Edited based on comments:
I am trying to edit files (js) within one project which are called by a package in Python, however I am unable to determine the steps to be able to do so. I am looking to add some functionality to the itkwidgets package by updating the annotations returned by some function calls within the js files.
I have forked itkwidgets from git and installed locally using python -m pip install -e .. I can import this package in my notebook and have confirmed that it is loaded and working as expected.
My expectation is that I should be able to point the package (itkwidgets) towards a local version of the js project (itk-vtk-viewer) so that any edits made can be observed in the notebook.
(Part I do not understand)
In a viewer.js file it specifies the location of the js code that I want to edit:
import createViewer from 'itk-vtk-viewer/src/createViewer'
This viewer.js file is pointed to in a index.js file:
const { ViewerModel, ViewerView } = require('./viewer.js');
and this index.js file is pointed to within the package.json file.
My original thoughts were that I should be able to change the location pointed to in viewer.js file to a local folder and it would point towards the new code. However, even if I change the line to import createViewer from '/<NON_EXISTENT_FOLDER>/src/createViewer'. The code still runs as before. If I point towards the local version, I would expect some added console.log's to be printed, but again this does not occur.
I have tried reinstalling the package using pip following the change but that did not help either.
I am at a loss as I do not really understand what is happening. Any help appreciated.
Related
I am new with programming, so it is maybe harder for me to understand but I have the following issue:
I have a script that imports "eurostag.dll", which according to its manual, should work until Python 3.6. (but the manual is not updated, so it may work also with later updates, I assume).\ The issue is that I have Python 3.8. and when running the script I receive the following message:
"Failed to load EUROSTAG library (Could not find module 'D:\Eurostag\eustag_esg.dll' (or one of its dependencies). Try using the full path with constructor syntax.)"
I have tried to move the .dll library where the script is, but nothing changed. I tried also changing the directory with os.chdir, but the same message appears (with the same 'D:\Eurostag\eustag_esg.dll', so the directory was not changed.
Does anybody know if there is any workaround for this?
Thank you!
We are building a User Interface APP (predicting a continuous variable through a machine learning model) through R Shiny.
Since we built the machine learning model in Python3 sklearn module, we hope that we could write python codes in R Shiny to call that model and corresponding functions.
We used R-package "reticulate" to create virtual python environment where it would save python packages, and through which we could call python3 functions.
We created the virtual environment using the following line of code (the function in R package "reticulate")
use_virtualenv("env", required = TRUE)
Where we indeed have the following directory "env/bin" in which there are python and python3 to execute.
The Shiny APP worked perfectly locally. HOWEVER, when we made attempts to publish, it gave the following error (please see picture) (after the APP was successfully deployed and on shinyapps.io, it said the APP was running).
The issue was "Error 126", which denied the permission for our APP to access the virtual environment. This issue had no previous (similar) case on Stackoverflow, and therefore we spent a long time to debug (issue not resolved).
If anyone knows how to solve this problem, would it be possible for you to kindly mark your solution tips below? (We hope your solution would not modify our basic layout, i.e. "calling python-made model in Shiny and publish through Shiny") We really appreciate your efforts to help us out!
Thank you so much!
Could you share the code where actual call to python script is being made? is it a python module function that you are calling from Rshiny? what does the python module/function do and return? I have used reticulate inside shiny to call Python scripts and it works fine. Didn't require to set the environment. Just provide the source to python script and call it like any other R function.
If you're trying to deploy to shinyapps.io, you may need to set the RETICULATE_PYTHON env variable so that reticulate uses the correct version of Python when running your app:
VIRTUALENV_NAME = 'env'
Sys.setenv(RETICULATE_PYTHON = paste0('/home/shiny/.virtualenvs/',
VIRTUALENV_NAME,
'/bin/python'))
Full example here demonstrates one method for configuring a Shiny + reticulate app so that it can easily run both locally and on shinyapps.io.
I'm trying to use python in a new OS X application for plugin scripting. I'm looking to offload some of the program logic to python for easy, on-the-fly modification. I had started by looking at the Big Nerd Ranch tutorial. That seemed to work, but it suggested an older method of linking Python. It appears that since Xcode 5, we are supposed to install python using this Mac Developer Library Tech Note. This process, however, seems to create a linked python instance, not an embedded one. I've tried following the guidelines in the answer to this question but it seems to break down.
So my question is this: what are the current best practices for building python for use as a plugin runtime in an Objective C Mac OS X app? How does one go about making sure that it is bundled with the application, and that it is possible to install any additional libraries that one might want before the final Objective C app is built?
I've come up with a method that seems to work fairly well.
First, download source of the python version you want to use from the official website. Extract the archive somewhere. I'm using Python 3.4.2. Adjust the commands on your system for the specific version you're using.
Create a build directory that you will use for this development python version. The entire directory should have no spaces in it to make sure that bash interprets the she-bang (#!) lines correctly. I used /Users/myaccount/development/python/devbuild/python3.4.2.
Go into the extracted Python directory and run the following commands:
./configure --prefix="/Users/myaccount/development/python/devbuild/python3.4.2"
make
make install
This will install python in that development build directory. Setup the Python path to use the correct directory:
export PYTHONPATH="/Users/myaccount/development/python/devbuild/python3.4.2/lib/python3.4/site-packages/"
Go into the python bin directory (/Users/myaccount/development/python/devbuild/python3.4.2/bin) and use the pip3 there to install any modules that you need. The $PYTHONPATH setting will ensure that the modules get installed into the correct site-packages directory.
Find a handy home for the PyObjC repository and clone it there. Then checkout the latest version tag and install it, making sure that your $PYTHONPATH is still correct:
hg clone https://bitbucket.org/ronaldoussoren/pyobjc
cd pyobjc
hg tags
hg checkout [the id of the latest version from the tag list]
/Users/myaccount/development/python/devbuild/python3.4.2/bin/python3 ./install.py
Whenever you need to update the python modules, just make sure to use the correct python bin and $PYTHONPATH.
Now to add python to an Xcode project.
Drag the /Users/myaccount/development/python/devbuild/python3.4.2 directory into the Xcode project, setting it to not copy items as necessary, and to create a folder reference.
Add /Users/myaccount/development/python/devbuild/python3.4.2/include/python3.4m to the Header Search Paths setting in the Xcode project's Build Settings. Not sure if there's a way to do this as a generalized step to just search the folder referenced directory we had just added.
Drag the `/Users/myaccount/development/python/devbuild/python3.4.2/lib/libpython3.4m.a library into the Xcode project, setting it to be added as a reference without copying as well.
The code from the Big Nerd Ranch scripting tutorial repository can now be used with a few modifications.
The Plugin Manager code will need an NSString extension to work with the wchar_t strings that the Python API seems to like so much:
#interface NSString (WcharEncodedString)
- (wchar_t*) getWideString;
#end
#implementation NSString (WcharEncodedString)
- (wchar_t*) getWideString {
const char* tmp = [self cStringUsingEncoding:NSUTF8StringEncoding];
unsigned long buflen = strlen(tmp) + 1;
wchar_t* buffer = malloc(buflen * sizeof(wchar_t));
mbstowcs(buffer, tmp, buflen);
return buffer;
}
#end
The Python header should be included as follows:
#include "Python.h"
The following code needs to be run before Py_Initialize() is called in order to set up the correct python executable, PYTHONPATH, and PYTHONHOME as suggested by Zorg on that other question.
NSString* executablePath = [[NSBundle mainBundle] pathForResource:#"python3.4" ofType:nil inDirectory:#"python3.4.2/bin"];
Py_SetProgramName([executablePath getWideString]);
NSString* pythonDirectory = [[NSBundle mainBundle] pathForResource:#"python3.4" ofType:nil inDirectory:#"python3.4.2/lib"];
Py_SetPath([pythonDirectory getWideString]);
Py_SetPythonHome([pythonDirectory getWideString]);
Finally, the python path needs to be expanded in the PluginExecutor.py file to include the various subdirectories of the high level lib path. Add the following code to the top of the Plugin Executor file:
import sys
from os import walk
path = sys.path.copy()
for p in path:
for root,dirs,files in walk(p):
if p is not root:
sys.path.append(root)
I'll post updates if things start to break down, but this seems a working solution for now.
Context
Steps taken:
Environment Setup
I've installed protobufs via Home Brew
I've also followed the steps in the proto-bufs python folder's readme on installing python protobufs - namely running the python setup.py install command
I've using the protobuf-2.4.1 files
Coding
I have a python file (generated from a .proto file I compiled) that contains the statement, among other import statements, but I believe this one is the one causing issues:
from google.protobuf import descriptor_pb2
The above python file, I'm importing in another python file, it's
this python file that I want to write up logic for parsing the
protobufs data files I receive
Error received
I get this error when running that file:
Steps taken to fix
Searched google for that error - didn't find much
Looked at this question/answer Why do I see "cannot import name descriptor_pb2" error when using Google Protocol Buffers?
I don't really understand the above questions selected answer,I tried to run the command in the above answer protoc descriptor.proto --python_out=gen/ by coping and pasting it in the terminal in different places but couldn't get it to work
Question
How do I fix this error?
What is the underlying cause?
How do I check if the rest of my protobuf python compiler/classes are set up correctly?
I've discovered the issue. I had not run the python install instructions the first time I tried to compile this file. I recompiled the file and this issue was fixed.
I am currently working on a project to embed a Python interpreter in my website--I would like users to be able to execute their own Python code on the server-side in a secure Python sandbox. I have been using PyPy's sandboxing features and have set my virtual tmp/ directory (which corresponds to the real directory that the sandbox can read from) to my server-side files. So ideally, users will be able to run their own code on the server and use whatever libraries I make available to them (with no ability to write to any of these files/make system calls/do anything in general that would mess up my files).
The issue is that within my server-side code I use standard Python libraries as well as others I have installed separately (e.g. "import datetime", "import pandas", etc.). While the sandbox can read my server-side code it ends up failing whenever I try to import additional libraries within this code. I have thought of setting my virtual tmp/ directory to include my server-side files + the standard Python libraries + separately installed libraries such as PANDAS. However, when I tried setting it to just the Python libraries it ended up not working, not to mention that this solution seems pretty inelegant.
Any thoughts on how to go about fixing this? I appreciate whatever advice anyone may have. Thanks!
EDIT: I think part of the answer lies in the following portion of pypy_interact.py (the full source code can be found here: https://github.com/ojii/sandlib/blob/master/sandlib/pypy_interact.py):
def build_virtual_root(self):
# build a virtual file system:
# * can access its own executable
# * can access the pure Python libraries
# * can access the temporary usession directory as /tmp
exclude = ['.pyc', '.pyo']
if self.tmpdir is None:
tmpdirnode = Dir({})
else:
tmpdirnode = RealDir(self.tmpdir, exclude=exclude)
libroot = str(LIB_ROOT)
return Dir({
'bin': Dir({
'pypy-c': RealFile(self.executable),
'lib-python': RealDir(os.path.join(libroot, 'lib-python'),
exclude=exclude),
'lib_pypy': RealDir(os.path.join(libroot, 'lib_pypy'),
exclude=exclude),
}),
'tmp': tmpdirnode,
})
I am relatively new to Python and can't seem to figure out how to use this method properly. Any suggestions would be greatly appreciated.