Conda activate fix and development environment

[sfarrens]

Summary

closes #651

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[sfarrens]

Hi @martinkilbinger, after discussing with @cailmdaley we decided to move towards a Conda-free distribution of ShapePipe. Therefore, I think this PR can be merged as it is to have a stable installation with passing CI in the develop branch. Don't be scared by the number of changed files as this just because I have moved everything into a src directory to better fit the current community standard.

The default environment.yml has not been properly checked, but this will be dropped soon anyway. Anyone wishing to install ShapePipe in the meantime can just install the development environment.

./install_shapepipe --env-dev

If all looks good to you, we can merge and @cailmdaley can create a new branch from develop.