As the native install of pymol provides a plugin interface for apbs, it should depend. Second for the right functionality of apbs with pymol two env variables should be set. From the ideas discussed in bug #213346 I rewrote the ebuild a little bit and introduced the USE flag apbs. It makes pymol depend on sci-chemistry/apbs and for the USE="-apbs" it removes the plugin. Additionally I added the python_mod_cleanup in the pkg_postrm section. Reproducible: Always
Created attachment 146328 [details] pymol-1.0-r2.ebuild
Created attachment 146934 [details] pymol-1.0-r2.ebuild Made it some more portable.
Hi Justin, That looks good, thanks much for your work. In general, it is better to post a diff to an exisiting ebuild rather than the ebuild itself since it is much easier to spot the differences that way! Unless of course the changes are very significant. I think you can pull the line APBS_VER="$(best_version sci-chemistry/apbs | cut -d/ -f2)" into the "if use apbs" conditional later on. Also, I will try to have apbs install its files into /usr/share/apbs rather than apbs-<version>. Otherwise pymol will hard depend on a particular apbs version forcing a recompile of pymol every time apbs will be bumped. In that case you can get rid of the APBS_VER alltogether and replace it by just apbs. I'll post back once this is done. cheers, Markus
(In reply to comment #3) > I think you can pull the line > APBS_VER="$(best_version sci-chemistry/apbs | cut -d/ -f2)" > into the "if use apbs" conditional later on. It must be in in the conditional, because there is no reason to have a "best_version sci-chemistry/apbs". I changed the lines and at a diff.
Created attachment 146996 [details, diff] pymol-1.0-r1.ebuild patch Now a diff.
Cool, thanks! I changed apbs to install into /usr/share/apbs. I did not bump abps to a new revision though, hence users that have apbs already installed will need to recompile it to pick up this change. You may want to add a few einfo lines pointing this out (probably wrapped in a "if use apbs") to the ebuild. Thanks, Markus
Hi Markus! I changed the lines and added the ewarn. Hope the test case is legal. If not, please correct me. Thanks, Justin
Created attachment 147156 [details] pymol.diff
Created attachment 147706 [details, diff] pymol.diff Forgott some dependencies.
Fixed in the science overlay. I noticed your ebuild had some apbs variables commented out, so could you clarify the status of bug #213346 on that bug?
The updated version of the apbs plugin allows to define default locations inside the plugin. I set the right paths there so that there is no need to set them somewhere else. BUG #213346 is obsolete now.
