I need to use the sksparse.chomod package however my pycharm does not let me install it as it can't seem to find it.
I found the sksparse package on github and downloaded it but I do not know how to add a package downloaded from the internet into a conda environment. So, my first question would be can you download a package from github and add it to your conda environment, and how do you do this?
As I did not know how to do the above I instead saved the package within my project and thought I could simply import sksparse.cholmod. However, the line in my code that says import sksparse.cholmod as sks has no errors with it, so I assumed that meant this was ok, but when I try to run my file I get this error:
import sksparse.cholmod as sks
ModuleNotFoundError: No module named 'sksparse.cholmod'
If I have downloaded the package into my project why can't it be found, yet there are no errors when importing?
The cholmod file is a pyx file which I've been told should not be a problem.
Please could anyone help, I am reasonably new to python and I am looking for a straight forward solution that won't be time consuming.
It was an issue with windows, I was able to fix this using the instructions on this link
https://github.com/EmJay276/scikit-sparse
We must follow these steps precisely:
(This was tested with a Anaconda 3 installation and Python 3.7)
Install these requirements in order:
'''
conda install -c conda-forge numpy - tested with v1.19.1
conda install -c anaconda scipy - tested with v1.5.0
conda install -c conda-forge cython - tested with v0.29.21
conda install -c conda-forge suitesparse - tested with v5.4.0
'''
Download Microsoft Build Tools for C++ from https://visualstudio.microsoft.com/de/visual-cpp-build-tools/ (tested with 2019, should work with 2015 or newer)
Install Visual Studio Build Tools
Choose Workloads
Check "C++ Buildtools"
Keep standard settings
Run ''' pip install git+https://github.com/EmJay276/scikit-sparse '''
Test ''' from sksparse.cholmod import cholesky '''
Use all the versions stated for numpy etc, however with scipy I installed the latest version and it worked fine.
I tried to install the pybiomed package by using this link:
1- Download the PyBioMed-1.0.zip
2- Extract the PyBioMed-1.0.zip file
3- cd PyBioMed-1.0
4-python setup.py install
Then I found out I need to install the rdkit package too. Based on this document I need to use conda while I have installed standalone python 3.6.8, so I installed miniconda then downgrade its python to 3.6.8 version and used the below command to install the Rdkit and successfully finished:
conda install -c conda-forge rdkit
Now, when I use this from PyBioMed.PyMolecule import moe, I get this ModuleNotFoundError: No module named 'rdkit'! May you help me how to declare, show or clarify the basic python that you can find Rdkit in conda's path?
Let me add the following points:
A- I am using the Windows 10.
B- I have added the below lines to the system path:
C:\Program Files\Python36\
C:\Program Files\Python36\Scripts\
C:\ProgramData\Miniconda3
C:\ProgramData\Miniconda3\Lib\site-packages
C:\ProgramData\Miniconda3\Library\mingw-w64\bin
C:\ProgramData\Miniconda3\Library\usr\bin
C:\ProgramData\Miniconda3\Library\bin
C:\ProgramData\Miniconda3\Scripts
I have started getting this error for a "plspm" module in python which is part of R library after I 'conda install plspm' on my windows 10 OS. Installation has been done properly but i could not able to import plspm in python getting "No module" error. Please anyone help me to resolve.Thanks.
version of r-plspm is -0.4.9
needed packages already installed(scipy,skit-learn,pandas,numpy,statsmodule).
command used to install:
conda install -c conda-forge r-plspm
Screen shot of installed plspm:
Error:
Window 10
anaconda v5.0.1 -python v3.6.3 runs
jupyter v4.3.0 -python v3.6.3 runs
on cmd : C:\User\KRX>python --version
And I got > Python 3.5.6 :: Anaconda, Inc.
Hi, I had ModuleNotfoundError: No module named 'word2vec' after installing 'word2vec' following this procedure below.
1.download get-pip.py on https://bootstrap.pypa.io/get-pip.py. On cmd python get-pip.py
2.Install gensim in windows
On cmd: pip install scipy,
On cmd: pip install gensim
3.Install word2vec
On anaconda prompt: conda install -c anaconda word2vec
Until then, I had no problem but when I tried to import word2vec on jupyter notebook, I had ModuleNotfoundError as I already mentioned above.
I tried to reinstall 'word2vec' but I fell into another error :
ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'anaconda::tqdm-4.43.0-py_0'.
CondaError: Cannot link a source that does not exist. C:\User\KRX\Anaconda3\Scripts\conda.exe
Running 'conda clean --packages' may resolve your problem
I tried conda clean --packages but nothing changed
I also tried conda update anaconda and got same error (CondaError : Cannot link a source that does not exist...etc)
ps. This is my first time asking a question so if you need any other details please let me know. I thank y'all.
Conda gives error when I run any command with it.
Traceback (most recent call last):
File "/usr/local/bin/conda", line 7, in <module>
from conda.cli.main import main
File "/usr/local/lib/python2.7/dist-packages/conda/cli/__init__.py", line 8, in <module>
from .main import main # NOQA
File "/usr/local/lib/python2.7/dist-packages/conda/cli/main.py", line 46, in <module>
from ..base.context import context
File "/usr/local/lib/python2.7/dist-packages/conda/base/context.py", line 18, in <module>
from ..common.configuration import (Configuration, MapParameter, PrimitiveParameter,
File "/usr/local/lib/python2.7/dist-packages/conda/common/configuration.py", line 40, in <module>
from ruamel.yaml.comments import CommentedSeq, CommentedMap # pragma: no cover
ImportError: No module named ruamel.yaml.comments
The module ruamel.yaml.comments will normally be loaded from site-packages/ruamel/yaml/comments.py, and not from site-packages/ruamel_yaml/comments.py
Conda seems to have problems with properly supporting namespaces (ruamel.) which I can only attribute to not (yet) being fully pip compatible. That although "namespaces are a honking good idea", and package namespaces have been around for many years.
Assuming you can extend "conda" installations with pip you could try to do a normal install of ruamel.yaml with:
pip install ruamel_yaml==0.11.14
I would not normally recommend such an old version, but that is more likely to work in combination with the version conda uses itself internally.
The alternative would be to switch to using python and pip without conda, that way you can just use the latest version of software from PyPI.
Try pip install ruamel.yaml
It works for me.
Try conda install ruamel.yaml ... pip didnt work for me
Try sudo pip install ruamel_yaml
I went into this file:
/anaconda2/lib/python2.7/site-packages/dateparser/utils/__init__.py
edited this line:
import ruamel.yaml as yaml
to read
import ruamel_yaml as yaml
Changing the dot to an underscore worked for me.... I hope it works for you.
this worked for me:
pip install --upgrade ruamel.yaml --ignore-installed ruamel.yaml
from an answer in matsci.org
https://matsci.org/t/modulenotfounderror-no-module-named-ruamel/36183
The above answer didn't work for me. I had to do a fresh install of the core conda components as described in the conda docs here. Copy and pasted below:
Issue: My conda is broken and I want to fix it without blowing away the current installation
I am getting a conda error and want to reinstall Miniconda to fix it but when I try, it gives me the error that Miniconda (or Anaconda) is already installed and will not let me continue. I want to force the installation.
Resolution: Install Miniconda using the -f (force) option
Download and install the appropriate Miniconda for your computer operating system from the Miniconda download page using the force or -f option as shown:
bash Miniconda3-latest-MacOSX-x86_64.sh -f
NOTE: Substitute the appropriate filename and version for your
operating system.
NOTE: Be sure that you install to same install location as your
existing install so it overwrites the core conda files and does not
install a duplicate in a new folder.
Go to anaconda3\lib\site-packages\rpcq_base.py
and change line #22 :
from ruamel import yaml
to
from ruamel_yaml as yaml
This might not be a popular answer, but it finally helped me after many hours of troubleshooting:
Uninstall conda (I used this stack overflow solution) and also rm -rf miniconda3 in my home directory, fwiw.
Reinstalled conda using data camp's tutorial.
No other solutions worked for me after lots of head banging.
For python3 use
pip3 install ruamel_yaml
if pip3 not installed try at first
sudo apt install python3-pip
For me this was a conda/pip error. I'd tried to install (cwltool in my case) through pip.
It completed successfully, but then running any command gave me the error like above.
ImportError: No module named ruamel.yaml.
It turned out that the pip binary wasn't part of my conda env and was installing cwltool into a completely separate location.
To resolve the issue I completed the following:
conda activate <env I want to install cwltool into>
conda install -y pip
# Run 'rehash' now if you're using zsh to ensure you're using the right pip
pip install cwltool
cwltool -h
To add to what #user612161 has said, go to the directory of parent module (dateparser in this case) requiring ruamel.yaml:
cd anaconda2/lib/python2.7/site-packages/dateparser
and change all occurrences of ruamel.yaml into ruamel_yaml by the following command (Linux):
find . -name '*.py' | xargs sed -i 's/ruamel.yaml/ruamel_yaml/g'
The quick and easy is to ignore the previously installed version in an upgrade
pip install --ignore-installed ruamel_yaml==0.17.4
I was trying to link Bloomberg to Python
pip install --index-url=https://bcms.bloomberg.com/pip/simple blpapi
pip install xbbg
so far, so good.... then I tried to import a module from the package xbbg:
from xbbg import blp
and I was faced with an error, it couldn't find "ruamel.yaml" within the "param.py" within the xbbg module
When I dug into the folder C:/Anaconda3/Lib/site-packages I could see that there was a folder there called ruamel_yaml so I went back to the param.py file and edited ruamel.yaml to be ruamel_yaml as suggested in other posts.
"from xbbg import blp" now worked and I'm able to take data directly from Bloomberg into Python now. Problem solved.
I have a feeling that this issue is being caused by downloading different versions at different times as I've found the learning curve to get setup on Python difficult with many false starts. I was tearing my hair out a bit because I just got Python up and running linked to Bloomberg on my work pc but when I tried to link Bloomberg up to Python on my laptop it kept getting stuck with the "ruamel" issue. The version of Python on my laptop is much older than the version on my work pc. What makes me think that its a version issue is that I did not have to edit ruamel.yaml to be ruamel_yaml in order for me to link Python and BB.
These are just ideas, I'm too inexperienced at this stage to offer much more than to share what happened.