Running tests at circleci in conda environment

I use conda, and and trying to figure out how to get things running at circleci. I have a very simple project in an environment called calculator with two functions (one addition, one subtraction and one test for each). I am using pylint8 to check the formatting, and pytest/pytest-cov for testing/coverage.

My configuration file is as follows, which seems to be working until I reach the test-running stage:

# Python CircleCI 2.0 configuration file
version: 2
      - image: continuumio/miniconda3

    working_directory: ~/repo

      # Step 1: obtain repo from GitHub
      - checkout
      # Step 2: create virtual env and install dependencies
      - run:
          name: install dependencies
          command: |
            conda env create -f environment.yml

      # Step 3: run linter and tests
      - run:
          name: run tests
          command: |
            conda init bash
            conda activate calculator
            flake8 --statistics
            pytest -v --cov

Steps 1 and 2 work ok, but Step 3 gives a fail with the following message:

#!/bin/bash -eo pipefail
conda init bash
conda activate calculator
flake8 --statistics
pytest -v --cov
no change     /opt/conda/condabin/conda
no change     /opt/conda/bin/conda
no change     /opt/conda/bin/conda-env
no change     /opt/conda/bin/activate
no change     /opt/conda/bin/deactivate
no change     /opt/conda/etc/profile.d/
no change     /opt/conda/etc/fish/conf.d/
no change     /opt/conda/shell/condabin/Conda.psm1
no change     /opt/conda/shell/condabin/conda-hook.ps1
no change     /opt/conda/lib/python3.7/site-packages/xontrib/conda.xsh
no change     /opt/conda/etc/profile.d/conda.csh
modified      /root/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

I am in Ubuntu 18. I previously wasn't running conda init bash, but based on the error, I put it in there, but it is still suggesting I initialize my shell even though I already did this.

1 answer

  • answered 2019-11-14 07:48 orangeInk

    conda init bash changes your .bashrc which then would have to be reloaded.

    You could try it in this order

    conda init bash
    source ~/.bashrc
    conda activate calculator

    or simply try the old fashioned way of source activate calculator (without running conda init bash at all).