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AllenNeuralDynamics / exa-spim-control

Acquisition control for the exaSPIM microscope system
MIT License
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Could not install #61

Closed nvladimus closed 3 months ago

nvladimus commented 3 months ago

Hi, everyone, I wanted to run the code in simulated mode, but the installation didn't succeed. I created a clean conda env (python 3.7) and tried to install there following the instructions, but pip install -e . failed due to permission denied issues: image

I also tried to install the spim-core manually, but that also failed: image

Is this a config issue, or some repositories remain private? Or am I doing something dumb? Many thanks! Nikita

aliddell commented 3 months ago

@nvladimus have you associated your SSH key with your GitHub account? If you don't want to do that it might be better to change the repos in the dependencies to use HTTPS rather than SSH. Both of them are public, so that shouldn't be the problem.

So you could try changing lines 25-26 in pyproject.toml to

    "tigerasi @ git+https://github.com/AllenNeuralDynamics/TigerASI.git@main#egg=TigerASI",
    "spim_core @ git+https://github.com/AllenNeuralDynamics/spim-core.git@main#egg=spim_core",

It almost worked for me. But here's what I get:

ERROR: Cannot install exaspim and exaspim==0.1.0 because these package versions have conflicting dependencies.

The conflict is caused by:
    exaspim 0.1.0 depends on tigerasi 0.0.26 (from git+https://github.com/AllenNeuralDynamics/TigerASI.git@main#egg=TigerASI)
    spim-core 0.1.0 depends on tigerasi 0.0.26 (from git+ssh://****@github.com/AllenNeuralDynamics/TigerASI.git@main#egg=TigerASI)

exaspim wants https and spim-core wants ssh. So what I'd suggest is to generate an SSH key pair and associate it with your GitHub account. Then it should work for you. Note for the maintainers, all those URLs in the pyproject.toml files for each project could change to https and avoid issues like this in the future.

nvladimus commented 3 months ago

Many thanks, I will try that!

adamkglaser commented 3 months ago

Hey @nvladimus. Apologies for the troubles, this repository has not been updated in quite some time. It is also inactive, we have been working on new repositories over the last 6+ months with new acquisition software. It would be best to dive into these if helpful/useful. Documentation and commenting in the code is scarce but coming soon to hopefully make it more usable by others.

Hardware driver repo that will construct a microscope from a configuration YAML file + classes for data writing https://github.com/AllenNeuralDynamics/voxel/tree/main

GUI repo that builds upon the generated instrument object https://github.com/AllenNeuralDynamics/view

ExA-SPIM specific repo that uses both of the above https://github.com/AllenNeuralDynamics/exaspim-control

nvladimus commented 3 months ago

Thanks, looks very cool! It wasn't obvious that there are exa-spim-control vs exaspim-control repos =)