I'm writing a program that executes short shell one liners (potentially including pipes and background tasks etc), and I'd like to make it "just work" cross platform as much as possible.
For mac/linux the following seems to work well:
shell = os.environ.get("SHELL", "/bin/bash")
subprocess.Popen([shell, "-c", script_content])
However given that on windows:
SHELL isn't usually set
Assuming that bash is installed, a usable bash executable might be found in a variety of different places
What's the best way to make this work as reliably as possible in windows?
Are you looking for C:\Windows\System32\cmd.exe?
And if you are doing cross platorm you could use sys.platorm to find the platform the user is using.
On Window, 'COMSPEC' holds the name of the current command program. You can write unconditional lookup to lookup in the environemnt. Usually, better to take this approach, as in many cases, python script may be executed from 'git-bash', WSL or similar. No need to explicitly program for specific platform.
First Using SHELL
If none, use COMSPEC
See: https://en.wikipedia.org/wiki/COMSPEC
If you have Windows git client installed, you should have git bash, so in a CMD window:
set SHELL="c:\Program Files\Git\bin\bash.exe"
then you can run you python program.
Related
I'd like to give my Python scripts the ability to detect whether it was executed in a Git Bash terminal, or the Windows cmd command line interface. For example, I'm trying to write a function to clear the terminal (regardless of which terminal it is), e.g. echoes the clear command if in Git Bash, or cls if in cmd.
I've tried using sys.platform to detect this, but it returns win32 regardless of which type of terminal it was ran in.
Please try using os and psutil modules.
For example,
import os, psutil # Get the parent process name.
pprocName = psutil.Process(os.getppid()).name()
Then you can have your logic depending on the shell.
Additionally, you may want to check https://www.geeksforgeeks.org/clear-screen-python/
I don't believe what you're asking for is possible, but there are several answers here that show all the detections you can do to use the correct type of clear. Usually, it's just best to either make your own window or not clear the screen, sadly.
I have the following problem: I wrote a bash script for data analysis that works perfectly fine when I run it from the terminal. To further automate the process I wanted to use a python script that runs the bash script (using subprocess.call), changes the working directory, and reruns the script (and so on). This also worked fine when I did it on my MacBook. However, I need to do the analysis on a Linux machine and here the problem occurred. Again, running the script from the terminal worked fine but once I tried doing this with my python script it fails to find the relevant functions for the analysis. The functions are stored inside the anaconda3/bin folder.
(Python does not even find other functions like "pip")
Of course, I could add the path to all the functions in the bash script but this seems very inefficient to me. So my question is: is there any better way of telling python where to look for the functions? And can you maybe explain to me why running the script from the terminal works but not when I use subprocess.call?
Here is the python script:
import subprocess
import os
path_list = ["Path1",
"Path2"
]
for path in path_list:
os.chdir(path)
subprocess.call("Users/.../bash_script", shell=True)
I'm just posting my series of comments as an answer since I think this at least constitutes a reasonable answer for anyone running into a similar issue (your question could definitely be common enough to index from search engine results).
Issue:
...running the script from the terminal worked fine but once I tried doing this with my python script it fails to find the relevant functions for the analysis
In general, you can troubleshoot this kind of problem with:
import subprocess
subprocess.call('echo $PATH', shell=True)
If the directory that contains the relevant binaries/scripts/etc. is not in the output, then you are facing a PATH issue in the shell created by subprocess.call.
The exact problem as confirmed by the OP in comments is that anaconda3/bin is not part of your PATH. Your script works in a regular terminal session because of the Anaconda initialization function that gets added to your .bashrc when installing.
Part of an answer that is very helpful here: Python - Activate conda env through shell script
The problem with your script, though, lies in the fact that the .bashrc is not sourced by the subshell that runs shell scripts (see this answer for more info). This means that even though your non-login interactive shell sees the conda commands, your non-interactive script subshells won't - no matter how many times you call conda init.
Solution 1: Manually use the Anaconda sourcing function in your script
As the OP mentioned in the comments, their workaround was to use the initialization function added to their .bashrc in the script they are trying to run. Although this perhaps feels like not a great solution, this is a "good enough" workaround. Unfortunately I don't use Anaconda on Linux so I don't have an exact snippet of what this looks like. See the next section for a possibly "cleaner" solution.
Solution 2: Use bash -i to run your script
As mentioned in the same answer linked above, you might be able to use:
bash -i Users/.../bash_script
This will tell bash to run in interactive mode, which then properly sources your .bashrc file when creating the shell. As a result, Anaconda and related functions should work properly.
Solution 3: Manually add anaconda3/bin to PATH
You can check out this answer to decide if this is something you want to do. Keep in mind they are speaking about a Windows OS but most of the same applies to Linux.
When you add the directory to your PATH, you are specifically telling your system to always look in that directory for commands when executing by name, e.g. ping or which. This can have unexpected behavior if you have conflicts (e.g. a command is found with the same name in /usr/bin and .../anaconda3/bin), and as such Anaconda does not add its bin folder to your PATH by default.
This is not necessarily "dangerous" per se, it's just not an ideal solution for most people. However, you are the boss of your own system. If you decide this works for your particular workflow, you can just add the export to your script:
export PATH="path/to/anaconda3/bin:$PATH"
This will set the PATH for use in the current shell and sub-processes.
Solution 4: Manually source the conda script (possibly outdated)
As mentioned in this answer, you can also opt to manually source the conda.sh script (keep in mind your conda.sh might be in another directory):
source /opt/anaconda/etc/profile.d/conda.sh
This will essentially run that shell script and add the included functionality to the current shell (e.g the one spawned by subprocess.call).
Keep in mind this answer is quite a bit older (~2013) and may not apply anymore, depending how much conda has changed over the years.
Notes
As I mentioned in the comments, you may want to post some related questions on https://unix.stackexchange.com/. You have an interesting configuration challenge that may be better suited for answers specifically pertaining to Linux, since your issue is sourcing directly from Linux shell behavior.
I know it might sound weird because I can do it using PowerShell, but I'd like to use Python to find what Windows Features are enabled.
I'll explain my reason and maybe you'll be able to guide me in a different direction, because from a quick google search, what I'm looking for is not possible.
I have a script that should be able to run on both Windows and Linux. It checks if a path to a directory exists, and if I have permissions to it. It does a bunch of other things and since it should work on both OSes, I need it to check that Windows Features thing. I don't want to run two different scripts, I'd rather have it all in one place and I'm not sure if maybe I'm able to call PowerShell inside my script.
Any idea what I can do?
I tried to search myself how to get the enabled windows features and found nothing, but i have some solution for you.
In my opinion you can run a powershell script inside your python script and get the result in a variable in you python script using subprocess module:
import subprocess
p = subprocess.Popen(["powershell.exe",
r"C:\Path\powershellscript.ps1"],
stdout=subprocess.PIPE)
output, err = p.communicate()
print(output)
The output variable will contain the data i believe you desire
Excuse the awkward question wording.
I've made a script. I would like for others to download it from github, and run it by typing programName argument1 argument2, similar to any other popular app used through the terminal such as Jupyter or even opening Atom/Sublime/etc. (ex:jupyter notebook, atom .). However, unlike Jupyter or sublime, my script isn't launching another app, it's a small app meant to be used in the shell.
Currently, to use my script, one must type into the command line python programName.py arg1 etc from within the file's directory.
How do I allow others to dl it and use it from anywhere (not having to be within the directory), without having to type out the whole python programName.py part, and only having to type programName arg1?
This blog post explains step by step how to create a distribution that you can install and it would turn into an executable.
You can refer to this github repo for a sample application.
The full documentation of setuptools is available here.
In general, you should configure your setup.py in order to use the command in the entry-point option:
setup(
name = "your_app_name",
packages = ["package_name"],
entry_points = {
"console_scripts": ['cmd_name = package_name.package_name:main']
},
....
)
This solution would work on every OS where you have installed python.
Your script may need to have an interpreter, "shebang", besides being "reachable" by the $PATH
#!interpreter [optional-arg]
For example, you could have something like
#!/usr/bin/env python
or to force a specific version
#!/usr/local/bin/python2.7
Next, your script needs to be available within the $PATH, check this answer that covers that part: https://unix.stackexchange.com/q/29608/53084
You can simply add your script to PATH variable in order to launch it from anywhere.
In Linux distros, you can simply do it by using a bash command PATH=$PATH:/path/to/your/script.
Make sure you don't have the space around the "=" operator.
Now, the second thing is you don't want your script to be named as pythonProgram.py.You can simply remove the extension .py from PythonProgram.py by adding a single line to the starting of your script.
Open up your script and at the very begining type #!/usr/bin/python.This should be the first line of your code.This line is called shebang and is used to tell the bash which interpreter to be used for compiling the script.
If everything went right, you will be able to run your script as pythonProgram arg1.
In addition to mabe02: Python is a scripting language and usually not compiled, which means you will need an interpreter to run your program.
Programms made in C f.e. can be run on its own because they were compiled into machine code by a compiler.
An interpreter is similar to a compiler as it reads your script and interprets it at runntime. That is why you need to write python before your programm, to tell your computer to interpret your script on runntime, using python. This doesn't mean that there are no possibilities to compile python as can be seen in the other answer and in this link Can a python program be run on a computer without Python? What about C/C++? (py2exe and py2app).
I have a set of python scripts which I run as a daemon services. These all work great, but when all the scripts are running and I use top -u <USER>, I see all my scripts running as python.
I would really like to know which script is running under which process id. So is there any way to execute a python script as a different process name?
I'm stuck here, and I'm not ever sure what terms to Google. :-)
Note: I'm using Ubuntu Linux. Not sure if the OS matters or not.
Try using setproctitle. It should work fine on Linux.
Don't have a linux system here to test this on appropriately, but if the above doesn't work, you should be able to use the same trick they use for things like gzip etc.
The script has to tell what to run it at the top like this:
#!/usr/local/bin/python
Use a softlink like this:
ln -s /usr/local/bin/python ~/bin/myutil
Then just change your script to
#!~/bin/myutil
and it should show up that way instead. You may need to use a hard link instead of a soft link.
Launching a python script using the python script itself (and file associations and/or shell magic) is not very portable, but you can use similar methods on nearly any OS.
The easiest way to get this is using she bang. The first line of your python script should be:
#!/usr/bin/python
or
#!/usr/bin/python3
depending upon whether you use python or python3
and then assign executable permissions to the script as follows:
chmod +x <scriptname>
and then run the script as
./scriptname
this will show up as scriptname in top.