I tried conda remove nodejs and pip uninstall nodejs but it doesn't work. I get this error message PackagesNotFoundError: The following packages are missing from the target environment: - nodejs
but when I use conda search nodejs. It turns out the package still exists.
The conda search command does not give information about local installations, but instead queries Anaconda Cloud to see what packages are available to install.
To check what is installed, use the conda list command. If you wish to check every environment for a given package, see Conda: list all environments that use a certain package.
Related
is there a way to specify for a given python package to install in a given conda env vs. the User's python?
I thought that if I did pip install <package> in a given conda environment, this would make the package accessible in that environment.
If I create a conda environment and install pySankey then do conda list, pySankey won't show but instead be installed in /Users/username/Python/3.7/lib/python/site-packages/
The package installs with "Defaulting to user installation because normal site-packages is not writeable". I looked at other stack posts associated with this, but I'm unclear how to modify ~/.bashrc, since my understanding is that ~/.bashrc is not unique to a conda environment. I also checked the path of the conda environment but there's no local as indicated here.
This has happened to me with a couple different packages (eg these packages do not pip install into the conda environment, other do), I'm using pySankey as an example.
thanks!
I am trying to create a conda environment that will enable me to use JupyterLab extensions as well as matplotlib (among other things). When installing JupyterLab extensions in the past, I have been prompted that I require nodejs>=12.0. When I try installing both nodejs and matplotlib in a new environment, I receive a conflict. Any suggestions for how to proceed?
I do the following:
conda create -n test python=3.10
conda activate test
conda install jupyterlab
conda install nodejs
conda install matplotlib
Installation proceeds without a problem until the final step, at which point I am informed:
The following NEW packages will be INSTALLED:
blas anaconda/linux-64::blas-1.0-mkl None
...
zstd anaconda/linux-64::zstd-1.5.2-ha4553b6_0 None
The following packages will be DOWNGRADED:
icu 68.1-h2531618_0 --> 58.2-he6710b0_3 None
nodejs 16.13.1-hb931c9a_0 --> 10.13.0-he6710b0_0 None
Proceed ([y]/n)?
Of course, if I allow it to downgrade nodejs, then I won't be able to use Jupyter Lab extensions, which require nodejs>=12.0. Any suggestions for how to proceed?
(Other packages want to downgrade nodejs to 10.3 as well, e.g. conda install jupyter, but for clarity, I've focused on matplotlib.)
I ran into a similar issue, and I got around it by not installing node via conda. I think node just needs to be on your path so you can install with https://nodejs.org/en/download/ or if you need to support multiple node versions you can use nvm.
I have a 2-part question about conda vs. pip virtual environments. I found great information on the answers What is the difference between pip and conda? and Does Conda replace the need for virtualenv? but still have something unclear.
I have a given python project (say PR) that I need to install and further develop on a linux server (say S) where python is installed with anaconda. Now, the usage/installation instructions of PR tell me to use python to create virtual environment and pip to install all packages. That is,
python3 -m venv PR
pip install --editable . (the dot included at the end)
According to "pip install --editable ./" vs "python setup.py develop" the latter reads the file setup.py (included in PR) which contains a function setup(...) with option install_requires listing all the required packages and installs them automatically. I have tested this on my own computer (which does not have conda) and it works fine. At least no error messages.
Now I need to further develop PR on S. My question Part 1: can I use conda instead of pip to create and update virtual environment? If yes, what would be the conda command replacing pip install --editable . ? I'm positive I will later need to install other packages as well. I'm worried about conflicts between conda/pip.
On S, I have Spyder and no other python IDEs. I have never used Spyder but I'm very familiar with PyCharm (Windows) and VS Code (Linux) so I assume debugging with Spyder will be similar to those. My question Part 2 (tied to Part 1): if I have to use pip to install packages, does Spyder see those? Or can it only see conda-installed packages?
(Edit/update): Thank you Carlos for comments. I continue my question:
I created and activated the virtual environment (VE) with conda
conda create PR_venv
conda activate PR_venv
Installed pip with
conda install pip
(this upgraded pip and installed several other packages too, including newer version of python). Installed PR and its required packages with pip
pip install -e .
Now, if I run the PR package inside this active VE interactively from the terminal, everything works fine. I would like to do the same from within spyder, to get the IDE debugging abilities in my hand.
When I start spyder, open a python file to be run, click "Run" button, it crashes in the import statements.
Spyder cannot see the installed packages. It can see only the local package PR but none of the packages installed by pip for this VE.
I am not sure what is the correct question here; I'm confused how are conda VEs related to spyder/jupyter/ipython ? I cannot find information in the conda documents about this.
I cannot find from spyder documents anything about VEs. Do I have to somehow re-install the packages (how?) inside Spyder? It seems pointless because the packages are installed already.
(Edit/Update 2): The information on https://docs.spyder-ide.org/current/installation.html makes me even more confused: Spyder is presented as both a stand-alone program and as a python package. So do I have to re-install Spyder inside the VE(?!) with
conda activate PR_venv
conda install spyder
Any clarification would be appreciated. I have always thought that the IDEs are stand-alone programs and that's it. This Spyder setup twists my brains into pretzel.
(Spyder maintainer here) About your questions:
can I use conda instead of pip to create and update virtual environment?
Yes, you can. Please see here to learn about the functionality offered by conda for managing environments.
If yes, what would be the conda command replacing pip install --editable . ?
Conda doesn't offer a good replacement for that command. However, you can still use it in a conda environment, as long as all you've installed all your package dependencies with conda before running it. That would avoid mixing conda and pip packages, which usually leads to really bad results.
if I have to use pip to install packages, does Spyder see those? Or can it only see conda-installed packages?
Spyder can work with pip and conda packages without problems. Just make sure of not mixing them (as I said above) and you'll be fine. In addition, please read our documentation to learn how to connect a local Spyder instance to a remote server.
Part 1: yes I can use conda to create VE and pip to install packages
conda create PR_venv
conda activate PR_venv
conda install pip
pip install --editable .
conda list
The last line shows which packages are installed by conda and which by pip (shown as pypi)
Part 2: spyder by default cannot see the packages. Need to do two things:
conda install spyder-kernels
Open Spyder and Tools > Preferences > Python Interpreter > Use the following interpreter > [full path to VE python command]
Restart Spyder. Now it can see the packages.
(Edit:) this link is great: https://github.com/spyder-ide/spyder/wiki/Working-with-packages-and-environments-in-Spyder
I have Spyder, clean Win10 installation, ver. 4.2.3.
When I run command pip, it gives message:
Note: you may need to restart the kernel to use updated packages.
C:\Users\UserName\AppData\Local\Programs\Spyder\Python\python.exe: No module named pip
I restarted Spyder, Win10, nothing helps.
How to fix it?
Thanks.
(Spyder maintainer here) We don't provide pip in our Windows app to prevent people breaking Spyder by installing any kind of packages with it.
The best way to use other packages that don't come with our app is to install Miniconda, create a conda environment after that with the packages you want to use and spyder-kernels, and finally connect Spyder to that env.
If you have python 3.4+ then pip should be installed with python.
To check that, you can run
pip help
in your windows command line.
However, if it isn't the case then download the get-pip.py file and run
python get-pip.py
and the pip installation should start. You can use pip help to verify this.
Another source of the problem might be that pip isn't listed in your PATH variables and thus isn't recognized by your command line.
For a project I made a virtual environment (venv) using Python3. I installed all the necessary dependencies using a simple bash script (see picture below) after I activated my venv. (I verified the installed packages using: pip3 list and concluded that every dependency was installed succesfully.)
My project uses snakemake, so I ran this snakemake commando:
snakemake --snakefile Snakefile.py all
I get this error:
I know it has to do something with the venv, because without the venv snakemake runs perfectly. I have read the Snakemake installation documents and it says I have to install conda and make & activate a conda venv. But, I do not have the sudo privileges to download and install conda (I work on a protected server).
What is happening and does someone know a fix?
One possible reason could be the difference in Python versions. What version of Python does the pip3 prepare environment for?
As I can see from the picture provided, the invalid syntax may be because of the version of Python doesn't support f-strings.
Imagine the following two scenarios: when you run Snakemake manually, you use the latest Python3 (e.g. 3.9). But if the pip3 is configured for an older version (e.g. 3.5), you can configure a very different environment for Python3.5 that doesn't support f-strings.