I wrote a script in Spyder IDE, but in order for clients to use it, I would like to make it easier to run it then opening Anaconda and then Spyder and running it from there.
The reason I used Spyder was because it allowed me to use many modules that otherwise wouldn't be allowed on company stations.
I researched a lot but could not find a way to do this.
I was thinking of enveloping the script in a batch file and running it. I tried updating the python script to look for modules in the Anaconda default directories:
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\python37.zip)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\DLLs)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\lib)
sys.path.insert(1, C:\\ProgramData\\Anaconda3)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\lib\\site-packages)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\lib\\site-packages\\win32)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\lib\\site-packages\\win32\\lib)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\lib\\site-packages\\Pythonwin)
sys.path.insert(1, C:\\ProgramData\\Anaconda3\\lib\\site-packages\\IPython\\extensions)
When running the script in Windows cmd, I got these errors when importing pandas module, so there is more to using Spyder then just accessing those modules (I couldn't figure out what):
Traceback (most recent call last):
File "script.py", line 32, in <module>
import pandas as pd
File "C:\ProgramData\Anaconda3\lib\site-packages\pandas\__init__.py", line 13, in <module>
__import__(dependency)
File "C:\ProgramData\Anaconda3\lib\site-packages\numpy\__init__.py", line 110, in <module>
import warnings
File "C:\ProgramData\Anaconda3\lib\warnings.py", line 494
f"coroutine '{coro.__qualname__}' was never awaited\n"
Another approach I tried was using pyinstaller, but that is not available for us and I cannot install it from the website.
Is there a way of running the python script and using all the modules offered by Anaconda without going through Spyder?
Have you tried py2exe? It's a great tool that does exactly what you're asking for.
Also look into cython. It's a lot easier to generate an executable from C code, and you'll get a performance boost as well.
Also try pyinstaller. It'll give you both an executable and settings for that, like icon or no-console. first go to the directory where your .py file is and run the below command:
pyinstaller script.py --onefile
Before this, you'll need to install that python module:
python* -m pip install pyinstaller
Where * is your specific python version, if you have multiple installed.
The first command will give you dist folder, here is where your executable is placed. and the script.spec file is your settings.
I want to call my Anaconda Python from the Windows shell. The goal is to eventually call it from MATLAB using a system call, so I have to use the plain Windows shell, and not the "Anaconda prompt".
I have a simple Python script that I want to run, but it doesn't get past the import statements:
> "C:\ProgramData\Anaconda3\python.exe" lhs.py
Traceback (most recent call last):
File "lhs.py", line 8, in <module>
import numpy
File "C:\ProgramData\Anaconda3\lib\site-packages\numpy\__init__.py", line 140, in <module>
from . import _distributor_init
File "C:\ProgramData\Anaconda3\lib\site-packages\numpy\_distributor_init.py", line 34, in <module>
from . import _mklinit
ImportError: DLL load failed: The specified module could not be found.
EDIT
I made a simplified Python script (error.py) containing only one line:
import numpy
I then call it as:
"C:\ProgramData\Anaconda3\python.exe" error.py
TL;DR
C:\ProgramData\Anaconda3\condabin\activate.bat YOURENVIRONMENTNAME && python N:\Temp\lhs.py
Long Answer
There is a similar issue reported on github. I found this by searching for the last few lines of your message. It is about this:
File "C:\Users\hanna\Anaconda3\lib\site-packages\tensorflow\python_init.py",
line 47, in
import numpy as np
File "C:\Users\hanna\Anaconda3\lib\site-packages\numpy_init_.py", line 140, in
from . import _distributor_init
File "C:\Users\hanna\Anaconda3\lib\site-packages\numpy_distributor_init.py",
line 34, in
from . import _mklinit
There, they link to a conda troubleshooting page:
Error messages like
Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll
Cause
NumPy is unable to load the correct MKL or Intel OpenMP runtime
libraries. This is almost always caused by one of two things:
The environment with NumPy has not been activated.
Another software vendor has installed MKL or Intel OpenMP
(libiomp5md.dll) files into the C:\Windows\System32 folder. These
files are being loaded before Anaconda's and they're not compatible.
If you are not activating your environments, start with doing that.
So let us try this first:
C:\\ProgramData\\Anaconda3\\condabin\\activate.bat
conda run -n yourenvironment C:\\path\\to\\your\\pythonfile\\lhs.py
(Yes, from a normal cmd terminal)
If that seems to work, you should be able to chain the two commands using &&. My own example looks like this:
F:\Programme\Programme\Anaconda3\condabin\activate.bat && conda run -n textrecognition N:\Temp\temp.py
This can be simplified further to
F:\Programme\Programme\Anaconda3\condabin\activate.bat textrecognition && python N:\Temp\temp.py
In case of the problem being number two, you have the option to load conda things before system32. This is supported in anaconda starting the following versions:
Python 2.7.15 build 14
Python 3.6.8 build 7
Python 3.7.2 build 8
To activate that, you need to set some environment variables to 1:
Control environment variables:
CONDA_DLL_SEARCH_MODIFICATION_ENABLE
CONDA_DLL_SEARCH_MODIFICATION_DEBUG
CONDA_DLL_SEARCH_MODIFICATION_NEVER_ADD_WINDOWS_DIRECTORY
CONDA_DLL_SEARCH_MODIFICATION_NEVER_ADD_CWD
To set variables on Windows, you may use either the CLI (Anaconda
Prompt, for example) or a Windows GUI.
CLI:
https://superuser.com/questions/79612/setting-and-getting-windows-environment-variables-from-the-command-prompt/79614
GUI:
http://www.dowdandassociates.com/blog/content/howto-set-an-environment-variable-in-windows-gui/
These should be set to a value of 1 to enable them. For example, in an
anaconda prompt terminal:
set CONDA_DLL_SEARCH_MODIFICATION_ENABLE=1
you need to activate your conda base in cmd before calling the script
call <path>\anaconda\Scripts\activate base
<path>\anaconda\python.exe <path>\scriptname.py
I am trying to run a code I downloaded from https://github.com/szieleniewski/NIFSIM to analyze data from JWSTelescope. While running the main file, jwsim.py, I get a module error on one of the definitions.
I am currently using Python 3.7, Ubuntu 16.04, and I work under an environment (called webbpsf-env). These details can not be changed, since WebbPSF (a program I am using with the code) requires such versions to work. The main jsim.py file is stored in the Downloads folder.
I get the following error:
(webbpsf-env) aleejandrof#aleejandrof-Satellite-C55t-B:~/Downloads/NIFSIM-master$ python jsim.py
*File* "jsim.py", line 18, in <module>
*from* src.JSIM_main *import* main
File "/home/aleejandrof/Downloads/NIFSIM-master/src/JSIM_main.py", line 22, in <module>
*from* JSIM_Specres *import* spectral_res
ModuleNotFoundError: No module named 'JSIM_Specres'
The mentioned line is this one:
from JSIM_Specres import spectral_res
I've been told, that if I work ouside the environment, the module could be found. For me this is not an option since Webbpsf requires working inside an environment. I have tried downloading the master file again inside the environment (through pip), but it could not be done. Is there a way to "insert" a file into an environment? what should I do?
The author likely anticipated you had a certain env var set. Try this:
$ cd ../NIFSIM-master && env PYTHONPATH=.:src python jsim.py
I recently added a tool to my makefile's toolchain that is written in python. It processes .json input and outputs some assembly data, and when in run the python tool from the console (e.g. python xxx.py -o yyy.s zzz.json) it works quite well. However when the same script is run from within the makefile, suddenly package imports fail (concretly spoken those I installed using pip).
The makefile outputs the following error:
Traceback (most recent call last):
File "tools/pyset2s.py", line 2, in <module>
import pymap.tileset
File "/cygdrive/d/Hacking/__Violet_Sources/tools/pymap/tileset.py", line 3, in <module>
from . import image, palette, agbimg
File "/cygdrive/d/Hacking/__Violet_Sources/tools/pymap/image.py", line 3, in <module>
import png
ImportError: No module named png
make: *** [makefile:135: bld/map/tileset/gfx_maptileset0.s] Error 1
make: *** Waiting for unfinished jobs....
The only cause of this problem I figured so far might be, that the package (in this case PyPng, but I suppose it will also fail on the other ones (being Pilow and numpy) was installed while being in administrator mode (I am working under Windows and using a cygwin shell for the make call). However reinstalling the package did not work, since I am told, that the requirements are already satisfied. I also do not know who to promote my IDE (I am using Netbeans) to use adminstrator rights when running the make command.
Is there any solution to that?
Since updating from Homebrew Python 2.7.11 (from 2.7.10) I'm suddenly unable to test register my package on PyPi from the PyCharm IDE console.
Running (as an "External Tool")
python -B setup.py register -r pypitest
I now get
Traceback (most recent call last):
File "setup.py", line 22, in <module>
from setuptools import setup
File "/usr/local/lib/python2.7/site-packages/setuptools/__init__.py", line 12, in <module>
from setuptools.extension import Extension
File "/usr/local/lib/python2.7/site-packages/setuptools/extension.py", line 8, in <module>
from .dist import _get_unpatched
File "/usr/local/lib/python2.7/site-packages/setuptools/dist.py", line 16, in <module>
from setuptools.depends import Require
File "/usr/local/lib/python2.7/site-packages/setuptools/depends.py", line 6, in <module>
from setuptools import compat
File "/usr/local/lib/python2.7/site-packages/setuptools/compat.py", line 17, in <module>
import httplib
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py", line 80, in <module>
import mimetools
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/mimetools.py", line 6, in <module>
import tempfile
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tempfile.py", line 32, in <module>
import io as _io
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/io.py", line 51, in <module>
import _io
ImportError: dlopen(/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyCodecInfo_GetIncrementalDecoder
Referenced from: /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
Expected in: flat namespace
in /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
Process finished with exit code 1
I'm not sure how to proceed. I only get this issue if I execute from within my IDE's console. If I do it directly at the system command line (Terminal on OS X) I have no problems.
OS X 10.11.3; Homebrew Python 2.7.11; PyCharm 5.0.3
tl;dr: Fix this issue by doing one of the following:
type hash -r python, OR
log out and log in.
EDIT: An answer to my related question makes it clear what's happening here. When you install a new version of python, you may need to run hash -r python to tell bash to reset the "cached" location to the python executable.
In my case, I was typing python, which was on my $PATH at /usr/local/bin/python. But bash was still using the old cache location /usr/bin/python. So, the old executable was called, but the new path was provided to python in sys.argv[0]. This means that the old executable was running, but the new sys.executable value caused all the wrong modules to get loaded (including the io module).
I'm having the same problem. I installed python 2.7.11 via an installer from Python.org. Strangely, the issue seems to be related to some subtle difference between how OSX launches python when I invoke it from the shell using the full path vs. using just the word python.
So, for me, this works (invoking python via the full path /usr/local/bin/python):
$ which python
/usr/local/bin/python
$ /usr/local/bin/python -c "import io"
$
... but this doesn't:
$ python -c "import io"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/io.py", line 51, in <module>
import _io
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyCodecInfo_GetIncrementalDecoder
Referenced from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
Expected in: flat namespace
in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
So, as a workaround, you can try doing the same thing.
Elsewhere, I've posted a separate question about this puzzling behavior. Maybe somehow merely calling python invokes some strange mix of the 2.7.11 executable with the 2.7.10 dylibs??
According to https://github.com/klen/python-mode/issues/634:
I had the same issue, but successfully fixed. In my case I compiled
python and vim with homebrew, when PYTHON_PATH has been specified and
set to one of my dev environments, where I also had some libraries,
including io. Workaround was simple: open new terminal, make sure that
you do not have custom PYTHON_PATH, uninstall python, uninstall vim.
Reinstall both of them.
and
Problem solved.
Culprit is the update from python 2.7.10 to 2.7.11.
If you are using conda package control, simply run "conda install
python=2.7.10" will solve this problem.
This doesn't give the root cause though. Since this happens with _io, this looks like a bug in python 2.7.11 (unlikely, there would be a world-scale outcry and a prompt fix if it was) or some packaging bug or version mismatch specifically with the homebrew version (and maybe some related ones, too).
Try to import _io in the console and if it succeeds, check if it was loaded from the same path.
Reinstall python.
brew unlink python && brew reinstall python
Secure the path
export PYTHONPATH=$PYTHONPATH:/usr/local/bin/
BACKUP and Change the order of "paths" file.
sudo nano /etc/paths
it seems, the order of paths, it is decisive to run python properly. In my case, the result was:
#sudo nano /etc/paths
/usr/bin
/usr/local/bin
/bin
/usr/sbin
/sbin
On my mac, path is like this.
$ which python
/usr/local/bin/python
Now I can run both:
$ /usr/local/bin/python -c "import io"
$ python -c "import io"
I had the same issue, it is successfully fixed by just replacing the _io.so file.
sudo find / -name _io.so
copy the path of the _io.so file which DOES NOT belong to python-2.7.11. For example, copy the path of _io.so which is under python-2.7.5:
/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
Replace the /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so file with the _io.so that you just found.
This happened to me as well in MacVim. I solved it by making sure :python print(sys.path) is using system Python (e.g. /Library/Python/2.7/...)
Since I installed MacVim via Homebrew, I just did that by:
Spawn a new shell that had which python -> /usr/bin/python. For my case I needed to remove the pyenv line from my .bash_profile. If you installed Python via Homebrew you may want to brew unlink python first
brew reinstall macvim
If your problem is caused by anaconda, it is unnecessary to remove //anaconda directory.
Just open your ~/.bash_profile, find the line
export PATH="//anaconda/bin:$PATH
and comment it out, then restart your terminal session.
Another quick workaround if you don't mind sticking with Python 2.7.10 is to specify the path of the Python interpreter executable that will be used for the virtualenv. On OSX that path is usually /usr/bin/python:
virtualenv venv --python=/usr/bin/python
Can't add comment (?) so this just to share my exp., downgrade to 2.7.10 works fr me.
I got this error after a failed NLTK download, I needed to uninstall anaconda:
sudo rm -rf ~/anaconda
update PATH variable
This happened when I already had tried to create a venv in a folder, and mistakenly was trying to initialize a second one! So I just removed venv directory and re-ran the command. Very likely this is not the answer to this solution, but searching my error brought me here, so it may help some others who are stuck.
I solved this issue by removing the symbolic link that was in /usr/local/bin and copying the actual python binary, that was pointed to by said link, there.
I had the same issue when I tried to use PyCharm. Solved by setting "python interpreter" in project configuration to point to the python virtual env I wanted to use, which was an Anaconda env. Somehow the interpreter path was missing the "anaconda" portion of ~/.../anaconda/.../_io.so. No need to uninstall anaconda.