pipenv install --selective-upgrade upgrades package it's not supposed to
See original GitHub issueHi
I think this looks like a bug, but I would like to learn how to debug this. I’m trying to install a new package (with dependencies) into my current environment, minimizing the amounts of upgrades.
I’m doing this:
pipenv install --keep-outdated --selective-upgrade cellrank
and this results in incompatible versions:
There are incompatible versions in the resolved dependencies:
tensorboard<1.16.0,>=1.15.0 (from tensorflow==1.15->scgen==1.1.5->-r /tmp/pipenvlt9kuaxwrequirements/pipenv-21k5ptmh-constraints.txt (line 7))
tensorboard>=2.2.0 (from pytorch-lightning==1.2.3->scvi-tools==0.9.0->-r /tmp/pipenvlt9kuaxwrequirements/pipenv-21k5ptmh-constraints.txt (line 12))
However, the current installed version of scvi-tools
is 0.8.1
and if I fix (pin) that version in Pipfile, then everything works.
I think it’s supposed to work with selective-upgrade
option as well, without fixing the version in the Pipfile
$ pipenv --support
Pipenv version: '2020.11.15'
Pipenv location: '/home/nmx5063/.local/lib/python3.7/site-packages/pipenv'
Python location: '/software/python-anaconda3/2019.10/bin/python'
Python installations found:
3.6.9
:/projects/b1038/tools/pyenv/versions/3.6.9/bin/python3
3.6.8
:/usr/bin/python3
3.6.8
:/usr/bin/python3.6
3.6.8
:/usr/bin/python3.6m
2.7.5
:/usr/bin/python2
2.7.5
:/usr/bin/python2.7
PEP 508 Information:
{'implementation_name': 'cpython',
'implementation_version': '3.7.4',
'os_name': 'posix',
'platform_machine': 'x86_64',
'platform_python_implementation': 'CPython',
'platform_release': '3.10.0-862.el7.x86_64',
'platform_system': 'Linux',
'platform_version': '#1 SMP Wed Mar 21 18:14:51 EDT 2018',
'python_full_version': '3.7.4',
'python_version': '3.7',
'sys_platform': 'linux'}
System environment variables:
XDG_SESSION_ID
HOSTNAME
PYENV_ROOT
__LMOD_REF_COUNT_MODULEPATH
SHELL
TERM
HISTSIZE
SSH_CLIENT
MODULEPATH_ROOT
PIPENV_VENV_IN_PROJECT
LMOD_PACKAGE_PATH
LMOD_PKG
OLDPWD
QTDIR
QTINC
LMOD_VERSION
LMOD_ADMIN_FILE
SSH_TTY
LC_ALL
QT_GRAPHICSSYSTEM_CHECKED
USER
LS_COLORS
TIMEFORMAT
SSH_AUTH_SOCK
TERMCAP
BASH_MYENV
PYENV_VIRTUALENV_INIT
PAGER
LSCOLORS
_ModuleTable001_
PATH
MAIL
STY
PWD
EDITOR
LANG
LMOD_PAGER
MODULEPATH
_ModuleTable_Sz_
KDEDIRS
CLOUDSDK_PYTHON
LMOD_CMD
HISTIGNORE
HISTCONTROL
SSH_ASKPASS
HOME
SHLVL
LESSCHARSET
PYENV_SHELL
__LMOD_REF_COUNT_PATH
_ModuleTable002_
LOGNAME
CVS_RSH
QTLIB
WINDOW
LC_CTYPE
SSH_CONNECTION
XDG_DATA_DIRS
MODULESHOME
LESSOPEN
LMOD_SETTARG_FULL_SUPPORT
XDG_RUNTIME_DIR
QT_PLUGIN_PATH
_INIT_LMOD
LMOD_DIR
HOSTFILE
HISTTIMEFORMAT
BASH_FUNC_module()
BASH_FUNC_ml()
_
PIP_DISABLE_PIP_VERSION_CHECK
PYTHONDONTWRITEBYTECODE
PIP_SHIMS_BASE_MODULE
PIP_PYTHON_PATH
PYTHONFINDER_IGNORE_UNSUPPORTED
Pipenv–specific environment variables:
PIPENV_VENV_IN_PROJECT
:1
Debug–specific environment variables:
PATH
:/home/nmx5063/.local/bin:/projects/b1038/Pulmonary/nmarkov/reverse-names:/projects/b1038/tools/pyenv/plugins/pyenv-virtualenv/shims:/projects/b1038/tools/pyenv/shims:/projects/b1038/tools/pyenv/bin:/hpc/slurm/northwestern/usertools:/home/nmx5063/google-cloud-sdk/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/home/nmx5063/bin
SHELL
:/bin/bash
EDITOR
:vim
LANG
:en_US.UTF-8
PWD
:/projects/b1038/Pulmonary/nmarkov/ssc-v2/code
Contents of Pipfile
(‘/projects/b1038/Pulmonary/nmarkov/ssc-v2/code/Pipfile’):
[[source]]
name = "pypi"
url = "https://pypi.org/simple"
verify_ssl = true
[dev-packages]
[packages]
scanpy = "*"
bbknn = "*"
ipykernel = "*"
snakemake = "*"
leidenalg = "*"
scrublet = "*"
annoy = "*"
synapseclient = "*"
scgen = "*"
scvi-tools = "*"
openpyxl = "*"
cellrank = "*"
[requires]
python_version = "3.7"
Contents of Pipfile.lock
(‘/projects/b1038/Pulmonary/nmarkov/ssc-v2/code/Pipfile.lock’):
{
"_meta": {
"hash": {
"sha256": "7e56947a3abb23332c31f66e62805514b8aaae1ab7eb4ebec89630c5b05e9382"
},
"pipfile-spec": 6,
"requires": {
"python_version": "3.7"
},
"sources": [
{
"name": "pypi",
"url": "https://pypi.org/simple",
"verify_ssl": true
}
]
},
"default": {
"absl-py": {
"hashes": [
"sha256:673cccb88d810e5627d0c1c818158485d106f65a583880e2f730c997399bcfa7",
"sha256:b3d9eb5119ff6e0a0125f6dabf2f9fae02f8acae7be70576002fac27235611c5"
],
"version": "==0.11.0"
},
"adjusttext": {
"hashes": [
"sha256:b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06"
],
"version": "==0.7.3"
},
"amply": {
"hashes": [
"sha256:baa05b059759807cdbe897624ed037e1b045e6282cd500ee87ec78b2e504a669",
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],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==0.1.4"
},
"anndata": {
"hashes": [
"sha256:2113a7463388013023f153e1a1446add4182883e3320b6e37dda18ee6210e038",
"sha256:4f7d47e731cdf4ddc37a635f7532893a10510112e5bf6c4a68802438fdc9e0ab"
],
"markers": "python_version >= '3.6'",
"version": "==0.7.5"
},
"annoy": {
"hashes": [
"sha256:78df35a7c2c74b74d94b4bdc74ab4faa9a5ff67cb83d12902673d0d9bd02219d",
"sha256:9891e264041d1dcf3af42f67fbb16cb273c5404bc8c869d0915a3087f71d58dd"
],
"version": "==1.17.0"
},
"appdirs": {
"hashes": [
"sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
"sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
],
"version": "==1.4.4"
},
"argon2-cffi": {
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"sha256:cc0e028b209a5483b6846053d5fd7165f460a1f14774d79e632e75e7ae64b82b",
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"sha256:da7f0445b71db6d3a72462e04f36544b0de871289b0bc8a7cc87c0f5ec7079fa",
"sha256:e2db6e85c057c16d0bd3b4d2b04f270a7467c147381e8fd73cbbe5bc719832be"
],
"version": "==20.1.0"
},
"astor": {
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],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==0.8.1"
},
"async-generator": {
"hashes": [
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],
"markers": "python_version >= '3.5'",
"version": "==1.10"
},
"attrs": {
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],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==20.3.0"
},
"backcall": {
"hashes": [
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"sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"
],
"version": "==0.2.0"
},
"bbknn": {
"hashes": [
"sha256:03293ee80cebbe50eef52addf9cbc365a6607a633fa5d62be297a8622c400faf",
"sha256:7dc5257baa278fc92349ac7865674ce70802dc4e3afdafed87a099dff9e91159"
],
"index": "pypi",
"version": "==1.3.12"
},
"bleach": {
"hashes": [
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"sha256:9f8ccbeb6183c6e6cddea37592dfb0167485c1e3b13b3363bc325aa8bda3adbd"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==3.2.1"
},
"cached-property": {
"hashes": [
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"sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"
],
"markers": "python_version < '3.8'",
"version": "==1.5.2"
},
"certifi": {
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],
"version": "==2020.11.8"
},
"cffi": {
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"chardet": {
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"colorama": {
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"configargparse": {
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],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
"version": "==3.3.1"
},
"cycler": {
"hashes": [
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],
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"cython": {
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Issue Analytics
- State:
- Created 3 years ago
- Reactions:3
- Comments:6 (1 by maintainers)
I just ran into the same thing with another package, so commenting again.
Seems like I found the thread: https://github.com/pypa/pipenv/issues/966 If I read it right, then, by default
pipenv
does not look intoPipfile.lock
when resolving dependencies afterinstall
, and so if a new version is available for some dependency and it’s not constrained in thePipfile
then it would get intoPipfile.lock
Since comments there are closed, but the issue still open, I wonder: — is work on that issue still in progress? — or is the recommendation to pin everything we need not changed in
Pipfile
? — or is the recommendation to use passa? https://github.com/sarugaku/passa@techalchemy if you have time, I would be grateful if you comment if my reading of the situation is correct and what are plans regarding that as of now?
@mxposed and @dvemnt Can you retest with pipenv '2022.1.8`?