propka/pdb2pqr

[Jack Howarth]

Joshua,
       Thanks. I used the deactivate hack in propka against pdb2pqr prior
to 3.6.1 and it solved the buildbot failures. The final set of commits to
add the py-mmcif_pdbx support package for the the new pdb2pqr 3.6.1 update
and the associated propka package to provide the python-based propka.

py-mmcif_pdbx 2.0.1, pdb2pqr 3.6.1 and propka 3.5.1 #24365
<https://github.com/macports/macports-ports/pull/24365>

          Jack

On Tue, Jun 4, 2024 at 4:14 PM Joshua Root <jmr at macports.org> wrote:

> On 4/6/2024 23:43, Jack Howarth wrote:
> > I am lost at sea about how to handle the newer pdb2pqr packaging. The
> > ancient 2.1.1 pdb2pqr sources built a c-based propka as part of the
> > pdb2pqr process. Upstream replaced this with propka entirely rewritten
> > in python and as its own project. I believe the buildbot failures that I
> > am seeing are due to propka trying to overwrite the propka binary in
> > /opt/local/bin on installation before the newer propka-free pdb2pqr
> > package is installed. We don't seem to have the granularity in MacPorts
> > to handle this cleanly short of creating a whole new pdb2pqr package
> > under a new name (which is throwing a major wrench in using
> > github.setup). Is there some way to handle movement of binaries across
> > existing packages without having to recreate the wheel with a new
> > package set?
>
> If the old version of pdb2pqr installed propka and the new version of
> pdb2pqr depends on a separate port that now installs propka, you will
> need to use the deactivate hack:
> <https://trac.macports.org/wiki/PortfileRecipes#deactivatehack>
>
> - Josh
>
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