Locking fails, preempting pipenv clean and pipenv uninstall

[irenatfh]

Issue description

I'm cloning a repo that automatically creates a Pipenv shell and install pandas. Locking fails because (based on my understanding of the errors) installing pandas automatically installs numpy, and there's some issue with the newest version of numpy and Macs. I thought I could get around this by uninstalling numpy with pipenv uninstall numpy, but locking failed again. I checked that there is no version of numpy listed in the Pipfile.lock, and tried to run pipenv clean. But that also failed, throwing the same error message I obtained when trying to install pandas and also when trying to uninstall numpy. When I run pip freeze from within the pipenv shell, numpy is still listed even though nothing is specified about numpy in Pipfile.lock. How can I uninstall a package with Pipenv if failure to lock makes it impossible to run pipenv clean and also pipenv uninstall?

Expected result

To be able to run pipenv clean and remove specific packages with pipenv uninstall

Actual result

I keep getting the following lock error when I try to run pipenv install pandas, pipenv uninstall numpy or pipenv clean:

init_dgelsd failed init
Traceback (most recent call last):
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 807, in <module>
    main()
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 802, in main
    _main(parsed.pre, parsed.clear, parsed.verbose, parsed.system, parsed.write,
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 785, in _main
    resolve_packages(pre, clear, verbose, system, write, requirements_dir, packages)
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 758, in resolve_packages
    results = clean_results(results, resolver, project)
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 640, in clean_results
    entry_dict = translate_markers(entry.get_cleaned_dict(keep_outdated=False))
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 239, in get_cleaned_dict
    self.validate_constraints()
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 565, in validate_constraints
    constraints = self.get_constraints()
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 493, in get_constraints
    pipfile_constraint = self.get_pipfile_constraint()
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 507, in get_pipfile_constraint
    return self.constraint_from_parent_conflicts()
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 527, in constraint_from_parent_conflicts
    if not p.requirements:
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 625, in __getattribute__
    return super(Entry, self).__getattribute__(key)
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/resolver.py", line 370, in requirements
    self.project.environment.get_package_requirements(self.name)
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/environment.py", line 708, in get_package_requirements
    return [self._get_requirements_for_package(p, key_tree) for p in nodes]
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/environment.py", line 708, in <listcomp>
    return [self._get_requirements_for_package(p, key_tree) for p in nodes]
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/environment.py", line 685, in _get_requirements_for_package
    d['dependencies'] = [
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/environment.py", line 686, in <listcomp>
    cls._get_requirements_for_package(c, key_tree, parent=node,
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/environment.py", line 677, in _get_requirements_for_package
    d = node.as_dict()
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/vendor/pipdeptree.py", line 284, in as_dict
    'installed_version': self.installed_version,
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/vendor/pipdeptree.py", line 251, in installed_version
    return guess_version(self.key, self.UNKNOWN_VERSION)
  File "/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv/vendor/pipdeptree.py", line 123, in guess_version
    m = import_module(pkg_key)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 790, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3/lib/python3.9/site-packages/numpy/__init__.py", line 286, in <module>
    raise RuntimeError(msg)
RuntimeError: Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.
RankWarning: Polyfit may be poorly conditioned

Steps to replicate

Checking Pipfile.lock:

>> vim Pipfile.lock
{
    "_meta": {
        "hash": {
            "sha256": "cb2ba58b2355a84b4bab907c8e6fd3253271e43f232f326b4a8c37caaaee05a2"
        },
        "pipfile-spec": 6,
        "requires": {
            "python_version": "3.9"
        },
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.org/simple",
                "verify_ssl": true
            }
        ]
    },
    "default": {
        "appnope": {
            "hashes": [
                "sha256:5b26757dc6f79a3b7dc9fab95359328d5747fcb2409d331ea66d0272b90ab2a0",
                "sha256:8b995ffe925347a2138d7ac0fe77155e4311a0ea6d6da4f5128fe4b3cbe5ed71"
            ],
            "markers": "sys_platform == 'darwin' and platform_system == 'Darwin'",
            "version": "==0.1.0"
        },
        "backcall": {
            "hashes": [
                "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e",
                "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"
            ],
            "version": "==0.2.0"
        },
        "decorator": {
            "hashes": [
                "sha256:41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760",
                "sha256:e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7"
            ],
            "version": "==4.4.2"
        },
        "ipykernel": {
            "hashes": [
                "sha256:9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d",
                "sha256:d6fbba26dba3cebd411382bc484f7bc2caa98427ae0ddb4ab37fe8bfeb5c7dd3"
            ],
            "index": "pypi",
            "version": "==5.3.4"
        },
        "ipython": {
            "hashes": [
                "sha256:2e22c1f74477b5106a6fb301c342ab8c64bb75d702e350f05a649e8cb40a0fb8",
                "sha256:a331e78086001931de9424940699691ad49dfb457cea31f5471eae7b78222d5e"
            ],
            "markers": "python_version >= '3.7'",
            "version": "==7.18.1"
        },
        "ipython-genutils": {
            "hashes": [
                "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8",
                "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"
            ],
            "version": "==0.2.0"
        },
        "jedi": {
            "hashes": [
                "sha256:86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20",
                "sha256:98cc583fa0f2f8304968199b01b6b4b94f469a1f4a74c1560506ca2a211378b5"
            ],
            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
            "version": "==0.17.2"
        },
        "jupyter-client": {
            "hashes": [
                "sha256:49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1",
                "sha256:c958d24d6eacb975c1acebb68ac9077da61b5f5c040f22f6849928ad7393b950"
            ],
            "markers": "python_version >= '3.5'",
            "version": "==6.1.7"
        },
        "jupyter-core": {
            "hashes": [
                "sha256:394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e",
                "sha256:a4ee613c060fe5697d913416fc9d553599c05e4492d58fac1192c9a6844abb21"
            ],
            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
            "version": "==4.6.3"
        },
        "parso": {
            "hashes": [
                "sha256:97218d9159b2520ff45eb78028ba8b50d2bc61dcc062a9682666f2dc4bd331ea",
                "sha256:caba44724b994a8a5e086460bb212abc5a8bc46951bf4a9a1210745953622eb9"
            ],
            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
            "version": "==0.7.1"
        },
        "pexpect": {
            "hashes": [
                "sha256:0b48a55dcb3c05f3329815901ea4fc1537514d6ba867a152b581d69ae3710937",
                "sha256:fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c"
            ],
            "markers": "sys_platform != 'win32'",
            "version": "==4.8.0"
        },
        "pickleshare": {
            "hashes": [
                "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca",
                "sha256:9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56"
            ],
            "version": "==0.7.5"
        },
        "prompt-toolkit": {
            "hashes": [
                "sha256:25c95d2ac813909f813c93fde734b6e44406d1477a9faef7c915ff37d39c0a8c",
                "sha256:7debb9a521e0b1ee7d2fe96ee4bd60ef03c6492784de0547337ca4433e46aa63"
            ],
            "index": "pypi",
            "version": "==3.0.8"
        },
        "ptyprocess": {
            "hashes": [
                "sha256:923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0",
                "sha256:d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f"
            ],
            "version": "==0.6.0"
        },
        "pygments": {
            "hashes": [
                "sha256:307543fe65c0947b126e83dd5a61bd8acbd84abec11f43caebaf5534cbc17998",
                "sha256:926c3f319eda178d1bd90851e4317e6d8cdb5e292a3386aac9bd75eca29cf9c7"
            ],
            "markers": "python_version >= '3.5'",
            "version": "==2.7.1"
        },
        "python-dateutil": {
            "hashes": [
                "sha256:73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c",
                "sha256:75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"
            ],
            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
            "version": "==2.8.1"
        },
        "pyzmq": {
            "hashes": [
                "sha256:00dca814469436455399660247d74045172955459c0bd49b54a540ce4d652185",
                "sha256:046b92e860914e39612e84fa760fc3f16054d268c11e0e25dcb011fb1bc6a075",
                "sha256:09d24a80ccb8cbda1af6ed8eb26b005b6743e58e9290566d2a6841f4e31fa8e0",
                "sha256:0a422fc290d03958899743db091f8154958410fc76ce7ee0ceb66150f72c2c97",
                "sha256:18189fc59ff5bf46b7ccf5a65c1963326dbfc85a2bc73e9f4a90a40322b992c8",
                "sha256:276ad604bffd70992a386a84bea34883e696a6b22e7378053e5d3227321d9702",
                "sha256:296540a065c8c21b26d63e3cea2d1d57902373b16e4256afe46422691903a438",
                "sha256:29d51279060d0a70f551663bc592418bcad7f4be4eea7b324f6dd81de05cb4c1",
                "sha256:36ab114021c0cab1a423fe6689355e8f813979f2c750968833b318c1fa10a0fd",
                "sha256:3fa6debf4bf9412e59353defad1f8035a1e68b66095a94ead8f7a61ae90b2675",
                "sha256:5120c64646e75f6db20cc16b9a94203926ead5d633de9feba4f137004241221d",
                "sha256:59f1e54627483dcf61c663941d94c4af9bf4163aec334171686cdaee67974fe5",
                "sha256:5d9fc809aa8d636e757e4ced2302569d6e60e9b9c26114a83f0d9d6519c40493",
                "sha256:654d3e06a4edc566b416c10293064732516cf8871a4522e0a2ba00cc2a2e600c",
                "sha256:720d2b6083498a9281eaee3f2927486e9fe02cd16d13a844f2e95217f243efea",
                "sha256:73483a2caaa0264ac717af33d6fb3f143d8379e60a422730ee8d010526ce1913",
                "sha256:8a6ada5a3f719bf46a04ba38595073df8d6b067316c011180102ba2a1925f5b5",
                "sha256:8b66b94fe6243d2d1d89bca336b2424399aac57932858b9a30309803ffc28112",
                "sha256:949a219493a861c263b75a16588eadeeeab08f372e25ff4a15a00f73dfe341f4",
                "sha256:99cc0e339a731c6a34109e5c4072aaa06d8e32c0b93dc2c2d90345dd45fa196c",
                "sha256:a7e7f930039ee0c4c26e4dfee015f20bd6919cd8b97c9cd7afbde2923a5167b6",
                "sha256:ab0d01148d13854de716786ca73701012e07dff4dfbbd68c4e06d8888743526e",
                "sha256:b1dd4cf4c5e09cbeef0aee83f3b8af1e9986c086a8927b261c042655607571e8",
                "sha256:c1a31cd42905b405530e92bdb70a8a56f048c8a371728b8acf9d746ecd4482c0",
                "sha256:c20dd60b9428f532bc59f2ef6d3b1029a28fc790d408af82f871a7db03e722ff",
                "sha256:c36ffe1e5aa35a1af6a96640d723d0d211c5f48841735c2aa8d034204e87eb87",
                "sha256:c40fbb2b9933369e994b837ee72193d6a4c35dfb9a7c573257ef7ff28961272c",
                "sha256:c6d653bab76b3925c65d4ac2ddbdffe09710f3f41cc7f177299e8c4498adb04a",
                "sha256:d46fb17f5693244de83e434648b3dbb4f4b0fec88415d6cbab1c1452b6f2ae17",
                "sha256:e36f12f503511d72d9bdfae11cadbadca22ff632ff67c1b5459f69756a029c19",
                "sha256:f1a25a61495b6f7bb986accc5b597a3541d9bd3ef0016f50be16dbb32025b302",
                "sha256:fa411b1d8f371d3a49d31b0789eb6da2537dadbb2aef74a43aa99a78195c3f76"
            ],
            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
            "version": "==19.0.2"
        },
        "six": {
            "hashes": [
                "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
                "sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
            ],
            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
            "version": "==1.15.0"
        },
        "tornado": {
            "hashes": [
                "sha256:0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc",
                "sha256:22aed82c2ea340c3771e3babc5ef220272f6fd06b5108a53b4976d0d722bcd52",
                "sha256:2c027eb2a393d964b22b5c154d1a23a5f8727db6fda837118a776b29e2b8ebc6",
                "sha256:5217e601700f24e966ddab689f90b7ea4bd91ff3357c3600fa1045e26d68e55d",
                "sha256:5618f72e947533832cbc3dec54e1dffc1747a5cb17d1fd91577ed14fa0dc081b",
                "sha256:5f6a07e62e799be5d2330e68d808c8ac41d4a259b9cea61da4101b83cb5dc673",
                "sha256:c58d56003daf1b616336781b26d184023ea4af13ae143d9dda65e31e534940b9",
                "sha256:c952975c8ba74f546ae6de2e226ab3cc3cc11ae47baf607459a6728585bb542a",
                "sha256:c98232a3ac391f5faea6821b53db8db461157baa788f5d6222a193e9456e1740"
            ],
            "markers": "python_version >= '3.5'",
            "version": "==6.0.4"
        },
        "traitlets": {
            "hashes": [
                "sha256:178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396",
                "sha256:69ff3f9d5351f31a7ad80443c2674b7099df13cc41fc5fa6e2f6d3b0330b0426"
            ],
            "markers": "python_version >= '3.7'",
            "version": "==5.0.5"
        },
        "wcwidth": {
            "hashes": [
                "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784",
                "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"
            ],
            "version": "==0.2.5"
        }
    },
    "develop": {}
}

When I run pip freeze from the Pipenv shell, I get the following output:

appnope==0.1.0
backcall==0.2.0
decorator==4.4.2
ipykernel==5.3.4
ipython==7.18.1
ipython-genutils==0.2.0
jedi==0.17.2
jupyter-client==6.1.7
jupyter-core==4.6.3
numpy==1.19.2
pandas==1.1.3
parso==0.7.1
pexpect==4.8.0
pickleshare==0.7.5
prompt-toolkit==3.0.8
ptyprocess==0.6.0
Pygments==2.7.1
python-dateutil==2.8.1
pytz==2020.1
pyzmq==19.0.2
six==1.15.0
tornado==6.0.4
traitlets==5.0.5
wcwidth==0.2.5

---

$ pipenv --support

Pipenv version: '2020.8.13'

Pipenv location: '/usr/local/Cellar/pipenv/2020.8.13_1/libexec/lib/python3.9/site-packages/pipenv'

Python location: '/usr/local/Cellar/pipenv/2020.8.13_1/libexec/bin/python'

Python installations found:

• 3.9.0: /Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3/bin/python3
• 3.9.0: /Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3/bin/python3.9
• 3.9.0: /Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3/bin/python3
• 3.9.0: /Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3/bin/python3.9
• 3.9.0: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3
• 3.9.0: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9
• 3.9.0: /usr/local/bin/python3
• 3.9.0: /usr/local/bin/python3.9
• 3.7.9: /Users/ihwang/.pyenv/versions/3.7.9/bin/python3
• 2.7.16: /usr/bin/python2.7

PEP 508 Information:

{'implementation_name': 'cpython',
 'implementation_version': '3.9.0',
 'os_name': 'posix',
 'platform_machine': 'x86_64',
 'platform_python_implementation': 'CPython',
 'platform_release': '18.7.0',
 'platform_system': 'Darwin',
 'platform_version': 'Darwin Kernel Version 18.7.0: Mon Aug 31 20:53:32 PDT '
                     '2020; root:xnu-4903.278.44~1/RELEASE_X86_64',
 'python_full_version': '3.9.0',
 'python_version': '3.9',
 'sys_platform': 'darwin'}

System environment variables:

• PATH
• TERM_PROGRAM
• TERM
• SHELL
• PIP_PYTHON_PATH
• TMPDIR
• Apple_PubSub_Socket_Render
• TERM_PROGRAM_VERSION
• TERM_SESSION_ID
• USER
• SSH_AUTH_SOCK
• __CF_USER_TEXT_ENCODING
• VIRTUAL_ENV
• PIPENV_ACTIVE
• _
• PWD
• SLACK_NO_AUTO_UPDATES
• LANG
• PYTHONSTARTUP
• XPC_FLAGS
• PYTHONDONTWRITEBYTECODE
• XPC_SERVICE_NAME
• HOME
• SHLVL
• LOGNAME
• PIP_DISABLE_PIP_VERSION_CHECK
• PIP_SHIMS_BASE_MODULE
• PYTHONFINDER_IGNORE_UNSUPPORTED

Pipenv–specific environment variables:

• PIPENV_ACTIVE: 1

Debug–specific environment variables:

• PATH: /usr/local/Cellar/pipenv/2020.8.13_1/libexec/tools:/Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3/bin:/usr/local/Cellar/pipenv/2020.8.13_1/libexec/tools:/Library/Frameworks/Python.framework/Versions/3.9/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
• SHELL: /bin/bash
• LANG: en_US.UTF-8
• PWD: /Users/ihwang/GDrive-irenatfh/Work/2020-NPR/projects/newsletter/2020.10.27-stimulus-packages/opportunity-insights-chart
• VIRTUAL_ENV: /Users/ihwang/.local/share/virtualenvs/opportunity-insights-chart-okFO_1O3

---

Contents of Pipfile ('/Users/ihwang/GDrive-irenatfh/Work/2020-NPR/projects/newsletter/2020.10.27-stimulus-packages/opportunity-insights-chart/Pipfile'):

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

[dev-packages]

[packages]
prompt-toolkit = ">=2.0.4"
ipykernel = "*"
pandas = "*"

[requires]
python_version = "3.9"

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[frostming]

The error is thrown by pipdeptree when trying to import numpy to get the installed version. IMO it is the package owner's responsibility to make that module importable or fail at the installation stage instead of runtime.

As a workaround, you can manually uninstall the problematic package by pipenv run pip uninstall numpy.

[matteius]

@irenatfh Are you able to verify if this is still an issue with the latest version of pipenv?