The code I am interested in is scientific software released under a CeCILL-A license (equivalent to GPL license). The code is quite widely used in a specific community (which is great and also one of the reasons why it was put under a open source license in the first place) but a team took the code, modified it, published several papers with it, and is very reluctant to share their modified version. They even somehow give the impression that their version is accessible, but the repository is private and they shun most requests to access the code.

There is an attempt at clarification on the distribution of a modified version of a software in the CeCILL FAQ (in French; the following is my own translation):

I modified a software under a CeCILL license and users access it through a web site. Do I have to publish the source on request?

Yes, absolutely. If paragraph 5.3.2 mentions distribution, it means, as stipulated in 5.3 preamble, "to publish, transmit and communicate the Software to the general public on any or all medium, and by any or all means". A distribution through a web site or a server is therefore an actual distribution even though the user does not have per se a copy of the software, and therefore the obligation to share the modified source code applies.

In this, it differs from the GPL license in the sense that it is closer to an Affero GPL than a normal GPL. It is not the situation I mentioned, but it shows that CeCILL is a bit stronger on the sharing aspects of modifications of the code than the GPL.

Anyway, even if the GPL license does not force you to release your modification (emphasis is mine):

The GPL does not require you to release your modified version, or any part of it. You are free to make modifications and use them privately, without ever releasing them. This applies to organizations (including companies), too; an organization can make a modified version and use it internally without ever releasing it outside the organization.

But if you release the modified version to the public in some way, the GPL requires you to make the modified source code available to the program's users, under the GPL.

Thus, the GPL gives permission to release the modified program in certain ways, and not in other ways; but the decision of whether to release it is up to you.

It stipulates that it concerns a private use of the code. Does the use of a code leading to published results in scientific journals constitute a private use of the code?

I am a bit afraid that the answer is "yes", but I was wondering if there were any resort. Also, even if it is a legal use of the license, it does not seem moral to me.

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    If you are working in France in some of the organizations (CEA, CNRS, INRIA) authoring CECILL, you could ask internally the lawyers. Apparently, like me, you are working at CEA. The CECILL lawyers at CEA are very nice and helpful. Contact them. Nov 14 '18 at 15:50

If I understand correctly, the team that took the publicly-available version and modified it have not made it available to the public either as source, or for remote interaction. They have merely used it to generate results which have themselves been published.

If this is so, they have no obligation to make their version of the program available. It is well-established that the GPL permits you to modify GPL software for internal use without triggering any obligation to re-distribute it, and the CeCILL licence appears to be similar. What they've done constitutes internal use.

Does the use of a code leading to published results in scientific journals constitute a private use of the code?

Yes. The output of a program is not generally a work derived from the program itself, and so (with certain specific exceptions) the license of the program doesn't generally cover its output.

There is debate in the scientific community about how proper it is to use unpublished code to generate published results, since the work becomes non-reproducible by this practice, and reproducibility is key to modern science. But sadly no consensus has yet been reached in favour of requiring publication, so unless they've published in a journal that would have required this as a condition of publishing their paper, that's likely no help to you either.

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