If there is no quick workaround that I could use on my side, I'd be happy to give a hand for a PR solving this issue, but I might need some help as I can't see an obvious solution.

• How are you configuring sphinx-gallery in this setup of yours, and from which folder do you launch the build?
• This is a tricky problem as app.builder.srcdir despite sphinx claiming is the location of conf.py it actually seems to be the directory sphinx-build is called. So dealing with relative and absolute paths is quite complex. Then absolute paths in the rst files have as root the source folder and not the filesystem root, complicating again dealing with paths.

Thanks for the quick answer!

For the configuration of sphinx-gallery, I have in source/conf.py:

sphinx_gallery_conf = {
    # path to your examples scripts
    'examples_dirs' : 'doc/source/examples',
    # path where to save gallery generated examples
    'gallery_dirs'  : 'doc/source/auto_examples',
    }

(I first tried without doc but then it couldn't find the examples dir, once again because of os.path.relpath(examples_dir, app.builder.srcdir)). And of course I added sphinx_gallery.gen_gallery to the list of extensions.

I launch the build from doc (the directory where the Makefile is), with make html. doc is the directory from which I executed the tree commands above, which contains all the architecture listed above.

I think I found a workaround, with a minor modification of gen_gallery.generate_gallery_rst: adding

os.chdir(app.builder.srcdir)

allows to get the right paths with os.path.relpath. I checked on minimal examples that this change makes possible to build the gallery for the two types of folder organization (with or without a source directory).

Should I submit a PR with this change, or could it be a problem to make this modification (of course, one can go back to the initial directory at the end of the function)?

Coming back to this issue: any opinion on whether the workaround I suggest is the way to go, or whether another approach should be used?

doing the os.chdir(app.builder.srcdir) looks harmless for now. I'm not entirely sure how to work on this with Sphinx as is know for now it behaves different to their specification. I also see Sphinx has released a new version recently. It might be relevant to test it with it too, things usually break with Sphinx updates.

See #119.

It turns out that it is necessary to be located in the source directory for other tasks as well, as in doc_resolv._embed_code_links. It would be possible to add the same workaround (cd into source directory) as in #119, or maybe it would be preferable to go to the source directory from the beginning, that is in gen_gallery.setup.

What do you think?