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我最近从 TravisCI 切换到 circleCI 2.0，当我尝试这样做时遇到了一个问题：export PATH="$MINICONDA/bin:$PATH"，它没有添加路径变量。
我尝试使用 SSH 连接对其进行调试。我首先检查了是否设置了路径变量（没有设置），后来我尝试手动设置它并且它起作用了。但是，自动执行构建时它不起作用。
这是错误消息：

 Complete output from command python setup.py egg_info: Traceback (most
 recent call last):   File "<string>", line 1, in <module>   File
 "/tmp/pip-build-m_klG2/snakemake/setup.py", line 13
     print("At least Python 3.5 is required.\n", file=sys.stderr)

它基本上看不到通过 conda 安装的 python (3.6) 并尝试pip install -r python-requirements.txt使用默认的 python (2.7) 运行命令。
我一定错过了一些东西，但我无法弄清楚。我在下面提供了完整的config.yml文件。如果您能解释这个问题，我将不胜感激。

 version: 2
 jobs:
   build:
     branches:
       only:
         -dev
     machine: true
     working_directory: ~/repo
     steps:
       - checkout
       - run:
           name: install miniconda
           command: |
             cd /home/circleci
             export MINICONDA=$HOME/miniconda
             export PATH="$MINICONDA/bin:$PATH"
             hash -r
             wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
             bash miniconda.sh -b -f -p $MINICONDA
             conda config --set always_yes yes
             conda update conda
             conda info -a
             conda create -n testenv python=3.6.0
             source activate testenv
       - run:
           name: install requirements
           command: |
             cd /home/circleci/repo
             pip install -r python-requirements.txt
             pip install pytest-ordering
       - run:
           name: download sample dataset
           command: |
             cd /home/circleci/repo/unit_tests/test_data
             wget http://cf.10xgenomics.com/samples/cell-exp/2.1.0/t_3k/t_3k_filtered_gene_bc_matrices.tar.gz
             tar -xvfz t_3k_filtered_gene_bc_matrices.tar.gz
       - run:
           name: run tests
           command: |
             cd /home/circleci/repo
             pytest ./unit_tests
       - store_artifacts:
           path: test-reports
           destination: test-reports
4

2 回答 2

3

最后，我使用docs 2.0中的 Interpolating Environment Variables 解决了这个问题。

脚步：

  1. 将环境变量附加到 ~/.bashrc
    echo 'export MINICONDA=$HOME/miniconda' >> ~/.bashrc

  2. 在要访问这些变量的规则中获取 ~/.bashrc
    source ~/.bashrc

配置文件：

    version: 2
    jobs:
      build:
        branches:
          only:
            -dev
        machine: true
        working_directory: ~/repo
        steps:
          - checkout
          - run:
              name: install miniconda
              command: |
                cd /home/circleci
                echo 'export MINICONDA=$HOME/miniconda' >> ~/.bashrc
                echo 'export PATH="$MINICONDA/bin:$PATH"' >> ~/.bashrc
                source ~/.bashrc
                hash -r
                wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
                bash miniconda.sh -b -f -p $MINICONDA
                conda config --set always_yes yes
                conda update conda
                conda info -a
                conda create -n testenv python=3.6.0
                echo 'source activate testenv' >> ~/.bashrc
                source ~/.bashrc
          - run:
              name: install requirements
              command: |
                source ~/.bashrc
                cd /home/circleci/repo
                # a requirement has install-time dependency on numpy
                pip install numpy
                pip install -r python-requirements.txt
                pip install pytest-ordering
          - run:
              name: download sample dataset
              command: |
                cd /home/circleci/repo/unit_tests/test_data
                wget http://cf.10xgenomics.com/samples/cell-exp/2.1.0/t_3k/t_3k_filtered_gene_bc_matrices.tar.gz
                tar -zxvf t_3k_filtered_gene_bc_matrices.tar.gz

          - run:
              name: run tests
              command: |
                source ~/.bashrc
                cd /home/circleci/repo
                pytest ./unit_tests
          - store_artifacts:
              path: test-reports
    destination: test-reports


  [1]: https://circleci.com/docs/2.0/env-vars/#interpolating-environment-variables
于 2018-05-17T15:55:06.733 回答
1

这似乎是environment flag的一个很好的用例。

- run:
    name: install miniconda
    environment:
      MINICONDA: $HOME/miniconda
      PATH: $MINICONDA/bin:$PATH
    command: |
      cd /home/circleci
      hash -r
      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
      bash miniconda.sh -b -f -p $MINICONDA
      conda config --set always_yes yes
      conda update conda
      conda info -a
      conda create -n testenv python=3.6.0
      source activate testenv
于 2018-05-17T11:56:36.863 回答