Install phyx via conda

[vmikk]

Hello!
Thanks a lot for phyx, it looks very promising!
However the installation instructions may seem a bit scary for some users.
Do you plan to distribute phyx via conda (e.g., through bioconda channel)? It's quite popular now and allows to easily handle package dependencies and update the software.

With best regards,
Vladimir

[blackrim]

That looks cool! Haven't looked into it but will do so and update this issue when it is done. Thanks

[druvus]

I started to generate a bioconda recipe for phyx but run into some issues. You can find the current PR here: bioconda/bioconda-recipes#4539
I managed to get it building on the linux image that is used by bioconda but forgot something in the recipe. I will try to come back and fix it later during the week but you might have a better understanding of the error.

[nickloman]

I'd also be keen to see this building on Conda.

[blackrim]

Cool. I will resurrect this starting with the PR

[druvus]

@blackrim I have a working recipe for phyx locally but it needs a rebuild of nlopt using cxx. I opened PR at conda-forge/nlopt-feedstock#12. You are probably more familiar with nlopt to comment issues raised by @jschueller that is maintainer of the nlopt recipe.

[jschueller]

You dont need to enable cxx. For nlopt what it really does is enable the algorithm that is written in c++, but the api of nlopt remains C. The C++ interface for nlopt exists but is header-only and is not related to the with-cxx option. What you just have to do is tell phyx to link to nlopt instead of nlopt_cxx, here is the relevant phyx configure.ac line:

AC_SEARCH_LIBS([nlopt_urand], [nlopt_cxx], [have_nlopt=yes], [have_nlopt=no], [-lstdc++])

This phyx nlopt detection has to be improved, first look for nlopt, then nlopt_cxx+lstdc++.

[blackrim]

Thanks @jschueller and @druvus we will have a look at this and hopefully deal with it in the next day or two.

[jfwalker]

Thanks @jschueller and @druvus ! I tried taking a look, is the edit needed as trivial as changing the line to:

AC_SEARCH_LIBS([nlopt_urand], [nlopt], [have_nlopt=yes], [have_nlopt=no], [-lstdc++])

or is there more that needs to be done? Sorry I don't have muct familiarity with conda. Thanks!

[blackrim]

@jfwalker thanks but I think I have a better general solution. Pushing in one sec

[blackrim]

OK, I believe this has remedied teh situation. No more nlopt_cxx in linking or configure 6372057
@druvus and @jschueller

[druvus]

@blackrim I have an open PR to build phyx that pass the tests: bioconda/bioconda-recipes#9119

I am currently using the latest commit but would it be possible to get a new tagged release that I could refer to?

[josephwb]

We are planning on a minor release update early next week.

[jamie-arcc]

Is there any update on this? This would be a requisite for FePhyFoFum/PyPHLAWD#27 as well

[josephwb]

Sorry this has dragged for so long. Let's get it closed. I have no knowledge of conda. What do you require from us? We should make a new release, as a few bugs have been fixed since the last one. Can you do this @blackrim?

[jamie-arcc]

bump

[josephwb]

I don't have the faintest clue what is needed on this from our side (sorry: no experience with conda whatsoever). We do have a recent release here. Is there something else?

[blackrim]

Back here, but still don't know what we need to do to get this through.

[druvus]

Finally got back to this and phyx is now available through Bioconda.

[josephwb]

@druvus Sweet, thanks! So, we can close this?

[druvus]

Yes, please close it. Upcoming updates will be handled by the Bioconda bot.