为什么PyPi (pip)在卸载包时会尝试删除站点包？

Question

下面是我尝试卸载包时会发生的情况：

(soothsayer_py3.8_env) jespinozlt2-osx:Prototype jespinoz$ pip uninstall soothsayer
Found existing installation: soothsayer 2020.5.1
Uninstalling soothsayer-2020.5.1:
  Would remove:
    /Users/jespinoz/anaconda3/envs/soothsayer_py3.8_env/bin/clairvoyance.py
    /Users/jespinoz/anaconda3/envs/soothsayer_py3.8_env/bin/run_soothsayer.py
    /Users/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/
  Would not remove (might be manually added):
    /Users/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/soothsayer-2020.5.1.dist-info/Icon

这是setup.py

import re, datetime
from setuptools import setup, find_packages

# Version
version = None
with open("./soothsayer/__init__.py", "r") as f:
    for line in f.readlines():
        line = line.strip()
        if line.startswith("__version__"):
            version = line.split("=")[-1].strip().strip('"')
assert version is not None, "Check version in soothsayer/__init__.py"

setup(name='soothsayer',
      version=version,
      description='High-level API for (bio-)informatics',
      url='https://github.com/jolespin/soothsayer',
      author='Josh L. Espinoza',
      author_email='jespinoz@jcvi.org',
      license='BSD-3',
      packages=find_packages(include=("*", "./*")),
      install_requires=[
    "matplotlib >= 2.2.2",
    "scipy >= 1.0",
    "scikit-learn >= 0.20.2",
    "numpy >= 1.13", #, < 1.14.0",
    'pandas >= 1.0',
    'networkx >= 2.0',
    'ete3 >= 3.0',
    'scikit-bio >= 0.5.1',
    "biopython >= 1.5",
    "xarray >= 0.10.3",
    "tqdm >=4.19",
    "openpyxl >= 2.5",
    # "astropy >= 3.0",
    "rpy2 >= 2.9.4, < 3.0",
    "matplotlib_venn",
    "palettable >= 3.0.0",
    "adjustText",
    "tzlocal",
    "statsmodels >= 0.10.0", #https://github.com/statsmodels/statsmodels/issues/5899 May need to use this separately: pip install git+https://github.com/statsmodels/statsmodels.git@maintenance/0.10.x
    "teneto",
    "mmh3",
    "soothsayer_utils >= 2020.4.30",

      ],
     include_package_data=True,
     scripts=['bin/clairvoyance.py', "bin/run_soothsayer.py"],


)

这是我的manifest.in

recursive-include soothsayer/io/data_type/ *.py
recursive-include soothsayer/feature_extraction/algorithms/ *.py
recursive-include soothsayer/r_wrappers/packages/ *.py
recursive-include soothsayer/tests/data/ *.py
recursive-include soothsayer/db/ *.pbz2
recursive-exclude releases/ *.tar.gz
global-exclude *.py[cod] __pycache__

以下是我的pip版本：

pip 20.1 from /Users/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/pip (python 3.8)

我好像想不出来？有没有人知道是什么导致了这个问题？

Answer 1

我假设导致问题的项目的PyPI页面和源代码存储库如下所示：

• https://pypi.org/project/soothsayer/
• https://github.com/jolespin/soothsayer

在源代码存储库的根目录下有一个名称包含异常字符的文件。它有时看起来像'Icon'$'\r'。该文件似乎也存在于soothsayer.egg-info目录的source distribution for 中。因此，当pip安装该发行版时，它会以某种方式生成正在安装的文件的奇怪记录：

$ pip show --files soothsayer
Name: soothsayer
Version: 2020.5.4
Summary: High-level package for (bio-)informatics
Home-page: https://github.com/jolespin/soothsayer
Author: Josh L. Espinoza
Author-email: jespinoz@jcvi.org
License: BSD-3
Location: /tmp/tmp.YDoTgEDb9A/.venv/lib/python3.6/site-packages
Requires: networkx, teneto, palettable, matplotlib-venn, rpy2, xarray, ete3, biopython, tqdm, pandas, scikit-learn, scipy, numpy, scikit-bio, openpyxl, mmh3, matplotlib, statsmodels, adjustText, soothsayer-utils, tzlocal
Required-by: 
Files:
  "
  "soothsayer-2020.5.4.dist-info/Icon
  .
  ../../../bin/__pycache__/clairvoyance.cpython-36.pyc
  ../../../bin/__pycache__/run_soothsayer.cpython-36.pyc
  ../../../bin/clairvoyance.py
  ../../../bin/run_soothsayer.py
  soothsayer-2020.5.4.dist-info/INSTALLER
  soothsayer-2020.5.4.dist-info/Icon
  soothsayer-2020.5.4.dist-info/METADATA
  soothsayer-2020.5.4.dist-info/RECORD
  soothsayer-2020.5.4.dist-info/WHEEL
  soothsayer-2020.5.4.dist-info/top_level.txt
  soothsayer/__init__.py

在上面，请注意第一个记录的3个Files。这些记录显然是错的。特别是，第三行可能会导致pip打算删除site-packages目录。

我建议那个占卜者项目的所有者应该：

• 找出这些文件是如何创建的，并在所有分支中禁用创建这些文件的软件所有分支中的源代码存储库，以防止在将来的releases
• publish维护或错误修复版本中发生这种情况。对于所有有故障的发行版和所有有故障的发行版，请参阅PyPI PyPI

上发布的类似索引

更新

经过进一步检查，似乎在源代码存储库的每个目录中都有一个类似的异常命名的Icon文件，这些文件很可能也需要消失(除了该存储库中的许多其他不寻常的东西之外)。