Conda activate fix and development environment

[sfarrens]

Summary

closes #651

Reviewer Checklist

Reviewers should tick the following boxes before approving and merging the PR.

• [ ] The PR targets the develop branch
• [ ] The PR is assigned to the developer
• [ ] The PR has appropriate labels
• [ ] The PR is included in appropriate projects and/or milestones
• [ ] The PR includes a clear description of the proposed changes
• [ ] If the PR addresses an open issue the description includes "closes #"
• [ ] The code and documentation style match the current standards
• [ ] Documentation has been added/updated consistently with the code
• [ ] All CI tests are passing
• [ ] API docs have been built and checked at least once (if relevant)
• [ ] All changed files have been checked and comments provided to the developer
• [ ] All of the reviewer's comments have been satisfactorily addressed by the developer

[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.