I'm using conda with Spyder/Python 3.8.8.
I'm trying to install the geopandas package through conda-install, but when running it, I receive no output.
I've input the command conda install -c conda-forge geopandas and let it run for 30 minutes so far, so I doubt it's just a large package or poor connection. I don't know if I'm supposed to be seeing progress updates, but if I am, I'm not.
Any help is appreciated, thanks!
If you are using the base Anaconda environment, then there are packages that are conflicting with geopandas. I suggest you to create new environment for geopandas:
open anaconda command line and run this command to create new environment:
conda create --name gis python==3.8
You can use any version of python you like of course. Then you need to activate it:
conda activate gis
Now you can install geopandas and jupyter lab if you need it (Personally recommend VSCode):
conda install -y -c conda-forge geopandas jupyterlab
enter code here
Use below command to install,
conda install geopandas
or
pip install geopandas
When using pip to install GeoPandas, you need to make sure that all dependencies are installed correctly.
fiona provides binary wheels with the dependencies included for Mac and Linux, but not for Windows.
pyproj, rtree, and shapely provide binary wheels with dependencies included for Mac, Linux, and Windows.
Windows wheels for shapely, fiona, pyproj and rtree can be found at Christopher Gohlke’s website.
Depending on your platform, you might need to compile and install their C dependencies manually. We refer to the individual packages for more details on installing those. Using conda (see above) avoids the need to compile the dependencies yourself.
This solution might not be exactly relevant, but since there is no marked solution, it might help...
I recently ran into a problem installing geopandas as well. Though I did mine through my terminal and I did receive an error message: OSError: could not find or load spatialindex_c-64.dll.
I used: conda install -c conda-forge rtree=0.9.3.
Check out this post for more info.
I'm trying to update the pandas library to the latest version, but conda doesn't seem to be doing so. I ran the following line
conda update pandas
and this is the output I got back
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
However, it doesn't appear to have updated since the version still isn't working in my Jupyter Notebook. I've also tested for this by running the command
conda list | grep "pandas"
and received this output
pandas 0.23.4
So clearly, it's not being updated for some reason. I even tested with pip3 which gave me an installed version of 0.25.3 so I'm not really sure why this is happening and I have a project that's due soon, so I would really appreciate some help here.
I found a fix. For some reason, it appears there was a conflict between pip / pip3 and conda that was causing conda to keep referencing the old pandas version. It might also be because pandas relies on other packages, which haven't been updated since the last command required me to update numpy and other packages for the command to be executed efficiently.
Anyways, here's the set of commands I ran to fix the issue:
pip uninstall pandas
pip3 uninstall pandas
conda install pandas=0.25.3
following code is giving me error.
import pandas as pd
df = pd.DataFrame({'a' : [1,2,3]})
df.to_hdf('temp.h5', key='df', mode='w')
This is giving me error.
Missing optional dependency 'tables'. Use pip or conda to install tables.
I already tried
ImportError HDFStore requires PyTables No module named tables. Still the same error.
I am getting the same error when reading hdf file. And tables are already installed for my python.
Some version info.
python 3.7.4
pandas 0.25.2
windows10
PS: You can reproduce this in repl https://repl.it/.
Update:
I tried runnig following.
import tables
and got this error:
ImportError: Could not load any of ['hdf5.dll', 'hdf5dll.dll'], please ensure that it can be found in the system path.
It looks like pandas is not giving accurate message for this. Its just saying missing dependency when its actually present.
If anyone knows how to resolve this. That will help.
For conda users:
conda install pytables
The issue was with tables.
When i was installing tables using pip into local user directory using following command it's not working.
pip install --user tables
Running import tables will result in this error.
ImportError: Could not load any of ['hdf5.dll', 'hdf5dll.dll'], please ensure that it can be found in the system path
The solution that worked for me is to uninstall tables. And install it into python's directory. (or where your python is installed). without --user option. You may require admin/root access for this depending upon location of your python.
For me my python path was C:\Program Files\Python37-64\python.exe and installing under c:\program files\python37-64\lib\site-packages\ worked for me.
Hope this helps. I don't know why installing in user directory is not working for tables. If anyone can find the reason for that please post here.
I got it to work by using
conda install snappy
using tables 3.6.1 worked for me to resolve the dependency
pip install tables==3.6.1
I used following command successfully resolved this problem:
pip install --upgrade tables
hope that work for you !
This problem has appeared for me when refreshing an existing conda virtal env using pip install -U -r requirements.txt. I resolved the issue as follows:
conda env remove -n <env> # remove your virtual env.
conda create -n <env> python==3.8 # create your virtual env again.
pip install -U -r requirements.txt
It's quite tedius to maintain a mix of conda and pip packages, so I just use the latter.
The above solutions did not work for me. Perhaps because I built the individual environment using the conda-forge channel, I had success with this:
conda install -c conda-forge pytables
I am trying to create a conda package using conda build and a meta.yaml file. Most of the dependencies are handled just fine but some of them are causing issues. I know these packages all work together because I am using them in my dev environment.
My requirements section for the yaml file is as follows:
requirements:
build:
- setuptools
- numpy
- python >=3.6
- matplotlib
- rdkit
- openforcefield
- openeye
- networkx
- psi4
run:
- numpy
- python >=3.6
- matplotlib
- rdkit
- openforcefield
- openeye
- networkx
- psi4
All of the packages causing issues (see error below) are installable through conda, for example:
conda install -c psi4 psi4
conda install -c omnia openforcefield
conda install -c openeye openeye-toolkits
conda install -c rdkit rdkit
However when calling conda build . I get the following error:
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'rdkit', 'openeye', 'psi4', 'openforcefield'}
I believe the rest of the .yaml is correct as there have been no errors raised with respect to anything else. Do I need to be more specific/use some special code for identifying package names? Or perhaps the issue is something else.
Thanks for any help.
I believe I have found the issue.
The above packages all come from different channels. Having added all of the channels I now get further through the build process. Channels are added with:
conda config --add channels <name of channel>
There may be an issue when it comes to distributing the package though. I think other people might have to add all the other channels as well.
Since yesterday I've had this error when I try to import packages on anaconda :
ImportError: Missing required dependencies ['numpy']
I have tried un-installing Anaconda and Python, switching to Python 2.7 but nothing works it's still the same error, here is the code I get :
Any help is really appreciated thanks !
I had this same issue immediately after upgrading pandas to 0.19.2. I fixed it with the following install/uninstall sequence from the windows cmd line:
pip uninstall pandas -y
pip uninstall numpy -y
pip install pandas
pip install numpy
This also broke my matplotlib install so I uninstalled/installed that as well.
Very odd behavior for a seemingly routine upgrade.
What happens if you try to import numpy?
Have you tried'
pip install --upgrade numpy
pip install --upgrade pandas
I had to install this other package:
sudo apt-get install libatlas-base-dev
Seems like it is a dependency for numpy but the pip or apt-get don't install it automatically for whatever reason.
I had this problem with last version of numpy 1.16.x
Problem resolved with
python3 -m pip uninstall numpy
python3 -m pip install numpy==1.14.0
Did you install miniconda and pandas without dependencies?
Try installing numpy first with conda install numpy or pip install numpy.
If you're on Windows you can get pre-compiled versions of most libraries that require compilation from here.
On Windows 10 Anaconda3-5.3.0-Windows-x86_64 I had the Missing required dependencies ['numpy'] error when running scripts as so, %HOMEPATH%\AppData\Local\Continuum\anaconda3\python.exe pandas_script_foo.py.
In my case the error was caused by missing Anaconda package PATH definitions when running Anaconda python.exe in a windows cmd.exe session. The numpy package is not missing. It just can't be found on the PATH.
The Anaconda installation includes windows shortcuts that give examples of configuring the PATH per script run. See the shortcuts in the %HOMEPATH%\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Anaconda3 (64-bit) directory for examples.
See the %HOMEPATH%\AppData\Local\Continuum\anaconda3\cwp.py script to see how Anaconda configures PATH.
Below is an example windows BAT file that calls cwp.py to setup PATH, and then run a python script. Its a copy of the commands the Anaconda jupyter-lab shortcut executes.
%HOMEPATH%\AppData\Local\Continuum\anaconda3\python.exe ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3\cwp.py ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3 ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3\python.exe ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3\Scripts\jupyter-lab-script.py
If you need to execute python scripts on Anaconda with the conveniance of running a BAT file, the above BAT file example should do the trick.
The data manipulation capabilities of pandas are built on top of the numpy library. In a way, numpy is a dependency of the pandas library. If you want to use pandas, you have to make sure you also have numpy. When you install pandas using pip, it automatically installs numpy. If it doesn't, try the following
pip install -U numpy pandas
For conda
conda install numpy pandas
I also faced the same issue. It happened to me after I upgraded my numpy library.
It was resolved in my case by upgrading my pandas library as well after upgrading my numpy library using the below command:
pip install --upgrade pandas
Try:
sudo apt-get install libatlas-base-dev
It should work now.
Else, try uninstall and reinstall numpy and pandas.
I had the same issue. It was because I had multiple versions of numpy installed. Remove all versions by repeatedly using:
pip uninstall numpy
Then re-install it with the command:
pip install numpy
First, try to import numpy on it's own, like so:
import numpy as np
I got this message:
ImportError: Something is wrong with the numpy installation. While importing
we detected an older version of numpy in
['/home/michael/.local/lib/python3.6/site-packages/numpy']. One method of
fixing this is to repeatedly uninstall numpy until none is found, then
reinstall this version.
So do what it says, keep uninstalling numpy until there is none, and then reinstall.
This worked for me.
I had the same issue while using Microsoft Visual Code with Python 3.7.3 64-bit('base':conda)as my python interpreter. Before running any code type the following three commands:
C:/ProgramData/Anaconda3/Scripts/activate #activate conda Scripts directory
conda activate base #activate conda
& C:/ProgramData/Anaconda3/python.exe #to run python
I have same problem.
I have got two version of numpy 1.16.6 and 1.15.4, fresh installed pandas did not work correctly.
I fixed it by uninstalling all versions of numpy and pandas and install the last versions.
$ pip uninstall numpy pandas -y
Uninstalling numpy-1.16.6:
Successfully uninstalled numpy-1.16.6
Uninstalling pandas-0.24.2:
Successfully uninstalled pandas-0.24.2
$ pip uninstall numpy pandas -y
Uninstalling numpy-1.15.4:
Successfully uninstalled numpy-1.15.4
Cannot uninstall requirement pandas, not installed
$ pip uninstall numpy pandas -y
Cannot uninstall requirement numpy, not installed
$ pip install numpy pandas
I had the same issue with anaconda package, it got updated.
anaconda {4.3.1 -> custom} ## I am not sure if this was the issue
Hit below command to know
conda list --revisions
what i did is just uninstall pandas with conda and re-install it
conda install pandas
Some new libs may also get installed with it.
It worked for me hope will do the same for you.
Uninstall all pip packages that you're having problems with. Manually remove all site-packages files. If you're using MacPorts, sudo port clean .
Then try reinstalling. Sometimes, there are files that should have been removed, but weren't if the installation was abruptly interrupted or something.
There could be an issue with conflicting versions of the package(s), as well as potentially issues with Pathing. Are you sure you've set the correct Path for your binaries? (/opt/local/bin, /anaconda2/bin, etc.)
Another issue could be some PYTHONPATH that's explicitly looking in the wrong place for the file.
I had a same issue recently with Anaconda with Python 3.7.
I solved this problem by downgrading python version to 3.6:
conda install python=3.6
and then by updating all the packages:
conda update --all
pandas is built on top of numpy so you need to have numpy to use the data manipulation feature, so install numpy first.
pip install numpy
This worked in my anaconda environment, but I do not know why conda does not work. For some reason conda uninstall was not sufficient. This only worked with conda remove.
conda remove pandas
conda remove numpy
conda install pip
pip install pandas
*With help from this answer
This raises the following import warning in python 3.6 and 3.7:
ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
If you with to ignore this warning (and maybe other ImportWarnings), add the following to your script before importing pandas:
import warnings
warnings.filterwarnings('ignore', category=ImportWarning, module='_bootstrap.py')
In my case even though I was using the above options of uninstall and installing using pip the code was still giving me same errors.
Finally, I created a vritual environment and Installed numpy and pandas using pip in my virtual env. Now the code is running.
Steps: for Anaconda3 - Please change according to your installation type:
[if you dont have virtual env package installed]
$ pip install virtualenv
[from command prompt go to the directory by c:\anadonda3\scripts
[write the following command to use virtual env to create a virtual env for you in your desired location]
$virtualenv c:\anaconda3\envs\my_virtual_env
[once created you will have to activate your virtual env]
$c:\anaconda3\envs\my_virtual_env\scripts activate
[now pip install numpy and pandas and other required packages using pip]
[once installations are done exit from the virtual env]
$c:\anaconda3\envs\my_virtual_env\scripts deactivate
now use the python.exe inside your virtual env folder to run the script and it will run even with python 3.7.
I am using Win10 and Conda, and this issue just append to me when upgrading python 3.7.2-h8c8aaf0_0 --> 3.7.2-h8c8aaf0_2.
I solved it by return to the previous version with
conda install python=3.7.2=h8c8aaf0_0
If you're running your program on PyCharm on Windows, there is a known bug, because PyCharm simply doesn't add env-related paths to PATH.
The issue is fixed in the 2019.1 Early Access Preview (EAP) build.
For me installing the EAP fixed the issue.
nothing worked for me ... except when I found this
I suspect that you have a local file called unittest.py that is getting imported instead of the standard module.
I was trying to upgrade my anaconda 2 with anaconda 3. I tried installing Anaconda3-2018.12-Windows-x86 and Anaconda3-2019.03-Windows-x86_64 on my Windows 10 machine and failed with this error. For me, using Anaconda3-4.4.0-Windows-x86_64 for anaconda 3 worked the trick after trying everything listed in answers here.
I fixed this using Anaconda by going to Environments > base(root), searching for numpy in the installed modules and clicking the tickbox alongside it and choosing > Mark for specific version installation > 1.14.0 (as suggested by another user on this thread). Then clicking Apply. Once it downgraded numpy I stopped getting errors when running py files on the command line.
Throughout this saga, I was still able to use https://pypi.org/project/auto-py-to-exe/ even when I was getting the numpy errors on the command line, but it was a hassle to create an exe every time I wanted to test a change. It's all sorted now. I guess there was a problem with numpy 1.16.4.
Anyway, I hope this helps someone who's using Anaconda as well.
The following worked for me.
Deleted the folders for numpy and pandas together with their contents completely from the site-packages folder. Check depending on whether you are using python2 or python3. Check the exact path as per your machine.
N.B handle with care "rm -rf" command. If you are not sure of what you are doing, please do it manually using any file explorer of your choice!!
rm -rf ~/anaconda2/envs/myenv/lib/pythonX/site-packages/pandas*
rm -rf ~/anaconda2/envs/myenv/lib/pythonX/site-packages/numpy*
Then i installed clean packages for pandas and numpy as usual with
pip install numpy
pip install pandas
I've got the same error recently. Before applying uninstall or install tools, try to update your Jupyter.
How? Go to 'Environments' and type on the Search Packages box 'pandas'. Afterwards, check the version (if that column shows a blue number with a diagonal arrow, it means that your pandas is out of date). Click on 'pandas' and a option will pop up (choose 'Apply' and wait for a couple of minutes to update the package). And then, make a quick test on any notebook to make sure that your Jupyter is running smoothly.
For those who couldn't solve with the above answers:
Ensure that you are running python3 with
$ python version
If not, install python3.
Then change default python to python3 with
$ alias python=python3
Next, close your jupyter lab/notebook environment and re-launch it with default python being python3.
build_exe_options = {"packages": ["os",'pandas','numpy']}
It works.
you are running python 3.7
create environment for python 3.6
python3.6 filename.py