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copip: conda-pip environment development overlays

A tool to better manage PyPI and source packages (installed using pip, with or without -e .) in a conda-based workflow.

The approach taken is to create a separate filesystem area where all non-conda installations go. Then, we "hijack" the --user flag of Python's installation process by always using --user during any pip-based installation. When using the conda root environment such area already exists: ~/.local/... (on *nix, there's a Windows-specific location too). When using custom conda environments, we set the $PYTHONUSERBASE variable to point to a location named the same as the conda environment but separate in the filesystem, and set $PATH accordingly.

This avoids the problem of conflicts arising after packages have been added to a conda environment and a conda update potentially overwrites them.

I have used this a fair amount for a few months, and so far it hasn't failed me. As usual, caveat emptor.

Setup

There's no packaging/installation yet. For now, you need to:

  • symlink/copy the mkcopip command somewhere in your $PATH.

Usage

Assuming your paths are properly set up as above, you can use this to manage an overlay on your conda env foo by running

mkcopip foo

Since this tool is designed to direct all pip installs to the user overlay, it sets the environment variable PIP_USER=True unconditionally on environment activation.

If you want to have the same behavior in your root conda env, you should:

  • Also set PIP_USER=True in your regular shell config file ( ~/.bashrc or equivalent).

  • Ensure that ~/.local/bin is in your PATH, so that script entry points installed by new packages are also found first.

Todo

Besides packaging/configurability, the key thing to test next is usage with complex C extensions built this way. That requires setting lots more environment variables related to compilers, linkers, etc. I have old code for that which can be reused if there's interest.

Requirements

The 'driver' script is Python 3.6-only. This would be easy to avoid, but I wanted to use it as an opportunity to play with some Python 3.6-specific features, like f-strings and standard library support for pathlib. The resulting code is indeed nicer, so I'm keeping it that way.

Advanced: cactivate with a sub-shell

I personally prefer to run my environments in a brand-new subshell. By having a subshell, I'm guaranteed to get back to my parent environment 100% unmodified once I'm done with the environment I activated, since exiting a sub-shell destroys any env. variables or other context. This is much more robust than trusting that source deactivate will do the right thing in all cases.

For this, I use the cactivate shell script included here helps, but I haven't made it portable yet. If you want to test this approach, you'll need to:

  • modify the cactivate shell script to include your path to the bash_condarc path on your system.

  • symlink the cactivate script somewhere in your $PATH.

Then, when you want to use environment foo, instead of source activate foo, you should run source cactivate foo (note the 'c'). This will activate your environment in a subshell, which you can terminate to exit the environment (no need to run source deactivate, you simply exit the subshell).

License

Released under the terms of the 3-clause ("new") BSD license.