Implement default submission template #338
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Actionable comments posted: 27
🧹 Outside diff range and nitpick comments (8)
pysqa/utils/basic.py (1)
514-523: LGTM! Consider adding type hints for improved code clarity.The refactoring to use
render_submission_templateimproves modularity and separates concerns. This change enhances maintainability and potentially allows for easier customization of submission templates for different queue systems.Consider adding type hints to the
render_submission_templatemethod call for improved code clarity and maintainability. For example:return self._commands.render_submission_template( command: str = command, submission_template: Template = active_queue["template"], working_directory: str = working_directory, job_name: str = job_name, cores: Optional[int] = cores, memory_max: Optional[int] = memory_max, run_time_max: Optional[int] = run_time_max, dependency_list: Optional[List[int]] = dependency_list, **kwargs )pysqa/wrapper/moab.py (1)
24-35: Include working directory change in the submission scriptThe
working_directoryparameter is accepted but not used in the submission script. To ensure the job executes in the correct working directory, include a command to change to that directory before executing the main command.Consider adding the following line before
{{command}}:{%- endif %} +cd {{ working_directory }} {{command}}This ensures the job runs in the intended directory.
pysqa/wrapper/flux.py (1)
101-101: Update docstring type forsubmission_templateparameterThe
submission_templateparameter is typed asUnion[str, Template]in the function signature but is documented as(str)in the docstring. For consistency and clarity, update the docstring to reflect the correct type.Correct the docstring as follows:
- submission_template (str): Submission script template pysqa.wrapper.flux.template + submission_template (Union[str, Template], optional): Submission script template. Defaults to `template`.pysqa/wrapper/lsf.py (1)
100-101: Document the usage of**kwargsin the methodThe method accepts
**kwargs, which are passed to the template rendering. However, there is no explanation in the docstring about what additional keyword arguments can be provided. To enhance clarity, consider updating the docstring to inform users about the possibility of passing extra parameters to the template.Suggested addition to the docstring:
**kwargs, ) -> str: """ Generate the job submission template. Args: ... + **kwargs: Additional keyword arguments to be passed to the template rendering.pysqa/wrapper/sge.py (3)
31-38: Validation formemory_maxandrun_time_maxunitsThe template uses
{{memory_max}}and{{run_time_max}}directly, but it's unclear what units are expected (e.g., bytes, kilobytes, megabytes, seconds, minutes). This might lead to incorrect resource requests.Consider adding unit validation or documentation to clarify the expected units for
memory_maxandrun_time_max.
105-105: Defaultworking_directorymight not be intuitiveThe default value for
working_directoryisos.path.abspath("."), which resolves to the current working directory when the script is run. This may not be the intended directory for job execution.Consider requiring the user to specify
working_directory, or clarify in the documentation that it defaults to the directory from which the script is executed.
114-127: Improve docstring formatting and consistencyThe docstring has some inconsistencies and could be formatted more clearly for better readability.
- Ensure all parameter descriptions are aligned and consistently formatted.
- Correct any typos or mismatches in parameter names and descriptions.
Suggested changes:
""" Generate the job submission template. Args: command (str): The command to be executed. job_name (str, optional): The job name. Defaults to "pysqa". working_directory (str, optional): The working directory. Defaults to the current directory. cores (int, optional): The number of cores. Defaults to 1. memory_max (int, optional): The maximum memory in megabytes. Defaults to None. run_time_max (int, optional): The maximum run time in seconds. Defaults to None. dependency_list (list[int], optional): The list of dependency job IDs. Defaults to None. - submission_template (str): Submission script template. + submission_template (Union[str, Template], optional): The submission script template. Defaults to the class-defined template. **kwargs: Additional template variables. Returns: str: The rendered job submission script. """pysqa/wrapper/torque.py (1)
25-41: Add usage ofworking_directoryin the template or remove the parameterThe
working_directoryparameter is currently not used within the submission template.If the working directory needs to be set, consider adding it to the template:
+#PBS -d {{ working_directory }}Alternatively, if setting the working directory is handled elsewhere, you might consider removing the
working_directoryparameter from the method signature to avoid confusion.
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📒 Files selected for processing (8)
- pysqa/utils/basic.py (1 hunks)
- pysqa/wrapper/flux.py (2 hunks)
- pysqa/wrapper/generic.py (3 hunks)
- pysqa/wrapper/lsf.py (3 hunks)
- pysqa/wrapper/moab.py (3 hunks)
- pysqa/wrapper/sge.py (3 hunks)
- pysqa/wrapper/slurm.py (3 hunks)
- pysqa/wrapper/torque.py (3 hunks)
🔇 Additional comments (9)
pysqa/utils/basic.py (2)
514-523: Summary: Improved modularity in job submission template rendering.The changes in this file are minimal but impactful. By introducing the
render_submission_templatemethod, the code now has better separation of concerns and improved modularity. This refactoring allows for easier customization of submission templates for different queue systems without affecting the overall functionality of theBasisQueueAdapterclass.Key points:
- The public API of the class remains unchanged.
- The change is localized to the
_job_submission_templatemethod.- The new implementation delegates template rendering to a separate method, likely implemented in subclasses of
SchedulerCommands.These changes align well with best practices for maintainable and extensible code.
514-523: Verify the implementation ofrender_submission_templatein the SchedulerCommands subclass.The refactoring introduces a new method
render_submission_templatewhich is called onself._commands. Ensure that this method is properly implemented in the appropriate subclass ofSchedulerCommandsfor each supported queue system.Run the following script to verify the implementation of
render_submission_template:pysqa/wrapper/generic.py (2)
6-6: Imports added for new functionalityThe addition of
List,Optional, andUnionfrom thetypingmodule andTemplatefromjinja2is appropriate and necessary for the new methods introduced.Also applies to: 8-8
57-65: Changedget_queue_status_commandfrom property to methodThe
get_queue_status_commandwas previously defined as a property with@propertyand@abstractmethoddecorators. It has now been changed to an abstract method by removing the@propertydecorator. This alteration changes how subclasses implement this method and may impact any code that accesses it as a property.Run the following script to identify subclasses that may need updates:
Ensure that all subclasses and code accessing
get_queue_status_commandare updated to reflect this change.✅ Verification successful
Verification Successful: No subclasses or instances are using
get_queue_status_commandas a property.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Find subclasses of SchedulerCommands with get_queue_status_command defined as a property. # Test: Search for subclasses using @property for get_queue_status_command. ast-grep --lang python --pattern $'class $_(SchedulerCommands):\n $$$\n @property\n def get_queue_status_command($_):\n $$$\n $$$'Length of output: 145
Script:
#!/bin/bash # Description: Find all instances where get_queue_status_command is defined as a property in Python files. ast-grep --lang python --pattern $'@property\n def get_queue_status_command($_):\n $$$'Length of output: 96
pysqa/wrapper/flux.py (2)
84-84: Unused parametermemory_maxThe parameter
memory_maxis accepted by the function but is not used in the submission template. Ifmemory_maxis not needed, consider removing it from the function parameters. If it is required, include it in the template to set the maximum memory for the job.Please verify whether
memory_maxshould be included in the submission template. If Flux supports specifying memory limits, incorporatememory_maxinto the template accordingly.Also applies to: 114-114
19-19: Verify time unit conversion forrun_time_maxIn the template,
run_time_maxis converted to minutes using integer division by 60:{{ [1, run_time_max // 60]|max }}. Please verify thatrun_time_maxis provided in seconds and that the-toption expects time in minutes.pysqa/wrapper/lsf.py (1)
34-34: Verify thatrun_time_maxandmemory_maxare in the correct unitsIn the template directives
#BSUB -W {{run_time_max}}and#BSUB -M {{memory_max}}, ensure that the values provided forrun_time_maxandmemory_maxare in the units expected by LSF. Typically:
-Wexpects the run time in minutes.-Mexpects the memory limit in kilobytes.Adjust the parameter units or include unit conversions if necessary to prevent scheduling issues.
Also applies to: 37-37
pysqa/wrapper/torque.py (1)
30-31: Validate units for thememory_maxparameterEnsure that the
memory_maxparameter is provided in gigabytes as an integer. If users provide memory in other units or as a string, it could result in scheduling errors.Consider adding validation in the
render_submission_templatemethod to confirm thememory_maxis an integer representing gigabytes.pysqa/wrapper/slurm.py (1)
33-33: Verify the calculation ofrun_time_maxfor SLURM's--timedirectiveThe calculation
{{ [1, run_time_max // 60]|max }}may not correctly reflect SLURM's expected time format. SLURM expects the--timeparameter in the formatminutes,hours:minutes:seconds, ordays-hours. Ensure thatrun_time_maxis converted appropriately.Run the following script to verify the correct handling of
run_time_max:
pysqa/wrapper/moab.py
Outdated
| memory_max (int, optional): The maximum memory. Defaults to None. | ||
| run_time_max (int, optional): The maximum run time. Defaults to None. | ||
| dependency_list (list[int], optional): The list of dependency job IDs. Defaults to None. | ||
| submission_template (str): Submission script template pysqa.wrapper.torque.template |
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Update the docstring to reference the correct template
The docstring for the submission_template parameter refers to pysqa.wrapper.torque.template, which is incorrect for the Moab scheduler. It should reference the Moab template to avoid confusion.
Please correct the docstring as follows:
- submission_template (str): Submission script template pysqa.wrapper.torque.template
+ submission_template (str): Submission script template for Moab scheduler📝 Committable suggestion
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| submission_template (str): Submission script template pysqa.wrapper.torque.template | |
| submission_template (str): Submission script template for Moab scheduler |
| #MSUB -l pmem={{ memory_max| int }}gb | ||
| {%- endif %} | ||
| {%- if run_time_max %} | ||
| #$ -l walltime={{run_time_max}} |
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Correct the resource directive prefix for consistency
The resource directive on line 31 uses #$, which is inconsistent with the other Moab directives that use #MSUB. This inconsistency may lead to the scheduler ignoring the line or causing unexpected behavior.
Please update the line to use the correct Moab directive prefix:
-#$ -l walltime={{run_time_max}}
+#MSUB -l walltime={{ run_time_max }}📝 Committable suggestion
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| #$ -l walltime={{run_time_max}} | |
| #MSUB -l walltime={{ run_time_max }} |
| template = """\ | ||
| #!/bin/bash | ||
| #MSUB -N {{job_name}} | ||
| {%- if memory_max %} | ||
| #MSUB -l pmem={{ memory_max| int }}gb | ||
| {%- endif %} | ||
| {%- if run_time_max %} | ||
| #$ -l walltime={{run_time_max}} | ||
| {%- endif %} | ||
|
|
||
| {{command}} | ||
| """ |
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Include the number of cores in the submission template
The cores parameter is accepted by the render_submission_template method but is not utilized in the submission script. To ensure the scheduler allocates the correct number of cores, include the appropriate resource directive in the submission template.
Add the following to the template to request the specified number of cores:
{%- if run_time_max %}
#MSUB -l walltime={{ run_time_max }}
{%- endif %}
+{%- if cores %}
+#MSUB -l nodes=1:ppn={{ cores }}
+{%- endif %}
{{command}}📝 Committable suggestion
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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.
| template = """\ | |
| #!/bin/bash | |
| #MSUB -N {{job_name}} | |
| {%- if memory_max %} | |
| #MSUB -l pmem={{ memory_max| int }}gb | |
| {%- endif %} | |
| {%- if run_time_max %} | |
| #$ -l walltime={{run_time_max}} | |
| {%- endif %} | |
| {{command}} | |
| """ | |
| template = """\ | |
| #!/bin/bash | |
| #MSUB -N {{job_name}} | |
| {%- if memory_max %} | |
| #MSUB -l pmem={{ memory_max| int }}gb | |
| {%- endif %} | |
| {%- if run_time_max %} | |
| #MSUB -l walltime={{run_time_max}} | |
| {%- endif %} | |
| {%- if cores %} | |
| #MSUB -l nodes=1:ppn={{ cores }} | |
| {%- endif %} | |
| {{command}} | |
| """ |
Handle job dependencies in the submission template
The dependency_list parameter is accepted but not utilized in the submission script. To properly manage job dependencies, include directives that specify the job IDs this job depends on.
Add the following lines to handle job dependencies:
{%- if run_time_max %}
#MSUB -l walltime={{ run_time_max }}
{%- endif %}
+{%- if dependency_list %}
+#MSUB -l depend={{ dependency_list | join(':') }}
+{%- endif %}
{{command}}This inclusion will ensure that the job submission respects any specified dependencies.
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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.
| template = """\ | |
| #!/bin/bash | |
| #MSUB -N {{job_name}} | |
| {%- if memory_max %} | |
| #MSUB -l pmem={{ memory_max| int }}gb | |
| {%- endif %} | |
| {%- if run_time_max %} | |
| #$ -l walltime={{run_time_max}} | |
| {%- endif %} | |
| {{command}} | |
| """ | |
| template = """\ | |
| #!/bin/bash | |
| #MSUB -N {{job_name}} | |
| {%- if memory_max %} | |
| #MSUB -l pmem={{ memory_max| int }}gb | |
| {%- endif %} | |
| {%- if run_time_max %} | |
| #MSUB -l walltime={{run_time_max}} | |
| {%- endif %} | |
| {%- if dependency_list %} | |
| #MSUB -l depend={{ dependency_list | join(':') }} | |
| {%- endif %} | |
| {{command}} | |
| """ |
| @property | ||
| def enable_reservation_command(self) -> list[str]: | ||
| """ | ||
| Returns the command to enable job reservation on the scheduler. | ||
|
|
||
| Returns: | ||
| list[str]: The command to enable job reservation. | ||
| """ | ||
| raise NotImplementedError() |
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Missing @abstractmethod decorator on enable_reservation_command
The enable_reservation_command property lacks the @abstractmethod decorator. Other abstract properties in the class, such as submit_job_command and delete_job_command, include both @property and @abstractmethod decorators. Adding the @abstractmethod decorator ensures consistency and enforces implementation in subclasses.
Apply this diff to add the decorator:
@property
+@abstractmethod
def enable_reservation_command(self) -> list[str]:
"""
Returns the command to enable job reservation on the scheduler.
Returns:
list[str]: The command to enable job reservation.
"""
- raise NotImplementedError()
+ pass📝 Committable suggestion
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| @property | |
| def enable_reservation_command(self) -> list[str]: | |
| """ | |
| Returns the command to enable job reservation on the scheduler. | |
| Returns: | |
| list[str]: The command to enable job reservation. | |
| """ | |
| raise NotImplementedError() | |
| @property | |
| @abstractmethod | |
| def enable_reservation_command(self) -> list[str]: | |
| """ | |
| Returns the command to enable job reservation on the scheduler. | |
| Returns: | |
| list[str]: The command to enable job reservation. | |
| """ | |
| pass |
pysqa/wrapper/generic.py
Outdated
| def render_submission_template( | ||
| command: str, | ||
| submission_template: Union[str, Template], | ||
| working_directory: str, | ||
| job_name: str = "pysqa", | ||
| cores: int = 1, | ||
| memory_max: Optional[int] = None, | ||
| run_time_max: Optional[int] = None, | ||
| dependency_list: Optional[List[int]] = None, | ||
| **kwargs, | ||
| ) -> str: | ||
| """ | ||
| Returns the command to get the status of the job queue. | ||
| Generate the job submission template. | ||
|
|
||
| Args: | ||
| command (str, optional): The command to be executed. | ||
| job_name (str, optional): The job name. Defaults to "pysqa". | ||
| working_directory (str, optional): The working directory. Defaults to ".". | ||
| cores (int, optional): The number of cores. Defaults to 1. |
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Inconsistencies between function signature and docstring in render_submission_template
There are discrepancies between the function signature and the docstring:
- Parameter Order: The order of parameters in the docstring does not match the function signature.
- Optional Parameters:
command: In the signature, it's required (command: str), but the docstring marks it as optional.working_directory: Required in the signature but marked as optional in the docstring with a default value that isn't reflected in the signature.
- Type Annotations:
submission_template: In the signature, it'sUnion[str, Template], but the docstring lists it asstr.
- Missing Parameters:
**kwargsis not documented in the docstring.
Apply this diff to correct the docstring:
"""
Generate the job submission template.
Args:
- command (str, optional): The command to be executed.
+ command (str): The command to be executed.
+ submission_template (Union[str, Template]): The submission script template.
working_directory (str): The working directory.
- job_name (str, optional): The job name. Defaults to "pysqa".
- working_directory (str, optional): The working directory. Defaults to ".".
+ job_name (str, optional): The job name. Defaults to "pysqa".
cores (int, optional): The number of cores. Defaults to 1.
memory_max (int, optional): The maximum memory. Defaults to None.
run_time_max (int, optional): The maximum run time. Defaults to None.
dependency_list (list[int], optional): The list of dependency job IDs. Defaults to None.
+ **kwargs: Additional keyword arguments.
- submission_template (str): Submission script template pysqa.wrapper.torque.template
Returns:
str: The rendered job submission template.
"""Ensure that the function signature and docstring parameters are consistent, accurately reflect default values, and document all parameters.
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| def render_submission_template( | |
| command: str, | |
| submission_template: Union[str, Template], | |
| working_directory: str, | |
| job_name: str = "pysqa", | |
| cores: int = 1, | |
| memory_max: Optional[int] = None, | |
| run_time_max: Optional[int] = None, | |
| dependency_list: Optional[List[int]] = None, | |
| **kwargs, | |
| ) -> str: | |
| """ | |
| Returns the command to get the status of the job queue. | |
| Generate the job submission template. | |
| Args: | |
| command (str, optional): The command to be executed. | |
| job_name (str, optional): The job name. Defaults to "pysqa". | |
| working_directory (str, optional): The working directory. Defaults to ".". | |
| cores (int, optional): The number of cores. Defaults to 1. | |
| def render_submission_template( | |
| command: str, | |
| submission_template: Union[str, Template], | |
| working_directory: str, | |
| job_name: str = "pysqa", | |
| cores: int = 1, | |
| memory_max: Optional[int] = None, | |
| run_time_max: Optional[int] = None, | |
| dependency_list: Optional[List[int]] = None, | |
| **kwargs, | |
| ) -> str: | |
| """ | |
| Generate the job submission template. | |
| Args: | |
| command (str): The command to be executed. | |
| submission_template (Union[str, Template]): The submission script template. | |
| working_directory (str): The working directory. | |
| job_name (str, optional): The job name. Defaults to "pysqa". | |
| cores (int, optional): The number of cores. Defaults to 1. | |
| memory_max (int, optional): The maximum memory. Defaults to None. | |
| run_time_max (int, optional): The maximum run time. Defaults to None. | |
| dependency_list (list[int], optional): The list of dependency job IDs. Defaults to None. | |
| **kwargs: Additional keyword arguments. | |
| Returns: | |
| str: The rendered job submission template. | |
| """ |
| {%- if dependency %} | ||
| #PBS -W depend=afterok:{{ dependency | join(':') }} | ||
| {%- endif %} |
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Fix variable name inconsistency between dependency_list and dependency
In the submission template, the variable dependency is used, but in the render_submission_template method, the parameter is named dependency_list. This inconsistency may cause a KeyError during template rendering.
Apply this diff to fix the inconsistency:
# In the template (lines 36-38):
-{%- if dependency %}
-#PBS -W depend=afterok:{{ dependency | join(':') }}
+{%- if dependency_list %}
+#PBS -W depend=afterok:{{ dependency_list | join(':') }}
{%- endif %}
# In the `render_submission_template` method (line 165):
- dependency_list=dependency_list,
+ dependency=dependency_list,Also applies to: 165-165
pysqa/wrapper/slurm.py
Outdated
| memory_max (int, optional): The maximum memory. Defaults to None. | ||
| run_time_max (int, optional): The maximum run time. Defaults to None. | ||
| dependency_list (list[int], optional): The list of dependency job IDs. Defaults to None. | ||
| submission_template (str): Submission script template pysqa.wrapper.torque.template |
There was a problem hiding this comment.
Update the docstring for submission_template parameter
The docstring for submission_template mentions pysqa.wrapper.torque.template, which is incorrect for the SLURM scheduler. Please update it to reflect the correct template.
Apply this diff to fix the docstring:
submission_template (str): Submission script template
- pysqa.wrapper.torque.template
+ Default SLURM submission script template.📝 Committable suggestion
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| submission_template (str): Submission script template pysqa.wrapper.torque.template | |
| submission_template (str): Submission script template | |
| Default SLURM submission script template. |
| {%- if dependency %} | ||
| #SBATCH --dependency=afterok:{{ dependency | join(',') }} | ||
| {%- endif %} |
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Inconsistent variable name dependency vs dependency_list
In the template, the variable dependency is used, but in the render_submission_template method, the parameter is named dependency_list. This inconsistency will lead to a KeyError when rendering the template. Please ensure that the variable names match between the template and the method.
Apply this diff to fix the issue:
-{%- if dependency %}
-#SBATCH --dependency=afterok:{{ dependency | join(',') }}
+{%- if dependency_list %}
+#SBATCH --dependency=afterok:{{ dependency_list | join(',') }}
{%- endif %}📝 Committable 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.
| {%- if dependency %} | |
| #SBATCH --dependency=afterok:{{ dependency | join(',') }} | |
| {%- endif %} | |
| {%- if dependency_list %} | |
| #SBATCH --dependency=afterok:{{ dependency_list | join(',') }} | |
| {%- endif %} |
| template = """\ | ||
| #!/bin/bash | ||
| #SBATCH --output=time.out | ||
| #SBATCH --job-name={{job_name}} | ||
| #SBATCH --chdir={{working_directory}} | ||
| #SBATCH --get-user-env=L | ||
| #SBATCH --partition={{partition}} | ||
| {%- if run_time_max %} | ||
| #SBATCH --time={{ [1, run_time_max // 60]|max }} | ||
| {%- endif %} | ||
| {%- if dependency %} | ||
| #SBATCH --dependency=afterok:{{ dependency | join(',') }} | ||
| {%- endif %} | ||
| {%- if memory_max %} | ||
| #SBATCH --mem={{memory_max}}G | ||
| {%- endif %} | ||
| #SBATCH --cpus-per-task={{cores}} | ||
|
|
||
| {{command}} | ||
| """ |
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Undefined variable partition in the template
The partition variable is used in the submission template but is not provided to the render_submission_template method or passed during template rendering. This will cause a KeyError when rendering the template. Consider adding a partition parameter to the method and passing it to the template.
Apply this diff to fix the issue:
def render_submission_template(
command: str,
job_name: str = "pysqa",
working_directory: str = os.path.abspath("."),
cores: int = 1,
memory_max: Optional[int] = None,
run_time_max: Optional[int] = None,
+ partition: str = "default",
dependency_list: Optional[List[int]] = None,
submission_template: Union[str, Template] = template,
**kwargs,
) -> str:
...
return submission_template.render(
command=command,
job_name=job_name,
working_directory=working_directory,
cores=cores,
memory_max=memory_max,
run_time_max=run_time_max,
+ partition=partition,
dependency_list=dependency_list,
**kwargs,
)Committable suggestion was skipped due to low confidence.
🛠️ Refactor suggestion
Enhance the submission template with optional email notifications
Consider adding optional parameters for email notifications to inform users about job start, completion, or failure events. This can improve user experience for long-running jobs.
Modify the template to include email options:
{%- if email %}
#SBATCH --mail-user={{ email }}
{%- endif %}
{%- if email_events %}
#SBATCH --mail-type={{ email_events | join(',') }}
{%- endif %}Update the method parameters and rendering context:
def render_submission_template(
command: str,
job_name: str = "pysqa",
working_directory: Optional[str] = None,
cores: int = 1,
memory_max: Optional[int] = None,
run_time_max: Optional[int] = None,
dependency_list: Optional[List[int]] = None,
+ email: Optional[str] = None,
+ email_events: Optional[List[str]] = None,
submission_template: Union[str, Template] = template,
**kwargs,
) -> str:
+ if working_directory is None:
+ working_directory = os.path.abspath(".")
...
return submission_template.render(
command=command,
job_name=job_name,
working_directory=working_directory,
cores=cores,
memory_max=memory_max,
run_time_max=run_time_max,
dependency_list=dependency_list,
+ email=email,
+ email_events=email_events,
**kwargs,
)Committable suggestion was skipped due to low confidence.
🛠️ Refactor suggestion
Consider simplifying the runtime calculation in the template
The expression {{ [1, run_time_max // 60]|max }} may be unnecessarily complex. If run_time_max is already provided in minutes or the appropriate SLURM time format, you can use it directly.
Modify the template line:
-#SBATCH --time={{ [1, run_time_max // 60]|max }}
+#SBATCH --time={{ run_time_max }}Ensure that run_time_max is provided in the correct format expected by SLURM (e.g., minutes, hours:minutes:seconds, or days-hours).
Committable suggestion was skipped due to low confidence.
| def render_submission_template( | ||
| command: str, | ||
| job_name: str = "pysqa", | ||
| working_directory: str = os.path.abspath("."), |
There was a problem hiding this comment.
Avoid using function calls in default parameter values
The default value os.path.abspath(".") is evaluated at function definition time, which may not reflect the current working directory when the function is called. It's better to set the default to None and compute it inside the function.
Apply this diff to fix the issue:
def render_submission_template(
command: str,
job_name: str = "pysqa",
- working_directory: str = os.path.abspath("."),
+ working_directory: Optional[str] = None,
cores: int = 1,
memory_max: Optional[int] = None,
run_time_max: Optional[int] = None,
dependency_list: Optional[List[int]] = None,
submission_template: Union[str, Template] = template,
**kwargs,
) -> str:
+ if working_directory is None:
+ working_directory = os.path.abspath(".")
...📝 Committable 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.
| working_directory: str = os.path.abspath("."), | |
| def render_submission_template( | |
| command: str, | |
| job_name: str = "pysqa", | |
| working_directory: Optional[str] = None, | |
| cores: int = 1, | |
| memory_max: Optional[int] = None, | |
| run_time_max: Optional[int] = None, | |
| dependency_list: Optional[List[int]] = None, | |
| submission_template: Union[str, Template] = template, | |
| **kwargs, | |
| ) -> str: | |
| if working_directory is None: | |
| working_directory = os.path.abspath(".") | |
| ... |
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
tests/test_scheduler_commands.py (1)
Line range hint
6-58: Consider expanding test coverage for SchedulerCommands.While the existing tests cover basic functionality and error cases, the move to an abstract base class might introduce new methods or behaviors that require testing.
Consider the following improvements:
- Review the abstract
SchedulerCommandsclass for any new methods or behaviors that aren't currently tested.- Add tests for any new functionality introduced in the abstract class.
- Ensure that the
TmpSchedularCommandsclass correctly implements all required methods from the abstract base class.To help identify any new methods that might need testing, you can run:
#!/bin/bash # Description: List methods in the SchedulerCommands class # Test: Extract method names from the SchedulerCommands class ast-grep --lang python --pattern 'class SchedulerCommands($_): $$$ def $METHOD($_) { $$$ } $$$ ' pysqa/wrapper/abstract.py | grep -oP '(?<=def )\w+'Compare the output with the existing tests and add coverage for any missing methods.
pysqa/wrapper/abstract.py (1)
68-107: LGTM with a minor suggestion: Consider improvingsubmission_templateparameter.The
render_submission_templatemethod is well-implemented and documented. It enhances the class's functionality by allowing dynamic job submission template generation. The use of type hints and comprehensive docstring is commendable.However, there's a minor inconsistency in the
submission_templateparameter:Consider updating the type hint and docstring for the
submission_templateparameter to reflect that it can be either a string or aTemplateobject. Here's a suggested change:- submission_template: Union[str, Template], + submission_template: Union[str, Template], job_name: str = "pysqa", working_directory: str = os.path.abspath("."), cores: int = 1, memory_max: Optional[int] = None, run_time_max: Optional[int] = None, dependency_list: Optional[List[int]] = None, **kwargs, ) -> str: """ Generate the job submission template. Args: command (str, optional): The command to be executed. job_name (str, optional): The job name. Defaults to "pysqa". working_directory (str, optional): The working directory. Defaults to ".". cores (int, optional): The number of cores. Defaults to 1. memory_max (int, optional): The maximum memory. Defaults to None. run_time_max (int, optional): The maximum run time. Defaults to None. dependency_list (list[int], optional): The list of dependency job IDs. Defaults to None. - submission_template (str): Submission script template pysqa.wrapper.torque.template + submission_template (Union[str, Template]): Submission script template as a string or Template object.This change would make the method signature and docstring more consistent with the actual implementation.
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📒 Files selected for processing (9)
- pysqa/utils/basic.py (2 hunks)
- pysqa/wrapper/abstract.py (3 hunks)
- pysqa/wrapper/flux.py (2 hunks)
- pysqa/wrapper/lsf.py (3 hunks)
- pysqa/wrapper/moab.py (3 hunks)
- pysqa/wrapper/sge.py (3 hunks)
- pysqa/wrapper/slurm.py (3 hunks)
- pysqa/wrapper/torque.py (3 hunks)
- tests/test_scheduler_commands.py (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (6)
- pysqa/utils/basic.py
- pysqa/wrapper/flux.py
- pysqa/wrapper/lsf.py
- pysqa/wrapper/moab.py
- pysqa/wrapper/sge.py
- pysqa/wrapper/slurm.py
🔇 Additional comments (8)
pysqa/wrapper/abstract.py (3)
25-33: LGTM: Well-defined abstract property method.The
enable_reservation_commandproperty method is correctly implemented as an abstract method. It follows the established pattern in the class, has appropriate type hints, and includes a clear docstring.
5-10: LGTM: Appropriate imports and consistent file structure.The addition of the Jinja2 Template import is necessary for the new
render_submission_templatemethod. The overall file structure remains consistent with the abstract base class pattern, maintaining good coding practices.
Line range hint
1-108: Summary: Well-implemented enhancements to the SchedulerCommands class.The changes to this file enhance the
SchedulerCommandsabstract base class by adding two new methods:
enable_reservation_command: A new abstract property method for enabling job reservation.render_submission_template: A static method for generating job submission templates using Jinja2.These additions improve the flexibility and functionality of the job scheduling system. The implementation maintains consistent coding style, proper use of type hints, and comprehensive documentation.
pysqa/wrapper/torque.py (5)
5-7: LGTM: Import statements are appropriateThe added import statements for
os,re, andUnionfrom typing are necessary for the new functionality and follow good practices.
9-10: LGTM: Additional imports are appropriateThe added import statements for
pandasandTemplatefrom jinja2 are necessary for the new template rendering functionality and follow good practices.
128-166: LGTM: render_submission_template method is well-structuredThe
render_submission_templatemethod is well-structured and properly usessuper()to call the parent class's method. The method signature and docstring are appropriate for the job submission requirements.However, please ensure that the previously mentioned issues are addressed:
- The inconsistency between
dependency_listanddependency.- The formatting of
run_time_maxtoHH:MM:SS.
Line range hint
1-166: Summary: Good implementation with minor issues to addressThe implementation of the default submission template for the Torque job scheduler is generally well-done. The new
render_submission_templatemethod and the template string enhance the functionality of theTorqueCommandsclass.However, there are two main issues that need to be addressed:
- The inconsistency between
dependency_listanddependencyin the template and method signature.- The potential incorrect formatting of
run_time_maxfor Torque'swalltimeparameter.Once these issues are resolved, the implementation will be robust and consistent with the requirements of the Torque job scheduler.
36-38:⚠️ Potential issueFix variable name inconsistency between
dependency_listanddependencyIn the submission template, the variable
dependencyis used, but in therender_submission_templatemethod, the parameter is nameddependency_list. This inconsistency may cause aKeyErrorduring template rendering.Apply this diff to fix the inconsistency:
{%- if dependency %} #PBS -W depend=afterok:{{ dependency | join(':') }} {%- endif %}to:
{%- if dependency_list %} #PBS -W depend=afterok:{{ dependency_list | join(':') }} {%- endif %}Also, update the
render_submission_templatemethod accordingly:- dependency_list=dependency_list, + dependency=dependency_list,Likely invalid or redundant comment.
| @@ -1,5 +1,5 @@ | |||
| import unittest | |||
| from pysqa.wrapper.generic import SchedulerCommands | |||
| from pysqa.wrapper.abstract import SchedulerCommands | |||
There was a problem hiding this comment.
💡 Codebase verification
Update tests to use concrete SchedulerCommands subclasses.
The SchedulerCommands class has been refactored to an abstract base class in pysqa/wrapper/abstract.py, and several concrete subclasses (e.g., TorqueCommands, SlurmCommands) now inherit from it. Ensure that tests/test_scheduler_commands.py imports and utilizes these concrete implementations instead of the abstract class to maintain valid and comprehensive test coverage.
🔗 Analysis chain
Verify test coverage after import change.
The import statement has been updated to import SchedulerCommands from pysqa.wrapper.abstract instead of pysqa.wrapper.generic. This change might indicate a significant refactoring or relocation of the SchedulerCommands class.
Please ensure that:
- The existing tests are still valid and cover all necessary aspects of the refactored
SchedulerCommandsclass. - Any new methods or behaviors introduced in the abstract version are adequately tested.
- The
TmpSchedularCommandsclass still correctly inherits from and implements the abstractSchedulerCommands.
To verify the changes in the SchedulerCommands class, you can run the following script:
This will help identify any changes in the class definition that might require updates to the tests.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Compare the old and new SchedulerCommands classes
# Test: Check the differences between the old and new SchedulerCommands classes
rg --type python -A 20 'class SchedulerCommands' pysqa/wrapper/
Length of output: 96
Script:
#!/bin/bash
# Description: Compare the old and new SchedulerCommands classes
# Test: Check the differences between the old and new SchedulerCommands classes
rg --type py -A 20 'class SchedulerCommands' pysqa/wrapper/
Length of output: 1169
Script:
#!/bin/bash
# Description: Find concrete implementations of SchedulerCommands
# Search for classes that inherit from SchedulerCommands and are not abstract
rg --type py 'class\s+\w+\(SchedulerCommands\):' pysqa/wrapper/
Length of output: 443
| #PBS -l walltime={{run_time_max}} | ||
| {%- endif %} |
There was a problem hiding this comment.
Ensure run_time_max is formatted as HH:MM:SS for Torque's walltime
Torque's walltime parameter expects time in HH:MM:SS format. Currently, run_time_max might be provided as an integer (e.g., total seconds), which could lead to incorrect scheduling.
Consider converting run_time_max to the appropriate format before rendering the template. Here's how you can adjust the code:
# In the `render_submission_template` method before rendering:
if run_time_max is not None:
run_time_max = "{:02d}:{:02d}:{:02d}".format(
run_time_max // 3600,
(run_time_max % 3600) // 60,
run_time_max % 60
)for more information, see https://pre-commit.ci
There was a problem hiding this comment.
Actionable comments posted: 9
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (2)
- pysqa/utils/basic.py (4 hunks)
- pysqa/utils/core.py (1 hunks)
🧰 Additional context used
🪛 Ruff
pysqa/utils/core.py
61-61: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
84-87: Do not call
getattrwith a constant attribute value. It is not any safer than normal property access.Replace
getattrwith attribute access(B009)
🔇 Additional comments (1)
pysqa/utils/basic.py (1)
190-190:⚠️ Potential issueEnsure compatibility of
submission_templateparameter with superclass methodAdding the
submission_templateparameter to_job_submission_templatemay cause issues if the superclass method does not accept this parameter. This could lead to aTypeErrorwhen callingsuper()._job_submission_template().Run the following script to verify if the superclass method accepts
submission_template:
| super().__init__( | ||
| queue_type=config["queue_type"], execute_command=execute_command | ||
| ) |
There was a problem hiding this comment.
Ensure 'queue_type' key exists in config to avoid KeyError
The call to super().__init__ uses config["queue_type"]. If 'queue_type' is not present in the config dictionary, this will raise a KeyError. Consider adding error handling or providing a default value to prevent this issue.
Apply this diff to handle missing 'queue_type' key:
def __init__(
self,
config: dict,
directory: str = "~/.queues",
execute_command: callable = execute_command,
):
+ queue_type = config.get("queue_type")
+ if queue_type is None:
+ raise ValueError("The 'queue_type' key is missing in the config dictionary.")
super().__init__(
- queue_type=config["queue_type"], execute_command=execute_command
+ queue_type=queue_type, execute_command=execute_command
)Alternatively, you can set a default queue_type if appropriate.
Committable suggestion was skipped due to low confidence.
| return super()._job_submission_template( | ||
| queue=None, | ||
| submission_template=active_queue["template"], |
There was a problem hiding this comment.
Ensure 'template' key exists in active_queue to avoid KeyError
The code accesses active_queue["template"]. If the 'template' key is missing in active_queue, this will raise a KeyError. Please ensure that all active queues have a 'template' defined or add error handling to manage missing templates.
Apply this diff to handle missing 'template' key:
if queue not in self.queue_list:
raise ValueError(
"The queue "
+ queue
+ " was not found in the list of queues: "
+ str(self.queue_list)
)
active_queue = self._config["queues"][queue]
+if "template" not in active_queue:
+ raise ValueError("The active queue does not have a 'template' defined.")
cores, run_time_max, memory_max = self.check_queue_parameters(
queue=None,
cores=cores,
run_time_max=run_time_max,
memory_max=memory_max,
active_queue=active_queue,
)
return super()._job_submission_template(
queue=None,
submission_template=active_queue["template"],
job_name=job_name,Alternatively, provide a default template or handle this scenario gracefully.
Committable suggestion was skipped due to low confidence.
| df_selected = df[df["jobid"] == process_id]["status"] | ||
| if len(df_selected) != 0: | ||
| results_lst.append(df_selected.values[0]) | ||
| else: | ||
| results_lst.append("finished") | ||
| return results_lst |
There was a problem hiding this comment.
Avoid assuming job status is 'finished' when not found
Setting the job status to "finished" when the job ID is not found may be inaccurate, as the job could be pending, failed, or cancelled. Consider setting the status to "unknown" or implementing additional checks.
Apply this diff:
if len(df_selected) != 0:
results_lst.append(df_selected.values[0])
else:
- results_lst.append("finished")
+ results_lst.append("unknown")📝 Committable 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.
| df_selected = df[df["jobid"] == process_id]["status"] | |
| if len(df_selected) != 0: | |
| results_lst.append(df_selected.values[0]) | |
| else: | |
| results_lst.append("finished") | |
| return results_lst | |
| df_selected = df[df["jobid"] == process_id]["status"] | |
| if len(df_selected) != 0: | |
| results_lst.append(df_selected.values[0]) | |
| else: | |
| results_lst.append("unknown") | |
| return results_lst |
| os.makedirs(working_directory) | ||
| queue_script_path = os.path.join(working_directory, "run_queue.sh") | ||
| with open(queue_script_path, "w") as f: | ||
| f.writelines(queue_script) |
There was a problem hiding this comment.
Use write() instead of writelines() when writing a string
The writelines() method expects an iterable of strings, but queue_script is a single string. Use write() to correctly write the content.
Apply this diff:
with open(queue_script_path, "w") as f:
- f.writelines(queue_script)
+ f.write(queue_script)📝 Committable 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.
| f.writelines(queue_script) | |
| with open(queue_script_path, "w") as f: | |
| f.write(queue_script) |
pysqa/utils/core.py
Outdated
| self._submission_template = getattr( | ||
| importlib.import_module(queue_type_dict[queue_type]["module_name"]), | ||
| "template", | ||
| ) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Avoid unnecessary use of getattr with a constant attribute
Since 'template' is a constant attribute name, you can access it directly for better readability.
Apply this diff:
- self._submission_template = getattr(
- importlib.import_module(queue_type_dict[queue_type]["module_name"]),
- "template",
- )
+ module = importlib.import_module(queue_type_dict[queue_type]["module_name"])
+ self._submission_template = module.template📝 Committable 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.
| self._submission_template = getattr( | |
| importlib.import_module(queue_type_dict[queue_type]["module_name"]), | |
| "template", | |
| ) | |
| module = importlib.import_module(queue_type_dict[queue_type]["module_name"]) | |
| self._submission_template = module.template |
🧰 Tools
🪛 Ruff
84-87: Do not call
getattrwith a constant attribute value. It is not any safer than normal property access.Replace
getattrwith attribute access(B009)
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
There was a problem hiding this comment.
Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (2)
pysqa/wrapper/gent.py (2)
21-22: Consider renaming the module-level template variable.The assignment of
template_slurmto a new variable namedtemplateis correct and likely part of a standardization effort. However, this creates a potential naming confusion sincetemplateis now both a module-level variable and an imported name.To improve clarity, consider renaming the module-level variable to something more specific, such as
gent_templateordefault_template.Here's a suggested change:
- template = template_slurm + gent_template = template_slurmThis change would make the code more explicit and reduce the potential for confusion.
Line range hint
26-95: Consider updating GentCommands to use the new template.The introduction of the
templateobject from theslurmmodule suggests a move towards standardization of job submission templates. However, theGentCommandsclass doesn't currently use this new template.To fully implement this change:
- Consider adding a
render_submission_templatemethod toGentCommandsthat uses the new template.- Update existing methods in
GentCommandsto use the new template where appropriate.This would ensure consistency with the apparent goal of standardizing template usage across different queue adapters.
📜 Review details
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📒 Files selected for processing (3)
- pysqa/queueadapter.py (2 hunks)
- pysqa/utils/core.py (1 hunks)
- pysqa/wrapper/gent.py (2 hunks)
🧰 Additional context used
🪛 Ruff
pysqa/utils/core.py
61-61: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
85-88: Do not call
getattrwith a constant attribute value. It is not any safer than normal property access.Replace
getattrwith attribute access(B009)
🔇 Additional comments (5)
pysqa/wrapper/gent.py (1)
8-8: LGTM: Import statement for template looks good.The import statement correctly brings in the
templateobject from theslurmmodule and aliases it astemplate_slurm. This prepares for its usage later in the file.pysqa/queueadapter.py (2)
5-5: LGTM: Import statement updated correctly.The import statement has been appropriately updated to include
TupleandUnionfrom thetypingmodule. This change is necessary to support the new type annotation in thecheck_queue_parametersmethod and follows best practices for type hinting in Python.
Line range hint
1-391: Overall assessment: Improvements in type safety with minor documentation update needed.The changes in this file enhance type safety and specificity, particularly in the
check_queue_parametersmethod. The updated import statement and method signature are well-implemented. The only remaining task is to update the method's docstring to reflect the new return type accurately.These changes contribute to better code quality and maintainability. Great job on improving the type annotations!
pysqa/utils/core.py (2)
343-343:⚠️ Potential issueUse
write()instead ofwritelines()for writing a single stringThe
writelines()method expects an iterable of strings, butqueue_scriptis a single string.Use
write()to correctly write the content. Apply this diff:with open(queue_script_path, "w") as f: - f.writelines(queue_script) + f.write(queue_script)Likely invalid or redundant comment.
246-251:⚠️ Potential issueReconsider default status for jobs not found in queue
Setting the job status to
"finished"when the job ID is not found may be inaccurate. The job could be in various states like pending, failed, or cancelled.Consider setting the status to
"unknown"or implementing additional checks to determine the actual status. Apply this diff as a starting point:if len(df_selected) != 0: results_lst.append(df_selected.values[0]) else: - results_lst.append("finished") + results_lst.append("unknown")Likely invalid or redundant comment.
| ) -> Tuple[ | ||
| Union[float, int, None], Union[float, int, None], Union[float, int, None] | ||
| ]: |
There was a problem hiding this comment.
Approve signature change and update docstring.
The method signature update improves type safety and code readability by providing a more specific return type annotation. This change is beneficial for maintainability and helps catch potential type-related errors early.
However, the method's docstring still mentions returning a List, which is now inconsistent with the new Tuple return type.
Please update the docstring to reflect the new return type. For example:
"""
...
Returns:
Tuple[Union[float, int, None], Union[float, int, None], Union[float, int, None]]: A tuple containing the checked parameters (cores, run_time_max, memory_max).
"""Also, ensure that the method implementation returns a tuple that matches this new type annotation.
| Returns: | ||
| SchedulerCommands: queuing system commands class instance | ||
| """ | ||
| if queue_type in queue_type_dict.keys(): |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Simplify dictionary membership check
The current check if queue_type in queue_type_dict.keys(): can be simplified to improve readability and performance slightly.
Apply this diff to simplify the dictionary membership check:
-if queue_type in queue_type_dict.keys():
+if queue_type in queue_type_dict:📝 Committable 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.
| if queue_type in queue_type_dict.keys(): | |
| if queue_type in queue_type_dict: |
🧰 Tools
🪛 Ruff
61-61: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
| process_id (int): The process ID. | ||
|
|
||
| Returns: | ||
| str: The status of the job.results_lst.append(df_selected.values[0]) |
There was a problem hiding this comment.
Correct the docstring return description in get_status_of_job
The return description includes an unintended code snippet, which may confuse users.
Apply this diff to fix the docstring:
- str: The status of the job.results_lst.append(df_selected.values[0])
+ str: The status of the job.📝 Committable 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.
| str: The status of the job.results_lst.append(df_selected.values[0]) | |
| str: The status of the job. |
| if queue_type_dict[queue_type]["module_name"] is not None: | ||
| self._submission_template = getattr( | ||
| importlib.import_module(queue_type_dict[queue_type]["module_name"]), | ||
| "template", | ||
| ) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Simplify attribute access for template
The use of getattr with a constant attribute name can be simplified for better readability.
Apply this diff to simplify the attribute access:
- self._submission_template = getattr(
- importlib.import_module(queue_type_dict[queue_type]["module_name"]),
- "template",
- )
+ module = importlib.import_module(queue_type_dict[queue_type]["module_name"])
+ self._submission_template = module.template📝 Committable 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.
| if queue_type_dict[queue_type]["module_name"] is not None: | |
| self._submission_template = getattr( | |
| importlib.import_module(queue_type_dict[queue_type]["module_name"]), | |
| "template", | |
| ) | |
| if queue_type_dict[queue_type]["module_name"] is not None: | |
| module = importlib.import_module(queue_type_dict[queue_type]["module_name"]) | |
| self._submission_template = module.template |
🧰 Tools
🪛 Ruff
85-88: Do not call
getattrwith a constant attribute value. It is not any safer than normal property access.Replace
getattrwith attribute access(B009)
| if queue is not None: | ||
| raise ValueError() | ||
| if submission_template is None: |
There was a problem hiding this comment.
Improve error handling when queue is specified
Raising a ValueError without a message when queue is not None can be unclear to users.
Consider providing a clear error message or removing the queue parameter if it's not supported. Here's an example of adding an informative error message:
if queue is not None:
- raise ValueError()
+ raise ValueError("Specifying 'queue' is not supported in this context.")Alternatively, if the queue parameter is not used at all, consider removing it from the method signature and any references within the method.
📝 Committable 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.
| if queue is not None: | |
| raise ValueError() | |
| if submission_template is None: | |
| if queue is not None: | |
| raise ValueError("Specifying 'queue' is not supported in this context.") | |
| if submission_template is None: |
| if isinstance(command, list): | ||
| command = "".join(command) | ||
| if working_directory is None: |
There was a problem hiding this comment.
Use appropriate separator when joining commands
Using "".join(command) concatenates the commands without any separators, which may result in invalid command strings.
Consider joining with a newline or space, depending on your specific use case. Apply this diff to join commands with newlines:
if isinstance(command, list):
- command = "".join(command)
+ command = "\n".join(command)📝 Committable 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.
| if isinstance(command, list): | |
| command = "".join(command) | |
| if working_directory is None: | |
| if isinstance(command, list): | |
| command = "\n".join(command) | |
| if working_directory is None: |
# Conflicts: # pysqa/utils/basic.py # pysqa/wrapper/abstract.py # pysqa/wrapper/flux.py # pysqa/wrapper/gent.py # pysqa/wrapper/lsf.py # pysqa/wrapper/moab.py # pysqa/wrapper/sge.py # pysqa/wrapper/slurm.py # pysqa/wrapper/torque.py
Summary by CodeRabbit
Release Notes
New Features
render_submission_templatemethod across multiple job scheduler classes (Flux, LSF, Moab, SGE, SLURM, Torque) for generating dynamic job submission scripts.enable_reservation_commandproperty toSchedulerCommandsclass to support job reservation functionality.CoreQueueAdapterclass to streamline job submission and management across various queuing systems.Refactor
SchedulerCommandsclass to improve abstraction and enforce implementation in subclasses.BasisQueueAdapterclass by removing redundant methods and leveraging functionality from the superclass.Bug Fixes
check_queue_parametersfunction for better clarity on expected output.