We Keep Coding

I keep having a error when running the script. It keeps sending "name input_file is not defined"

I am trying to create a python def to unzip a few .gz files within a folder. I know that the main script works if it is not in the def. The script I have created is similar to others I have done but this one give me the error
File "unzip.py", line 24, in
decompressed_files(input_folder)
NameError: name 'input_folder' is not defined
I copied the script below so someone can help me to see where the error is. I haven't done any BioInformatics for the last couple of years and I am a bit rusty.
import glob
import sys
import os
import argparse
import subprocess
import gzip
def decompressed_files(input_folder):
print ('starting decompressed_files')
output_folder=input_folder + '/fasta_files'
if os.path.exists(output_folder):
print ('folder already exists')
else:
os.makedirs(output_folder)
for f in input_folder:
fastqs=glob.glob(input_folder + '/*.fastq.gz')
cmd =[gunzip, -k, fastqs, output_folder]
my_file=subprocess.Popen(cmd)
my_file.wait
print ('The programme has finished doing its job')
decompressed_files(input_folder)
This is done for python 2.7, I know that is old but it is the one that it is installed in my work server.

That's why when you call decompressed_files(input_folder) in the last line, you didn't define input_folder before. you should do it like this :
input_folder = 'C:/Some Address/'
decompressed_files(input_folder)

Compile Python code with Openpyxl into executable using PyInstaller Error cannot import '__versions__' [duplicate]

My traceback from running pandas takes me to:
site-packages\pandas\io\excel.py line 58, in get_writer
AttributeError: 'module' object has no attribute '__version__'
I found this link to a git issue in the PyInstaller repo
https://github.com/pyinstaller/pyinstaller/issues/1890 and found my openpyxl version, manually added it into the get_writer method like so:
def get_writer(engine_name):
if engine_name == 'openpyxl':
try:
import openpyxl
#remove when conda update available
openpyxl.__version__ = '2.3.2'
# with version-less openpyxl engine
# make sure we make the intelligent choice for the user
if LooseVersion(openpyxl.__version__) < '2.0.0':
return _writers['openpyxl1']
elif LooseVersion(openpyxl.__version__) < '2.2.0':
return _writers['openpyxl20']
else:
return _writers['openpyxl22']
except ImportError:
# fall through to normal exception handling below
pass
try:
return _writers[engine_name]
except KeyError:
raise ValueError("No Excel writer '%s'" % engine_name)
Still no dice. The line number given in the error traceback doesn't even change. I then updated the openpyxl version to 2.3.5, still receiving the error. The openpyxl init file has a version variable in it:
try:
here = os.path.abspath(os.path.dirname(__file__))
src_file = os.path.join(here, ".constants.json")
with open(src_file) as src:
constants = json.load(src)
__author__ = constants['__author__']
__author_email__ = constants["__author_email__"]
__license__ = constants["__license__"]
__maintainer_email__ = constants["__maintainer_email__"]
__url__ = constants["__url__"]
__version__ = constants["__version__"]
except IOError:
# packaged
pass
Any known or potential fixes or workarounds?

Edits were not making an impact because the process was compiled into an exe that these modules were running through. Exported the sections I needed outside of my anaconda environment and now the process works without a hitch.

I will add my workaround to this discussion as I was having the same problem using openpyxl 2.4.0 and maybe a few others are stuck too.
I found that to create a .exe file you have to revert to an older version of openpyxl. To do so:
Open the command prompt and uninstall openpyxl with 'pip uninstall openpyxl'
Reinstall openpyxl using an older version 'pip install openpyxl==2.3.5'
Now you should be able to create your .exe file using py2exe, cx_freeze, etc.

This is my fix: go to your openpyxl site-package folder (for me it's: C:\Python27\Lib\site-packages\openpyxl). Copy all variables in your .constant.json file directly into the _ init _.py file, so it looks like:
import json
import os
__author__= "See AUTHORS"
__author_email__= "eric.gazoni#gmail.com"
__license__= "MIT/Expat",
__maintainer_email__= "openpyxl-users#googlegroups.com"
__url__= "http://openpyxl.readthedocs.org"
__version__= "2.4.0"
try:
here = os.path.abspath(os.path.dirname(__file__))

How to create a shortcut in startmenu using setuptools windows installer

I want to create a start menu or Desktop shortcut for my Python windows installer package. I am trying to follow https://docs.python.org/3.4/distutils/builtdist.html#the-postinstallation-script
Here is my script;
import sys
from os.path import dirname, join, expanduser
pyw_executable = sys.executable.replace('python.exe','pythonw.exe')
script_file = join(dirname(pyw_executable), 'Scripts', 'tklsystem-script.py')
w_dir = expanduser(join('~','lsf_files'))
print(sys.argv)
if sys.argv[1] == '-install':
print('Creating Shortcut')
create_shortcut(
target=pyw_executable,
description='A program to work with L-System Equations',
filename='L-System Tool',
arguments=script_file,
workdir=wdir
)
I also specified this script in scripts setup option, as indicated by aforementioned docs.
Here is the command I use to create my installer;
python setup.py bdist_wininst --install-script tklsystem-post-install.py
After I install my package using created windows installer, I can't find where my shorcut is created, nor I can confirm whether my script run or not?
How can I make setuptools generated windows installer to create desktop or start menu shortcuts?

Like others have commented here and elsewhere the support functions don't seem to work at all (at least not with setuptools). After a good day's worth of searching through various resources I found a way to create at least the Desktop shortcut. I'm sharing my solution (basically an amalgam of code I found here and here). I should add that my case is slightly different from yasar's, because it creates a shortcut to an installed package (i.e. an .exe file in Python's Scripts directory) instead of a script.
In short, I added a post_install function to my setup.py, and then used the Python extensions for Windows to create the shortcut. The location of the Desktop folder is read from the Windows registry (there are other methods for this, but they can be unreliable if the Desktop is at a non-standard location).
#!/usr/bin/env python
import os
import sys
import sysconfig
if sys.platform == 'win32':
from win32com.client import Dispatch
import winreg
def get_reg(name,path):
# Read variable from Windows Registry
# From https://stackoverflow.com/a/35286642
try:
registry_key = winreg.OpenKey(winreg.HKEY_CURRENT_USER, path, 0,
winreg.KEY_READ)
value, regtype = winreg.QueryValueEx(registry_key, name)
winreg.CloseKey(registry_key)
return value
except WindowsError:
return None
def post_install():
# Creates a Desktop shortcut to the installed software
# Package name
packageName = 'mypackage'
# Scripts directory (location of launcher script)
scriptsDir = sysconfig.get_path('scripts')
# Target of shortcut
target = os.path.join(scriptsDir, packageName + '.exe')
# Name of link file
linkName = packageName + '.lnk'
# Read location of Windows desktop folder from registry
regName = 'Desktop'
regPath = r'Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders'
desktopFolder = os.path.normpath(get_reg(regName,regPath))
# Path to location of link file
pathLink = os.path.join(desktopFolder, linkName)
shell = Dispatch('WScript.Shell')
shortcut = shell.CreateShortCut(pathLink)
shortcut.Targetpath = target
shortcut.WorkingDirectory = scriptsDir
shortcut.IconLocation = target
shortcut.save()
setup(name='mypackage',
...,
...)
if sys.argv[1] == 'install' and sys.platform == 'win32':
post_install()
Here's a link to a full setup script in which I used this:
https://github.com/KBNLresearch/iromlab/blob/master/setup.py

If you want to confirm whether the script is running or not, you can print to a file instead of the console. Looks like text you print to console in the post-install script won't show up.
Try this:
import sys
from os.path import expanduser, join
pyw_executable = join(sys.prefix, "pythonw.exe")
shortcut_filename = "L-System Toolsss.lnk"
working_dir = expanduser(join('~','lsf_files'))
script_path = join(sys.prefix, "Scripts", "tklsystem-script.py")
if sys.argv[1] == '-install':
# Log output to a file (for test)
f = open(r"C:\test.txt",'w')
print('Creating Shortcut', file=f)
# Get paths to the desktop and start menu
desktop_path = get_special_folder_path("CSIDL_COMMON_DESKTOPDIRECTORY")
startmenu_path = get_special_folder_path("CSIDL_COMMON_STARTMENU")
# Create shortcuts.
for path in [desktop_path, startmenu_path]:
create_shortcut(pyw_executable,
"A program to work with L-System Equations",
join(path, shortcut_filename),
script_path,
working_dir)

At least with Python 3.6.5, 32bit on Windows, setuptools does work for this. But based on the accepted answer, by trial and error I found some issues that may have caused your script to fail to do what you wanted.
create_shortcut does not accept keyword arguments, only positional, so its usage in your code is invalid
You must add a .lnk extension for Windows to recognise the shortcut
I found sys.executable will be the name of the installer executable, not the python executable
As mentioned, you can't see stdout or stderr so you might want to log to a text file. I would suggest also redirecting sys.stdout and sys.stderr to the log file.
(Maybe not relevant) as mentioned in this question there appears to be a bug with the version string generated by bdist_wininst. I used the hexediting hack from an answer there to work around this. The location in the answer is not the same, you have to find the -32 yourself.
Full example script:
import sys
import os
import datetime
global datadir
datadir = os.path.join(get_special_folder_path("CSIDL_APPDATA"), "mymodule")
def main(argv):
if "-install" in argv:
desktop = get_special_folder_path("CSIDL_DESKTOPDIRECTORY")
print("Desktop path: %s" % repr(desktop))
if not os.path.exists(datadir):
os.makedirs(datadir)
dir_created(datadir)
print("Created data directory: %s" % repr(datadir))
else:
print("Data directory already existed at %s" % repr(datadir))
shortcut = os.path.join(desktop, "MyModule.lnk")
if os.path.exists(shortcut):
print("Remove existing shortcut at %s" % repr(shortcut))
os.unlink(shortcut)
print("Creating shortcut at %s...\n" % shortcut)
create_shortcut(
r'C:\Python36\python.exe',
"MyModuleScript",
shortcut,
"",
datadir)
file_created(shortcut)
print("Successfull!")
elif "-remove" in sys.argv:
print("Removing...")
pass
if __name__ == "__main__":
logfile = r'C:\mymodule_install.log' # Fallback location
if os.path.exists(datadir):
logfile = os.path.join(datadir, "install.log")
elif os.environ.get("TEMP") and os.path.exists(os.environ.get("TEMP"),""):
logfile = os.path.join(os.environ.get("TEMP"), "mymodule_install.log")
with open(logfile, 'a+') as f:
f.write("Opened\r\n")
f.write("Ran %s %s at %s" % (sys.executable, " ".join(sys.argv), datetime.datetime.now().isoformat()))
sys.stdout = f
sys.stderr = f
try:
main(sys.argv)
except Exception as e:
raise
f.close()
sys.exit(0)

UPD: on an off chance that the client machine has pywin32 installed, we try in-process creation first. Somewhat cleaner that way.
Here is another take. This assumes the package is called myapp, and that also becomes the executable that you want a shortcut to. Substitute your own package name and your own shortcut text.
Uses a Windows Scripting Host COM class - in process if possible, inside a Powershell command line as a subprocess if not. Tested on Python 3.6+.
from setuptools import setup
from setuptools.command.install import install
import platform, sys, os, site
from os import path, environ
def create_shortcut_under(root, exepath):
# Root is an env variable name -
# either ALLUSERSPROFILE for the all users' Start menu,
# or APPDATA for the current user specific one
profile = environ[root]
linkpath = path.join(profile, "Microsoft", "Windows", "Start Menu", "Programs", "My Python app.lnk")
try:
from win32com.client import Dispatch
from pywintypes import com_error
try:
sh = Dispatch('WScript.Shell')
link = sh.CreateShortcut(linkpath)
link.TargetPath = exepath
link.Save()
return True
except com_error:
return False
except ImportError:
import subprocess
s = "$s=(New-Object -COM WScript.Shell).CreateShortcut('" + linkpath + "');$s.TargetPath='" + exepath + "';$s.Save()"
return subprocess.call(['powershell', s], stdout = subprocess.DEVNULL, stderr = subprocess.DEVNULL) == 0
def create_shortcut(inst):
try:
exepath = path.join(path.dirname(sys.executable), "Scripts", "myapp.exe")
if not path.exists(exepath):
# Support for "pip install --user"
exepath = path.join(path.dirname(site.getusersitepackages()), "Scripts", "myapp.exe")
# If can't modify the global menu, fall back to the
# current user's one
if not create_shortcut_under('ALLUSERSPROFILE', exepath):
create_shortcut_under('APPDATA', exepath)
except:
pass
class my_install(install):
def run(self):
install.run(self)
if platform.system() == 'Windows':
create_shortcut(self)
#...
setup(
#...
cmdclass={'install': my_install},
entry_points={"gui_scripts": ["myapp = myapp.__main__:main"]},

Python - create object of class from one package in different package

I started using Python few days back and I think I have a very basic question where I am stuck. Maybe I am not doing it correctly in Python so wanted some advice from the experts:
I have a config.cfg & a class test in one package lib as follows:
myProj/lib/pkg1/config.cfg
[api_config]
url = https://someapi.com/v1/
username=sumitk
myProj/lib/pkg1/test.py
class test(object):
def __init__(self, **kwargs):
config = ConfigParser.ConfigParser()
config.read('config.cfg')
print config.get('api_config', 'username')
#just printing here but will be using this as a class variable
def some other foos()..
Now I want to create an object of test in some other module in a different package
myProj/example/useTest.py
from lib.pkg1.test import test
def temp(a, b, c):
var = test()
def main():
temp("","","")
if __name__ == '__main__':
main()
Running useTest.py is giving me error:
...
print config.get('api_config', 'username')
File "C:\Python27\lib\ConfigParser.py", line 607, in get
raise NoSectionError(section)
ConfigParser.NoSectionError: No section: 'api_config'
Now if I place thie useTest.py in the same package it runs perfectly fine:
myProj/lib/pkg1/useTest.py
myProj/lib/pkg1/test.py
myProj/lib/pkg1/config.cfg
I guess there is some very basic package access concept in Python that I am not aware of or is there something I am doing wrong here?

The issue here is that you have a different working directory depending on which module is your main script. You can check the working directory by adding the following lines to the top of each script:
import os
print os.getcwd()
Because you just provide 'config.cfg' as your file name, it will attempt to find that file inside of the working directory.
To fix this, give an absolute path to your config file.
You should be able to figure out the absolute path with the following method since you know that config.cfg and test.py are in the same directory:
# inside of test.py
import os
config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'config.cfg')

Python - How do you run a .py file?

I've looked all around Google and its archives. There are several good articles, but none seem to help me out. So I thought I'd come here for a more specific answer.
The Objective: I want to run this code on a website to get all the picture files at once. It'll save a lot of pointing and clicking.
I've got Python 2.3.5 on a Windows 7 x64 machine. It's installed in C:\Python23.
How do I get this script to "go", so to speak?
=====================================
WOW. 35k views. Seeing as how this is top result on Google, here's a useful link I found over the years:
http://learnpythonthehardway.org/book/ex1.html
For setup, see exercise 0.
=====================================
FYI: I've got zero experience with Python. Any advice would be appreciated.
As requested, here's the code I'm using:
"""
dumpimages.py
Downloads all the images on the supplied URL, and saves them to the
specified output file ("/test/" by default)
Usage:
python dumpimages.py http://example.com/ [output]
"""
from BeautifulSoup import BeautifulSoup as bs
import urlparse
from urllib2 import urlopen
from urllib import urlretrieve
import os
import sys
def main(url, out_folder="C:\asdf\"):
"""Downloads all the images at 'url' to /test/"""
soup = bs(urlopen(url))
parsed = list(urlparse.urlparse(url))
for image in soup.findAll("img"):
print "Image: %(src)s" % image
filename = image["src"].split("/")[-1]
parsed[2] = image["src"]
outpath = os.path.join(out_folder, filename)
if image["src"].lower().startswith("http"):
urlretrieve(image["src"], outpath)
else:
urlretrieve(urlparse.urlunparse(parsed), outpath)
def _usage():
print "usage: python dumpimages.py http://example.com [outpath]"
if __name__ == "__main__":
url = sys.argv[-1]
out_folder = "/test/"
if not url.lower().startswith("http"):
out_folder = sys.argv[-1]
url = sys.argv[-2]
if not url.lower().startswith("http"):
_usage()
sys.exit(-1)
main(url, out_folder)

On windows platform, you have 2 choices:
In a command line terminal, type
c:\python23\python xxxx.py
Open the python editor IDLE from the menu, and open xxxx.py, then press F5 to run it.
For your posted code, the error is at this line:
def main(url, out_folder="C:\asdf\"):
It should be:
def main(url, out_folder="C:\\asdf\\"):

Usually you can double click the .py file in Windows explorer to run it. If this doesn't work, you can create a batch file in the same directory with the following contents:
C:\python23\python YOURSCRIPTNAME.py
Then double click that batch file. Or, you can simply run that line in the command prompt while your working directory is the location of your script.

Since you seem to be on windows you can do this so python <filename.py>. Check that python's bin folder is in your PATH, or you can do c:\python23\bin\python <filename.py>. Python is an interpretive language and so you need the interpretor to run your file, much like you need java runtime to run a jar file.

use IDLE Editor {You may already have it} it has interactive shell for python and it will show you execution and result.

Your command should include the url parameter as stated in the script usage comments.
The main function has 2 parameters, url and out (which is set to a default value)
C:\python23\python "C:\PathToYourScript\SCRIPT.py" http://yoururl.com "C:\OptionalOutput\"

If you want to run .py files in Windows, Try installing Git bash
Then download python(Required Version) from python.org and install in the main c drive folder
For me, its :
"C:\Python38"
then open Git Bash and go to the respective folder where your .py file is stored :
For me, its :
File Location : "Downloads"
File Name : Train.py
So i changed my Current working Directory From "C:/User/(username)/" to "C:/User/(username)/Downloads"
then i will run the below command
" /c/Python38/python Train.py "
and it will run successfully.
But if it give the below error :
from sklearn.model_selection import train_test_split
ModuleNotFoundError: No module named 'sklearn'
Then Do not panic :
and use this command :
" /c/Python38/Scripts/pip install sklearn "
and after it has installed sklearn go back and run the previous command :
" /c/Python38/python Train.py "
and it will run successfully.
!!!!HAPPY LEARNING !!!!