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scipion-em / scipion-installer

Scipion app installer for version 3. Compatible with python2 and python3. It creates virtualenv or conda environments.
GNU General Public License v3.0
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scipion3 not found #12

Closed DStrelak closed 2 months ago

DStrelak commented 4 years ago

Steps to reproduce:

installscipion -conda -dev ~/git/scipion3 -httpsClone
cd git/scipion3/xmipp-bundle
conda activate .scipion3env
./xmipp

results in No scipion3 found. If you intended to use Xmipp in the Scipion framework, check the binding at SCIPION_HOME/software/binding...

Expectation: Scipion3 should be in the environment path. No error should be reported

pconesa commented 4 years ago

Do you expect to have SCIPION_HOME define when you activate the environment? It would be nice ... Is it possible?

Do you mean something else?

dmaluenda commented 4 years ago

We can link the scipion3 script in the environ/bin in order to get ot visible when the environ is actived.

On the other hand, an alternative is to run xmipp by using the scipion3 as wraper, just after the installation (no activation is needed):

./scipion3 run xmipp-bundle/xmipp [args]

In this way, the wraper activates the environ and properly sets the env.vars. for the xmipp command.

DStrelak commented 4 years ago

I think it would be cleaner to have Scipion home set in the environment, but I'll leave it up to you.

dmaluenda commented 4 years ago

Is it possible to set an enviromemtal variable while activating the virtualenv? TBH, I don't know. But if possible, it makes sense.

On the other hand, I think linking the scipion3 launcher in the env/bin also makes sense.

However, the 'usual' way to run commands under scipion's environ is by using the wrapper 'scipion3 run'.

pconesa commented 4 years ago

This is a developer issue. I do not expect regular users to activate the environment.

As developers....there are many ways to do this, once you know it.