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Shell command from Python "env: node: No such file or directory"

I got a Node.js CLI program called meyda installed (Mac OS 10.14) using:
sudo npm install --global meyda
From the Terminal I can call the program and it works as expected; like:
meyda --bs=256 --o=apagodis2.csv DczN6842.wav rms
Now, I want to call it from inside a python script (using Spyder) at the same location and tried this – but getting error:
import os
os.system ('/usr/local/bin/meyda --bs=256 --o=apagodis4.csv samples_training/DczN6842.wav rms')
>>> env: node: No such file or directory
I can issue more "traditional" shell commands like this from the same Python script and it works:
os.system ('cp samples_training/DczN6842.wav copy.wav')
Also tried subprocess call with same result. I confirmed the executable is at /usr/local/bin/
To make sure I also removed all file arguments calling the program using only the help flag but same, error.
os.system ('/usr/local/bin/meyda -h')
>>> env: node: No such file or directory
Why is the command not found from inside Python but sucessfully in the macOS Terminal?

Why is $PATH in remote deployment path different from $PATH in remote system?

I'm currently working on Pycharm with remote python Interpreter(miniconda3/bin/python).
So when I type echo $PATH in remote server, it prints
/home/woosung/bin:/home/woosung/.local/bin:/home/woosung/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
I created project in Pycharm and set remote python Interpreter as miniconda3 python, it works well when I just run some *.py files.
But when I typed some os.system() lines, weird things happened.
For instance, in test.py from Pycharm project
import os
os.system('echo $PATH')
os.system('python --version')
Output is
ssh://woosung#xxx.xxx.xxx.xxx:xx/home/woosung/miniconda3/bin/python -u /tmp/pycharm_project_203/test.py
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
Python 2.7.12
Process finished with exit code 0
I tried same command in remote server,
woosung#test-pc:~$ echo $PATH
/home/woosung/bin:/home/woosung/.local/bin:/home/woosung/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
woosung#test-pc:~$ python --version
Python 3.6.6 :: Anaconda, Inc.
PATH and the version of python are totally different! How can I fix this?
I've already tried add os.system('export PATH="$PATH:$HOME/miniconda3/bin"') to test.py. But it still gives same $PATH.(/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games)
EDIT
Thanks to the comment of #Dietrich Epp, I successfully add interpreter path to the shell $PATH.
(os.environ["PATH"] += ":/home/woosung/miniconda3/bin")
But I stuck the more basic problem. When I add the path and execute command the some *.py file including import library which is only in miniconda3, the shell gives ImportError.
For instance, in test.py
import matplotlib
os.environ["PATH"] += ":/home/woosung/miniconda3/bin"
os.system("python import_test.py")
and import_test.py
import matplotlib
And when I run test.py,
Traceback (most recent call last):
File "import_test.py", line 1, in <module>
import matplotlib
ImportError: No module named matplotlib
Looks like the shell doesn't understand how to utilize modified $PATH.

I find the solution.
It is not direct but quite simple.
I changed os.system("python import_test.py") to os.system(sys.executable + ' import_test.py').
This makes the shell uses the Pycharm remote interpreter(miniconda3), not original.

Why can't the Python command "subprocess.Popen" find the jar file to run?

I'm trying to run code from this repo: https://github.com/tylin/coco-caption, specifically from https://github.com/tylin/coco-caption/blob/master/pycocoevalcap/tokenizer/ptbtokenizer.py, line 51-52:
p_tokenizer = subprocess.Popen(cmd, cwd=path_to_jar_dirname, \
stdout=subprocess.PIPE)
The error I get running this is
OSError: [Errno 2] No such file or directory
I can't figure out why the file can't be found.
The jar I'm trying to run is:
stanford-corenlp-3.4.1.jar
You can see the structure of directory by going to https://github.com/tylin/coco-caption/tree/master/pycocoevalcap/tokenizer. For more specificity into what my actual arguments are when I run the line of code:
cmd= ['java', '-cp', 'stanford-corenlp-3.4.1.jar', 'edu.stanford.nlp.process.PTBTokenizer', '-preserveLines', '-lowerCase', 'tmpWS5p0Z'],
and
path_to_dirname =abs_path_to_folder/tokenizer
I can see the jar that needs to be run, and it looks to be in the right place, so why can't python find it. (Note: I'm using python2.7.) And the temporary File 'tmpWS5p0Z' is where it should be.
Edit: I'm using Ubuntu

try an absolute path ( meaning the path beginning from root / )
https://en.wikipedia.org/wiki/Path_(computing)#Absolute_and_relative_paths
for relative paths in python see i.e. Relative paths in Python , How to refer to relative paths of resources when working with a code repository in Python
UPDATE:
As a test try subprocess.Popen() with the shell=True option and give an absolute path for any involved file, including tmpWS5p0Z
in this subprocess.Popen() call are involved two paths :
1) the python path, python has to find the java executable and the stanford-corenlp-3.4.1.jar which is essentially a java program with its own path
2) the java path of stanford-corenlp-3.4.1.jar
as this is all too complicated try
p_tokenizer = subprocess.Popen(['/absolute_path_to/java -cp /absolute_path_to/stanford-corenlp-3.4.1.jar /absolute_path_to/edu.stanford.nlp.process.PTBTokenizer -preserveLines -lowerCase /absolute_path_to/tmpWS5p0Z' ], shell=True)
Python specify popen working directory via argument
Python subprocess.Popen() error (No such file or directory)

Just in case it might help someone:
I was struggling with the same problem (same https://github.com/tylin/coco-caption code). Might be relevant to say that I was running the code with python 3.7 on CentOS using qsub. So I changed
cmd = ['java', '-cp', 'stanford-corenlp-3.4.1.jar', 'edu.stanford.nlp.process.PTBTokenizer', '-preserveLines', '-lowerCase', 'tmpWS5p0Z']
to
cmd = ['/abs/path/to/java -cp /abs/path/to/stanford-corenlp-3.4.1.jar edu.stanford.nlp.process.PTBTokenizer -preserveLines -lowerCase ', ' /abs/path/to/temporary_file']
Using absolute paths fixed the OSError: [Errno 2] No such file or directory. Notice that I still put '/abs/path/to/temporary_file' as second element in the cmd list, because it got added later on. But then something went wrong in the tokenizer java subprocess, I don't know why or what, just observing because:
p_tokenizer = subprocess.Popen(cmd, cwd=path_to_jar_dirname, stdout=subprocess.PIPE, shell=True)
token_lines = p_tokenizer.communicate(input=sentences.rstrip())[0]
Here token_lines was an empty list (which is not the wanted behavior). Executing this in IPython resulted in the following (just the subprocess.Popen(..., not the communicate).
Exception in thread "main" edu.stanford.nlp.io.RuntimeIOException: java.io.IOException: Input/output error
at edu.stanford.nlp.process.PTBTokenizer.getNext(PTBTokenizer.java:278)
at edu.stanford.nlp.process.PTBTokenizer.getNext(PTBTokenizer.java:163)
at edu.stanford.nlp.process.AbstractTokenizer.hasNext(AbstractTokenizer.java:55)
at edu.stanford.nlp.process.PTBTokenizer.tokReader(PTBTokenizer.java:444)
at edu.stanford.nlp.process.PTBTokenizer.tok(PTBTokenizer.java:416)
at edu.stanford.nlp.process.PTBTokenizer.main(PTBTokenizer.java:760)
Caused by: java.io.IOException: Input/output error
at java.base/java.io.FileInputStream.readBytes(Native Method)
at java.base/java.io.FileInputStream.read(FileInputStream.java:279)
at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:290)
at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351)
at java.base/sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at java.base/sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at java.base/sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.base/java.io.InputStreamReader.read(InputStreamReader.java:185)
at java.base/java.io.BufferedReader.read1(BufferedReader.java:210)
at java.base/java.io.BufferedReader.read(BufferedReader.java:287)
at edu.stanford.nlp.process.PTBLexer.zzRefill(PTBLexer.java:24511)
at edu.stanford.nlp.process.PTBLexer.next(PTBLexer.java:24718)
at edu.stanford.nlp.process.PTBTokenizer.getNext(PTBTokenizer.java:276)
... 5 more
Again, I don't know why or what, but I just wanted to share that doing this fixed it:
cmd = ['/abs/path/to/java -cp /abs/path/to/stanford-corenlp-3.4.1.jar edu.stanford.nlp.process.PTBTokenizer -preserveLines -lowerCase /abs/path/to/temporary_file']
And changing cmd.append(os.path.join(path_to_jar_dirname, os.path.basename(tmp_file.name))) into cmd[0] += os.path.join(path_to_jar_dirname, os.path.basename(tmp_file.name)).
So making cmd into a list with only 1 element, containing the entire command with absolute paths at once. Thanks for your help!

As #Lars mentioned above the issue I had was that I Java wasn't installed. Solved it with:
sudo apt update
sudo apt install default-jdk
sudo apt install default-jre
Making this post since I had this issue twice (due to reinstallation problems) and forgot about it.

How do I make a python script executable?

How can I run a python script with my own command line name like myscript without having to do python myscript.py in the terminal?

Add a shebang line to the top of the script:
#!/usr/bin/env python
Mark the script as executable:
chmod +x myscript.py
Add the dir containing it to your PATH variable. (If you want it to stick, you'll have to do this in .bashrc or .bash_profile in your home dir.)
export PATH=/path/to/script:$PATH

The best way, which is cross-platform, is to create setup.py, define an entry point in it and install with pip.
Say you have the following contents of myscript.py:
def run():
print('Hello world')
Then you add setup.py with the following:
from setuptools import setup
setup(
name='myscript',
version='0.0.1',
entry_points={
'console_scripts': [
'myscript=myscript:run'
]
}
)
Entry point format is terminal_command_name=python_script_name:main_method_name
Finally install with the following command.
pip install -e /path/to/script/folder
-e stands for editable, meaning you'll be able to work on the script and invoke the latest version without need to reinstall
After that you can run myscript from any directory.

I usually do in the script:
#!/usr/bin/python
... code ...
And in terminal:
$: chmod 755 yourfile.py
$: ./yourfile.py

Another related solution which some people may be interested in. One can also directly embed the contents of myscript.py into your .bashrc file on Linux (should also work for MacOS I think)
For example, I have the following function defined in my .bashrc for dumping Python pickles to the terminal, note that the ${1} is the first argument following the function name:
depickle() {
python << EOPYTHON
import pickle
f = open('${1}', 'rb')
while True:
try:
print(pickle.load(f))
except EOFError:
break
EOPYTHON
}
With this in place (and after reloading .bashrc), I can now run depickle a.pickle from any terminal or directory on my computer.

The simplest way that comes to my mind is to use "pyinstaller".
create an environment that contains all the lib you have used in your code.
activate the environment and in the command window write pip install pyinstaller
Use the command window to open the main directory that codes maincode.py is located.
remember to keep the environment active and write pyinstaller maincode.py
Check the folder named "build" and you will find the executable file.
I hope that this solution helps you.
GL

I've struggled for a few days with the problem of not finding the command py -3 or any other related to pylauncher command if script was running by service created using Nssm tool.
But same commands worked when run directly from cmd.
What was the solution? Just to re-run Python installer and at the very end click the option to disable path length limit.
I'll just leave it here, so that anyone can use this answer and find it helpful.

Starting module shell command from python subprocess module

I'm trying to run vnc server, but in order to do it first I need to run 'module load vnc'.
If I call which module in loaded bash shell then the command in not found is the PATH but in the same time it's available. It looks like the command is built-in.
In other words it looks like I need to execute two commands at once module load vnc;vncserver :8080 -localhost and I'm writing script to start it from python.
I have tried different variants with subprocess.Popen like
subprocess.Popen('module load vnc;vncserver :8080 -localhost', shell=True)
which returns 127 exit code or command not found.
subprocess.Popen('module load vnc;vncserver :8080 -localhost', shell=False)
showing
File <path>/subprocess.py line 621, in \__init__
errread, errwrite)
OSError: [Errno 2] No such file or directory.
If I specify shell=True, it executes from /bin/sh but I need it from /bin/bash.
Specifying executable='/bin/bash' doesn't help as it loads new bash shell but it starts as string but not as process, i.e. I see in ps list exactly the same command I would like to start.
Would you please advise how to do start this command from subprocess module? Is it possible to have it started with shell=False?

Environment Modules usually just modifies a couple environment variables for you. It's usually possible to skip the module load whatever step altogether and just not depend on those modules. I recommend
subprocess.Popen(['/possibly/path/to/vncserver', ':8080', '-localhost'],
env={'WHATEVER': 'you', 'MAY': 'need'})
instead of loading the module at all.
If you do insist on using this basic method, then you want to start bash yourself with Popen(['bash',....

If you want to do it with shell=False, just split this into two Popen calls.
subprocess.check_call('module load vnc'.split())
subprocess.Popen('vncserver :8080 -localhost'.split())

You can call module from a Python script. The module command is provided by the environment-modules software, which also provides a python.py initialization script.
Evaluating this script in a Python script enables the module python function. If environment-modules is installed in /usr/share/Modules, you can find this script at /usr/share/Modules/init/python.py.
Following code enables module python function:
import os
exec(open('/usr/share/Modules/init/python.py').read())
Thereafter you can load your module and start your application:
module('load', 'vnc')
subprocess.Popen(['vncserver', ':8080', '-localhost'])