Openms 2.5 preparation #19989
Openms 2.5 preparation #19989
Conversation
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@jpfeuffer any idea about the OSX error? Do you have a local OSX box around? |
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Yes, I have a Mac here. But it is probably the "fixup dependencies" patch that has to be redone. |
…me if building for multiple python versions. init.py.Patch was incomplete.
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Looks good. We could test adding the GUI tools as well but maybe we do this in another PR later. |
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@jpfeuffer At the moment we build for 2.7, 3.6 and 3.7 (we'll likely drop 3.6 and add 3.8 soon). |
recipes/openms/meta.yaml
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| - seqan-library ==1.4.2 | ||
| - coinmp | ||
| - sqlite | ||
| - python {{ python }} |
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here you could skip python2 and build everything against python 3x with python >=3
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But how can we otherwise build pyopenms for multiple python versions? |
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Our Cython modules are probably not using the limited Python API that is compatible across minor versions. cython/cython#2542 |
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There's a project-wide (actually multiple project wide, since conda-forge uses it too) conda_build_config.yaml file that already lists 3 python versions, so it should be needed to specify that again (though we can judge that in an hour or two once we see what's built now). |
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Aaaah great. Then, let's see |
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We can recythonize things in each python build if there's a build flag to do that. I think we have to do the same thing with other recipes, like pysam. |
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By the way: I think we should wait for the official release, then I will update the source package and it will be available under a stable github release tag artifact. |
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@bioconda-bot please fetch artifacts |
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Ok so in case such incompatibility happens, we just have to find the affected package and request a rebuild, right? |
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Correct, just open an issue and maybe mention something in the gitter channel. |
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What is happening? This feels unrelated. |
…act same dependencies
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I have the same problem now, that during tests, it suddenly resolves to boost 1.70 as requirement (instead of 1.72 as used during build). |
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@BiocondaBot update |
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@BiocondaBot please update |
| - thermorawfileparser ==1.2.1 | ||
| - xtandem ==15.12.15.2 | ||
| - gnuplot | ||
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Really like this.
For Galaxy wrappers I currently also inlcude
- bumbershoot 3_0_11579 (for myrimatch)
- tpp 5.0.0 (for SpectraSTAdapter)
For you reference here is a list of requirements that is not yet in conda: #18953 .. essentially only MaraCluster is left (and a few which will not make it to conda due to licensing)
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Ah, that's what they are for, thanks, I will add them! Yes, we also figured it would be great if there is an all-in package. And with the new structure, it should be up to the user to choose which parts they need.
Release will hopefully be tomorrow if everything works out.
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This is some awesome work! Thanks a lot @jpfeuffer and all others!
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@jpfeuffer congrats for the release. The PR title is still about preparation, do you want this PR to be merged now or is this still WIP? |
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Was about to request the review and merge label. Good to go for me. |
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@BiocondaBot please merge |
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I will attempt to upload artifacts and merge this PR. This may take some time, please have patience. |
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Wuhu!
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Already 5 downloads .. one is from a |
This updates the OpenMS recipe to use the release candidate of 2.5.
(otherwise, please submit to the more general purpose conda-forge channel).