CODEWITHSUNDEEP
pythontravis-ci
ericmjl
ericmjl

Reputation: 14724

Travis CI python imports do not work

On my project, I have issues with my test scripts on Travis CI. I installed the packages that I needed using conda, and then ran my test scripts. The build fails because of import errors. How can I fix this?

My travis YAML file is as such:

language: python
python:
  - "2.7"
  - "3.4"
  - "nightly"

# command to install dependencies
# setup anaconda
before_install:
  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
  - chmod +x miniconda.sh
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - conda update -y conda

# install packages
install:
  - conda install -y numpy scipy matplotlib networkx biopython
  - echo $PATH
  - which python


# command to run tests
script: py.test

One of my test scripts requires BioPython, and the test script fails because it cannot find biopython.

__________________ ERROR collecting test_genotype_network.py ___________________
test_genotype_network.py:1: in <module>
    import genotype_network as gn
genotype_network.py:1: in <module>
    from Bio import SeqIO
E   ImportError: No module named 'Bio'

Is there a way to fix this?

Upvotes: 2

Views: 626

Answers (1)

ericmjl
ericmjl

Reputation: 14724

Turns out the problem was py.test - I didn't install it in the conda environment. Adding pytest to the packages to install when creating the new environment made those import errors go away.

Upvotes: 1

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