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Setup Necessary Software and links

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Adam Wright edited this page Jul 5, 2023 · 2 revisions

Setup stuff

You'll need links, python packages, and compiled cython files to make everything work!

Links to other directories

This repo is not entirely stand-alone, you'll need three github repos working together:

  1. https://github.com/deapplegate/wtgpipeline : has all of the pre-processing and image-calibration and measurement stuff that's needed prior to calculating masses and getting the final lensing catalogs
  2. https://github.com/arwright3/gravitas : has stuff for calulating CC masses, p(z) masses, and Cosmos Mass Bias
  3. https://github.com/arwright3/quick : has some general tools you'll likely need (e.g. imagetools.py and cattools.py)

In order to get everything to work, you're going to have to make sure you clone my quick gravitas and wtgpipeline repos as well. You'll need tools from each of these directories, and the easiest way to do this is with links. Since github doesn't like repos that link outside the repo, I've included a script called setup_symlinks.sh to help you get the right links in place.

Note: this script isn't as important anymore, at least not for the quick and gravitas repo. Instead you should place paths to the quick/gravitas/wtgpipeline repos in your .bash_profile like this:

export quickpypath=/u/ki/awright/quick/pythons/
export gravitaspath=/u/ki/awright/gravitas/                                                                          export wtgpipelinepath=/u/ki/awright/wtgpipeline/

For most python scripts this should take care of everything since we've placed a sys.path.append(os.environ['quickpypath']) in the scripts importing modules from that repo, likewise for gravitas and wtgpipeline.

Then use setup_symlinks.sh to get the necessary links to .sh and other non-python scripts like this:

## make links in wtgpipeline/
cd ${wtgpipeline_repo_path}
./setup_symlinks.sh $quick_repo_path $gravitas_repo_path 

## make links in gravitas/
cd $gravitas_repo_path4
./setup_symlinks.sh $quick_repo_path ${wtgpipeline_repo_path}

Python Packages Needed:

Setup and compile the *.pyx files

You can compile all of the .pyx files by running make_pyx_setup.sh with the one input being your anaconda path.

./make_pyx_setup.sh ${anaconda_path}
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