From 1f94020e82e54d6296b932c8b65d6bc771ad9845 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Sun, 17 Mar 2024 20:16:18 -0500
Subject: [PATCH] Add type hints

---
 pysqa/cmd.py               |   2 +-
 pysqa/executor/backend.py  |   6 +-
 pysqa/executor/executor.py |   6 +-
 pysqa/executor/helper.py   |  12 ++--
 pysqa/ext/modular.py       |  30 +++++-----
 pysqa/ext/remote.py        |  79 +++++++++++++++-----------
 pysqa/queueadapter.py      |  56 +++++++++----------
 pysqa/utils/basic.py       | 110 ++++++++++++++++++-------------------
 pysqa/utils/config.py      |   2 +-
 pysqa/utils/execute.py     |  12 ++--
 pysqa/wrapper/flux.py      |  10 ++--
 pysqa/wrapper/generic.py   |  12 ++--
 pysqa/wrapper/gent.py      |   8 +--
 pysqa/wrapper/lsf.py       |  10 ++--
 pysqa/wrapper/moab.py      |   6 +-
 pysqa/wrapper/sge.py       |  10 ++--
 pysqa/wrapper/slurm.py     |  12 ++--
 pysqa/wrapper/torque.py    |  10 ++--
 18 files changed, 204 insertions(+), 189 deletions(-)

diff --git a/pysqa/cmd.py b/pysqa/cmd.py
index 747bb8e2..7aa72682 100644
--- a/pysqa/cmd.py
+++ b/pysqa/cmd.py
@@ -7,7 +7,7 @@
 from pysqa.utils.execute import execute_command
 
 
-def command_line(arguments_lst=None, execute_command=execute_command):
+def command_line(arguments_lst: list=None, execute_command: callable = execute_command):
     """
     Parse the command line arguments.
 
diff --git a/pysqa/executor/backend.py b/pysqa/executor/backend.py
index 776e7643..599dc8e3 100644
--- a/pysqa/executor/backend.py
+++ b/pysqa/executor/backend.py
@@ -10,7 +10,7 @@
 )
 
 
-def execute_files_from_list(tasks_in_progress_dict, cache_directory, executor):
+def execute_files_from_list(tasks_in_progress_dict: dict, cache_directory: str, executor):
     file_lst = os.listdir(cache_directory)
     for file_name_in in file_lst:
         key = file_name_in.split(".in.pl")[0]
@@ -37,7 +37,7 @@ def execute_files_from_list(tasks_in_progress_dict, cache_directory, executor):
             )
 
 
-def execute_tasks(cores, cache_directory):
+def execute_tasks(cores: int, cache_directory: str):
     tasks_in_progress_dict = {}
     with PyMPIExecutor(
         max_workers=cores,
@@ -58,7 +58,7 @@ def execute_tasks(cores, cache_directory):
             )
 
 
-def command_line(arguments_lst=None):
+def command_line(arguments_lst: list=None):
     if arguments_lst is None:
         arguments_lst = sys.argv[1:]
     cores_arg = arguments_lst[arguments_lst.index("--cores") + 1]
diff --git a/pysqa/executor/executor.py b/pysqa/executor/executor.py
index 1f6e9087..a5a1245d 100644
--- a/pysqa/executor/executor.py
+++ b/pysqa/executor/executor.py
@@ -12,7 +12,7 @@
 
 
 class Executor(FutureExecutor):
-    def __init__(self, cwd=None, queue_adapter=None, queue_adapter_kwargs=None):
+    def __init__(self, cwd: str=None, queue_adapter=None, queue_adapter_kwargs: dict=None):
         self._task_queue = queue.Queue()
         self._memory_dict = {}
         self._cache_directory = os.path.abspath(os.path.expanduser(cwd))
@@ -42,7 +42,7 @@ def __init__(self, cwd=None, queue_adapter=None, queue_adapter_kwargs=None):
         )
         self._process.start()
 
-    def submit(self, fn, *args, **kwargs):
+    def submit(self, fn: callable, *args, **kwargs):
         funct_dict = serialize_funct(fn, *args, **kwargs)
         key = list(funct_dict.keys())[0]
         if key not in self._memory_dict.keys():
@@ -53,7 +53,7 @@ def submit(self, fn, *args, **kwargs):
             self._task_queue.put({key: self._memory_dict[key]})
         return self._memory_dict[key]
 
-    def shutdown(self, wait=True, *, cancel_futures=False):
+    def shutdown(self, wait: bool = True, *, cancel_futures: bool = False):
         if cancel_futures:
             cancel_items_in_queue(que=self._task_queue)
         self._task_queue.put({"shutdown": True, "wait": wait})
diff --git a/pysqa/executor/helper.py b/pysqa/executor/helper.py
index 0dd250f9..d99980da 100644
--- a/pysqa/executor/helper.py
+++ b/pysqa/executor/helper.py
@@ -14,7 +14,7 @@ def deserialize(funct_dict):
         return {}
 
 
-def find_executed_tasks(future_queue, cache_directory):
+def find_executed_tasks(future_queue: queue.Queue, cache_directory: str):
     task_memory_dict = {}
     while True:
         task_dict = {}
@@ -32,13 +32,13 @@ def find_executed_tasks(future_queue, cache_directory):
             )
 
 
-def read_from_file(file_name):
+def read_from_file(file_name: str) -> dict:
     name = file_name.split("/")[-1].split(".")[0]
     with open(file_name, "rb") as f:
         return {name: f.read()}
 
 
-def reload_previous_futures(future_queue, future_dict, cache_directory):
+def reload_previous_futures(future_queue: queue.Queue, future_dict: dict, cache_directory: str):
     file_lst = os.listdir(cache_directory)
     for f in file_lst:
         if f.endswith(".in.pl"):
@@ -54,16 +54,16 @@ def reload_previous_futures(future_queue, future_dict, cache_directory):
                 future_queue.put({key: future_dict[key]})
 
 
-def serialize_result(result_dict):
+def serialize_result(result_dict: dict):
     return {k: cloudpickle.dumps(v) for k, v in result_dict.items()}
 
 
-def serialize_funct(fn, *args, **kwargs):
+def serialize_funct(fn: callable, *args, **kwargs):
     binary = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
     return {fn.__name__ + _get_hash(binary=binary): binary}
 
 
-def write_to_file(funct_dict, state, cache_directory):
+def write_to_file(funct_dict: dict, state, cache_directory: str):
     file_name_lst = []
     for k, v in funct_dict.items():
         file_name = _get_file_name(name=k, state=state)
diff --git a/pysqa/ext/modular.py b/pysqa/ext/modular.py
index 3036bc70..ce3a3f25 100644
--- a/pysqa/ext/modular.py
+++ b/pysqa/ext/modular.py
@@ -8,7 +8,7 @@
 
 
 class ModularQueueAdapter(BasisQueueAdapter):
-    def __init__(self, config, directory="~/.queues", execute_command=execute_command):
+    def __init__(self, config: dict, directory: str = "~/.queues", execute_command: callable = execute_command):
         super(ModularQueueAdapter, self).__init__(
             config=config, directory=directory, execute_command=execute_command
         )
@@ -26,16 +26,16 @@ def __init__(self, config, directory="~/.queues", execute_command=execute_comman
 
     def submit_job(
         self,
-        queue=None,
-        job_name=None,
-        working_directory=None,
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        dependency_list=None,
-        command=None,
+        queue: str = None,
+        job_name: str = None,
+        working_directory: str = None,
+        cores: int = None,
+        memory_max: str = None,
+        run_time_max: int = None,
+        dependency_list: list[str] = None,
+        command: str = None,
         **kwargs,
-    ):
+    ) -> int:
         """
 
         Args:
@@ -79,7 +79,7 @@ def submit_job(
         else:
             return None
 
-    def enable_reservation(self, process_id):
+    def enable_reservation(self, process_id: int):
         """
 
         Args:
@@ -103,7 +103,7 @@ def enable_reservation(self, process_id):
         else:
             return None
 
-    def delete_job(self, process_id):
+    def delete_job(self, process_id: int):
         """
 
         Args:
@@ -127,7 +127,7 @@ def delete_job(self, process_id):
         else:
             return None
 
-    def get_queue_status(self, user=None):
+    def get_queue_status(self, user: str = None) -> pandas.DataFrame:
         """
 
         Args:
@@ -155,11 +155,11 @@ def get_queue_status(self, user=None):
             return df[df["user"] == user]
 
     @staticmethod
-    def _resolve_queue_id(process_id, cluster_dict):
+    def _resolve_queue_id(process_id: int, cluster_dict: dict):
         cluster_queue_id = int(process_id / 10)
         cluster_module = cluster_dict[process_id - cluster_queue_id * 10]
         return cluster_module, cluster_queue_id
 
     @staticmethod
-    def _switch_cluster_command(cluster_module):
+    def _switch_cluster_command(cluster_module: str):
         return ["module", "--quiet", "swap", "cluster/{};".format(cluster_module)]
diff --git a/pysqa/ext/remote.py b/pysqa/ext/remote.py
index d36f4f1c..8219dd17 100644
--- a/pysqa/ext/remote.py
+++ b/pysqa/ext/remote.py
@@ -15,7 +15,7 @@
 
 
 class RemoteQueueAdapter(BasisQueueAdapter):
-    def __init__(self, config, directory="~/.queues", execute_command=execute_command):
+    def __init__(self, config: dict, directory: str = "~/.queues", execute_command: callable = execute_command):
         super(RemoteQueueAdapter, self).__init__(
             config=config, directory=directory, execute_command=execute_command
         )
@@ -78,22 +78,37 @@ def __init__(self, config, directory="~/.queues", execute_command=execute_comman
         self._ssh_proxy_connection = None
         self._remote_flag = True
 
-    def convert_path_to_remote(self, path):
+    def convert_path_to_remote(self, path: str):
         working_directory = os.path.abspath(os.path.expanduser(path))
         return self._get_remote_working_dir(working_directory=working_directory)
 
     def submit_job(
         self,
-        queue=None,
-        job_name=None,
-        working_directory=None,
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        dependency_list=None,
-        command=None,
+        queue: str = None,
+        job_name: str = None,
+        working_directory: str = None,
+        cores: int = None,
+        memory_max: int = None,
+        run_time_max: int = None,
+        dependency_list: list[str] = None,
+        command: str = None,
         **kwargs,
-    ):
+    ) -> int:
+        """
+
+        Args:
+            queue (str/None):
+            job_name (str/None):
+            working_directory (str/None):
+            cores (int/None):
+            memory_max (int/None):
+            run_time_max (int/None):
+            dependency_list (list/None):
+            command (str/None):
+
+        Returns:
+            int:
+        """
         if dependency_list is not None:
             raise NotImplementedError(
                 "Submitting jobs with dependencies to a remote cluster is not yet supported."
@@ -102,7 +117,7 @@ def submit_job(
         output = self._execute_remote_command(command=command)
         return int(output.split()[-1])
 
-    def enable_reservation(self, process_id):
+    def enable_reservation(self, process_id: int) -> str:
         """
 
         Args:
@@ -115,7 +130,7 @@ def enable_reservation(self, process_id):
             command=self._reservation_command(job_id=process_id)
         )
 
-    def delete_job(self, process_id):
+    def delete_job(self, process_id: int) -> str:
         """
 
         Args:
@@ -128,7 +143,7 @@ def delete_job(self, process_id):
             command=self._delete_command(job_id=process_id)
         )
 
-    def get_queue_status(self, user=None):
+    def get_queue_status(self, user: str = None) -> pandas.DataFrame:
         """
 
         Args:
@@ -147,7 +162,7 @@ def get_queue_status(self, user=None):
         else:
             return df[df["user"] == user]
 
-    def get_job_from_remote(self, working_directory):
+    def get_job_from_remote(self, working_directory: str):
         """
         Get the results of the calculation - this is necessary when the calculation was executed on a remote host.
         """
@@ -176,7 +191,7 @@ def get_job_from_remote(self, working_directory):
         if self._ssh_delete_file_on_remote:
             self._execute_remote_command(command="rm -r " + remote_working_directory)
 
-    def transfer_file(self, file, transfer_back=False, delete_file_on_remote=False):
+    def transfer_file(self, file: str, transfer_back: bool = False, delete_file_on_remote: bool = False):
         working_directory = os.path.abspath(os.path.expanduser(file))
         remote_working_directory = self._get_remote_working_dir(
             working_directory=working_directory
@@ -200,7 +215,7 @@ def _check_ssh_connection(self):
         if self._ssh_connection is None:
             self._ssh_connection = self._open_ssh_connection()
 
-    def _transfer_files(self, file_dict, sftp=None, transfer_back=False):
+    def _transfer_files(self, file_dict: dict, sftp=None, transfer_back: bool = False):
         if sftp is None:
             if self._ssh_continous_connection:
                 self._check_ssh_connection()
@@ -346,13 +361,13 @@ def _get_queue_status_command(self):
 
     def _submit_command(
         self,
-        queue=None,
-        job_name=None,
-        working_directory=None,
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        command_str=None,
+        queue: str = None,
+        job_name: str = None,
+        working_directory: str = None,
+        cores: int = None,
+        memory_max: int = None,
+        run_time_max: int = None,
+        command_str: str = None,
     ):
         command = self._remote_command() + "--submit "
         if queue is not None:
@@ -371,13 +386,13 @@ def _submit_command(
             command += '--command "' + command_str + '" '
         return command
 
-    def _delete_command(self, job_id):
+    def _delete_command(self, job_id: int) -> str:
         return self._remote_command() + "--delete --id " + str(job_id)
 
-    def _reservation_command(self, job_id):
+    def _reservation_command(self, job_id: int) -> str:
         return self._remote_command() + "--reservation --id " + str(job_id)
 
-    def _execute_remote_command(self, command):
+    def _execute_remote_command(self, command: str):
         if self._ssh_continous_connection:
             self._check_ssh_connection()
             ssh = self._ssh_connection
@@ -390,13 +405,13 @@ def _execute_remote_command(self, command):
             ssh.close()
         return output
 
-    def _get_remote_working_dir(self, working_directory):
+    def _get_remote_working_dir(self, working_directory: str):
         return os.path.join(
             self._ssh_remote_path,
             os.path.relpath(working_directory, self._ssh_local_path),
         )
 
-    def _create_remote_dir(self, directory):
+    def _create_remote_dir(self, directory: str):
         if isinstance(directory, str):
             self._execute_remote_command(command="mkdir -p " + directory)
         elif isinstance(directory, list):
@@ -407,7 +422,7 @@ def _create_remote_dir(self, directory):
         else:
             raise TypeError()
 
-    def _transfer_data_to_remote(self, working_directory):
+    def _transfer_data_to_remote(self, working_directory: str):
         working_directory = os.path.abspath(os.path.expanduser(working_directory))
         remote_working_directory = self._get_remote_working_dir(
             working_directory=working_directory
@@ -432,7 +447,7 @@ def _transfer_data_to_remote(self, working_directory):
         self._create_remote_dir(directory=new_dir_list)
         self._transfer_files(file_dict=file_dict, sftp=None, transfer_back=False)
 
-    def _get_user(self):
+    def _get_user(self) -> str:
         """
 
         Returns:
@@ -441,7 +456,7 @@ def _get_user(self):
         return self._ssh_username
 
     @staticmethod
-    def _get_file_transfer(file, local_dir, remote_dir):
+    def _get_file_transfer(file: str, local_dir: str, remote_dir: str) -> str:
         return os.path.abspath(
             os.path.join(remote_dir, os.path.relpath(file, local_dir))
         )
diff --git a/pysqa/queueadapter.py b/pysqa/queueadapter.py
index 812e5472..e052c28f 100644
--- a/pysqa/queueadapter.py
+++ b/pysqa/queueadapter.py
@@ -45,7 +45,7 @@ class QueueAdapter(object):
             Queues available for auto completion QueueAdapter().queues.<queue name> returns the queue name.
     """
 
-    def __init__(self, directory="~/.queues", execute_command=execute_command):
+    def __init__(self, directory: str = "~/.queues", execute_command: callable = execute_command):
         queue_yaml = os.path.join(directory, "queue.yaml")
         clusters_yaml = os.path.join(directory, "clusters.yaml")
         self._adapter = None
@@ -76,7 +76,7 @@ def __init__(self, directory="~/.queues", execute_command=execute_command):
             )
         self._adapter = self._queue_dict[primary_queue]
 
-    def list_clusters(self):
+    def list_clusters(self) -> list[str]:
         """
         List available computing clusters for remote submission
 
@@ -85,7 +85,7 @@ def list_clusters(self):
         """
         return list(self._queue_dict.keys())
 
-    def switch_cluster(self, cluster_name):
+    def switch_cluster(self, cluster_name: str):
         """
         Switch to a different computing cluster
 
@@ -104,11 +104,11 @@ def config(self):
         return self._adapter.config
 
     @property
-    def ssh_delete_file_on_remote(self):
+    def ssh_delete_file_on_remote(self) -> bool:
         return self._adapter.ssh_delete_file_on_remote
 
     @property
-    def remote_flag(self):
+    def remote_flag(self) -> bool:
         """
 
         Returns:
@@ -117,7 +117,7 @@ def remote_flag(self):
         return self._adapter.remote_flag
 
     @property
-    def queue_list(self):
+    def queue_list(self) -> list[str]:
         """
 
         Returns:
@@ -126,7 +126,7 @@ def queue_list(self):
         return self._adapter.queue_list
 
     @property
-    def queue_view(self):
+    def queue_view(self) -> pandas.DataFrame:
         """
 
         Returns:
@@ -135,21 +135,21 @@ def queue_view(self):
         return self._adapter.queue_view
 
     @property
-    def queues(self):
+    def queues(self) -> list[str]:
         return self._adapter.queues
 
     def submit_job(
         self,
-        queue=None,
-        job_name=None,
-        working_directory=None,
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        dependency_list=None,
-        command=None,
+        queue: str = None,
+        job_name: str = None,
+        working_directory: str = None,
+        cores: int = None,
+        memory_max: int = None,
+        run_time_max: int = None,
+        dependency_list: list[str] = None,
+        command: str = None,
         **kwargs,
-    ):
+    ) -> int:
         """
         Submits command to the given queue.
 
@@ -181,7 +181,7 @@ def submit_job(
             **kwargs,
         )
 
-    def enable_reservation(self, process_id):
+    def enable_reservation(self, process_id: int) -> str:
         """
 
         Args:
@@ -192,7 +192,7 @@ def enable_reservation(self, process_id):
         """
         return self._adapter.enable_reservation(process_id=process_id)
 
-    def get_job_from_remote(self, working_directory):
+    def get_job_from_remote(self, working_directory: str):
         """
         Get the results of the calculation - this is necessary when the calculation was executed on a remote host.
 
@@ -202,7 +202,7 @@ def get_job_from_remote(self, working_directory):
         self._adapter.get_job_from_remote(working_directory=working_directory)
 
     def transfer_file_to_remote(
-        self, file, transfer_back=False, delete_file_on_remote=False
+        self, file: str, transfer_back: bool = False, delete_file_on_remote: bool = False
     ):
         """
         Transfer file from remote host to local host
@@ -218,7 +218,7 @@ def transfer_file_to_remote(
             delete_file_on_remote=delete_file_on_remote,
         )
 
-    def convert_path_to_remote(self, path):
+    def convert_path_to_remote(self, path: str) -> str:
         """
 
         Args:
@@ -229,7 +229,7 @@ def convert_path_to_remote(self, path):
         """
         return self._adapter.convert_path_to_remote(path=path)
 
-    def delete_job(self, process_id):
+    def delete_job(self, process_id: int) -> str:
         """
 
         Args:
@@ -240,7 +240,7 @@ def delete_job(self, process_id):
         """
         return self._adapter.delete_job(process_id=process_id)
 
-    def get_queue_status(self, user=None):
+    def get_queue_status(self, user: str=None) -> pandas.DataFrame:
         """
 
         Args:
@@ -251,7 +251,7 @@ def get_queue_status(self, user=None):
         """
         return self._adapter.get_queue_status(user=user)
 
-    def get_status_of_my_jobs(self):
+    def get_status_of_my_jobs(self) -> pandas.DataFrame:
         """
 
         Returns:
@@ -259,7 +259,7 @@ def get_status_of_my_jobs(self):
         """
         return self._adapter.get_status_of_my_jobs()
 
-    def get_status_of_job(self, process_id):
+    def get_status_of_job(self, process_id: int) -> str:
         """
 
         Args:
@@ -270,7 +270,7 @@ def get_status_of_job(self, process_id):
         """
         return self._adapter.get_status_of_job(process_id=process_id)
 
-    def get_status_of_jobs(self, process_id_lst):
+    def get_status_of_jobs(self, process_id_lst: list[int]) -> list[str]:
         """
 
         Args:
@@ -282,7 +282,7 @@ def get_status_of_jobs(self, process_id_lst):
         return self._adapter.get_status_of_jobs(process_id_lst=process_id_lst)
 
     def check_queue_parameters(
-        self, queue, cores=1, run_time_max=None, memory_max=None, active_queue=None
+        self, queue: str, cores: int = 1, run_time_max: int = None, memory_max: int = None, active_queue: dict = None
     ):
         """
 
@@ -305,7 +305,7 @@ def check_queue_parameters(
         )
 
 
-def set_queue_adapter(config, directory, execute_command=execute_command):
+def set_queue_adapter(config: dict, directory: str, execute_command: callable=execute_command):
     """
     Initialize the queue adapter
 
diff --git a/pysqa/utils/basic.py b/pysqa/utils/basic.py
index 29d8ab5b..5db323d0 100644
--- a/pysqa/utils/basic.py
+++ b/pysqa/utils/basic.py
@@ -44,7 +44,7 @@ class BasisQueueAdapter(object):
             Queues available for auto completion QueueAdapter().queues.<queue name> returns the queue name.
     """
 
-    def __init__(self, config, directory="~/.queues", execute_command=execute_command):
+    def __init__(self, config: dict, directory: str = "~/.queues", execute_command: callable = execute_command):
         self._config = config
         self._fill_queue_dict(queue_lst_dict=self._config["queues"])
         self._load_templates(queue_lst_dict=self._config["queues"], directory=directory)
@@ -89,11 +89,11 @@ def __init__(self, config, directory="~/.queues", execute_command=execute_comman
         self._execute_command_function = execute_command
 
     @property
-    def ssh_delete_file_on_remote(self):
+    def ssh_delete_file_on_remote(self) -> bool:
         return self._ssh_delete_file_on_remote
 
     @property
-    def remote_flag(self):
+    def remote_flag(self) -> bool:
         return self._remote_flag
 
     @property
@@ -106,7 +106,7 @@ def config(self):
         return self._config
 
     @property
-    def queue_list(self):
+    def queue_list(self) -> list:
         """
 
         Returns:
@@ -115,7 +115,7 @@ def queue_list(self):
         return list(self._config["queues"].keys())
 
     @property
-    def queue_view(self):
+    def queue_view(self) -> pandas.DataFrame:
         """
 
         Returns:
@@ -131,16 +131,16 @@ def queues(self):
 
     def submit_job(
         self,
-        queue=None,
-        job_name=None,
-        working_directory=None,
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        dependency_list=None,
-        command=None,
+        queue: str = None,
+        job_name: str = None,
+        working_directory: str = None,
+        cores: int = None,
+        memory_max: int = None,
+        run_time_max: int = None,
+        dependency_list: list[str] = None,
+        command: str = None,
         **kwargs,
-    ):
+    ) -> int:
         """
 
         Args:
@@ -182,14 +182,14 @@ def submit_job(
         else:
             return None
 
-    def _list_command_to_be_executed(self, dependency_list, queue_script_path) -> list:
+    def _list_command_to_be_executed(self, dependency_list: list[str], queue_script_path: str) -> list:
         return (
             self._commands.submit_job_command
             + self._commands.dependencies(dependency_list)
             + [queue_script_path]
         )
 
-    def enable_reservation(self, process_id):
+    def enable_reservation(self, process_id: int):
         """
 
         Args:
@@ -207,7 +207,7 @@ def enable_reservation(self, process_id):
         else:
             return None
 
-    def delete_job(self, process_id):
+    def delete_job(self, process_id: int) -> str:
         """
 
         Args:
@@ -225,7 +225,7 @@ def delete_job(self, process_id):
         else:
             return None
 
-    def get_queue_status(self, user=None):
+    def get_queue_status(self, user: str = None) -> pandas.DataFrame:
         """
 
         Args:
@@ -243,7 +243,7 @@ def get_queue_status(self, user=None):
         else:
             return df[df["user"] == user]
 
-    def get_status_of_my_jobs(self):
+    def get_status_of_my_jobs(self) -> pandas.DataFrame:
         """
 
         Returns:
@@ -251,7 +251,7 @@ def get_status_of_my_jobs(self):
         """
         return self.get_queue_status(user=self._get_user())
 
-    def get_status_of_job(self, process_id):
+    def get_status_of_job(self, process_id: int) -> str:
         """
 
         Args:
@@ -267,14 +267,14 @@ def get_status_of_job(self, process_id):
         else:
             return None
 
-    def get_status_of_jobs(self, process_id_lst):
+    def get_status_of_jobs(self, process_id_lst: list[int]) -> list[str]:
         """
 
         Args:
-            process_id_lst:
+            process_id_lst list[int]:
 
         Returns:
-             list: ['running', 'pending', 'error', ...]
+             list[str]: ['running', 'pending', 'error', ...]
         """
         df = self.get_queue_status()
         results_lst = []
@@ -286,21 +286,21 @@ def get_status_of_jobs(self, process_id_lst):
                 results_lst.append("finished")
         return results_lst
 
-    def get_job_from_remote(self, working_directory):
+    def get_job_from_remote(self, working_directory: str):
         """
         Get the results of the calculation - this is necessary when the calculation was executed on a remote host.
         """
         raise NotImplementedError
 
-    def convert_path_to_remote(self, path):
+    def convert_path_to_remote(self, path: str):
         raise NotImplementedError
 
-    def transfer_file(self, file, transfer_back=False, delete_file_on_remote=False):
+    def transfer_file(self, file: str, transfer_back: bool = False, delete_file_on_remote: bool = False):
         raise NotImplementedError
 
     def check_queue_parameters(
-        self, queue, cores=1, run_time_max=None, memory_max=None, active_queue=None
-    ):
+        self, queue: str, cores: int = 1, run_time_max: int = None, memory_max: int = None, active_queue: dict = None
+    ) -> list:
         """
 
         Args:
@@ -330,13 +330,13 @@ def check_queue_parameters(
 
     def _write_queue_script(
         self,
-        queue=None,
-        job_name=None,
-        working_directory=None,
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        command=None,
+        queue: str = None,
+        job_name: str = None,
+        working_directory: str = None,
+        cores: int = None,
+        memory_max: int = None,
+        run_time_max: int = None,
+        command: str = None,
         **kwargs,
     ):
         """
@@ -374,15 +374,15 @@ def _write_queue_script(
 
     def _job_submission_template(
         self,
-        queue=None,
-        job_name="job.py",
-        working_directory=".",
-        cores=None,
-        memory_max=None,
-        run_time_max=None,
-        command=None,
+        queue: str = None,
+        job_name: str = "job.py",
+        working_directory: str = ".",
+        cores: int = None,
+        memory_max: int = None,
+        run_time_max: int = None,
+        command: str = None,
         **kwargs,
-    ):
+    ) -> str:
         """
 
         Args:
@@ -428,12 +428,12 @@ def _job_submission_template(
 
     def _execute_command(
         self,
-        commands,
-        working_directory=None,
-        split_output=True,
-        shell=False,
-        error_filename="pysqa.err",
-    ):
+        commands: str,
+        working_directory: str = None,
+        split_output: bool = True,
+        shell: bool = False,
+        error_filename: str = "pysqa.err",
+    ) -> str:
         """
 
         Args:
@@ -455,7 +455,7 @@ def _execute_command(
         )
 
     @staticmethod
-    def _get_user():
+    def _get_user() -> str:
         """
 
         Returns:
@@ -464,7 +464,7 @@ def _get_user():
         return getpass.getuser()
 
     @staticmethod
-    def _fill_queue_dict(queue_lst_dict):
+    def _fill_queue_dict(queue_lst_dict: dict):
         """
 
         Args:
@@ -476,7 +476,7 @@ def _fill_queue_dict(queue_lst_dict):
                 queue_dict[key] = None
 
     @staticmethod
-    def _load_templates(queue_lst_dict, directory="."):
+    def _load_templates(queue_lst_dict: dict, directory: str = "."):
         """
 
         Args:
@@ -498,7 +498,7 @@ def _load_templates(queue_lst_dict, directory="."):
                         )
 
     @staticmethod
-    def _value_error_if_none(value):
+    def _value_error_if_none(value: str):
         """
 
         Args:
@@ -548,7 +548,7 @@ def _value_in_range(cls, value, value_min=None, value_max=None):
             return value
 
     @staticmethod
-    def _is_memory_string(value):
+    def _is_memory_string(value: str) -> bool:
         """
         Tests a string if it specifies a certain amount of memory e.g.: '20G', '60b'. Also pure integer strings are
         also valid.
@@ -564,7 +564,7 @@ def _is_memory_string(value):
 
     @classmethod
     def _memory_spec_string_to_value(
-        cls, value, default_magnitude="m", target_magnitude="b"
+        cls, value: str, default_magnitude: str = "m", target_magnitude: str = "b"
     ):
         """
         Converts a valid memory string (tested by _is_memory_string) into an integer/float value of desired
diff --git a/pysqa/utils/config.py b/pysqa/utils/config.py
index a831ea72..8b80dc1d 100644
--- a/pysqa/utils/config.py
+++ b/pysqa/utils/config.py
@@ -1,7 +1,7 @@
 import yaml
 
 
-def read_config(file_name="queue.yaml"):
+def read_config(file_name: str = "queue.yaml") -> dict:
     """
 
     Args:
diff --git a/pysqa/utils/execute.py b/pysqa/utils/execute.py
index 9bd560c1..6c663db8 100644
--- a/pysqa/utils/execute.py
+++ b/pysqa/utils/execute.py
@@ -3,12 +3,12 @@
 
 
 def execute_command(
-    commands,
-    working_directory=None,
-    split_output=True,
-    shell=False,
-    error_filename="pysqa.err",
-):
+    commands: str,
+    working_directory: str = None,
+    split_output: bool = True,
+    shell: bool = False,
+    error_filename: str = "pysqa.err",
+) -> str:
     """
     A wrapper around the subprocess.check_output function.
 
diff --git a/pysqa/wrapper/flux.py b/pysqa/wrapper/flux.py
index 1c84171e..efa52099 100644
--- a/pysqa/wrapper/flux.py
+++ b/pysqa/wrapper/flux.py
@@ -7,25 +7,25 @@
 
 class FluxCommands(SchedulerCommands):
     @property
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         return ["flux", "batch"]
 
     @property
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         return ["flux", "cancel"]
 
     @property
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         return ["flux", "jobs", "-a", "--no-header"]
 
     @staticmethod
-    def get_job_id_from_output(queue_submit_output):
+    def get_job_id_from_output(queue_submit_output: str) -> int:
         return int(
             JobID(queue_submit_output.splitlines()[-1].rstrip().lstrip().split()[-1])
         )
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         line_split_lst = [line.split() for line in queue_status_output.splitlines()]
         job_id_lst, user_lst, job_name_lst, status_lst = [], [], [], []
         for entry in line_split_lst:
diff --git a/pysqa/wrapper/generic.py b/pysqa/wrapper/generic.py
index 327b6e9a..05715b27 100644
--- a/pysqa/wrapper/generic.py
+++ b/pysqa/wrapper/generic.py
@@ -19,12 +19,12 @@
 class SchedulerCommands(ABC):
     @property
     @abstractmethod
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         pass
 
     @property
     @abstractmethod
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         pass
 
     @property
@@ -33,20 +33,20 @@ def enable_reservation_command(self):
 
     @property
     @abstractmethod
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         pass
 
     @staticmethod
-    def dependencies(dependency_list) -> list:
+    def dependencies(dependency_list: list[str]) -> list:
         if dependency_list is not None:
             raise NotImplementedError()
         else:
             return []
 
     @staticmethod
-    def get_job_id_from_output(queue_submit_output):
+    def get_job_id_from_output(queue_submit_output: str) -> int:
         raise NotImplementedError()
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         raise NotImplementedError()
diff --git a/pysqa/wrapper/gent.py b/pysqa/wrapper/gent.py
index fe5a643d..3d6e8fd7 100644
--- a/pysqa/wrapper/gent.py
+++ b/pysqa/wrapper/gent.py
@@ -20,15 +20,15 @@
 
 class GentCommands(SlurmCommands):
     @staticmethod
-    def get_job_id_from_output(queue_submit_output):
+    def get_job_id_from_output(queue_submit_output: str) -> int:
         return int(queue_submit_output.splitlines()[-1].rstrip().lstrip().split(";")[0])
 
     @staticmethod
-    def get_queue_from_output(queue_submit_output):
+    def get_queue_from_output(queue_submit_output: str) -> str:
         return str(queue_submit_output.splitlines()[-1].rstrip().lstrip().split(";")[1])
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         qstat = queue_status_output.splitlines()
         queue = qstat[0].split(":")[1].strip()
         if len(qstat) <= 1:  # first row contains cluster name, check if there are jobs
@@ -52,7 +52,7 @@ def convert_queue_status(queue_status_output):
         )
 
     @staticmethod
-    def dependencies(dependency_list) -> list:
+    def dependencies(dependency_list: list[str]) -> list:
         if dependency_list is not None:
             raise NotImplementedError()
         else:
diff --git a/pysqa/wrapper/lsf.py b/pysqa/wrapper/lsf.py
index 0a22a630..cf04fabc 100644
--- a/pysqa/wrapper/lsf.py
+++ b/pysqa/wrapper/lsf.py
@@ -20,23 +20,23 @@
 
 class LsfCommands(SchedulerCommands):
     @property
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         return ["bsub"]
 
     @property
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         return ["bkill"]
 
     @property
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         return ["bjobs"]
 
     @staticmethod
-    def get_job_id_from_output(queue_submit_output):
+    def get_job_id_from_output(queue_submit_output: str) -> int:
         return int(queue_submit_output.split("<")[1].split(">")[0])
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         job_id_lst, user_lst, status_lst, job_name_lst = [], [], [], []
         line_split_lst = queue_status_output.split("\n")
         if len(line_split_lst) > 1:
diff --git a/pysqa/wrapper/moab.py b/pysqa/wrapper/moab.py
index 19a6d0e6..e9300265 100644
--- a/pysqa/wrapper/moab.py
+++ b/pysqa/wrapper/moab.py
@@ -18,13 +18,13 @@
 
 class MoabCommands(SchedulerCommands):
     @property
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         return ["msub"]
 
     @property
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         return ["mjobctl", "-c"]
 
     @property
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         return ["mdiag", "-x"]
diff --git a/pysqa/wrapper/sge.py b/pysqa/wrapper/sge.py
index c5dbc66f..5025bb2a 100644
--- a/pysqa/wrapper/sge.py
+++ b/pysqa/wrapper/sge.py
@@ -21,23 +21,23 @@
 
 class SunGridEngineCommands(SchedulerCommands):
     @property
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         return ["qsub", "-terse"]
 
     @property
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         return ["qdel"]
 
     @property
-    def enable_reservation_command(self):
+    def enable_reservation_command(self) -> list[str]:
         return ["qalter", "-R", "y"]
 
     @property
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         return ["qstat", "-xml"]
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         def leaf_to_dict(leaf):
             return [
                 {sub_child.tag: sub_child.text for sub_child in child} for child in leaf
diff --git a/pysqa/wrapper/slurm.py b/pysqa/wrapper/slurm.py
index 6be70969..4cfd5424 100644
--- a/pysqa/wrapper/slurm.py
+++ b/pysqa/wrapper/slurm.py
@@ -20,23 +20,23 @@
 
 class SlurmCommands(SchedulerCommands):
     @property
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         return ["sbatch", "--parsable"]
 
     @property
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         return ["scancel"]
 
     @property
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         return ["squeue", "--format", "%A|%u|%t|%.15j|%Z", "--noheader"]
 
     @staticmethod
-    def get_job_id_from_output(queue_submit_output):
+    def get_job_id_from_output(queue_submit_output: str) -> int:
         return int(queue_submit_output.splitlines()[-1].rstrip().lstrip().split()[-1])
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         line_split_lst = [line.split("|") for line in queue_status_output.splitlines()]
         if len(line_split_lst) != 0:
             job_id_lst, user_lst, status_lst, job_name_lst, working_directory_lst = zip(
@@ -67,7 +67,7 @@ def convert_queue_status(queue_status_output):
         return df
 
     @staticmethod
-    def dependencies(dependency_list) -> list:
+    def dependencies(dependency_list: list[str]) -> list:
         if dependency_list is not None:
             return ["--dependency=afterok:" + ",".join(dependency_list)]
         else:
diff --git a/pysqa/wrapper/torque.py b/pysqa/wrapper/torque.py
index b1da1e96..060e6b27 100644
--- a/pysqa/wrapper/torque.py
+++ b/pysqa/wrapper/torque.py
@@ -22,19 +22,19 @@
 
 class TorqueCommands(SchedulerCommands):
     @property
-    def submit_job_command(self):
+    def submit_job_command(self) -> list[str]:
         return ["qsub"]
 
     @property
-    def delete_job_command(self):
+    def delete_job_command(self) -> list[str]:
         return ["qdel"]
 
     @property
-    def get_queue_status_command(self):
+    def get_queue_status_command(self) -> list[str]:
         return ["qstat", "-f"]
 
     @staticmethod
-    def get_job_id_from_output(queue_submit_output):
+    def get_job_id_from_output(queue_submit_output: str) -> int:
         # strip last line from output, leading and trailing whitespaces,
         # and separates the queue id from the stuff after "."
         # Adjust if your system doesn't have output like below!
@@ -45,7 +45,7 @@ def get_job_id_from_output(queue_submit_output):
         )
 
     @staticmethod
-    def convert_queue_status(queue_status_output):
+    def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         # # Run the qstat -f command and capture its output
         # output = subprocess.check_output(["qstat", "-f"]) -> output is the
         # queue_status_output that goes into this function