New install of lsst_stack, numpy not found

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#21

Sorry, had this bookmarked but didn’t have any fresh ideas.

The fundamental problem is that you don’t appear to have a directory with envs/lsst-scipipe-4d7b902/bin in it in your PATH. This is supposed to be set by the source activate line in loadLSST.bash. If it’s not, then something is wrong with your conda installation or possibly your shell startup files (.bash_profile, .bash_login, .profile, .bashrc).

You mentioned a fresh install. What version of newinstall.sh (what URL) did you use, and what version of the stack did you install?

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#22

Thanks @ktl.

I do have the directory: /Users/blum/lsst_stack/python/miniconda3-4.7.10/envs/lsst-scipipe-4d7b902/bin/

But numpy is not there.

numpy conda package is here:

ls /Users/blum/lsst_stack/python/miniconda3-4.7.10/envs/lsst-scipipe-4d7b902/pkgs/nump*

numpy-1.16.2-py37hacdab7b_0
numpy-1.16.2-py37hacdab7b_0.conda
numpy-base-1.16.2-py37h6575580_0
numpy-base-1.16.2-py37h6575580_0.conda

Appears not to be installed in the bin directory?

#23

numpy does not belong in the bin directory. The point is for you to use the python in the envs/.../bin directory which will have access to the numpy in the pkgs directory.

#24

Check.

Yes, so the path to the envs version of python is in PATH but it comes after the miniconda/bin in the PATH. This appears after I execute setup obs_sdss.

#25

So I guess the issue is why does the path end up that way after running setup obs_sdss. If I always want the lsstpipe version of python while using the stack, I guess this is easy to fix manually.

#26

setup obs_sdss should prepend .../obs_sdss/.../bin: to your PATH. If it’s also prepending .../miniconda3-4.7.10/bin, something is quite strange.

Basically, which python or command -v python should always give a path with envs/lsst-scipipe in it. If it’s not, we need to figure out what is overriding it.

#27

as soon as I source loadLSST.bash, the paths are reversed and the envs/lsst-scipipe is second

#28

Interesting that is go to csh and source loadLSST.csh, the paths come out right.

#29

I seem to have resolved this. I disabled .bash_profile file that was setting up a conda environment from an independent conda installation.

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