Re: Missing functions in the statistics package.

[Oliver Heimlich]

On 13.09.2015 11:52, Dag wrote:
> Thanks everyone for your help.
>
> There are many ways to write and test code. I have this procedure in mind:
>
> 1. Download the source code of Octave and do a local installation.
>
> I downloaded v. 3.8.2 and compiled it in Linux Mint after installing
> relevant Debian packages ( http://wiki.octave.org/Octave_for_Debian_systems
> <http://wiki.octave.org/Octave_for_Debian_systems>  ). All the tests run by
> "make check" complete successfully.

When you plan to contribute to the source code, you should not get the 
source tarball, but clone the source repository into a local workspace. 
You will then be able to create patches for the maintainers. If you make 
changes to version 3.8.2, it might become impossible to apply them to 
the upcoming 4.2.0.

If you are only contributing to packages, you could install any 
reasonably recent octave version, preferably from the package 
repositories of your distribution.

> 2. Make a local installation of the package to be edited.
>
> I installed the statistics package v. 1.2.4 using the command  "pkg install
> -local statistics-1.2.4.tar.gz". It loads successfully.

Again, if you plan to make changes to the packages, it is much easier to 
clone the source repository and export patches. There have been several 
changes to the source code since the 1.2.4 release of the statistics 
package.

> 3. Make some edits of code including test cases and reinstall (uninstall +
> install) the relevant package.

When you have a local clone of the package's repository, you can use 
`make run` to experiment with the package without (re-)installing all 
the time. Whether `make run` is available for a particular package 
depends, but the statistics package has it.

> 4. Run tests and see if there are any errors.
>
> 5. Run 3-4 iteratively until the goal has been attained and there are no
> known bugs.

ok

> 6. Upload code to a repository or something.

You could push your modified version to a private repository or provide 
patches for the official repository. Later it will be possible to grant 
push access to the official repository if you plan more substantial 
contributions.

> I am about to start doing step 3 now. I will take a look at the code
> guidelines and internal information that you have and proceed accordingly.
>
> Some questions:
>
> * An attempt to run all the tests ("make check") failed with Octave 4.0.0,
> so I cannot test my code there. But since I am not dealing with the core,
> this may not be important until at a later stage.

You should file a bug report for octave, unless the error is already 
known or caused by some misconfiguration.

> * I have an Octave installation that comes with Linux Mint packages. But I
> do not want to make changes to this one when doing my coding, because I need
> a stable installation for other purposes. I will be using the local
> installation for code writing and testing.

When you have several octave versions on your machine, you have to 
export OCTAVE and MKOCTFILE environment variables and make them point to 
the correct binaries. Otherwise working with the package sources might 
fail because the wrong mkoctfile version is used in combination with a 
particular octave version.

> * Bounds checking is good for debugging purposes. I will try this and
> reinstall my local Octave if it makes debugging easier.
>
> * I am used to writing code in Eclipse and save them with git. There is no
> indication that Octave programmers are using these tools. Should I just make
> edits in a simple text editor and reinstall iteratively the package being
> edited?

Most of our repositories use mercurial instead of git. You can use 
whatever editor you prefer. For example you should have mercurial 
integration in Eclipse. Instead of reinstalling the package, you can use 
`make run` to see your changes to the source code in action.

> * I can run "make check" for testing Octave core. But how do I test a
> package?

Just like `make run` you can use `make check` for some packages. You 
have to clone the official source repository, because the Makefile is 
not included in the package tarball.

To test an installed package, you could use
>> pkg load statistics
>> __run_test_suite__ ({'octave/statistics-1.2.4/'}, {})
…
Summary:

  PASS       223
  FAIL        21


> * As for coding, I was thinking of writing the prob.* statistical functions
> listed in  http://wiki.octave.org/Statistics_package
> <http://wiki.octave.org/Statistics_package>  . If this succeeds and is fun,
> I will be doing more later. But what do the functions entail? Is it random
> number generation, PDFs, or CDFs? Are they based on function declarations in
> Matlab? MathWorks has got a lot of information on the Internet. Where can I
> find are the function declarations in that case? (If we are writing
> independent code, this does not apply and we will make our own.)

If you implement a function that is also available in matlab or one of 
its toolboxes, you should make sure that its interface is compatible, so 
user code can run in octave without much rewriting.

Oliver