I'm new with IPython and I had this awkward problem with using a notebook:
When I try to use matplotlib
%matplotlib inline
I get this error:
ImportError: /home/ipython/anaconda2/bin/../lib/libgfortran.so.3:
version `GFORTRAN_1.4' not found (required by /usr/lib/liblapack.so.3)
But.. If I execute the code below before:
import sys
sys.path.reverse()
It works!
The question is: Does the order of python path matters? Do I need to install python dependencies in a correct order or set the python path to a correct order?
Thanks!
PS: I'm using jupyter server 4.
I'm sure paths do matter but the same way like for any other python program.
When a module named spam is imported, the interpreter first searches
for a built-in module with that name. If not found, it then searches
for a file named spam.py in a list of directories given by the
variable sys.path.
https://docs.python.org/2/tutorial/modules.html#the-module-search-path
Anyway, I think you should try first this workaround, i.e. add to your .bashrc:
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgfortran.so.3
If it doesn't help you could try change PYTHONPATH in .bashrc. Anaconda adds itself there. So you could interchange it.
Don't forget to reload .bashrc after changing with source ~/.bashrc
I'm using Pelican for a static blog, and attempting to install the figure-ref extension. Since I'm using Markdown, the plugin relies on the figureAltCaption third-party Markdown extension. However I have no idea how to install it.
Pelican has an MD_EXTENSIONS configuration option, but I've tried a few obvious options with no luck. It seems like this is a dead-simple gimme but it's not clear how to proceed. Would love some suggestions.
Unfortunately, the author of figureAltCaption appears to have not provided an install script. My suggestion would be to create one and contribute it as a pull request. This tutorial about creating Extensions for Python-Markdown covers creating an install script as well.
However, as a shortcut, you should be able to just copy the figureAltCaption.py file to the appropriate directory. Usually you want the site-packages directory. As this answer shows, just do the following from Python:
>>> import site; site.getsitepackages()
Then copy the figureAltCaption.py file to the first directory returned.
Now that the extension is on your PYTHONPATH, it should be importable. From the Python prompt, try:
import figureAltCaption
If you get no errors, then it worked and you just need to tell Pelican about it.
MD_EXTENSIONS = ['figureAltCaption']
I have a decently long program that I have been trying to compile. I have tried py2exe and cx_Freeze, both seem to come up with this problem.
I used the following setup.py file to compile my program:
import sys
from cx_Freeze import setup, Executable
base = None
if sys.platform == 'win32':
base = 'Win32GUI'
executables = [
Executable('version_3_2.py', base=base)
]
setup(name='version_3_2',
version='0.32',
description='desc',
executables=executables
)
From running this using
python setup.py build
The executable is created.
From running the executable, i was given a traceback stating that
TclError: Can't find a usable init.tcl in the following directories:
C:/Python27/build/lib/tcl8.5
and a bunch of other directories
From adding all of the tkinter and tcl files and folers into a couple of those directories i get the next traceback from executing:
C:/Python27/build/lib/tcl8.5/init.tcl: version conflict for package "Tcl":
have 8.5.15, need exactly 8.5.2
version conflict for package "Tcl": have 8.5.15, need exactly 8.5.2
while executing
"package require -exact Tcl 8.5.2"
(file "C:/Python27/build/lib/tcl8.5/init.tcl" line 20)
invoked from within
"source C:/Python27/build/lib/tcl8.5/init.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $tclfile]"
I'm not entirely sure what to do. Several solutions like How to correct TCL_LIBRARY and TK_LIBRARY with py2exe and Py2exe with Tkinter have not worked.
Any Ideas?
You need to match exactly the libtcl8.5.dll (or whatever the name is on your system) and the init.tcl (and related files) because they are both part of the same Tcl installation. If you change one out, you must change the other as well. How exactly you've mangled your installation I'm not quite sure, but mangled it surely is. Also be aware that in Tcl 8.5 (and before), it's strongly advised to match the Tk version precisely to it as well; we relax this requirement in 8.6 but you're not using that…
(Note that this is different from the way that normal dependencies work in Tcl; typically a program will depend on a minimum API version, not an exact one.)
Since you've got a binary build of 8.5.15 in use, you might as well use the script files for that version too. I suggest getting the Tcl source distribution for 8.5.15 from SourceForge and grabbing the files out of the library directory in there. You probably only need the .tcl files directly in there (especially init.tcl of course!) and not in any of the subdirectories, as the subdirectories are for official add on packages and those aren't so tightly bound to Tcl versions.
I am trying to install a homegrown package that will be used , but python package installation is still a bit of a quagmire for me, and I haven't gotten this to work.
I created a package using setup.py sdist, which I uploaded to a repository
I am trying to install my package on another machine. I tried three methods, each time on an entirely clean machine. But none are doing what I want them to.
Method 1
easy_install http://mysite/mypkg.zip
RESULT: mypkg.egg gets added to \Python27\Lib\site-packages. But none of my folder structure is there
Method 2
pip install http://mysite/mypkg.zip
RESULT: two folders, mypkg and mypkg-1.0-py2.7.egg-info, get added to Python27\Lib\site-packages. All of the files seem to be there. But when I got to import or run nosetests on the folder, I get all sorts of import errors that reference mypkg modules. I have played with PATH and PYTHONPATH to get all variations of including the folder, but nothing has worked.
Method 3
download .zip
extract locally
add folder to PATH
run easy_install . in the local dir
RESULT: unpacks pkg locally. When I run nosetests on this folder, everything runs as expected.
Thing is, I don't want each user to have to do all of the steps in Method 3. I will eventually be running nosetests in a .bat file that does various things with the output. I don't want every user to have to modify the .bat file to indicate where the testsuite is located. Which is why Python27\Lib\site-packages appealed to me.
Any insight as to why these three methods behave so differently would be very helpful!
I am attempting to put together a simple c++ test project that uses an embedded python 3.2 interpreter. The project builds fine but Py_Initialize raises a fatal error:
Fatal Python error: Py_Initialize: unable to load the file system codec
LookupError: no codec search functions registered: can't find encoding
Minimal code:
#include <Python.h>
int main (int, char**)
{
Py_Initialize ();
Py_Finalize ();
return 0;
}
The OS is 32bit Vista.
The python version used is a python 3.2 debug build, built from sources using VC++ 10.
The python_d.exe file from the same build runs without any problems.
Could someone explain the problem and how to fix it? My own google-fu fails me.
EDIT 1
After going through the python source code I've found that, as the error says, no codec search functions have been registered. Both codec_register and PyCodec_Register are as they should be. It's just that nowhere in the code are any of these functions called.
I don't really know what this means as I still have no idea when and from where these functions should have been called. The code that raises the error is entirely missing from the source of my other python build (3.1.3).
EDIT 2
Answered my own question below.
Check the PYTHONPATH and PYTHONHOME environment variables and make sure they don't point to Python 2.x.
http://bugs.python.org/issue11288
Parts of this have been mentioned before, but in a nutshell this is what worked for my environment where I have multiple Python installs and my global OS environment set-up to point to a different install than the one I attempt to work with when encountering the problem.
Make sure your (local or global) environment is fully set-up to point to the install you aim to work with, e.g. you have two (or more) installs of, let's say a python27 and python33 (sorry these are windows paths but the following should be valid for equivalent UNIX-style paths just as well, please let me know about anything I'm missing here (probably the DLLs path might differ)):
C:\python27_x86
C:\python33_x64
Now, if you intend to work with your python33 install but your global environment is pointing to python27, make sure you update your environment as such (while PATH and PYTHONHOME may be optional (e.g. if you temporarily work in a local shell)):
PATH="C:\python33_x64;%PATH%"
PYTHONPATH="C:\python33_x64\DLLs;C:\python33_x64\Lib;C:\python33_x64\Lib\site-packages"
PYTHONHOME=C:\python33_x64
Note, that you might need/want to append any other library paths to your PYTHONPATH if required by your development environment, but having your DLLs, Lib and site-packages properly set-up is of prime importance.
Hope this helps.
The core reason is quite simple: Python does not find its modules directory, so it can of course not load encodings, too
Python doc on embedding says "Py_Initialize() calculates the module search path based upon its best guess" ... "In particular, it looks for a directory named lib/pythonX.Y"
Yet, if the modules are installed in (just) lib - relative to the python binary - above guess is wrong.
Although docs says that PYTHONHOME and PYTHONPATH are regarded, we observed that this was not the case; their actual presence or content was completely irrelevant.
The only thing that had an effect was a call to Py_SetPath() with e.g. [path-to]\lib as argument before Py_Initialize().
Sure this is only an option for an embedding scenario where one has direct access and control over the code; with a ready-made solution, special steps may be necessary to solve the issue.
Ran into the same thing trying to install brew's python3 under Mac OS! The issue here is that in Mac OS, homebrew puts the "real" python a whole layer deeper than you think. You would think from the homebrew output that
$ echo $PYTHONHOME
/usr/local/Cellar/python3/3.6.2/
$ echo $PYTHONPATH
/usr/local/Cellar/python3/3.6.2/bin
would be correct, but invoking $PYTHONPATH/python3 immediately crashes with the abort 6 "can't find encodings." This is because although that $PYTHONHOME looks like a complete installation, having a bin, lib etc, it is NOT the actual Python, which is in a Mac OS "Framework". Do this:
PYTHONHOME=/usr/local/Cellar/python3/3.x.y/Frameworks/Python.framework/Versions/3.x
PYTHONPATH=$PYTHONHOME/bin
(substituting version numbers as appropriate) and it will work fine.
From python3k, the startup need the encodings module, which can be found in PYTHONHOME\Lib directory.
In fact, the API Py_Initialize () do the init and import the encodings module.
Make sure PYTHONHOME\Lib is in sys.path and check the encodings module is there.
I had this issue with python 3.5, anaconda 3, windows 7 32 bit. I solved it by moving my pythonX.lib and pythonX.dll files into my working directory and calling
Py_SetPythonHome(L"C:\\Path\\To\\My\\Python\\Installation");
before initialize so that it could find the headers that it needed, where my path was to "...\Anaconda3\". The extra step of calling Py_SetPythonHome was required for me or else I'd end up getting other strange errors where python import files.
I just ran into the exact same problem (same Python version, OS, code, etc).
You just have to copy Python's Lib/ directory in your program's working directory ( on VC it's the directory where the .vcproj is )
There appears to be something going wrong with the release build either failing to include the appropriate codecs or else misidentifying the codec to use for system APIs. Since the python_d executable is working, what does that return for os.getfsencoding()? (Use the C API to call that between your Initialize/Finalize calls)
I had the same issue and found this question. However from the answers here I was not able to solve my problem. I started debugging the cpython code and thought that I might be discovered a bug. Therefore I opened a issue on the python issue tracker.
My mistake was that I did not understand that Py_SetPath clears all inferred paths.
So one needs to set all paths when calling this function.
Link to the issue conversation
For completion I also copied the most important part of the conversation below.
My original issue text
I compiled the source of CPython 3.7.3 myself on Windows with Visual Studio 2017 together with some packages like e.g numpy. When I start the Python Interpreter I am able to import and use numpy. However when I am running the same script via the C-API I get an ModuleNotFoundError.
So the first thing I did, was to check if numpy is in my site-packages directory and indeed there is a folder named numpy-1.16.2-py3.7-win-amd64.egg. (Makes sense because the python interpreter can find numpy)
The next thing I did was to get some information about the sys.path variable created when running the script via the C-API.
#### sys.path content ####
C:\Work\build\product\python37.zip
C:\Work\build\product\DLLs
C:\Work\build\product\lib
C:\PROGRAM FILES (X86)\MICROSOFT VISUAL STUDIO\2017\PROFESSIONAL\COMMON7\IDE\EXTENSIONS\TESTPLATFORM
C:\Users\rvq\AppData\Roaming\Python\Python37\site-packages
Examining the content of sys.path I noticed two things.
C:\Work\build\product\python37.zip has the correct path 'C:\Work\build\product\'. There was just no zip file. All my files and directory were unpacked. So I zipped the files to an archive named python37.zip and this resolved the import error.
C:\Users\rvq\AppData\Roaming\Python\Python37\site-packages is wrong it should be C:\Work\build\product\Lib\site-packages but I dont know how this wrong path is created.
The next thing I tried was to use Py_SetPath(L"C:/Work/build/product/Lib/site-packages") before calling Py_Initialize(). This led to
Fatal Python Error 'unable to load the file system encoding'
ModuleNotFoundError: No module named 'encodings'
I created a minimal c++ project with exact these two calls and started to debug Cpython.
int main()
{
Py_SetPath(L"C:/Work/build/product/Lib/site-packages");
Py_Initialize();
}
I tracked the call of Py_Initialize() down to the call of
static int
zipimport_zipimporter___init___impl(ZipImporter *self, PyObject *path)
inside of zipimport.c
The comment above this function states the following:
Create a new zipimporter instance. 'archivepath' must be a path-like
object to a zipfile, or to a specific path inside a zipfile. For
example, it can be '/tmp/myimport.zip', or
'/tmp/myimport.zip/mydirectory', if mydirectory is a valid directory
inside the archive. 'ZipImportError' is raised if 'archivepath'
doesn't point to a valid Zip archive. The 'archive' attribute of the
zipimporter object contains the name of the zipfile targeted.
So for me it seems that the C-API expects the path set with Py_SetPath to be a path to a zipfile. Is this expected behaviour or is it a bug?
If it is not a bug is there a way to changes this so that it can also detect directories?
PS: The ModuleNotFoundError did not occur for me when using Python 3.5.2+, which was the version I used in my project before. I also checked if I had set any PYTHONHOME or PYTHONPATH environment variables but I did not see one of them on my system.
Answer
This is probably a documentation failure more than anything else. We're in the middle of redesigning initialization though, so it's good timing to contribute this feedback.
The short answer is that you need to make sure Python can find the Lib/encodings directory, typically by putting the standard library in sys.path. Py_SetPath clears all inferred paths, so you need to specify all the places Python should look. (The rules for where Python looks automatically are complicated and vary by platform, which is something I'm keen to fix.)
Paths that don't exist are okay, and that's the zip file. You can choose to put the stdlib into a zip, and it will be found automatically if you name it the default path, but you can also leave it unzipped and reference the directory.
A full walk through on embedding is more than I'm prepared to type on my phone. Hopefully that's enough to get you going for now.
I had the problem and was tinkering with different solutions mentioned here. Since I was running my project from Visual Studio, apparently, I needed to set the environment path inside Visual Studio and not the system path.
Adding a simple PYTHONHOME=PATH\TO\PYTHON\DIR in the project solution\properties\environment solved the problem.
For me this happened when I updated Python 64 bit from 3.6.4 to 3.6.5. It threw some error like "unable to extract python.dll. Do you have permissions."
Pycharm also failed to load interpreter, even though I reloaded it in settings. Running python command gave same error, with and without administrator mode.
Reason
There was error in installation of Python, include folder in python installation directory C:\Users\USERNAME\AppData\Local\Programs\Python\Python36 was missing
Reinstalling Python also dint solve the issue.(Not removal and install)
Solution
Uninstall Python and Install of Python again.
Because running installer was just extracting same files excluding include folder
In my cases, for windows, if you have multiple python versions installed, if PYTHONPATH is pointing to one version the other ones didn't work. I found that if you just remove PYTHONPATH, they all work fine
For those working in Visual Studio simply add the include, Lib and libs directories to the Include Directories and Library Directories under
Projects Properties -> Configuration Properties > VC++ Directories :
For example I have Anaconda3 on my system and working with Visual Studio 2015 This is how the settings looks like (note the Include and Library directories) :
Edit:
As also pointed out by bossi setting PYTHONPATH in your user Environment Variables section seems necessary.
a sample input can be like this (in my case):
C:\Users\Master\Anaconda3\Lib;C:\Users\Master\Anaconda3\libs;C:\Users\Master\Anaconda3\Lib\site-packages;C:\Users\Master\Anaconda3\DLLs
is necessary it seems.
Also, you need to restart Visual Studio after you set up the PYTHONPATH in your user Environment Variables for the changes to take effect.
Also note that :
Make sure the PYTHONHOME environment variable is set to the Python
interpreter you want to use. The C++ projects in Visual Studio rely on
this variable to locate files such as python.h, which are used when
creating a Python extension.
So, for some reason the python dll fails to locate the encodings module. The python.exe executable apparently finds it because it has the expected relative path. Modifying the search path works.
The reason for all of this? Don't know but at least it works. I highly suspect a typo on my part somewhere, that's usually the reason for odd bugs it seems.