How do I keep track of pip-installed packages in an Anaconda (Conda) environment?

conda-env now does this automatically (if pip was installed with conda).

You can see how this works by using the export tool used for migrating an environment:

conda env export -n <env-name> > environment.yml

The file will list both conda packages and pip packages:

name: stats
channels:
  - javascript
dependencies:
  - python=3.4
  - bokeh=0.9.2
  - numpy=1.9.*
  - nodejs=0.10.*
  - flask
  - pip:
    - Flask-Testing

If you're looking to follow through with exporting the environment, move environment.yml to the new host machine and run:

conda env create -f path/to/environment.yml

conda will only keep track of the packages it installed. And pip will give you the packages that were either installed using the pip installer itself or they used setuptools in their setup.py so conda build generated the egg information. So you have basically three options.

1. You can take the union of the conda list and pip freeze and manage packages that were installed using conda (that show in the conda list) with the conda package manager and the ones that are installed with pip (that show in pip freeze but not in conda list) with pip.

2. Install in your environment only the python, pip and distribute packages and manage everything with pip. (This is not that trivial if you're on Windows...)

3. Build your own conda packages, and manage everything with conda.

I would personally recommend the third option since it's very easy to build conda packages. There is a git repository of example recipes on the continuum's github account. But it usually boils down to:

 conda skeleton pypi PACKAGE
 conda build PACKAGE

or just:

conda pipbuild PACKAGE

Also when you have built them once, you can upload them to https://binstar.org/ and just install from there.

Then you'll have everything managed using conda.