issue with pipx dependency conflicting with package dependency, Click

I’m running into an issue with the clokta package. It depends on Click. It seems like it is pipx thinks it is already installed because Click is a dependency of pipx itself.

Requirement already satisfied: click in /usr/local/Cellar/pipx/0.14.0.0/libexec/lib/python3.7/site-packages (from clokta) (7.0)

╰─ pipx install clokta --verbose
pipx > (run_pipx_command:134): Virtual Environment location is /Users/johria/.local/pipx/venvs/clokta
pipx > (run:97): running /usr/local/opt/python/bin/python3.7 -m venv --without-pip /Users/johria/.local/pipx/venvs/clokta
pipx > (run:97): running /Users/johria/.local/pipx/venvs/clokta/bin/python -m pip install clokta
Collecting clokta
  Using cached https://files.pythonhosted.org/packages/7c/de/02c8f5a51ebacea04e52745852a3dc691d40e78d0fdf0be9f53ea2855561/clokta-4.1.0-py3-none-any.whl
Collecting enum-compat (from clokta)
Collecting boto3 (from clokta)
  Using cached https://files.pythonhosted.org/packages/42/b5/03da45c451b4e7d31bc42e3b844cbb2e9fc6e8757705504d828a7295b27e/boto3-1.9.245-py2.py3-none-any.whl
Collecting beautifulsoup4 (from clokta)
  Using cached https://files.pythonhosted.org/packages/3b/c8/a55eb6ea11cd7e5ac4bacdf92bac4693b90d3ba79268be16527555e186f0/beautifulsoup4-4.8.1-py3-none-any.whl
Collecting keyring (from clokta)
  Using cached https://files.pythonhosted.org/packages/b1/08/ad1ae7262c8146bee3be360cc766d0261037a90b44872b080a53aaed4e84/keyring-19.2.0-py2.py3-none-any.whl
Collecting requests (from clokta)
  Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting configparser (from clokta)
  Using cached https://files.pythonhosted.org/packages/7a/2a/95ed0501cf5d8709490b1d3a3f9b5cf340da6c433f896bbe9ce08dbe6785/configparser-4.0.2-py2.py3-none-any.whl
Requirement already satisfied: click in /usr/local/Cellar/pipx/0.14.0.0/libexec/lib/python3.7/site-packages (from clokta) (7.0)
Collecting botocore<1.13.0,>=1.12.245 (from boto3->clokta)
  Using cached https://files.pythonhosted.org/packages/0e/84/b13b233a344de26796b7b457571c16f2b3d1fab8fb48931208d650cc4d97/botocore-1.12.245-py2.py3-none-any.whl
Collecting s3transfer<0.3.0,>=0.2.0 (from boto3->clokta)
  Using cached https://files.pythonhosted.org/packages/16/8a/1fc3dba0c4923c2a76e1ff0d52b305c44606da63f718d14d3231e21c51b0/s3transfer-0.2.1-py2.py3-none-any.whl
Collecting jmespath<1.0.0,>=0.7.1 (from boto3->clokta)
  Using cached https://files.pythonhosted.org/packages/83/94/7179c3832a6d45b266ddb2aac329e101367fbdb11f425f13771d27f225bb/jmespath-0.9.4-py2.py3-none-any.whl
Collecting soupsieve>=1.2 (from beautifulsoup4->clokta)
  Using cached https://files.pythonhosted.org/packages/5d/42/d821581cf568e9b7dfc5b415aa61952b0f5e3dede4f3cbd650e3a1082992/soupsieve-1.9.4-py2.py3-none-any.whl
Collecting entrypoints (from keyring->clokta)
  Using cached https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests->clokta)
  Using cached https://files.pythonhosted.org/packages/e0/da/55f51ea951e1b7c63a579c09dd7db825bb730ec1fe9c0180fc77bfb31448/urllib3-1.25.6-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests->clokta)
  Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests->clokta)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests->clokta)
  Using cached https://files.pythonhosted.org/packages/18/b0/8146a4f8dd402f60744fa380bc73ca47303cccf8b9190fd16a827281eac2/certifi-2019.9.11-py2.py3-none-any.whl
Collecting python-dateutil<3.0.0,>=2.1; python_version >= "2.7" (from botocore<1.13.0,>=1.12.245->boto3->clokta)
  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Collecting docutils<0.16,>=0.10 (from botocore<1.13.0,>=1.12.245->boto3->clokta)
  Using cached https://files.pythonhosted.org/packages/22/cd/a6aa959dca619918ccb55023b4cb151949c64d4d5d55b3f4ffd7eee0c6e8/docutils-0.15.2-py3-none-any.whl
Collecting six>=1.5 (from python-dateutil<3.0.0,>=2.1; python_version >= "2.7"->botocore<1.13.0,>=1.12.245->boto3->clokta)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Installing collected packages: enum-compat, six, python-dateutil, jmespath, urllib3, docutils, botocore, s3transfer, boto3, soupsieve, beautifulsoup4, entrypoints, keyring, idna, chardet, certifi, requests, configparser, clokta
Successfully installed beautifulsoup4-4.8.1 boto3-1.9.245 botocore-1.12.245 certifi-2019.9.11 chardet-3.0.4 clokta-4.1.0 configparser-4.0.2 docutils-0.15.2 entrypoints-0.3 enum-compat-0.0.2 idna-2.8 jmespath-0.9.4 keyring-19.2.0 python-dateutil-2.8.0 requests-2.22.0 s3transfer-0.2.1 six-1.12.0 soupsieve-1.9.4 urllib3-1.25.6
pipx > (_symlink_package_apps:551): Same path /Users/johria/.local/bin/clokta and /Users/johria/.local/pipx/venvs/clokta/bin/clokta
  installed package clokta 4.1.0, Python 3.7.4
  These apps are now globally available
    - clokta
done! ✨ 🌟 ✨

This is installed via the latest homebrew release.

$ clokta --version
clokta, version 4.1.0

[cs01]

It looks fine to me. If you make the change in a PR and the unit tests still pass then I will merge it.

[AlJohri]

as a quick proof of concept, this patch fixes the issue:

diff --git a/pipx/util.py b/pipx/util.py
index 94732d8..ba27eee 100644
--- a/pipx/util.py
+++ b/pipx/util.py
@@ -93,11 +93,12 @@ def get_site_packages(python: Path) -> Path:
 def run(cmd: Sequence[Union[str, Path]], check=True) -> int:
     """Run arbitrary command as subprocess"""
 
+    env = {k:v for k,v in os.environ.items() if k != 'PYTHONPATH'}
     cmd_str = " ".join(str(c) for c in cmd)
     logging.info(f"running {cmd_str}")
     # windows cannot take Path objects, only strings
     cmd_str_list = [str(c) for c in cmd]
-    returncode = subprocess.run(cmd_str_list).returncode
+    returncode = subprocess.run(cmd_str_list, env=env).returncode
     if check and returncode:
         raise PipxError(f"{cmd_str!r} failed")
     return returncode