regression: pipenv check not checking requirements inside venv

[thehesiod]

Issue description

With the latest pipenv release we're noticing that the pipenv check command seems to be using the modules outside the venv instead of venv

Expected result

Should be checking vulnerabities of modules inside venv

Actual result

When possible, provide the verbose output (--verbose), especially for locking and dependencies resolving issues.

Steps to replicate

We have a Pipenv.lock file with:

 958         "pyyaml": {
 959             "hashes": [
 960                 "sha256:06a0d7ba600ce0b2d2fe2e78453a470b5a6e000a985dd4a4e54e436cc36b0e97",
 961                 "sha256:240097ff019d7c70a4922b6869d8a86407758333f02203e0fc6ff79c5dcede76",
 962                 "sha256:4f4b913ca1a7319b33cfb1369e91e50354d6f07a135f3b901aca02aa95940bd2",
 963                 "sha256:69f00dca373f240f842b2931fb2c7e14ddbacd1397d57157a9b005a6a9942648",
 964                 "sha256:73f099454b799e05e5ab51423c7bcf361c58d3206fa7b0d555426b1f4d9a3eaf",
 965                 "sha256:74809a57b329d6cc0fdccee6318f44b9b8649961fa73144a98735b0aaf029f1f",
 966                 "sha256:7739fc0fa8205b3ee8808aea45e968bc90082c10aef6ea95e855e10abf4a37b2",
 967                 "sha256:95f71d2af0ff4227885f7a6605c37fd53d3a106fcab511b8860ecca9fcf400ee",
 968                 "sha256:b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d",
 969                 "sha256:cc8955cfbfc7a115fa81d85284ee61147059a753344bc51098f3ccd69b0d7e0c",
 970                 "sha256:d13155f591e6fcc1ec3b30685d50bf0711574e2c0dfffd7644babf8b5102ca1a"
 971             ],
 972             "markers": "python_version != '3.4'",
 973             "version": "==5.3.1"
 974         },

install pyyaml 5.1 outside the venv.

then run pipenv sync followed by pipenv check and you'll get:

38100: pyyaml <5.3.1 resolved (5.1 installed)!
A vulnerability was discovered in the PyYAML library in versions before 5.3.1, where it is susceptible to arbitrary code execution when it processes untrusted YAML files through the full_load method or with the FullLoader loader. Applications that use the library to process untrusted input may be vulnerable to this flaw. An attacker could use this flaw to execute arbitrary code on the system by abusing the python/object/new constructor. See: CVE-2020-1747.

---

$ pipenv --support

Pipenv version: '2020.5.28'

Pipenv location: '/usr/local/lib/python3.8/site-packages/pipenv'

Python location: '/usr/local/opt/python@3.8/bin/python3.8'

Python installations found:

• 3.8.2: /usr/local/opt/python@3.8/bin/python3
• 3.8.2: /usr/local/opt/python@3.8/bin/python3.8
• 3.8.0: /usr/local/bin/python3.8
• 3.7.3: /usr/bin/python3
• 3.7.0: /usr/local/bin/python3
• 3.7.0: /usr/local/bin/python3.7m
• 3.7.0: /usr/local/bin/python3.7
• 3.6.7: /usr/local/bin/python3.6
• 3.6.7: /usr/local/bin/python3.6m
• 3.5.9: /Users/alex/.pyenv/versions/3.5.9/bin/python3
• 2.7.16: /usr/bin/python2
• 2.7.16: /usr/bin/python2.7
• 2.7.15: /usr/local/bin/python2
• 2.7.15: /usr/local/bin/python2.7

PEP 508 Information:

{'implementation_name': 'cpython',
 'implementation_version': '3.8.2',
 'os_name': 'posix',
 'platform_machine': 'x86_64',
 'platform_python_implementation': 'CPython',
 'platform_release': '19.5.0',
 'platform_system': 'Darwin',
 'platform_version': 'Darwin Kernel Version 19.5.0: Thu Apr 30 18:25:59 PDT '
                     '2020; root:xnu-6153.121.1~7/RELEASE_X86_64',
 'python_full_version': '3.8.2',
 'python_version': '3.8',
 'sys_platform': 'darwin'}

System environment variables:

• SHELL
• XPC_FLAGS
• HISTCONTROL
• TERM_PROGRAM_VERSION
• PKG_CONFIG_PATH
• HISTSIZE
• HDF5_DIR
• SSH_AUTH_SOCK
• TERM_SESSION_ID
• GPG_TTY
• serverFlavor
• PWD
• LOGNAME
• MANPATH
• LaunchInstanceID
• HOME
• LANG
• SECURITYSESSIONID
• TMPDIR
• CLICOLOR
• FBNSECRETS_FORCE_USER
• OPENSC_LIBS
• NVM_DIR
• TERM
• USER
• DISPLAY
• SHLVL
• XPC_SERVICE_NAME
• HOMEBREW_GITHUB_API_TOKEN
• PS1
• PATH
• GOPATH
• TERM_PROGRAM
• _
• __CF_USER_TEXT_ENCODING
• PIP_DISABLE_PIP_VERSION_CHECK
• PYTHONDONTWRITEBYTECODE
• PIP_SHIMS_BASE_MODULE
• PIP_PYTHON_PATH
• PYTHONFINDER_IGNORE_UNSUPPORTED

Pipenv–specific environment variables:

Debug–specific environment variables:

• PATH: ~/.local/bin:/usr/local/opt/python@3.8/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/alex/bin:/usr/local/opt/go/libexec/bin:/Users/alex/gowork/bin:/Applications/Postgres.app/Contents/Versions/9.6/bin:/usr/local/bin:/usr/local/sbin:/Users/alex/Downloads/google-cloud-sdk/bin:/Users/alex/dev/fbn.com/ops/docker/ecr/bin
• SHELL: /usr/local/bin/bash
• LANG: en_US.UTF-8
• PWD: /Users/alex/dev/fbn.com/api/commodities

---

Contents of Pipfile ('/Users/alex/dev/fbn.com/api/commodities/Pipfile'):

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

[dev-packages]
# This version pin fixes a security vuln https://github.com/warner/python-ecdsa/security/advisories/GHSA-pwfw-mgfj-7g3g
#  until a new version of moto that bumps this comes out
ecdsa = ">=0.3.13"
moto = {extras = ["server"],version = "~=1.3.13"}
pytest = "<5.4"
pytest-asyncio = "<0.11"
pytest-cov = "*"
pytest-xdist = "*"
async-mock = "*"
freezegun = "*"
netifaces = "*"
bpython = "*"
coverage = "<5.0"

[packages]
fbn-async-server = {extras = ["database"],version = "~=13.0"}
fbn-pcdu-client3 = "~=5.0"
fbn-pcdu-plugin3 = "~=8.0"
fbn-weather = "~=2.0"
aiomcache = "~=0.6.0"
hdx-python-country = ">=1.5.0,<1.6.0"
aioodbc = "~=0.3.3"
python-dateutil = "~=2.8"
pytz = "*"
pandas = "~=0.24.2"
# Pinning this to fix a testing bug
tenacity = "~=6.0.0"
simplejson = "*"
feather-format = "~=0.4.0"
pyarrow = "~=0.16"
lz4 = "~=2.2"
pysftp = "~=0.2.9"
APScheduler = "~=3.6"
Babel = "~=2.7"
Pillow = "~=6.2"
docutils = '~=0.15'
# For a sql building corner-case, not used generally.
pypika = '~=0.9'
# Pinning google dependencies to avoid google update breakages
google-auth = '~=1.6.3'
# Pinning to fix security vuln
httplib2 = ">=0.18.0"
hdx-python-utilities = "~=1.9"
fbn-googleapi-helpers = '~=0.1'
fbn-redshift-extract = '>=0.3.6'

# pipenv doesn't pull the editable requirement from fbn-googleapi: https://github.com/pypa/pipenv/issues/3964
google-api-python-client = {editable = true,git = "https://github.com/thehesiod/google-api-python-client.git",ref = "thehesiod/batch-retries"}

[requires]
python_version = "3.8"

Contents of Pipfile.lock ('/Users/alex/dev/fbn.com/api/commodities/Pipfile.lock'):

{
    "_meta": {
        "hash": {
            "sha256": "aebb5ccb90258c2f1a311b5e79f32b2c26dc0b002666eb8e90f2a6d8081b64d0"
        },
        "pipfile-spec": 6,
        "requires": {
            "python_version": "3.8"
        },
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.fbn.org/simple",
                "verify_ssl": true
            }
        ]
    },
    "default": {
        "aiobotocore": {
            "extras": [
                "awscli",
                "boto3"
            ],
            "hashes": [
                "sha256:1e89ef97c52eb77d89c7c4a9130cab162ae3b89d2709c6e45da30824163ed8d3",
                "sha256:4103d90b9e162176203dc5295124b15f56c37eee0ddbcddc6929760443714ff8"
            ],
            "version": "==1.0.4"
        },
        "aiodns": {
            "hashes": [
                "sha256:815fdef4607474295d68da46978a54481dd1e7be153c7d60f9e72773cd38d77d",
                "sha256:aaa5ac584f40fe778013df0aa6544bf157799bd3f608364b451840ed2c8688de"
            ],
            "version": "==2.0.0"
        },
        "aiohttp": {
            "hashes": [
                "sha256:46c86926fd02f42a335baf89be3e6ab97929402abbfd6adbfd0904158e0e3978"
            ],
            "version": "==3.3.2.2"
        },
        "aioitertools": {
            "hashes": [
                "sha256:341cb05a0903177ef1b73d4cc12c92aee18e81c364e0138f4efc7ec3c47b8177",
                "sha256:e931a2f0dcabd4a8446b5cc2fc71b8bb14716e6adf37728a70869213f1f741cd"
            ],
            "version": "==0.7.0"
        },
        "aiomcache": {
            "hashes": [
                "sha256:17d82e0586c8500a7a3dac0fdef67e2d0300c82d4acb1595a9925783b7c382b5",
                "sha256:b38062efca87f2e6ac3b406bd816ca790900b03fef1c5c38fa61c18212c38825"
            ],
            "index": "pypi",
            "version": "==0.6.0"
        },
        "aioodbc": {
            "hashes": [
                "sha256:16d5dcc529a5a8dd91cf96d73521d0408c59f4289a81254bad155e1b3142584f"
            ],
            "index": "pypi",
            "version": "==0.3.3"
        },
        "aiopg": {
            "hashes": [
                "sha256:32da3c9c73c248c715883fbb0876d66015d9fb6b4946058eb9fd40e86cfff9b4",
                "sha256:5da7763028b735ebc4c2980ba39ef1ce4f48df1fc05900e036674edd50f0727c"
            ],
            "version": "==1.0.0"
        },
        "apscheduler": {
            "hashes": [
                "sha256:3bb5229eed6fbbdafc13ce962712ae66e175aa214c69bed35a06bffcf0c5e244",
                "sha256:e8b1ecdb4c7cb2818913f766d5898183c7cb8936680710a4d3a966e02262e526"
            ],
            "index": "pypi",
            "version": "==3.6.3"
        },
        "async-timeout": {
            "hashes": [
                "sha256:0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f",
                "sha256:4291ca197d287d274d0b6cb5d6f8f8f82d434ed288f962539ff18cc9012f9ea3"
            ],
            "version": "==3.0.1"
        },
        "asyncpg": {
            "hashes": [
                "sha256:058baec9d6b75612412baa872a1aa47317d0ff88c318a49f9c4a2389043d5a8d",
                "sha256:0c336903c3b08e970f8af2f606332f1738dba156bca83ed0467dc2f5c70da796",
                "sha256:1388caa456070dab102be874205e3ae8fd1de2577d5de9fa22e65ba5c0f8b110",
                "sha256:25edb0b947eb632b6b53e5a4b36cba5677297bb34cbaba270019714d0a5fed76",
                "sha256:2af6a5a705accd36e13292ea43d08c20b15e52d684beb522cb3a7d3c9c8f3f48",
                "sha256:391aea89871df8c1560750af6c7170f2772c2d133b34772acf3637e3cf4db93e",
                "sha256:394bf19bdddbba07a38cd6fb526ebf66e120444d6b3097332b78efd5b26495b0",
                "sha256:5664d1bd8abe64fc60a0e701eb85fa1d8c9a4a8018a5a59164d27238f2caf395",
                "sha256:57666dfae38f4dbf84ffbf0c5c0f78733fef0e8e083230275dcb9ccad1d5ee09",
                "sha256:74510234c294c6a6767089ba9c938f09a491426c24405634eb357bd91dffd734",
                "sha256:95cd2df61ee00b789bdcd04a080e6d9188693b841db2bf9a87ebaed9e53147e0",
                "sha256:a981500bf6947926e53c48f4d60ae080af1b4ad7fa78e363465a5b5ad4f2b65e",
                "sha256:a9e6fd6f0f9e8bd77e9a4e1ef9a4f83a80674d9136a754ae3603e915da96b627",
                "sha256:ad5ba062e09673b1a4b8d0facaf5a6d9719bf7b337440d10b07fe994d90a9552",
                "sha256:ba90d3578bc6dddcbce461875672fd9bdb34f0b8215b68612dd3b65a956ff51c",
                "sha256:c773c7dbe2f4d3ebc9e3030e94303e45d6742e6c2fc25da0c46a56ea3d83caeb",
                "sha256:da238592235717419a6a7b5edc8564da410ebfd056ca4ecc41e70b1b5df86fba",
                "sha256:e39aac2b3a2f839ce65aa255ce416de899c58b7d38d601d24ca35558e13b48e3",
                "sha256:ec6e7046c98730cb2ba4df41387e10cb8963a3ac2918f69ae416f8aab9ca7b1b",
                "sha256:f0c9719ac00615f097fe91082b785bce36dbf02a5ec4115ede0ebfd2cd9500cb",
                "sha256:f7184689177eeb5a11fa1b2baf3f6f2e26bfd7a85acf4de1a3adbd0867d7c0e2"
            ],
            "version": "==0.20.1"
        },
        "attrs": {
            "hashes": [
                "sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c",
                "sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"
            ],
            "version": "==19.3.0"
        },
        "awscli": {
            "hashes": [
                "sha256:399f6f60174854ef3e59d5c23ce71c401216837e248002a716601a27a602678c",
                "sha256:6ccd4b81de4c46fae4db15c8a540e650248e669b000fd56c389c7efaeeed795d"
            ],
            "version": "==1.18.32"
        },
        "babel": {
            "hashes": [
                "sha256:1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38",
                "sha256:d670ea0b10f8b723672d3a6abeb87b565b244da220d76b4dba1b66269ec152d4"
            ],
            "index": "pypi",
            "version": "==2.8.0"
        },
        "basicauth": {
            "hashes": [
                "sha256:d79ebe09ec4a46955539ed2e66a6543375511e0f00b3c37be735d15f8e63ac02"
            ],
            "version": "==0.4.1"
        },
        "bcrypt": {
            "hashes": [
                "sha256:0258f143f3de96b7c14f762c770f5fc56ccd72f8a1857a451c1cd9a655d9ac89",
                "sha256:0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42",
                "sha256:19a4b72a6ae5bb467fea018b825f0a7d917789bcfe893e53f15c92805d187294",
                "sha256:5432dd7b34107ae8ed6c10a71b4397f1c853bd39a4d6ffa7e35f40584cffd161",
                "sha256:6305557019906466fc42dbc53b46da004e72fd7a551c044a827e572c82191752",
                "sha256:69361315039878c0680be456640f8705d76cb4a3a3fe1e057e0f261b74be4b31",
                "sha256:6fe49a60b25b584e2f4ef175b29d3a83ba63b3a4df1b4c0605b826668d1b6be5",
                "sha256:74a015102e877d0ccd02cdeaa18b32aa7273746914a6c5d0456dd442cb65b99c",
                "sha256:763669a367869786bb4c8fcf731f4175775a5b43f070f50f46f0b59da45375d0",
                "sha256:8b10acde4e1919d6015e1df86d4c217d3b5b01bb7744c36113ea43d529e1c3de",
                "sha256:9fe92406c857409b70a38729dbdf6578caf9228de0aef5bc44f859ffe971a39e",
                "sha256:a190f2a5dbbdbff4b74e3103cef44344bc30e61255beb27310e2aec407766052",
                "sha256:a595c12c618119255c90deb4b046e1ca3bcfad64667c43d1166f2b04bc72db09",
                "sha256:c9457fa5c121e94a58d6505cadca8bed1c64444b83b3204928a866ca2e599105",
                "sha256:cb93f6b2ab0f6853550b74e051d297c27a638719753eb9ff66d1e4072be67133",
                "sha256:ce4e4f0deb51d38b1611a27f330426154f2980e66582dc5f438aad38b5f24fc1",
                "sha256:d7bdc26475679dd073ba0ed2766445bb5b20ca4793ca0db32b399dccc6bc84b7",
                "sha256:ff032765bb8716d9387fd5376d987a937254b0619eff0972779515b5c98820bc"
            ],
            "version": "==3.1.7"
        },
        "beautifulsoup4": {
            "hashes": [
                "sha256:73cc4d115b96f79c7d77c1c7f7a0a8d4c57860d1041df407dd1aae7f07a77fd7",
                "sha256:a6237df3c32ccfaee4fd201c8f5f9d9df619b93121d01353a64a73ce8c6ef9a8",
                "sha256:e718f2342e2e099b640a34ab782407b7b676f47ee272d6739e60b8ea23829f2c"
            ],
            "version": "==4.9.1"
        },
        "boto3": {
            "hashes": [
                "sha256:57398de1b5e074e715c866441e69f90c9468959d5743a021d8aeed04fbaa1078",
                "sha256:60ac1124597231ed36a7320547cd0d16a001bb92333ab30ad20514f77e585225"
            ],
            "version": "==1.12.32"
        },
        "botocore": {
            "hashes": [
                "sha256:3ea89601ee452b65084005278bd832be854cfde5166685dcb14b6c8f19d3fc6d",
                "sha256:a963af564d94107787ff3d2c534e8b7aed7f12e014cdd609f8fcb17bf9d9b19a"
            ],
            "version": "==1.15.32"
        },
        "cachetools": {
            "hashes": [
                "sha256:1d057645db16ca7fe1f3bd953558897603d6f0b9c51ed9d11eb4d071ec4e2aab",
                "sha256:de5d88f87781602201cde465d3afe837546663b168e8b39df67411b0bf10cefc"
            ],
            "version": "==4.1.0"
        },
        "cchardet": {
            "hashes": [
                "sha256:0f6e4e464e332da776b9c1a34e4e83b6301d38c2724efc93848c46ade66d02bb",
                "sha256:217a7008bd399bdb61f6a0a2570acc5c3a9f96140e0a0d089b9e748c4d4e4c4e",
                "sha256:27b0f23088873d1dd36d2c8a2e45c9167e312e1aac7e4baeb47f7428a2669638",
                "sha256:2a958fb093f69ee5f16be7a1aee5122e07aff4350fa4dc9b953b87c34468e605",
                "sha256:2aa1b008965c703ad6597361b0f6d427c8971fe94a2c99ec3724c228ae50d6a6",
                "sha256:2c05b66b12f9ab0493c5ffb666036fd8c9004a9cc9d5a9264dc24738b50ab8c3",
                "sha256:4096759825a130cb27a58ddf6d58e10abdd0127d29fbf53fde26df7ad879737b",
                "sha256:40c199f9c0569ac479fae7c4e12d2e16fc1e8237836b928474fdd228b8d11477",
                "sha256:4486f6e5bdf06f0081d13832f2a061d9e90597eb02093fda9d37e3985e3b2ef2",
                "sha256:54d2653520237ebbd2928f2c0f2eb7c616ee2b5194d73d945060cd54a7846b64",
                "sha256:5e38cfad9d3ca0f571c4352e9ca0f5ab718508f492a37d3236ae70810140e250",
                "sha256:68409e00d75ff13dd7a192ec49559f5527ee8959a51a9f4dd7b168df972b4d44",
                "sha256:79b0e113144c2ef0050bc9fe647c7657c5298f3012ecd8937d930b24ddd61404",
                "sha256:7a2d98df461d3f36b403fdd8d7890c823ed05bd98eb074412ed56fbfedb94751",
                "sha256:7bba1cbb4358dc9a2d2da00f4b38b159a5483d2f3b1d698a7c2cae518f955170",
                "sha256:84d2ce838cf3c2fe7f0517941702d42f7e598e5173632ec47a113cd521669b98",
                "sha256:8b1d02c99f6444c63336a76638741eaf4ac4005b454e3b8252a40074bf0d84a1",
                "sha256:8f7ade2578b2326a0a554c03f60c8d079331220179a592e83e143c9556b7f5b2",
                "sha256:953fe382304b19f5aa8fc2da4b092a3bb58a477d33af4def4b81abdce4c9288c",
                "sha256:acc96b4a8f756af289fa90ffa67ddef57401d99131e51e71872e3609483941ce",
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}

[thehesiod]

@techalchemy seems kinda critical

[frostming]

This seems similar to #4276 , closing it now.