update ssh interface + config file structure

config/example_task.toml

@@ -1,7 +1,6 @@
 woking_directory = "~"                                  # working directory of the running process
 environment = "venv"                                    # activate virtual environment relative to working directory
-output = "output"                                       # redirect stdout of all processes | 
-error = "error"                                         # redirect stderr of all processes \- into files in a directory relative to working directory
+output = "fib_run"                                       # redirect stdout and stderr of all processes into files, relative to working directory
 assign = "assignments.csv"                              # file containing the assignments for the runs with their numbers
 executable = "python fib.py"                            # executable file relative to working directory
 fix_arguments = ""                                      # Arguments which are always the same for every run

src/pisa/config.py

@@ -1,12 +1,11 @@
-__version__ = "0.1.1"
+__version__ = "0.1.2"
 
 # a list of all the keys which have to be present in the task configuration file
 task_necessary_keys = {
     "woking_directory",
     "environment",
     "output",
     "assign",
-    "error",
     "executable",
     "var_arguments"
 }

src/pisa/dispatcher/task_list.py

@@ -55,8 +55,8 @@ def fill_queue(task_queue: queue.Queue, config: dict, add_args: list[running_var
             args=current_args,  # the shlex.split() function transforms a string containing a collection of arguments into a list of single arguments
             w_dir=config['woking_directory'],
             env=config['environment'],
-            out=config['output'],
-            err=config['error'],
+            out=f"{config['output']}/stdout",
+            err=f"{config['output']}/stderr",
         ))
         # write the task with its parameters and the corresponding number into the assignment file
         assignto.write(f"{num}, {config['executable']} {current_args}\n")

src/pisa/ssh/ssh.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 
-import fcntl
 import os
 import subprocess
 
@@ -19,13 +18,9 @@ def connect(self):
             stderr=subprocess.PIPE,
         )
 
-        # weird hack to transform stdout and stderr into other fds where reading is non blocking
-        # first get the file descriptors of the pipes
-        # then use the fcntl system call to change the file descriptor flags
-        stdout_fd = self.ssh_process.stdout.fileno()
-        stderr_fd = self.ssh_process.stderr.fileno()
-        fcntl.fcntl(stdout_fd, fcntl.F_SETFL, os.O_NONBLOCK)
-        fcntl.fcntl(stderr_fd, fcntl.F_SETFL, os.O_NONBLOCK)
+        # set stdout and stderr to non blocking read mode
+        os.set_blocking(self.ssh_process.stdout.fileno(), False)
+        os.set_blocking(self.ssh_process.stderr.fileno(), False)
 
         return self  # monadic return
 
@@ -41,17 +36,11 @@ def send_command(self, command):
 
     def read_stdout(self):
         self._check_connected()
-        try:
-            return self.ssh_process.stdout.read1().decode('utf-8')
-        except BlockingIOError:
-            return None
+        return self.ssh_process.stdout.read1().decode('utf-8')
 
     def read_stderr(self):
         self._check_connected()
-        try:
-            return self.ssh_process.stderr.read1().decode('utf-8')
-        except BlockingIOError:
-            return None
+        return self.ssh_process.stderr.read1().decode('utf-8')
 
     def wait(self):
         self._check_connected()