我在 Ubuntu 14.04 Linux 上尝试安装软件包时运行了以下命令：
export PYTHONPATH=/usr/local/lib/python2.7/ && sudo python setup.py install
我试图安装的包是http://github.com/ewels/MultiQC
从那时起，很多与Python相关的事情都出了问题。例如，virtualenv 不再起作用，这个包也不起作用：
http://wiki.dnanexus.com/images/files/dx-toolkit-v0.240.1-ubuntu-14.04-amd64.tar.gz
source Downloads/dx-toolkit/environment
dx login
Traceback (most recent call last):
File "/home/avilella/Downloads/dx-toolkit/bin/dx", line 7, in <module>
from dxpy.scripts.dx import main
File "/home/avilella/Downloads/dx-toolkit/share/dnanexus/lib/python2.7/site-packages/dxpy/__init__.py", line 143, in <module>
from . import exceptions
File "/home/avilella/Downloads/dx-toolkit/share/dnanexus/lib/python2.7/site-packages/dxpy/exceptions.py", line 211, in <module>
network_exceptions = (requests.packages.urllib3.exceptions.ProtocolError,
AttributeError: 'module' object has no attribute 'packages'
如何将其恢复到运行此命令行之前的阶段？即使从新的 bash 终端开始，它现在也找不到我的任何其他 python 库。即使在同一台计算机上新创建的 Linux 用户，错误也是相同的。
相关问题未得到解答：修复损坏的 PYTHONPATH 环境变量
[编辑]
我不知道如何恢复到之前的文件夹列表，但我认为它是 /usr/lib/python2.7 和 /usr/local/lib/python2.7 的组合
尝试 virtualenv 现在也失败了：
virtualenv
Fatal Python error: Py_Initialize: Unable to get the locale encoding
File "/usr/lib/python2.7/encodings/__init__.py", line 123
raise CodecRegistryError,\
^
SyntaxError: invalid syntax
Aborted (core dumped)
交互式 python 可以在我下面尝试的范围内工作：
avilella@ubuntu14:~$ python
Python 2.7.6 (default, Oct 26 2016, 20:30:19)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> print "foo"
foo
>>> import urllib3
>>>
我现在已经浏览了该文件夹并尝试了以下两个pip install操作apt-get install python-${package}：
ls /usr/local/lib/python2.7/dist-packages/*/ | grep -v egg | grep '\:' | tr ':' ' ' | grep -v dist-info | xargs -n1 basename | while read i; do sudo pip install $i; done
还：
ls /usr/local/lib/python2.7/dist-packages/*/ | grep -v egg | grep '\:' | tr ':' ' ' | grep -v dist-info | xargs -n1 basename | while read i; do sudo apt-get install -y python-${i}; done
但仍然存在同样的问题。
包裹请求在那里：
ls -l /usr/lib/python2.7/dist-packages/requests/
total 304
-rw-r--r-- 1 root root 14594 Mar 26 2015 adapters.py
-rw-rw-r-- 1 root root 13750 Sep 4 16:05 adapters.pyc
-rw-r--r-- 1 root root 4333 Sep 24 2013 api.py
-rw-rw-r-- 1 root root 5261 Sep 4 16:05 api.pyc
-rw-r--r-- 1 root root 6173 Dec 5 2013 auth.py
-rw-rw-r-- 1 root root 7206 Sep 4 16:05 auth.pyc
-rw-r--r-- 1 root root 527 Mar 26 2015 certs.py
-rw-rw-r-- 1 root root 736 Sep 4 16:05 certs.pyc
-rw-r--r-- 1 root root 2531 Mar 26 2015 compat.py
-rw-rw-r-- 1 root root 2541 Sep 4 16:05 compat.pyc
-rw-r--r-- 1 root root 16686 Jan 8 2014 cookies.py
-rw-rw-r-- 1 root root 20167 Sep 4 16:05 cookies.pyc
-rw-r--r-- 1 root root 1599 Mar 26 2015 exceptions.py
-rw-rw-r-- 1 root root 3863 Sep 4 16:05 exceptions.pyc
-rw-r--r-- 1 root root 820 Sep 24 2013 hooks.py
-rw-rw-r-- 1 root root 1055 Sep 4 16:05 hooks.pyc
-rw-r--r-- 1 root root 1846 Mar 26 2015 __init__.py
-rw-rw-r-- 1 root root 2501 Sep 4 16:05 __init__.pyc
-rw-r--r-- 1 root root 25332 Mar 26 2015 models.py
-rw-rw-r-- 1 root root 23051 Sep 4 16:05 models.pyc
-rw-r--r-- 1 root root 22042 Mar 26 2015 sessions.py
-rw-rw-r-- 1 root root 18049 Sep 4 16:05 sessions.pyc
-rw-r--r-- 1 root root 3136 Sep 24 2013 status_codes.py
-rw-rw-r-- 1 root root 4439 Sep 4 16:05 status_codes.pyc
-rw-r--r-- 1 root root 3575 Sep 24 2013 structures.py
-rw-rw-r-- 1 root root 6359 Sep 4 16:05 structures.pyc
-rw-r--r-- 1 root root 19642 Mar 26 2015 utils.py
-rw-rw-r-- 1 root root 19386 Sep 4 16:05 utils.pyc
我检查了我拥有的另一个虚拟机的工作版本，其中与 python 相关的所有内容都可以工作，并且 requests 文件夹包含确切地相同的文件。
非工作 Linux 中对 urllib 的任何提及（如下）与工作 Linux 中的相同（下文进一步介绍），其中有 2 个文件在彼此之间更改了日期：
[ 4096 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3
[ 3346 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/_collections.pyc
[ 22000 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/connectionpool.pyc
[ 4096 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/contrib
[ 6015 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/exceptions.pyc
[ 6511 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/fields.pyc
[ 3162 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/filepost.pyc
[ 2074 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/__init__.pyc
[ 4096 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/packages
[ 9076 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/poolmanager.pyc
[ 5850 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/request.pyc
[ 9879 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/response.pyc
[ 19662 Sep 4 16:05] /usr/lib/python2.7/dist-packages/urllib3/util.pyc
[ 28639 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/connectionpool.py
[ 5961 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/fields.py
[ 2486 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/filepost.py
[ 10159 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/response.py
[ 20575 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/util.py
[ 1703 Sep 25 2013] /usr/lib/python2.7/dist-packages/urllib3/__init__.py
[ 3274 Sep 25 2013] /usr/lib/python2.7/dist-packages/urllib3/exceptions.py
[ 2898 Aug 14 2013] /usr/lib/python2.7/dist-packages/urllib3/_collections.py
[ 9009 Aug 14 2013] /usr/lib/python2.7/dist-packages/urllib3/poolmanager.py
[ 5874 Aug 14 2013] /usr/lib/python2.7/dist-packages/urllib3/request.py
[ 17079 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3-1.7.1.egg-info
[ 7142 Oct 5 14:47] /usr/lib/python2.7/lib2to3/fixes/fix_urllib.pyc
[ 8385 Oct 26 2016] /usr/lib/python2.7/lib2to3/fixes/fix_urllib.py
[ 46549 Oct 5 14:47] /usr/lib/python2.7/urllib2.pyc
[ 50626 Oct 5 14:47] /usr/lib/python2.7/urllib.pyc
[ 51788 Oct 26 2016] /usr/lib/python2.7/urllib2.py
[ 59371 Oct 26 2016] /usr/lib/python2.7/urllib.py
下面的工作：
[ 4096 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3
[ 3346 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/_collections.pyc
[ 22000 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/connectionpool.pyc
[ 4096 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/contrib
[ 6015 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/exceptions.pyc
[ 6511 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/fields.pyc
[ 3162 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/filepost.pyc
[ 2074 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/__init__.pyc
[ 4096 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/packages
[ 9076 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/poolmanager.pyc
[ 5850 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/request.pyc
[ 9879 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/response.pyc
[ 19662 Jul 10 9:06] /usr/lib/python2.7/dist-packages/urllib3/util.pyc
[ 28639 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/connectionpool.py
[ 5961 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/fields.py
[ 2486 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/filepost.py
[ 10159 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/response.py
[ 20575 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3/util.py
[ 1703 Sep 25 2013] /usr/lib/python2.7/dist-packages/urllib3/__init__.py
[ 3274 Sep 25 2013] /usr/lib/python2.7/dist-packages/urllib3/exceptions.py
[ 2898 Aug 14 2013] /usr/lib/python2.7/dist-packages/urllib3/_collections.py
[ 9009 Aug 14 2013] /usr/lib/python2.7/dist-packages/urllib3/poolmanager.py
[ 5874 Aug 14 2013] /usr/lib/python2.7/dist-packages/urllib3/request.py
[ 17079 Oct 12 2015] /usr/lib/python2.7/dist-packages/urllib3-1.7.1.egg-info
[ 46549 Jul 12 11:47] /usr/lib/python2.7/urllib2.pyc
[ 50626 Jul 12 11:47] /usr/lib/python2.7/urllib.pyc
[ 7142 Jul 12 11:47] /usr/lib/python2.7/lib2to3/fixes/fix_urllib.pyc
[ 8385 Oct 26 2016] /usr/lib/python2.7/lib2to3/fixes/fix_urllib.py
[ 51788 Oct 26 2016] /usr/lib/python2.7/urllib2.py
[ 59371 Oct 26 2016] /usr/lib/python2.7/urllib.py
另一个不再起作用的示例工具是tosheets https://github.com/kren1/tosheets:
tosheets
Traceback (most recent call last):
File "/usr/local/bin/tosheets", line 7, in <module>
from tosheets.tosheets import main
File "/usr/local/lib/python2.7/dist-packages/tosheets/tosheets.py", line 27, in <module>
from apiclient import discovery
ImportError: cannot import name discovery
做完之后unset PYTHON，然后：
>>> import sys
>>> sys.path
['', '/usr/local/lib/python2.7/dist-packages/multiqc-1.4dev-py2.7.egg', '/usr/lib/python2.7/dist-packages', '/usr/lib/pymodules/python2.7', '/home/avilella/Downloads/dx-toolkit/share/dnanexus/lib/python2.7/site-packages', '/home/avilella/Downloads/dx-toolkit/lib/python', '/home/avilella', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/home/avilella/.local/lib/python2.7/site-packages', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/python2.7/dist-packages/ubuntu-sso-client']
取消设置 PYTHON，即 python3：
>>> import sys
>>> sys.path
['', '/home/avilella/Downloads/dx-toolkit/share/dnanexus/lib/python2.7/site-packages', '/home/avilella/Downloads/dx-toolkit/lib/python', '/home/avilella', '/usr/lib/python3.4', '/usr/lib/python3.4/plat-x86_64-linux-gnu', '/usr/lib/python3.4/lib-dynload', '/usr/local/lib/python3.4/dist-packages', '/usr/lib/python3/dist-packages']
在进行任何源操作之前 $PYTHONPATH 的内容是空的。
其内容Downloads/dx-toolkit/environment如下：
# -*- Mode: shell-script -*-
#
# Copyright (C) 2013-2016 DNAnexus, Inc.
#
# This file is part of dx-toolkit (DNAnexus platform client libraries).
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy
# of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
#
#
# Source this file in a bash shell to initialize DNAnexus environment
# variables:
# $ source environment
# This line is compatible with both bash and csh/tcsh. If running in csh, it sources the file "environment.csh" and quits.
test ! -z "$version" && echo "$shell" | grep -q csh && set SOURCE=`echo $_ | cut -f 2 -d " "` && set SOURCE=`dirname "$SOURCE"` && source "$SOURCE/environment.csh" && exit
# Resolve the location of this file
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ] ; do SOURCE="$(readlink "$SOURCE")"; done
# Get RHEL version
if [ -e /etc/redhat-release ] ; then
RHEL_MAJOR_VERSION=$(grep -o "Red Hat Enterprise Linux .* release [0-9]\+" /etc/redhat-release | sed -e "s/Red Hat Enterprise Linux .* release //")
fi
export DNANEXUS_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
# Detect system installation of dx-toolkit
if [ "$DNANEXUS_HOME" == "/etc/profile.d" ]; then
export DNANEXUS_HOME="/usr/share/dnanexus"
# Private Python packages. We really ought not pollute PYTHONPATH with these though.
export PYTHONPATH="/usr/share/dnanexus/lib/python2.7/site-packages:$PYTHONPATH"
export CLASSPATH="/usr/share/java/dnanexus-api-0.1.0.jar:${CLASSPATH}"
else
export PATH="${DNANEXUS_HOME}/bin:$PATH"
export CLASSPATH="${DNANEXUS_HOME}/lib/java/*:${CLASSPATH}"
if [ "$RHEL_MAJOR_VERSION" == "7" ]; then
export PYTHONPATH="${DNANEXUS_HOME}/share/dnanexus/lib/python2.7/site-packages:${DNANEXUS_HOME}/lib64/python2.7/site-packages:$PYTHONPATH"
else
export PYTHONPATH="${DNANEXUS_HOME}/share/dnanexus/lib/python2.7/site-packages:${DNANEXUS_HOME}/lib/python:$PYTHONPATH"
fi
fi
# Note: The default I/O stream encoding in Python 2.7 (as configured on ubuntu) is ascii, not UTF-8 or the system locale
# encoding. We reset it here to avoid having to set it for every I/O operation explicitly.
export PYTHONIOENCODING=UTF-8
eval "$(register-python-argcomplete dx|sed 's/-o default//')"
# Clean up old session files
(shopt -s nullglob;
if [[ $HOME != "" ]]; then
for session_dir in "${HOME}/.dnanexus_config/sessions/"*; do
if ! ps -p $(basename "$session_dir") &> /dev/null; then
rm -rf "$session_dir"
fi
done
fi
)
if [[ -z "$DX_SECURITY_CONTEXT" && -n "$DX_AUTH_TOKEN" ]]; then
export DX_SECURITY_CONTEXT="{\"auth_token_type\":\"Bearer\",\"auth_token\":\"$DX_AUTH_TOKEN\"}"
fi
我有一个类似的 Ubuntu 14.04 VM 正在工作，是否可以将某些文件夹同步到它，以便非工作的 Ubuntu 14.04 恢复正常？
我似乎陷入了困境，不知道如何继续下去。
答案1
setup.py 的模式develop会将您的本地代码路径链接到PYTHONPATH.
如果你通过安装本地包
python setup.py develop
，这会改变系统PYTHONPATH并让你疯狂地从环境变量中删除它。
我找到了卸载它们并恢复默认设置的正确PYTHONPATH方法这里。您需要使用--uninstall或-u选项来开发，即：
python setup.py develop --uninstall
PS：如果第一次无法卸载该软件包，请尝试重新安装并再次卸载。
答案2
我发现唯一的解决方案是从头开始重新安装操作系统。