sys.path will use user site-packages over the environment's site-packages

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#171 创建于 2018年3月14日 13 条评论 8 个 reaction 已指派 0 人在 GitHub 查看

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还没有人认领这个 Issue。

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难度: 4/5
预计耗时: 3-5 天
新手友好度: 35/100

Issue 类型: 缺陷
描述清晰度: 需要澄清
活跃度: 停滞
技术栈: python
领域: build-system

调研方向

使用 issue 中所示的 user-site 设置和命令，分别在 root 和全新的 conda 环境中检查 sys.path，以复现所报告的行为。阅读 PEP 370 和 Python site-path 初始化入口；完成的标准是环境的 site-packages 没有被 user site-packages 意外遮蔽。

由索引模型根据 Issue 内容生成。

描述

Hello,

I'm following up on a recommendation from @jakirkham in the R-base feedstock in this issue:
https://github.com/conda-forge/r-base-feedstock/issues/37 where we see similar behavior in R with respect to .libPaths().

According to PEP 370 there are platform-specific paths in which users can install packages which will be included in sys.path. The unfortunate result is that if you have a package installed there, it may be incompatible with a given conda environment's binaries and cause issues. Worse, the user-package is always preferred in import-order, so this will impact every environment (including root).

I'm kind of torn as to whether this is or is not a bug, but I'm reporting it in any case for further discussion.

Here is a demonstration showing this in a root environment from defaults and a conda-forge environment using the Python from this feedstock.

boring conda-info for completeness

16:33:55 ~
§ conda info

     active environment : None
       user config file : /home/evan/.condarc
 populated config files : 
          conda version : 4.4.11
    conda-build version : 3.0.28
         python version : 3.6.1.final.0
       base environment : /opt/Miniconda3  (read only)
           channel URLs : https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
          package cache : /opt/Miniconda3/pkgs
                          /home/evan/.conda/pkgs
       envs directories : /home/evan/.conda/envs
                          /opt/Miniconda3/envs
               platform : linux-64
             user-agent : conda/4.4.11 requests/2.14.2 CPython/3.6.1 Linux/4.15.7-1-ARCH arch/ glibc/2.26
                UID:GID : 1000:100
             netrc file : None
           offline mode : False

Set up the user-site packages and add a Hello World package:

16:33:59 ~
§ mkdir -p ~/.local/lib/python3.6/site-packages
16:34:07 ~
§ echo "print('Hello World')" > ~/.local/lib/python3.6/site-packages/hello.py

Try it in the root environment:

16:34:13 ~
§ which python
/opt/Miniconda3/bin/python
16:34:20 ~
§ python
Python 3.6.1 |Continuum Analytics, Inc.| (default, May 11 2017, 13:09:58) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/opt/Miniconda3/lib/python36.zip', '/opt/Miniconda3/lib/python3.6', '/opt/Miniconda3/lib/python3.6/lib-dynload', '/home/evan/.local/lib/python3.6/site-packages', '/opt/Miniconda3/lib/python3.6/site-packages']
>>>             
>>> import hello
Hello World
>>>

Note the end of sys.path: '/home/evan/.local/lib/python3.6/site-packages', '/opt/Miniconda3/lib/python3.6/site-packages'] the .local site-packages takes precedence over the environment's.

Try it in a fresh conda-forge environment:

16:34:40 ~
§ conda create -n example -c conda-forge python=3.6

Boring output of install plan

Solving environment: done

## Package Plan ##

  environment location: /home/evan/.conda/envs/example

  added / updated specs: 
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2018.1.18          |           py36_0         143 KB  conda-forge
    setuptools-38.5.2          |           py36_0         525 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         668 KB

The following NEW packages will be INSTALLED:

    ca-certificates: 2018.1.18-0      conda-forge
    certifi:         2018.1.18-py36_0 conda-forge
    ncurses:         5.9-10           conda-forge
    openssl:         1.0.2n-0         conda-forge
    pip:             9.0.1-py36_1     conda-forge
    python:          3.6.4-0          conda-forge
    readline:        7.0-0            conda-forge
    setuptools:      38.5.2-py36_0    conda-forge
    sqlite:          3.20.1-2         conda-forge
    tk:              8.6.7-0          conda-forge
    wheel:           0.30.0-py36_2    conda-forge
    xz:              5.2.3-0          conda-forge
    zlib:            1.2.11-0         conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
certifi 2018.1.18: ##################################################### | 100% 
setuptools 38.5.2: ##################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate example
#
# To deactivate an active environment, use:
# > source deactivate
#

Run the same test:

16:35:21 ~
§ source activate example
(example) 16:35:27 ~
§ which python
/home/evan/.conda/envs/example/bin/python
(example) 16:35:29 ~
§ python
Python 3.6.4 | packaged by conda-forge | (default, Dec 23 2017, 16:31:06) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/home/evan/.conda/envs/example/lib/python36.zip', '/home/evan/.conda/envs/example/lib/python3.6', '/home/evan/.conda/envs/example/lib/python3.6/lib-dynload', '/home/evan/.local/lib/python3.6/site-packages', '/home/evan/.conda/envs/example/lib/python3.6/site-packages']
>>> 
>>> import hello
Hello World
>>>

Same behavior for .local site-packages as in root.

主要语言: Shell
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sys.path will use user site-packages over the environment's site-packages

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