Virtual Environment Being Ignored or Overridden - python

I have been having an issue where pip and python seem to be ignoring the fact that they are in a virtualenv. I found the following:
pip command in virtualenv ignored in favour of system pip command
pip not pointing to virtual enviroment, in virtual enviroment
But neither seem to answer my issue.
The key issue seems to be when pip is trying to install modules it is detecting the module at the system level and then thinking it is already there, tries to uninstall it then fails because it isn't in the same environment.
For example, I need to update Wernzeug, so I try:
[venv] me#somemachine: pip install werkzeug
which results in:
Requirement already satisfied: werkzeug in /python/3.7.2/rh60_64/modules (0.15.2)
The weird bit starts if I run an uninstall:
[venv] me#somemachine: pip uninstall werkzeug
When I get:
Not uninstalling werkzeug at
/python/3.7.2/rh60_64/modules, outside environment
/venv Can't uninstall 'Werkzeug'. No files were found to uninstall.
Here's the kicker, due to the way the server is built I'm having to use the 'sw' command to get python (in this case 3.7.2). I'm wondering if this has something to do with the venv getting confused with where it is supposed to be looking. I do not have root access to the server, nor am I likely to get it, so I can't mess with the system installed modules.
Other useful info:
The base system is REHL 6.6
pip -V output:
pip 22.0.4 from /venv/lib/python3.7/site-packages/pip (python 3.7)
Any pointers or ideas that might help this are more than welcome.

Related

pipenv install installs dependencies every time / Pycharm doesn't recognize them

I'm having a variety of problems with my pipenv setup (another question here differences between users even after using Pipfile and Pipfile.lock with explicit versions) and I just noticed something else that seems funky.
It turns out in my project folder (with both a Pipfile and Pipfile lock created, with an initial pipenv install having been run, and without pipenv shell invoked), I can run pipenv install as many times as I want and every time it says that it is installing 74 dependencies. Does this mean that the pipenv install isn't taking effect, or does it just mean it's running through the dependencies to make sure they are installed?
It seems like there might be a problem, because when I open Pycharm for the project for that folder, it gives me the below alert ("Package requirements..." with the option to install requirements from Pipfile.lock).
I'm on the latest Pycharm which is setup to use the pipenv environment that I created with pipenv install, and I can confirm that it's using that environment based on Pycharm->Preferences->Project->Project Interpreter where it shows that it's using the right virtualenv for this folder.
But it seems that both pipenv install and Pycharm don't think the dependencies have been installed.
To answer your second question, the requirements are not being installed again. Every time you run pipenv install it will say that it's installing all requirements from your Pipfile.lock file, but if you run pipenv install -v to make it verbose and see the output, you'll see things like the following:
Installed version (4.1.2) is most up-to-date (past versions: 4.1.2)
Requirement already up-to-date: whitenoise==4.1.2 in c:\users\mihai\.virtualenvs\pipenvtest-1zyry8jn\lib\site-packages (from -r C:\Users\Mihai\AppData\Local\Temp\pipenv-1th31ie1-requirements\pipenv-r4e3zcr7-requirement.txt (line 1))
(4.1.2)
Since it is already installed, we are trusting this package without checking its hash. To ensure a completely repeatable environment, install into an empty virtualenv.
Cleaning up...
Removed build tracker 'C:\\Users\\Mihai\\AppData\\Local\\Temp\\pip-req-tracker-ip_gjf7h'
So to answer your question, it just runs through them to check if they're installed, installing them only if necessary.

pip uninstall fails with "owned by OS" - even under sudo

I'm working on a DevOps project for a client who's using Python. Though I never used it professionally, I know a few things, such as using virtualenv and pip - though not in great detail.
When I looked at the staging box, which I am trying to prepare for running a functional test suite, I saw chaos. Tons of packages installed globally, and those installed inside a virtualenv not matching the requirements.txt of the project. OK, thought I, there's a lot of cleaning up. Starting with global packages.
However, I ran into a problem at once:
➜ ~ pip uninstall PyYAML
Not uninstalling PyYAML at /usr/lib/python2.7/dist-packages, owned by OS
OK, someone must've done a 'sudo pip install PyYAML'. I think I know how to fix it:
➜ ~ sudo pip uninstall PyYAML
Not uninstalling PyYAML at /usr/lib/python2.7/dist-packages, owned by OS
Uh, apparently I don't.
A search revealed some similar conflicts caused by users installing packages bypassing pip, but I'm not convinced - why would pip even know about them, if that was the case? Unless the "other" way is placing them in the same location pip would use - but if that's the case, why would it fail to uninstall under sudo?
Pip denies to uninstall these packages because Debian developers patched it to behave so. This allows you to use both pip and apt simultaneously. The "original" pip program doesn't have such functionality
Update: my answer is relevant only to old versions of Pip. For the latest versions, Pip is configured to modify only the files which reside only in its "home directory" - that is /usr/local/lib/python3.* for Debian. For the latest tools, you will get these errors when you try to delete the package, installed by apt:
For pip 9.0.1-2.3~ubuntu1 (installed from Ubuntu repository):
Not uninstalling pyyaml at /usr/lib/python3/dist-packages, outside environment /usr
For pip 10.0.1 (original, installed from pypi.org):
Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
The point is not that pip cannot install the package because you don't have enough permissions, but because it is not a package installed through pip, so it doesn't want to uninstall it.
dist-packages is where packages installed by the OS package manager reside; as they are handled by another package manager (e.g. apt on Ubuntu/Debian, pacman on Arch, rpm/yum on CentOS, ... ) pip won't touch them (but still has to know about them as they are installed packages, so they can be used to satisfy dependencies of pip-installed packages).
You should also probably avoid to touch them unless you use the correct package manager, and even so, they may have been installed automatically to satisfy the dependencies of some program, so you may not remove them without breaking it. This can usually be checked quite easily, although the exact way depends from the precise Linux distribution you are using.

How to make 'pip install' not uninstall other versions?

I am managing several modules on an HPC, and want to install some requirements for a tool using pip.
I won't use virtualenv because they don't work well with our module system. I want to install module-local versions of packages and will set PYTHONPATH correctly when the module is loaded, and this has worked just fine when the packages I am installing are not also installed in the default python environment.
What I do not want to do is uninstall the default python's versions of packages while I am installing module-local versions.
For example, one package requires numpy==1.6, and the default version installed with the python I am using is 1.8.0. When I
pip install --install-option="--prefix=$RE_PYTHON" numpy==1.6
where RE_PYTHON points to the top of the module-local site-packages directory, numpy==1.6 installs fine, then pip goes ahead and starts uninstalling 1.8.0 from the tree of the python I am using (why it wants to uninstall a newer version is beyond me but I want to avoid this even when I am doing a local install of e.g. numpy==1.10.1).
How can I prevent pip from doing that? It is really annoying and I have not been able to find a solution that doesn't involve virtualenv.
You have to explicitly tell pip to ignore the current installed package by specifying the -I option (or --ignore-installed). So you should use:
PYTHONUSERBASE=$RE_PYTHON pip install -I --user numpy==1.6
This is mentioned in this answer by Ian Bicking.

Python imports wrong version of library outside of virtualenv

Need help updating a python package.
I have an implementation that requires the following import
from twisted.internet.ssl import optionsForClientTLS
"optionsForClientTLS" was added to the twisted framework with version 14(?). I think the non-virtualenv import is getting a dated version-- If that import is within a virtualenv that has twisted installed via pip, everything is fine. Import fails outside the virtualenv.
In the virtualenv
twistd --version
Shows 15.2.1. On the bare system it shows 13.2.0.
pip install twisted
....
pip freeze
shows
Twisted==15.2.1
Uninstalling twisted using pip and reinstalling didn't help. You can install twisted from apt-get using
sudo apt-get install python-twisted
and it installs the older version, but after purging it and installing using only pip I still get the older version.
Possibly related.
I solved the issue in a terrible way. It was a few days ago, so the paths may not be exactly right.
The assumption that there were two python packages was correct (I think.) I suspect the order of the paths in PYTHONPATH meant that the wrong version was being imported first, while pip was installing in a version that was later on in the path.
My "solution" was to copy the twisted directory from the up to date version to the older version. This was either from usr/local/lib/python... to usr/lib/python... or from ... site-packages to ... dist-packages. I can check again if someone has the same issue and can't resolve it.

Why is pip installing an old version of my package?

I've just uploaded a new version of my package to PyPi (1.2.1.0-r4): I can download the egg file and install it with easy_install, and the version checks out correctly. But when I try to install using pip, it installs version 1.1.0.0 instead. Even if I explicitly specify the version to pip with pip install -Iv tome==1.2.1.0-r4, I get this message: Requested tome==1.2.1.0-r4, but installing version 1.1.0.0, but I don't understand why.
I double checked with parse_version and confirmed that the version string on 1.2.1 is greater than that on 1.1.0 as shown:
>>> from pkg_resources import parse_version as pv
>>> pv('1.1.0.0') < pv('1.2.1.0-r4')
True
>>>
So any idea why it's choosing to install 1.1.0 instead?
This is an excellent question. It took me forever to figure out. This is the solution that works for me:
Apparently, if pip can find a local version of the package, pip will prefer the local versions to remote ones. I even disconnected my computer from the internet and tried it again -- when pip still installed the package successfully, and didn't even complain, the source was obviously local.
The really confusing part, in my case, was that pip found the newer versions on pypi, reported them, and then went ahead and re-installed the older version anyway ... arggh. Also, it didn't tell me what it was doing, and why.
So how did I solve this problem?
You can get pip to give verbose output using the -v flag ... but one isn't enough. I RTFM-ed the help, which said you can do -v multiple times, up to 3x, for more verbose output. So I did:
pip install -vvv <my_package>
Then I looked through the output. One line caught my eye:
Source in /tmp/pip-build-root/ has version 0.0.11, which satisfies requirement <my_package>
I deleted that directory, after which pip installed the newest version from pypi.
Try forcing download the package again with:
pip install --no-cache-dir --upgrade <package>
Thanks to Marcus Smith, who does amazing work as a maintener of pip, this was fixed in version 1.4 of pip which was released on 2013-07-23.
Relevant information from the changelog for this version
Fixed a number of issues (#413, #709, #634, #602, and #939) related to
cleaning up and not reusing build directories. (Pull #865, #948)
I found here that there is a known bug in pip that it won't check the version if there's a build directory with unpacked sources. I have checked this on my troubling package and after deleting its sources from build directory pip installed the required version.
If you are using a pip version that comes with some distribution packages (ex. Ubuntu python-pip), you may need to install a newer pip version:
Update pip to latest version:
sudo pip install -U pip
In case of "virtualenv", skip "sudo":
pip install -U pip
Following command may be required, if your shell report something like -bash: /usr/bin/pip: No such file or directory after pip update:
hash -d pip
Now install your package as usual:
pip install -U foo
or
pip install foo==package.version.here
Got the same issue to update pika 0.9.5 to 0.9.8. The only working way was to install from tarball: pip install https://pypi.python.org/packages/source/p/pika/pika-0.9.8.tar.gz.
In my case the python version used (3.4) didn't satisfy Django 2.1 dependencies requirements (python >= 3.5).
For my case I had to delete the .pip folder in my home directory and then I was able to get later versions of multiple libraries. Note that this was on linux.
pip --version
pip 18.1 from /usr/lib/python2.7/site-packages/pip (python 2.7)
virtualenv --version
15.1.0
Just in case that anyone else hassles with upgrading torchtext (or probably any other torch library):
Although https://pypi.org/project/torchtext/ states that you could run pip install torchtext I had to install it similiar to torch by specifying --find-links aka -f:
pip install torchtext===0.8.1 -f https://download.pytorch.org/whl/torch_stable.html
What irritated me was that PyCharm pointed me to the new version, but couldn't find it when attempting to upgrade to it. I guess that PyCharm uses its own mechanism to spot new versions. Then, when invoking pip under the hood, it didn't find the new version without the --find-links option.
In my case I am pip installing a .tar.gz package from Artifactory that I make a lot of updates to. In order to overwrite my cached Python files and always grab/install the latest I was able to run:
pip install --no-cache-dir --force-reinstall <path/to/tar.gz>
You should see this re-download any necessary files and install those, instead of using your local cache.
10 years on and pip still fails to work as expected 😖.
I wasted a couple of hours now banging my head against the wall trying to find out why pip won't install a development version of my package. In my case, there are versions 0.0.4 and 0.0.5.dev1 in a private gitlab.com package registry (hence the --extra-index-url argument below), but I believe that's not relevant to the problem.
Following a lot of the advice on this page, I create a test venv in a far away folder, clear the pip cache, uninstall the package in question, etc. first to rule out the most common problems:
$ pip cache purge && \
pip uninstall --yes my-package && \
pip install --extra-index-url "https://_:${GITLAB_PASSWORD_TOOLS_VAULTTOOLS}#gitlab.com/api/v4/projects/<project-id>/packages/pypi/simple" \
--no-cache-dir \
--pre \
--upgrade my-package
output (using empty lines to separate output for commands):
WARNING: No matching packages
Files removed: 0
Found existing installation: my-package 0.0.4
Uninstalling my-package-0.0.4:
Successfully uninstalled my-package-0.0.4
Looking in indexes: https://pypi.org/simple, https://_:****#gitlab.com/api/v4/projects/<project-id>/packages/pypi/simple
Collecting my-package
Downloading https://gitlab.com/api/v4/projects/<project-id>/packages/pypi/files/f07 ... 397/my_package-0.0.5.dev1-py3-none-any.whl (16 kB)
Downloading https://gitlab.com/api/v4/projects/<project-id>/packages/pypi/files/775 ... 70e/my_package-0.0.4-py3-none-any.whl (16 kB)
...
Successfully installed my-package-0.0.4
So pip does see the dev package version, but chooses the earlier one nonetheless.
In an attempt to figure out what's going on, I published a 0.0.5 version: Error persists, pip sees all three versions, but still installs 0.0.4.
In a further, increasingly desperate attempt, I removed any versions prior to 0.0.5* from the gitlab.com package registry.
Only now, pip would bother to actually display some useful information:
$ (same command as above)
... (similar output as above) ...
ERROR: Cannot install my-package==0.0.5 and my-package==0.0.5.dev1 because these package versions have conflicting dependencies.
The conflict is caused by:
my-package 0.0.5 depends on my-other-package<0.2.5 and >=0.2.4
my-package 0.0.5.dev1 depends on my-other-package<0.2.5 and >=0.2.4
To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
OK, so there is something wrong with my package dependencies. Thanks for letting me know.
Seriously - I tried hard for a couple of hours using all kinds of pip ... -vvv and/or fixed versions such as e.g. my-package==0.0.5.dev1 - but I did not manage to get any useful output out of pip - until I wiped the entire history from my package registry 🤬.
Hope this at least helps someone in the same situation.
I found that if you use microversions, pip doesn't seem to recognize them. For example, we couldn't get version 1.9.9.1 to upgrade.
In my case, someone had published the latest version of a package with python2, so attempting to pip3 install it grabbed an older version that had been built with python3.
Handy things to check when debugging this:
If pip install claims to not be able to find the version, see whether pip search can see it.
Take a look at the "Download Files" section on the pypi repo -- the filenames might suggest what's wrong (in my case i saw -py2- there clear as day).
As suggested by others, try running pip install --no-cache-dir in case pip isn't bothering to ask the internet because it already has your answer locally.
I had hidden unversioned files under the Git tab in PyCharm that were being installed with pip install . even though I didn't see the files anywhere else.
Took a long time to find it for me, posting this in hope that it'll help somebody else.
if you need the path for your package do pip -v list. Example see related post when using pip -e Why is an old version of a package of my python library installing by itself with pip -e?

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