When I copy this text:
and paste it into a text field, I just get:
scipy.special.softmax([1,1])
array([0.5, 0.5])
I would like to get:
>>> scipy.special.softmax([1,1])
array([0.5, 0.5])
This is the behaviour when using the Python interactive console normally outside PyCharm.
this seems to be reported already, please see https://youtrack.jetbrains.com/issue/PY-52621/Unable-to-copy-code-from-the-console-as-plain-text and feel free to vote in order to increase the priority.
I apologize for the inconvenience.
I am new to PyCharm and I have 'Process finished with exit code 0' instead of getting (683, 11) as a result (please see attachment), could you guys help me out please? Much appreciate it!
That is good news! It means that there is no error with your code. You have run it right through and there is nothing wrong with it. Pycharm returns 0 when it has found no errors (plus any output you give it) and returns 1 as well as an error message when it encounters errors.
Editors and scripts do not behave like the interactive terminal, when you run a function it does not automatically show the the result. You need to actually tell it to do it yourself.
Generally you just print the results.
If you use print(data.shape) it should return what you expect with the success message Process finished with exit code 0.
exit code 0 means you code run with no error.
Let's give a error code for example(clearly in the below image): in below code, the variable lst is an empty list,
but we get the 5 member in it(which not exists), so the program throws IndexError, and exit 1 which means there is error with the code.
You can also define exit code for analysis, for example:
ERROR_USERNAME, ERROR_PASSWORD, RIGHT_CODE = 683, 11, 0
right_name, right_password = 'xy', 'xy'
name, password = 'xy', 'wrong_password'
if name != right_name:
exit(ERROR_USERNAME)
if password != right_password:
exit(ERROR_PASSWORD)
exit(RIGHT_CODE)
I would recommend you to read up onexit codes.
exit 0 means no error.
exit 1 means there is some error in your code.
This is not pyCharm or python specific. This is a very common practice in most of the programming languages. Where exit 0 means the successful execution of the program and a non zero exit code indicates an error.
Almost all the program(C++/python/java..) return 0 if it runs successful.That isn't specific to pycharm or python.
In program there is no need to invoke exit function explicitly when it runs success it invoke exit(0) by default, invoke exit(not_zero_num) when runs failed.
You can also invoke exit function with different code(num) for analysis.
You can also see https://en.wikipedia.org/wiki/Exit_(system_call) for more details.
What worked for me when this happened was to go to
Run --> Edit Configurations --> Execution --> check the box Run with
Python Console (which was unchecked).
This means that the compilation was successful (no errors). PyCharm and command prompt (Windows OS), terminal (Ubuntu) don't work the same way. PyCharm is an editor and if you want to print something, you explicitly have to write the print statement:
print(whatever_you_want_to_print)
In your case,
print(data.shape)
I think there's no problem in your code and you could find your print results (and other outputs) in the tab 5: Debug rather than 4: Run.
I just ran into this, but couldn't even run a simple print('hello world') function.
Turns out Comodo's Firewall was stopping the script from printing. This is a pretty easy fix by deleting Python out of the Settings > Advanced > Script Analysis portion of Comodo.
Good Luck
I had same problem with yours. And I finally solve it
I see you are trying to run code "Kaggle - BreastCancer.py"
but your pycharm try to run "Breast.py" instead of your code.
(I think Breast.py only contains functions so pycharm can run without showing any result)
Check on tab [Run] which code you are trying to run.
Your starting the program's run from a different file than you have open there. In Run (alt+shift+F10), set the python file you would like to run or debug.
while True:
string = input('Enter some text to print. \nType "done" to quit>')
if string == 'done':
break
print(string)
print('Done!')
SyntaxError: invalid syntax
image of issue
Image after idz's suggestion
I think your problem is that you wrote:
while true:
instead of
while True:
However, if you are using Python 2 you should be aware that input will attempt to evaluate what you type in as Python. Depending on what your aim is, you may want to use raw_input instead. This is not an issue if your are using Python 3.
For example, if I have a pipe function:
def process_data(weighting, period, threshold):
# do stuff
Can I get autocompletion on the process data arguments?
There are a lot of arguments to remember and I would like to make sure they get passed in correctly. In ipython, the function can autocomplete to show me the keyword args which is really neat, but I would like it to do this when piping a pandas dataframe too!
I don't see how this would be possible, but then again, I'm truly in awe of ipython and all its greatness. So, is this possible? If not, are there other hacks that people have come up with?
Install the pyreadline library.
$ pip install pyreadline
Update:
It seems like this problem is specific to some versions of ipython. The solution is the following:
Run below command from the terminal:
$ ipython profile create
It will create a default profile at ~/.ipython/profile_default/ipython_config.py
Now edit this ipython_config.py and add the below lines and it will solve the issue.
c = get_config()
c.Completer.use_jedi = False
Reference:
https://github.com/jupyter/notebook/issues/2435
https://ipython.readthedocs.io/en/stable/config/intro.html
My attempts to construct DAG or rulegraph from RNA-seq pipeline using snakemake results in error message from graphviz. 'Error: : syntax error in line 1 near 'File'.
The error can be corrected by commenting out two print commands with no visible syntax errors. I have tried converting the scripts from UTF-8 to Ascii in Notepad++. Graphviz seems to have issues with these two specific print statements because there are other print statements within the pipeline scripts. Even though the error is easily corrected, it's still annoying because I would like colleagues to be able to construct these diagrams for their publications without hassle, and the print statements inform them of what is happening in the workflow. My pipeline consists of a snakefile and multiple rule files, as well as a config file. If the offending line is commented out in the Snakefile, then graphviz takes issue with another line in a rule script.
#######Snakefile
!/usr/bin/env Python
import os
import glob
import re
from os.path import join
import argparse
from collections import defaultdict
import fastq2json
from itertools import chain, combinations
import shutil
from shutil import copyfile
#Testing for sequence file extension
directory = "."
MainDir = os.path.abspath(directory) + "/"
## build the dictionary with full path for each for sequence files
fastq=glob.glob(MainDir+'*/*'+'R[12]'+'**fastq.gz')
if len(fastq) > 0 :
print('Sequence file extensions have fastq')
os.system('scripts/Move.sh')
fastq2json.fastq_json(MainDir)
else :
print('File extensions are good')
######Rule File
if not config["GroupdFile"]:
os.system('Rscript scripts/Table.R')
print('No GroupdFile provided')
snakemake --forceall --rulegraph | dot -Tpdf > dag.pdf should result in an pdf output showing the snakemake workflow, but if the two lines aren't commented out it results in Error: : syntax error in line 1 near
To understand what is going on take a close look at the command to generate your dag.pdf.
Try out the first part of your command:
snakemake --forceall --rulegraph
What does that do? It prints out the dag in text form.
By using a | symbol you 'pipe' (pass along) this print to the next part of your command:
dot -Tpdf > dag.pdf
And this part makes the actual pdf from the text that is 'piped' and stores in in dag.pdf. The problem is that when your snakefile makes print statements these prints also get 'piped' to the second half of your command, which interferes with the making of your dag.pdf.
A kinda hackish way how I solved the issue to be able to print, but also to be able to generate the dag is to use the logging functionality of snakemake. It is not a documented way, and a bit hackish, but works really well for me:
from snakemake.logging import logger
logger.info("your print statement here!")