PHP's passthru function does not have the elegant method for which you may be searching of passing environment variables. If you must use passthru, then export your variables directly in the command:

passthru("SOMEVAR=$yourVar PATH=$newPATH ... /path/to/executable $arg1 $arg2 ...")

If you are inclined toward shell_exec, you may appreciate putenv for the slightly cleaner interface:

putenv("SOMEVAR=$yourVar");
putenv("PATH=$newPATH");
echo shell_exec("/path/to/executable $arg1 $arg2 ...");

If you are open to a more robust (if tedious) approach, consider proc_open:

$cmd = "/path/to/executable arg1 arg2 ..."

# Files 0, 1, 2 are the standard "stdin", "stdout", and "stderr"; For details
# read the PHP docs on proc_open.  The key here is to give the child process a
# pipe to write to, and from which we will read and handle the "passthru"
# ourselves
$fileDescriptors = array(
    0 => ["pipe", "r"],
    1 => ["pipe", "w"],
    2 => ["pipe", "w"]
);

$cwd = '/tmp';
$env = [
    'PATH' => $newPATH,
    'SOMEVAR' => $someVar,
    ...
];

# "pHandle" = "Process handle".  Note that $pipes is new here, and will be
# given back to us
$pHandle = proc_open($cmd, $fileDescriptors, $pipes, $cwd, $env);

# crucial: did proc_open work?
if ( is_resource( $pHandle ) ) {
    # $pipes is now valid
    $pstdout = $pipes[ 1 ];

    # Hey, whaddya know?  PHP has just what we need...
    fpassthru( $pstdout );

    # Whenever you proc_open, you must also proc_close.  Just don't
    # forget to close any open file handles
    fclose( $pipes[0] );
    fclose( $pipes[1] );
    fclose( $pipes[2] );
    proc_close( $pHandle );
}

Acc to your reply, as you want to execute the python script from PHP

I was able to execute it using the following code

$command = escapeshellcmd('/var/www/yourscript.py');
$output = shell_exec($command);
echo $output;

Please use the above PHP code with the same python script. Try to run the python script as a GCI script first to make sure it is working and set the permissions to public directory and script as I mentioned before

===================old ans============================

From what you asked, I guess this is what you are trying to do is that you are trying to run it as a CGI script like http://localhost/yourscript.py

And why are you using PHP to execute python script when you can run it directly as a CGI script?

here is what you need to do to make it work like a web page:

1. enable python CGI in apache ( or in the web server you are using ).
2. put the script in CGI configured directory
3. add proper code to your script to make it work as a CGI script

#!/usr/local/bin/python
from pydub import AudioSegment
AudioSegment.converter = "/usr/local/bin/ffmpeg"
sound = AudioSegment.from_file("/var/www/dev.com/public_html/track.mp3")
sound.export("/var/www/dev.com/public_html/test.mp3", format="mp3", bitrate="96k")

print "Content-type: text/html"
print
print ""
print ""
print ""
print "Done/ you can perform some conditions and print useful info here"
print ""

4. Give permissions to the script and make the public directory writable
5. Access the script http://localhost/your-path-to-script.py

I was able to run this properly. let me know if that's not your case if you want something else

In my case, I did this code.

<?php
chdir('/home/pythontest') ; // python code dir
$commandline="/usr/bin/python3 test.py parameter" ;
exec($commandline, $output, $error) ;
echo $output ;
?>

If you need to set some environments for python, add environment vars like this.

$commmandline="LANG=en_US.utf8 LC_ALL=en_US.utf8 /usr/bin/python3 ..." ;

and check the httpd log.