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Update peer to compile and work on modern platforms. #1

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Update peer to compile and work on modern platforms. #1

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pettyalex
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I've got this building locally with an external Eigen in Conda, I'm going to figure out a better way to do that but this works for now.

This is mostly updating CMakeLists, and I got it compiling on my apple silicon mac!

pettyalex added 30 commits March 4, 2024 22:49
@pettyalex
Initial exploration: Updating peer to work in modern environments.
86b612e
@pettyalex
Get peer building on a modern system, R libraries included
9ad7518
@pettyalex
Update alglib to 4.01.0
3991939
@pettyalex
Add conda env for github action
3ba56b8
@pettyalex
Manually point cmake at the conda dir?
b6896f2
@pettyalex
Actually lets see everything
6cb14f2
@pettyalex
it only works with bash
f84d0ab
@pettyalex
Fix up SWIG / R to put generated files in a specified place.
bf3de1a
@pettyalex
Get the dest paths for swig correct.
036d93e
@pettyalex
Check a vendored eigen back in. Fix standalone package build for R an…
51eb82d 
…d Python using vendored Eigen.
@pettyalex
R CMD build is lower case. Also remove unintentionally checked in bin…
76a994a 
…ary and no longer necessary numpy include script.
@pettyalex
Fixup R package build and move whole thing into the script.
c67437b
@pettyalex
Add python-build to the conda environment
039f0ec
@pettyalex
Check in empty src dir in the template via gitignore. We could also s…
56f5238 
…cript it?
@pettyalex
Add another build step to try cibuildwheel on the python packages.
5fb3b6e
@pettyalex
Fix matrix build
ada9ac4
@pettyalex
Replace alglib with boost
fc6c3e3
@pettyalex
Add boost to the conda environment we're building in
cc9a7da
@pettyalex
Try compiling with boost and eigen from repo or conda env
195d1b7
@pettyalex
Remove vendored alglib, fix path in wheel / r build
6f3dfc6
@pettyalex
Fix paths in github actions build. Dont copy in description from R dir
05d22ce
@pettyalex
Correct python standalone build. Add a script to build and install bo…
813c3b5 
…th python and R locally
@pettyalex
Github actions calls it arm64 on mac os
c35b652
@pettyalex
Remove extraneous R data artifacts.
bc150e4
@pettyalex
Add minimum python 3.7
73dfe52
@pettyalex
Install boost in cibuildwheel job
9ef666b
@pettyalex
Specify boost version
d14fd2c
@pettyalex
Go ahead and vendor boost::math. Maybe this is a bad idea?
7c4d614
@pettyalex
Marked python package version 2.0
8035e40
@pettyalex
Work towards a standalone R package build without Cmake
8754c95
pettyalex added 13 commits March 14, 2024 20:44
@thebigcorporation
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Thanks for this work. I had just started the the original and subsequent bioFAM fork, with the objective of getting things building in a container. I also started checking whether we can use https://github.com/bioFAM/MOFA2, which seems to have originated as a re-implementation of peer. In any case, if you are interested in PR's I'll be happy to put things up against this branch as I find / fix things.

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@pettyalex @thebigcorporation