Setting the root directory in a python-chunk with the following code line results in an error while for an ordinary r-chunk it works just fine
knitr::opts_knit$set(root.dir ="..")
knitr::opts_knit$set(root.dir ="..")
Optimally there should exist the following options for each knitr-chunk:
- directory to find code to be imported / executed
- directory to find files / dependencies that are needed for code execution
- directory to save any code output
Does something similar exist?
What it looks like here is that you have told it that it is to look for python code:
```{python}
knitr::opts_knit$set(root.dir ="..")
```
When you run this in R studio it will give you an error:
Error: invalid syntax (, line 1)
You fed it python code instead. This makes sense as the call knit::opt_knit$set means to look in the knitr package for the opts_knit$set and set it to…. This doesn’t exist in python… yet. The python compiler does not recognize it as python code and returns a syntax error. Whereas when you run it as an R chunk, it knows to look into the knitr package. Error handling can be huge issue to deal with. It makes more sense to handle error categories than to account for every type of error. If you want to control the settings for a code chunk, you would do so in the parenthesis ie:
```{python, args }
codeHere
```
I have not seen args for any other language than R, but that does not mean it doesn’t exist. I have just not seen them. I also do not believe that this will fix your issue. You could try some of the following ideas:
Writing your python in a separate file and link to it. This would allow for you to take advantage of the language and utilize things like the OS import. This may be something you want to consider as even python has its ways of navigating around the various operating systems. This may be helpful if you are just running quick scripts and not loading or running python programs.
# OS module
import os
# Your os name
print(os.name)
# Gets PWD or present working directory
os.getcwd()
# change your directory
os.chdir("path")
You could try using the reticulate library within an R chunk and load your python that way
Another thought is that you could try
library(reticulate)
use_python(“path”)
Knitr looks in the same directory as your markdown file to find other files if needed. This is just like about any other IDE
At one point in time knitr would not accept R’s setwd() command. Trying to call setwd() may not do you any good.
It may not the best idea to compute paths relative to what's being executed. If possible they should be determined relative to where the user calls the code from.
This site may help.
The author of the knitr package is very active and involved. Good luck with what you are doing!
Related
I'm trying to perform a simple Swap from DAI to WETH with Uniswap in my own SmartContract on the Kovan Testnet. Unfortunately my transaction keeps getting reverted even after setting the gas limit manually.
I also discovered that I can not verify the contract on Kovan via etherscan-API nor manually. Instead I keep getting this error for every library I import:
Source "#uniswap/v3-periphery/contracts/interfaces/ISwapRouter.sol" not found: File import callback not supported
Accordingly I have the feeling something is going wrong during compilation and I'm stuck without any further ideas to work out my problem.
Here are a couple infos on what I've tried so far and how to reproduce:
Brownie Version 1.16.4, Tested on Windows 10 and Ubuntu 21.04
I've tried:
Importing libraries with Brownie package manager
Importing libraries with npm and using relative paths
All kinds of different compiler remappings in the brownie-config.yaml
Adding all dependency files to project folders manually
Here's a link to my code for reproducing my error:
https://github.com/MjCage/swap-demo
It'd be fantastic if someone could help.
It's very unlikely that something is "going wrong during compilation". If your contract compiles but what it does does not match the sources, you have found a very serious codegen bug in the compiler and you should report it so that it can be fixed quickly. From experience I'd say that it's much more likely that you have a bug in your contract though.
As for the error during verification - the problem is that to properly compile a multi-file project, you have to provide all the source files and have them in the right directories. This applies to library code as well so if your contract imports ISwapRouter.sol, you need to also submit that file and all files it in turn imports too.
The next hurdle is that as far as I can tell, the multi-file verification option at Etherscan only allows you to submit files from a single directory so it only gets their names, not the whole paths (not sure if it's different via the API). You need Etherscan to see the file as #uniswap/v3-periphery/contracts/interfaces/ISwapRouter.sol but it sees just ISwapRouter.sol instead and the compiler will not treat them as the same (both could exist after all).
The right solution is to use the Standard JSON verification option - this way you submit the whole JSON input that your framework passes to the compiler and that includes all files in the project (including libraries) and relevant compiler options. The issue is that Brownie does not give you this input directly. You might be able to recreate it from the JSON it stores on disk (Standard JSON input format is documented at Compiler Input and Output JSON Description) but that's a bit of manual work. Unfortunately Brownie does not provide any way to request this on the command line. The only other way to get it that I know of is to use Brownie's API and call compiler.generate_input_json().
Since this is a simple project with just one contract and does not have deep dependencies, it might be easier for you to follow #Jacopo Mosconi's answer and just "flatten" the contract by replacing all imports by sources pasted directly into the main contract. You might also try copying the file to your project dir and altering the import so that it only contains the file name, without any path component - this might pass the multi-file verification. Flattening is ultimately how Brownie and many other frameworks currently do verification and Etherscan's check is lax enough to allow sources modified in such a way - it only checks bytecode so you can still verify even if you completely change the import structure, names, comments or even any code that gets removed by the optimizer.
the compiler can't find ISwapRouter.sol
you can add the code of ISwapRouter.sol directly on your swap.sol and delate that line from your code, this is the code https://github.com/Uniswap/v3-periphery/blob/main/contracts/interfaces/ISwapRouter.sol
I'm trying to restrict write and read access to a Python file. Suppose I have the following code:
with open('test.py', 'w+') as file:
file.write('''
open("document.txt", "w+").write("Hello, World!")
open("document.txt", "r+").read()
''')
By executing this code, a new file is created that in the new file there are two lines of code to write and read a another file.
I want the file created by executing this code (test.py) to hit PermissionError while running and not be able to create a new file or read it; Also, this file is only executable and normal commands work in it, but it can not access other files.
If I read you correctly, this is not a python problem, but an environment problem. I understand the question as something like 'how do I prevent python code from executing arbitrary reads or writes?'. There would be a trivial solution (modifying the generated test.py so it throws an error) but presumably that's not what you want.
The easiest way to make python hit a PermissionError... is to make sure it doesn't have permissions. So run your code as a user with extremely limited permissions---specifically no write permissions anywhere---or perhaps no default permissions at all, and use something like facls to grant permission to read specific files explicitly from a more priveleged sentinel process. (This assumes you are running Linux, but there are likely other ways to do this in different OSs).
Alternatively, look into various sandboxing techniques to give you a python interpreter with the relavent modules replaced with modules which throw errors, or an environment where outside modification is impossible.
It would help if you made it clearer why this is important, and why you are writing a python script with another python script (is this just an example of malicious action?).
You could technically change the permission of the file itself on the filesystem your trying to access.
Check the previous thread about changing permissions
os.chmod(path, <permission value>)
Where 000 is to disable anyone other than root to edit on linux.
I feel this question needs a better title and I will amend it if someone suggests something better. The problem is I'm not sure of the terminology of the feature that I'm using here.
The best way to describe my problem is to show what I've done. The project is here: https://github.com/jeffnyman/quendor
This project is setup so it can be executed as a module. For example, from the project root someone could do this:
python3 -m quendor
I also have a build script to generate an in-memory zip (if I'm using that terminology correctly):
https://github.com/jeffnyman/quendor/blob/master/build.py
That works in that if you run build.py it will generate a quendor.py file that executes the entire project. That worked fine up until I included other directories (like my utilities and zinterface).
With the project as it is in the repo right now, if you run the build (.\build.py) and then run the generated file:
./quendor.py
You get the following error:
File "./quendor.py/quendor/__main__.py", line 6, in <module>
ModuleNotFoundError: No module named 'quendor.zinterface'
So a key point: if all of my files are in the same directory (i.e., in quendor) this build script works fine in terms of producing an executable script file.
But once I include the subdirectories and files in those directories, things go south on me with the above error.
I'm sure all the files are being gathered. I handle that starting on line 18 (https://github.com/jeffnyman/quendor/blob/master/build.py#L18). And if you were to add to line 24 this statement:
print(f"* {file_path}")
You would see it outputs the following:
* quendor/__init__.py
* quendor/__version__.py
* quendor/zinterface/fileio.py
* quendor/utilities/messages.py
* quendor/__main__.py
So I'm suspecting it might have to do with the code where I write the string at line 28 (https://github.com/jeffnyman/quendor/blob/master/build.py#L28). I feel I have to do more to let the executable zipped script file know about the modules.
But I'm not sure if (1) I'm accurate and (2) even if I'm accurate, if that's possible. I'm finding I'm in a bit over my head here.
Any thoughts would be appreciated and I'm happy to update with any necessarily clarifications or terminology.
So it won't let me comment unless I have more reputation but I can post an answer. Even though I don't have an answer, but rather a comment. I think the above comment was not meant for your actual __main__.py file but rather the one that is getting generated in your quendor.py file. You might want to try adding the import statements to your packed string that you write.
For example, see what happens if on line 32 you add this: import quendor.zinterface.fileio as zio. (Don't replace the line that's there. Just put my line and then keep your others.) I'm not sure how the zip process works but if it tries to mirror the module process that should work. However, if it doesn't, that won't work. You might also just want to try doing import quendor.zinterface. By itself that won't work but it would be interesting to see if it gave you a different error.
Actually, it turns out I found a way to do this! It required using os.walk rather than os.listdir. This required taking a few ideas that people here discussed. Here is the script that does the trick:
https://github.com/jeffnyman/quendor/blob/master/build.py
You can compare that with my previous commit that was trying to handle this a different way.
Eldritch was right that I couldn't just flatten the directory nor could I just add imports to the string I was writing to the final zip file. Jean-François was correct that I had to focus on the __main__.py that was being generated. My contribution was figuring out os.walk() and then parameterizing the written string to handle the different directories.
Finally, this solution does require, as per HTF's suggestion, that I put an empty __init__.py file in each package.
With my solution in place, you can run build.py which then generates the quendor.py script. That script then executes correctly, in terms of recognizing the imports to various packages.
Playing around with just about every variation of import and file gathering that I can think of with your repo, there's a good news / bad news thing.
The bad news is that the answer is this: it isn't possible.
The good news is this: you do have a working implementation if you just keep all files in the quendor directory rather than having subdirectories.
The other good news is you stumbled on something, and posed a problem, that Python gurus aren't able to answer. And there's a certain pleasure to be found in that! I guarantee you will not get an answer to this that works (except for the "all files in one directory" solution).
A refinement to the answer is that if you're setting up the program to run as a module anyway, just use a pip configuration. That basically does the same thing that you want but without having to go through the contortions. (Unless there's a reason you were doing the build the way you were rather than using pip.)
I may sound rather uninformed writing this, and unfortunately, my current issue may require a very articulate answer to fix. Therefore, I will try to be specific as possible as to ensure that my problem can be concisely understood.
My apologizes for that- as this Python code was merely obtained from a friend of mine who wrote it for me in order to complete a certain task. I myself had had extremely minimal programming knowledge.
Essentially, I am running Python 3.6 on a Mac. I am trying to work out a code that allows Python to scan through a bulk of a particular website's potentially existent subdomains in order to find possibly-existent JPG images files contained within said subdomains, and download any and all of the resulting found files to a distinct folder on my Desktop.
The Setup-
The code itself, named "download.py" on my computer, is written as follows:
import urllib.request
start = int(input("Start range:100000"))
stop = int(input("End range:199999"))
for i in range(start, stop + 1):
filename = str(i).rjust(6, '0') + ".jpg"
url = "http://website.com/Image_" + filename
urllib.request.urlretrieve(url, filename)
print(url)
(Note that the words "website" and "Image" have been substituted for the actual text included in my code).
Before I proceed, perhaps some explanation would be necessary.
Basically, the website in question contains several subdomains that include .JPG images, however, the majority of the exact URLs that allow the user to access these sub-domains are unknown and are a hidden component of the internal website itself. The format is "website.com/Image_xxxxxx.jpg", wherein x indicates a particular digit, and there are 6 total numerical digits by which only when combined to make a valid code pertain to each of the existent images on the site.
So as you can see, I have calibrated the code so that Python will initially search through number values in the aforementioned URL format from 100000 to 199999, and upon discovering any .JPG images attributed to any of the thousands of link combinations, will directly download all existent uncovered images to a specific folder that resides within my Desktop. The aim would be to start from that specific portion of number values, and upon running the code and fetching any images (or not), continually renumbering the code to work my way through all of the possible 6-digit combos until the operation is ultimately a success.
(Possible Side-Issue- Although I am fairly confident that my friend's code is written in a manner so that Python will only download .JPG files to my computer from images that actually do exist on that particular URL, rather than swarming my folder with blank/bare files from every single one of URL attempts regardless of whether that URL happens to be successful or not, I am admittedly not completely certain. If the latter is the case, informing me of a more suitable edit to my code would be tremendously appreciated.)
The Execution-
Right off the bat, the code experienced a large error. I'll list through the series of steps that led to the creation of said error.
#1- Of course, I first copy-pasted the code into a text document, and saved it as "download.py". I saved it inside of a folder named "Images" where I sought the images to be directly downloaded to. I used BBEdit.
#2- I proceeded, in Terminal, to input the commands "cd Desktop/Images" (to account for the file being held within the "Images" folder on my Desktop), followed by the command "Python download.py" (to actually run the code).
As you can see, the error which I obtained following my attempt to run the code was the ImportError: No module named request. Despite me guessing that the answer to solving this is simple, I can legitimately say I have got such minimal knowledge regarding Python that I've absolutely no idea how to solve this.
Hint: Prior to making the download.py file, the folder, and typing the Terminal code the only interactions I made with Python were downloading the program (3.6) and placing it in my toolbar. I'm not even quite sure if I am required to create any additional scripts/text files, or make any additional downloads before a script like this would work and successfully download the resulting images into my "Images" folder as is my desired goal. If I sincerely missed something integral at any point during this long read, hopefully, someone in here can provide a thoroughly detailed explanation as to how to solve my issue.
Finishing statements for those who've managed to stick along this far:
Thank you. I know this is one hell of a read, and I'm getting more tired as I go along. What I hope to get out of this question is
1.) Obviously, what would constitute a direct solution to the "No module named request" Input Error in Terminal. In other words, what I did wrong there or am missing.
2.) Any other helpful information that you know would assist this code, for example, if there is any integral step or condition I've missed or failed to meet that would ultimately cause the entirety of my code to cease to work. If you do see a fault in this, I only ask of you to be specific, as I've not got much experience in the programming world. After all, I know there is a lot of developers out here that are far more informed and experienced than am I. Thanks.
urllib.request is in Python 3 only. When running 'python' on a Mac, you're running Python 2 by default. Try running executing with python3.
python --version
might need to
brew install python3
urllib.request is a Python 3 construct. Most systems run Python 2 as default and this is what you get when you run simply python.
To install Python 3, go to https://brew.sh/ and follow the instructions to install the Hombrew package manager. Then run
brew install python3
python3 download.py
So I downloaded some compiled matlab files. I see the following files in a folder.
makemesh.mexmaci64
makemesh.mexw32
makemesh.mexw64
I added this folder to userpath, and now the path variable shows that this folder exists in it.
I try to run a test script that came with these files, and I get this error message.
Undefined function 'makemesh' for input arguments of type 'struct'.
Now to trouble shoot, I need to find,
Does it find the function, but the data type is wrong.
It doesn't even find the function.
And if it is case 1.
1a. How do I find out what is the proper data structure that function expects.
I am good with python, but new to matlab, so any tips you can add regarding how to query the help string of a function, how to print out the function signature given a function name (like ?function_name in ipython interface) would be super useful.
thank you,
computer('arch') returns glnxa64 which stands for GnuLiNuX 64bit. You have downloaded binaries for Win32bit (mexw32), Win64bit (mexw64) and IOS on Intel (mexmaci64). Either get the source files to compile it yourself or the binaries for linux.
You can find the location of a file on your path by using the which command. For example:
which makemesh.mexw64
should print the location of that file to the terminal. If you get
'makemesh.mexmaci64' not found.
then it means that the file does not exist on your path.
As for finding out what the function wants, I'd start with "help"
help makemesh.mexw64
and see if that gives you anything useful.
I suspect that somehow or other, your matlab is not recognizing the mex file as a function, so I'd start looking there.
You can use the command which <functionName> to see if Matlab is seeing your function.
Have you tried help <functionName> to see if there are any useful comments on what your function is expecting?