pipenv clean doesn't uninstall package not specified in Pipfile.lock

[HuangShaoyan]

Issue description

pipenv clean doesn't uninstall package not specified in Pipfile.lock.

Expected result

pipenv clean should uninstall all packages not specified in Pipfile.lock only.

Actual result

pipenv clean doesn't uninstall package that not specify in Pipfile.lock, but always show uninstalling package "pipenv" and "virtualenv".

$ pipenv clean -v
Ignoring 'pip'.
Ignoring 'setuptools'.
Ignoring 'wheel'.
Uninstalling 'virtualenv'…
Uninstalling 'virtualenv-clone'…
Uninstalling 'pipenv'…
Uninstalling 'certifi'…                                                                                                                                                     

Steps to replicate

1. install package sh
   $ pipenv install sh

2. pip list it

   $ pipenv run pip list
   Package    Version
   ---------- -------
   pip        18.1
   setuptools 40.4.3
   sh         1.12.14
   wheel      0.32.1

   I can't use pipenv graph to show dependencies. It is still broken. Please refer to pipenv graph fails: No module named 'pipenv' #2952

   Pipfile:

   [packages]
   sh = "*"
   

3. comment package sh in Pipfile
   Pipfile:

   [packages]
   # sh = "*"
   

4. clean

   $ pipenv clean -v
   Ignoring 'pip'.
   Ignoring 'setuptools'.
   Ignoring 'wheel'.
   Uninstalling 'virtualenv'…
   Uninstalling 'virtualenv-clone'…
   Uninstalling 'pipenv'…
   Uninstalling 'certifi'…

   package "sh" not uninstall

   $ pipenv run pip list
   Package    Version
   ---------- -------
   pip        18.1
   setuptools 40.4.3
   sh         1.12.14
   wheel      0.32.1

---

$ pipenv --support

Pipenv version: '2018.10.9'

Pipenv location: '/usr/local/Cellar/pipenv/2018.10.9/libexec/lib/python3.7/site-packages/pipenv'

Python location: '/usr/local/Cellar/pipenv/2018.10.9/libexec/bin/python3.7'

Python installations found:

• 3.7.0: /Users/huangshaoyan/.pyenv/versions/3.7.0/bin/python3.7
• 3.7.0: /Users/huangshaoyan/.pyenv/versions/3.7.0/bin/python3.7m
• 3.7.0: /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/bin/python3.7
• 3.7.0: /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/bin/python3.7m
• 3.6.5: /Users/huangshaoyan/.pyenv/shims/python3
• 3.6.5: /Users/huangshaoyan/.pyenv/shims/python
• 3.6.5: /Users/huangshaoyan/.pyenv/shims/python3.6
• 3.6.5: /Users/huangshaoyan/.pyenv/shims/python3.6m
• 3.6.5: /Users/huangshaoyan/.pyenv/versions/3.6.5/bin/python3.6
• 3.6.5: /Users/huangshaoyan/.pyenv/versions/3.6.5/bin/python3.6m
• 3.6.4: /Users/huangshaoyan/.pyenv/versions/3.6.4/bin/python3.6
• 3.6.4: /Users/huangshaoyan/.pyenv/versions/3.6.4/bin/python3.6m
• 3.6.3: /Users/huangshaoyan/.pyenv/versions/3.6.3/bin/python3.6
• 3.6.3: /Users/huangshaoyan/.pyenv/versions/3.6.3/bin/python3.6m
• 3.6.1: /Users/huangshaoyan/.pyenv/versions/3.6.1/bin/python3.6
• 3.6.1: /Users/huangshaoyan/.pyenv/versions/3.6.1/bin/python3.6m
• 3.5.2: /Users/huangshaoyan/.pyenv/versions/3.5.2/bin/python3.5
• 3.5.2: /Users/huangshaoyan/.pyenv/versions/3.5.2/bin/python3.5m
• 2.7.15: /usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
• 2.7.14: /Users/huangshaoyan/.pyenv/versions/2.7.14/bin/python2.7
• 2.7.10: /usr/bin/python
• 2.7.10: /usr/bin/pythonw
• 2.7.10: /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7

PEP 508 Information:

{'implementation_name': 'cpython',
 'implementation_version': '3.7.0',
 'os_name': 'posix',
 'platform_machine': 'x86_64',
 'platform_python_implementation': 'CPython',
 'platform_release': '18.0.0',
 'platform_system': 'Darwin',
 'platform_version': 'Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT '
                     '2018; root:xnu-4903.201.2~1/RELEASE_X86_64',
 'python_full_version': '3.7.0',
 'python_version': '3.7',
 'sys_platform': 'darwin'}

System environment variables:

• PATH
• MANPATH
• rvm_use_flag
• SSH_AGENT_PID
• rvm_bin_path
• TERM_PROGRAM
• rvm_quiet_flag
• GEM_HOME
• NVM_CD_FLAGS
• PIPENV_PYTHON
• PYENV_ROOT
• ANDROID_HOME
• rvm_gemstone_url
• TERM
• SHELL
• rvm_docs_type
• IRBRC
• TMPDIR
• NVM_PATH
• Apple_PubSub_Socket_Render
• TERM_PROGRAM_VERSION
• SELENIUM_CDNURL
• rvm_hook
• MY_RUBY_HOME
• TERM_SESSION_ID
• SDKMAN_PLATFORM
• ZSH
• NVM_DIR
• USER
• rvm_gemstone_package_file
• _system_type
• SDKMAN_CANDIDATES_API
• rvm_path
• SSH_AUTH_SOCK
• __CF_USER_TEXT_ENCODING
• rvm_proxy
• rvm_ruby_file
• PAGER
• MAVEN_OPTS
• LSCOLORS
• rvm_silent_flag
• rvm_prefix
• rvm_ruby_make
• _
• NVM_NODEJS_ORG_MIRROR
• PWD
• CHROMEDRIVER_CDNURL
• rvm_sdk
• LANG
• SDKMAN_VERSION
• ITERM_PROFILE
• _system_arch
• XPC_FLAGS
• AUTOJUMP_DATA_DIR
• _system_version
• XPC_SERVICE_NAME
• rvm_version
• rvm_script_name
• rvm_pretty_print_flag
• PYENV_SHELL
• SHLVL
• HOME
• COLORFGBG
• rvm_ruby_mode
• PHANTOMJS_CDNURL
• ITERM_SESSION_ID
• LESS
• LOGNAME
• rvm_alias_expanded
• GROOVY_HOME
• SDKMAN_DIR
• rvm_wrapper_name
• GEM_PATH
• LC_CTYPE
• NVM_BIN
• rvm_nightly_flag
• NVM_IOJS_ORG_MIRROR
• rvm_ruby_make_install
• SDKMAN_CANDIDATES_DIR
• ANDROID_NDK_HOME
• rvm_niceness
• DISPLAY
• rvm_ruby_bits
• rvm_bin_flag
• rvm_only_path_flag
• RUBY_VERSION
• _system_name
• COLORTERM
• PYTHONDONTWRITEBYTECODE
• PIP_SHIMS_BASE_MODULE
• PIP_PYTHON_PATH

Pipenv–specific environment variables:

• PIPENV_PYTHON: /Users/huangshaoyan/.pyenv/shims/python

Debug–specific environment variables:

• PATH: /usr/local/Cellar/pipenv/2018.10.9/libexec/tools:/Users/huangshaoyan/.rvm/gems/ruby-2.4.1/bin:/Users/huangshaoyan/.rvm/gems/ruby-2.4.1@global/bin:/Users/huangshaoyan/.rvm/rubies/ruby-2.4.1/bin:/Users/huangshaoyan/.pyenv/shims:/Users/huangshaoyan/.sdkman/candidates/groovy/current/bin:/Users/huangshaoyan/.nvm/versions/node/v8.12.0/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/deployd/bin:/usr/local/go/bin:/usr/local/opt/android-ndk/bin:/Users/huangshaoyan/.rvm/bin
• SHELL: /bin/zsh
• LANG: en_US.UTF-8
• PWD: /Users/huangshaoyan/workspace/pipenvbug

---

Contents of Pipfile ('/Users/huangshaoyan/workspace/pipenvbug/Pipfile'):

[[source]]
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"

[packages]
sh = "*"

[dev-packages]

[requires]
python_version = "3.6"

Contents of Pipfile.lock ('/Users/huangshaoyan/workspace/pipenvbug/Pipfile.lock'):

{
    "_meta": {
        "hash": {
            "sha256": "0d85e69ff0ba710b723eeb2afa6eccc783788971ac59f87a764a116203ddb902"
        },
        "pipfile-spec": 6,
        "requires": {
            "python_version": "3.6"
        },
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.org/simple",
                "verify_ssl": true
            }
        ]
    },
    "default": {
        "sh": {
            "hashes": [
                "sha256:ae3258c5249493cebe73cb4e18253a41ed69262484bad36fdb3efcb8ad8870bb",
                "sha256:b52bf5833ed01c7b5c5fb73a7f71b3d98d48e9b9b8764236237bdc7ecae850fc"
            ],
            "index": "pypi",
            "version": "==1.12.14"
        }
    },
    "develop": {}
}

Contents of Pipfile.lock after comment out package "sh":

{
    "_meta": {
        "hash": {
            "sha256": "415dfdcb118dd9bdfef17671cb7dcd78dbd69b6ae7d4f39e8b44e71d60ca72e7"
        },
        "pipfile-spec": 6,
        "requires": {
            "python_version": "3.6"
        },
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.org/simple",
                "verify_ssl": true
            }
        ]
    },
    "default": {},
    "develop": {}
}

[uranusjr]

(Misread the issue. Please ignore.)

[techalchemy]

pipenv clean is also fixed in master. Sorry for the difficulty, see #2976