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pypa / pipenv

Python Development Workflow for Humans.
https://pipenv.pypa.io
MIT License
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pipenv install --selective-upgrade upgrades package it's not supposed to #4650

Closed mxposed closed 2 years ago

mxposed commented 3 years ago

Hi

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I'm doing this: pipenv install --keep-outdated --selective-upgrade cellrank and this results in incompatible versions: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'): ```toml [[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'): ```json { "_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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frostming commented 3 years ago

What happens if you run pipenv install --keep-outdated cellrank?

mxposed commented 3 years ago

Same. And if I run with --selective-upgrade option alone it's the same

dvemnt commented 3 years ago

Same. It's totally broken and unusable. I faced really annoying situation when I can't update... dev dependency (!) because pipenv trying update all listed dependencies.

romanek-adam commented 3 years ago

Looks like a duplicate of #4536

mxposed commented 3 years ago

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 into Pipfile.lock when resolving dependencies after install, and so if a new version is available for some dependency and it's not constrained in the Pipfile then it would get into Pipfile.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?

matteius commented 2 years ago

@mxposed and @dvemnt Can you retest with pipenv '2022.1.8`?