Add docstrings and typehints with github co-pilot #317
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Sequence Diagram(s)sequenceDiagram
participant User
participant CommandLine
participant BackendExecutor
participant Helper
User->>CommandLine: execute_command(arguments)
CommandLine->>BackendExecutor: execute_files_from_list()
BackendExecutor->>Helper: find_executed_tasks()
Helper-->>BackendExecutor: tasks_in_progress
BackendExecutor-->>CommandLine: execution_result
CommandLine-->>User: display_result()
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There was a problem hiding this comment.
Actionable comments posted: 3
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (19)
- pysqa/cmd.py (1 hunks)
- pysqa/executor/backend.py (3 hunks)
- pysqa/executor/executor.py (3 hunks)
- pysqa/executor/helper.py (4 hunks)
- pysqa/ext/modular.py (6 hunks)
- pysqa/ext/remote.py (14 hunks)
- pysqa/queueadapter.py (11 hunks)
- pysqa/utils/basic.py (18 hunks)
- pysqa/utils/config.py (1 hunks)
- pysqa/utils/execute.py (2 hunks)
- pysqa/utils/queues.py (1 hunks)
- pysqa/wrapper/flux.py (1 hunks)
- pysqa/wrapper/generic.py (1 hunks)
- pysqa/wrapper/gent.py (2 hunks)
- pysqa/wrapper/lsf.py (1 hunks)
- pysqa/wrapper/moab.py (1 hunks)
- pysqa/wrapper/sge.py (1 hunks)
- pysqa/wrapper/slurm.py (2 hunks)
- pysqa/wrapper/torque.py (1 hunks)
Files skipped from review due to trivial changes (7)
- pysqa/cmd.py
- pysqa/utils/config.py
- pysqa/wrapper/flux.py
- pysqa/wrapper/generic.py
- pysqa/wrapper/lsf.py
- pysqa/wrapper/moab.py
- pysqa/wrapper/torque.py
Additional context used
Ruff
pysqa/utils/queues.py
11-11: Undefined name
List(F821)
40-40: Undefined name
List(F821)
pysqa/executor/helper.py
133-133: Undefined name
List(F821)
pysqa/ext/remote.py
598-598: Undefined name
Union(F821)
598-598: Undefined name
List(F821)
Additional comments not posted (72)
pysqa/utils/queues.py (1)
21-34: Fix the undefined nameList.The type hint
List[str]requires importingListfrom thetypingmodule.+ from typing import ListLikely invalid or redundant comment.
pysqa/utils/execute.py (2)
12-24: LGTM!The type annotations and docstring are correct and complete.
3-3: Fix the undefined nameList.The type hint
List[str]requires importingListfrom thetypingmodule.+ from typing import ListLikely invalid or redundant comment.
pysqa/wrapper/sge.py (5)
25-25: LGTM!The docstring is correct and complete.
30-30: LGTM!The docstring is correct and complete.
35-35: LGTM!The docstring is correct and complete.
40-40: LGTM!The docstring is correct and complete.
45-53: LGTM!The docstring is correct and complete.
pysqa/wrapper/slurm.py (6)
24-24: Docstring added forsubmit_job_command.The docstring clearly describes the purpose of the property. The type hint
list[str]is appropriate.
29-29: Docstring added fordelete_job_command.The docstring clearly describes the purpose of the property. The type hint
list[str]is appropriate.
34-34: Docstring added forget_queue_status_command.The docstring clearly describes the purpose of the property. The type hint
list[str]is appropriate.
39-39: Docstring added forget_job_id_from_output.The docstring clearly describes the purpose of the method. The type hint
intis appropriate.
44-44: Docstring added forconvert_queue_status.The docstring clearly describes the purpose of the method. The type hint
pandas.DataFrameis appropriate.
75-76: Docstring and type hint added fordependencies.The docstring clearly describes the purpose of the method. The type hint
list[str]is appropriate.pysqa/executor/backend.py (4)
18-28: Docstring and return type hint added forexecute_files_from_list.The docstring clearly describes the purpose of the function and its parameters. The return type hint
Noneis appropriate.
56-65: Docstring and return type hint added forexecute_tasks.The docstring clearly describes the purpose of the function and its parameters. The return type hint
Noneis appropriate.
85-94: Docstring and return type hint added forcommand_line.The docstring clearly describes the purpose of the function and its parameters. The return type hint
Noneis appropriate.
99-99: Ensure proper type conversion forcores_arg.The explicit conversion of
cores_argto an integer ensures type safety.pysqa/wrapper/gent.py (4)
24-33: Docstring added forget_job_id_from_output.The docstring clearly describes the purpose of the method. The type hint
intis appropriate.
38-47: Docstring added forget_queue_from_output.The docstring clearly describes the purpose of the method. The type hint
stris appropriate.
52-61: Docstring added forconvert_queue_status.The docstring clearly describes the purpose of the method. The type hint
pandas.DataFrameis appropriate.
85-98: Docstring and type hint added fordependencies.The docstring clearly describes the purpose of the method. The type hint
list[str]is appropriate. The docstring also specifies the potentialNotImplementedError, which is a good practice.pysqa/executor/executor.py (3)
24-31: Docstring added for__init__method.The docstring clearly describes the parameters and their default values. This enhances the readability and maintainability of the code.
61-72: Docstring and return type annotation added forsubmitmethod.The docstring and return type annotation enhance the usability and maintainability of the method. The descriptions of the parameters and return type are clear and accurate.
84-90: Docstring added forshutdownmethod.The docstring clearly describes the parameters and their default values. This enhances the readability and maintainability of the code.
pysqa/executor/helper.py (11)
11-20: Docstring added fordeserializefunction.The docstring clearly describes the parameter and return type. This enhances the readability and maintainability of the code.
27-38: Docstring and return type annotation added forfind_executed_tasksfunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
57-66: Docstring and return type annotation added forread_from_filefunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameter and return type are clear and accurate.
74-86: Docstring and return type annotation added forreload_previous_futuresfunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
102-112: Docstring and return type annotation added forserialize_resultfunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameter and return type are clear and accurate.
116-128: Docstring and return type annotation added forserialize_functfunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
133-145: Docstring and return type annotation added forwrite_to_filefunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
Tools
Ruff
133-133: Undefined name
List(F821)
155-166: Docstring and return type annotation added for_get_file_namefunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
170-180: Docstring and return type annotation added for_get_hashfunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
186-197: Docstring and return type annotation added for_set_futurefunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
203-217: Docstring and return type annotation added for_update_task_dictfunction.The docstring and return type annotation enhance the usability and maintainability of the function. The descriptions of the parameters and return type are clear and accurate.
pysqa/ext/modular.py (7)
12-26: Docstring added forModularQueueAdapterclass.The docstring clearly describes the constructor arguments, attributes, and exceptions. This enhances the readability and maintainability of the code.
62-76: Docstring and type annotations added forsubmit_jobmethod.The docstring and type annotations enhance the usability and maintainability of the method. The descriptions of the parameters and return type are clear and accurate.
109-116: Docstring and type annotations added forenable_reservationmethod.The docstring and type annotations enhance the usability and maintainability of the method. The descriptions of the parameter and return type are clear and accurate.
135-142: Docstring and type annotations added fordelete_jobmethod.The docstring and type annotations enhance the usability and maintainability of the method. The descriptions of the parameter and return type are clear and accurate.
161-168: Docstring and type annotations added forget_queue_statusmethod.The docstring and type annotations enhance the usability and maintainability of the method. The descriptions of the parameter and return type are clear and accurate.
190-200: Docstring and type annotations added for_resolve_queue_idmethod.The docstring and type annotations enhance the usability and maintainability of the method. The descriptions of the parameters and return type are clear and accurate.
207-216: Docstring and type annotations added for_switch_cluster_commandmethod.The docstring and type annotations enhance the usability and maintainability of the method. The descriptions of the parameters and return type are clear and accurate.
pysqa/queueadapter.py (7)
91-96: LGTM!The change to use
List[str]from thetypingmodule aligns with Python's type hinting conventions.
110-115: LGTM!The addition of the return type
dictenhances code clarity and type safety.
140-145: LGTM!The change to use
List[str]from thetypingmodule aligns with Python's type hinting conventions.
160-166: LGTM!The change to use
List[str]from thetypingmodule aligns with Python's type hinting conventions.
Line range hint
177-198: LGTM!The addition of the
dependency_listparameter with the typeOptional[List[str]]enhances type safety and clarity.
310-318: LGTM!The changes to use
List[int]andList[str]from thetypingmodule align with Python's type hinting conventions.
329-341: LGTM!The addition of the return type
Listenhances code clarity and type safety.pysqa/utils/basic.py (10)
105-110: LGTM!The addition of the return type
dictenhances code clarity and type safety.
117-120: LGTM!The change to use
Listfrom thetypingmodule aligns with Python's type hinting conventions.
138-143: LGTM!The method now returns
Queues, a custom type, which aligns with Python's type hinting conventions.
154-172: LGTM!The addition of the
dependency_listparameter with the typeOptional[List[str]]enhances type safety and clarity.
295-303: LGTM!The changes to use
List[int]andList[str]from thetypingmodule align with Python's type hinting conventions.
315-320: LGTM!The method now raises a
NotImplementedError, indicating that it is not yet implemented.
399-414: LGTM!The method now returns a
Tuple[str, str], which is a custom type, aligning with Python's type hinting conventions.
572-584: LGTM!The method now raises a
ValueErrorif the value isNone, indicating that it is not yet implemented.
589-604: LGTM!The method now returns a
Union[int, float, None], which is a custom type, aligning with Python's type hinting conventions.
549-555: LGTM!The method now raises a
TemplateSyntaxErrorif the template is invalid, indicating that it is not yet implemented.pysqa/ext/remote.py (12)
153-162: LGTM!The addition of the return type
strenhances code clarity and type safety.
179-192: LGTM!The addition of the
dependency_listparameter with the typeOptional[List[str]]enhances type safety and clarity.
204-210: LGTM!The addition of the return type
strenhances code clarity and type safety.
218-224: LGTM!The addition of the return type
strenhances code clarity and type safety.
232-238: LGTM!The addition of the return type
pandas.DataFrameenhances code clarity and type safety.
252-255: LGTM!The method now raises a
NotImplementedError, indicating that it is not yet implemented.
288-295: LGTM!The addition of the return type
Noneenhances code clarity and type safety.
358-364: LGTM!The addition of the return type
paramiko.SSHClientenhances code clarity and type safety.
477-483: LGTM!The addition of the return type
strenhances code clarity and type safety.
486-492: LGTM!The addition of the return type
strenhances code clarity and type safety.
504-519: LGTM!The addition of the return type
strenhances code clarity and type safety.
561-570: LGTM!The addition of the return type
strenhances code clarity and type safety.
| def __dir__(self) -> List[str]: | ||
| """ | ||
| Get the list of queues. | ||
|
|
||
| Returns: | ||
| List[str]: The list of queues. | ||
|
|
||
| """ |
There was a problem hiding this comment.
Fix the undefined name List.
The type hint List[str] requires importing List from the typing module.
+ from typing import ListCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def __dir__(self) -> List[str]: | |
| """ | |
| Get the list of queues. | |
| Returns: | |
| List[str]: The list of queues. | |
| """ | |
| from typing import List | |
| def __dir__(self) -> List[str]: | |
| """ | |
| Get the list of queues. | |
| Returns: | |
| List[str]: The list of queues. | |
| """ |
Tools
Ruff
40-40: Undefined name
List(F821)
| def __init__(self, list_of_queues: List[str]): | ||
| """ | ||
| Initialize the Queues object. | ||
|
|
||
| Args: | ||
| list_of_queues (List[str]): A list of queue names. | ||
|
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||
| """ |
There was a problem hiding this comment.
Fix the undefined name List.
The type hint List[str] requires importing List from the typing module.
+ from typing import ListCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def __init__(self, list_of_queues: List[str]): | |
| """ | |
| Initialize the Queues object. | |
| Args: | |
| list_of_queues (List[str]): A list of queue names. | |
| """ | |
| from typing import List | |
| def __init__(self, list_of_queues: List[str]): | |
| """ | |
| Initialize the Queues object. | |
| Args: | |
| list_of_queues (List[str]): A list of queue names. | |
| """ |
Tools
Ruff
11-11: Undefined name
List(F821)
| binary = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs}) | ||
| return {fn.__name__ + _get_hash(binary=binary): binary} | ||
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| def write_to_file(funct_dict: dict, state, cache_directory: str): | ||
| def write_to_file(funct_dict: dict, state: str, cache_directory: str) -> List[str]: |
There was a problem hiding this comment.
Fix undefined name List.
The List type hint is used but not imported. Import List from typing to fix this issue.
+ from typing import ListCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def write_to_file(funct_dict: dict, state: str, cache_directory: str) -> List[str]: | |
| + from typing import List | |
| def write_to_file(funct_dict: dict, state: str, cache_directory: str) -> List[str]: |
Tools
Ruff
133-133: Undefined name
List(F821)
There was a problem hiding this comment.
Actionable comments posted: 1
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (2)
- pysqa/executor/helper.py (4 hunks)
- pysqa/utils/queues.py (2 hunks)
Files skipped from review due to trivial changes (1)
- pysqa/utils/queues.py
Additional comments not posted (10)
pysqa/executor/helper.py (10)
12-21: Docstring addition looks good.The added docstring is clear and enhances the readability of the function.
28-39: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
58-67: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
75-87: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
103-113: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
117-129: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
156-167: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
171-181: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
187-198: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
204-218: Docstring and type hint additions look good.The added docstring and type hints are clear and enhance the readability of the function.
| def write_to_file(funct_dict: dict, state: str, cache_directory: str) -> List[str]: | ||
| """ | ||
| Write the contents of a dictionary to files in the cache directory. | ||
|
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||
| Args: | ||
| funct_dict (dict): A dictionary containing the contents to be written. | ||
| state (str): The state of the files to be written. | ||
| cache_directory (str): The directory where the files will be written. | ||
|
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| Returns: | ||
| List[str]: A list of file names that were written. | ||
|
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||
| """ |
There was a problem hiding this comment.
Fix undefined name List.
The List type hint is used but not imported. Import List from typing to fix this issue.
+ from typing import ListCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def write_to_file(funct_dict: dict, state: str, cache_directory: str) -> List[str]: | |
| """ | |
| Write the contents of a dictionary to files in the cache directory. | |
| Args: | |
| funct_dict (dict): A dictionary containing the contents to be written. | |
| state (str): The state of the files to be written. | |
| cache_directory (str): The directory where the files will be written. | |
| Returns: | |
| List[str]: A list of file names that were written. | |
| """ | |
| from typing import List | |
| def write_to_file(funct_dict: dict, state: str, cache_directory: str) -> List[str]: | |
| """ | |
| Write the contents of a dictionary to files in the cache directory. | |
| Args: | |
| funct_dict (dict): A dictionary containing the contents to be written. | |
| state (str): The state of the files to be written. | |
| cache_directory (str): The directory where the files will be written. | |
| Returns: | |
| List[str]: A list of file names that were written. | |
| """ |
There was a problem hiding this comment.
Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (1)
pysqa/ext/remote.py (1)
Line range hint
598-617:
Fix the undefined nameList.The name
Listis undefined. Import it fromtyping.+ from typing import ListTools
Ruff
598-598: Undefined name
List(F821)
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- pysqa/ext/remote.py (15 hunks)
Additional context used
Ruff
pysqa/ext/remote.py
598-598: Undefined name
List(F821)
Additional comments not posted (19)
pysqa/ext/remote.py (19)
153-162: LGTM!The docstring and type hinting for the
convert_path_to_remotemethod look good.
179-192: LGTM!The docstring and type hinting for the
submit_jobmethod look good. TheNotImplementedErrorfordependency_listis a good practice.
204-210: LGTM!The docstring and type hinting for the
enable_reservationmethod look good.
218-224: LGTM!The docstring and type hinting for the
delete_jobmethod look good.
232-238: LGTM!The docstring and type hinting for the
get_queue_statusmethod look good.
252-255: LGTM!The docstring and type hinting for the
get_job_from_remotemethod look good.
288-295: LGTM!The docstring and type hinting for the
transfer_filemethod look good.
310-312: LGTM!The docstring for the
__del__method looks good.
319-321: LGTM!The docstring for the
_check_ssh_connectionmethod looks good.
326-333: LGTM!The docstring and type hinting for the
_transfer_filesmethod look good.
358-364: LGTM!The docstring and type hinting for the
_open_ssh_connectionmethod look good.
477-483: LGTM!The docstring and type hinting for the
_remote_commandmethod look good.
486-492: LGTM!The docstring and type hinting for the
_get_queue_status_commandmethod look good.
504-519: LGTM!The docstring and type hinting for the
_submit_commandmethod look good.
561-570: LGTM!The docstring and type hinting for the
_execute_remote_commandmethod look good.
583-592: LGTM!The docstring and type hinting for the
_get_remote_working_dirmethod look good.
618-627: LGTM!The docstring and type hinting for the
_transfer_data_to_remotemethod look good.
654-657: LGTM!The docstring and type hinting for the
_get_usermethod look good.
663-673: LGTM!The docstring and type hinting for the
_get_file_transfermethod look good.
Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Refactor
Chores