AttributeError: 'dict' object has no attribute 'split'

[sebastian-luna-valero]

Hi,

I get an AttributeError exception when doing:

bioconda-utils build recipes config.yml --mulled-test --packages cgat-scripts

Full output is here

I think the error was caused after adding a pip dependency on my meta.yaml file, like

requirements:
   build:
      - python 3.5
      - pip
         - bx-python==0.7.3

Do you know why?

Best regards,
Sebastian

[daler]

looks like you have an extra indentation on the bx-python line

[sebastian-luna-valero]

Sorry, I meant:

requirements:
   build:
      - python 3.5
      - pip:
         - bx-python==0.7.3

I guess, I should rephrase my question. How can I included pypi deps in the meta.yaml?

It works in a conda environment file.

EDIT: This is what I want to install:
https://pypi.python.org/pypi/bx-python/0.7.3

[sebastian-luna-valero]

@daler could you please let me know your thoughts on this issue?

[daler]

Ah, sorry I misunderstood. Pip dependencies work in a conda env file but this is not supported (that I know of) by conda when building recipes. Anyway I think it's better to have checksummed downloads be the only input to a recipe rather than arbitrary pip packages.

For a recipe, any deps need to be in either defaults, conda-forge, or bioconda channels. But if you're looking specifically for bx-python, it's in bioconda (https://anaconda.org/bioconda/bx-python).

[sebastian-luna-valero]

Thanks @daler

The thing is that our scripts depend on bx-python for certain tasks. We have ported our scripts from Py2 to Py3, but bx-python is not officially Py3 yet [1]. Therefore, the bioconda package is only Py2 [2]. However, we found that you can still pip install bx-python with Py3 and it does the job. Obviously this is a temporary solution until bx-python is fully ported to Py3.

On the other hand, I don't understand why pip dependencies are not supported when building recipes, if the version of the pip package is fixed. We need bx-python=0.7.3

Any suggestions?

[1] bxlab/bx-python#9
[2] bioconda/bioconda-recipes#1639

[daler]

If you run conda-build on your recipe directly, you will get an error like:

Received dictionary as spec. Note that pip requirements are not supported
in conda-build meta.yaml.

Installing from pip is not supported by conda-build for building packages from recipes. It's only supported by conda when building environments from requirements files.

An individual recipe can install from pip (that's how pretty much all python packages in bioconda are built). If you want bx-python on py3, then you need a working recipe and package for bx-python on py3. You can try getting a py3 package to run and pass tests, and work with upstream as necessary to get that to work.

[sebastian-luna-valero]

Thanks @daler