I'd tend to think that creating a copy of trunk in
the
Commons's sandbox part of the repository will be more productive.
Why sandbox? Just use a temporary
On Thu, 15 Aug 2013 11:07:20 -0500, Phil Steitz wrote:
On Aug 15, 2013, at 7:31 AM, Gilles gil...@harfang.homelinux.org
wrote:
On Wed, 14 Aug 2013 23:40:58 +0100, sebb wrote:
On 14 August 2013 23:34, Gilles gil...@harfang.homelinux.org
wrote:
At this point, I'd tend to think that creating
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