Add FileExecutor #344
Add FileExecutor #344
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Actionable comments posted: 2
Outside diff range and nitpick comments (2)
pympipool/cache/shared.py (2)
13-26: Consider adding docstrings to theFutureItemclass and its methods.Adding docstrings would improve the maintainability and readability of the code by providing a clear description of the class's purpose and its methods' functionalities.
90-93: Optimize the regular expression in_get_hash.Consider pre-compiling the regular expression for performance improvement, especially if
_get_hashis called frequently.pattern = re.compile(b"(?<=/ipykernel_)(.*)(?=/)") binary_no_ipykernel = pattern.sub(b"", binary)
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (15)
- .ci_support/environment-docs.yml (1 hunks)
- .ci_support/environment-mpich.yml (1 hunks)
- .ci_support/environment-old.yml (1 hunks)
- .ci_support/environment-openmpi.yml (1 hunks)
- .ci_support/environment-win.yml (1 hunks)
- binder/environment.yml (1 hunks)
- pympipool/init.py (2 hunks)
- pympipool/cache/backend.py (1 hunks)
- pympipool/cache/executor.py (1 hunks)
- pympipool/cache/hdf.py (1 hunks)
- pympipool/cache/shared.py (1 hunks)
- pyproject.toml (1 hunks)
- tests/executables/test_cache_shared.py (1 hunks)
- tests/test_cache_file_executor.py (1 hunks)
- tests/test_cache_hdf.py (1 hunks)
Files skipped from review due to trivial changes (7)
- .ci_support/environment-docs.yml
- .ci_support/environment-mpich.yml
- .ci_support/environment-old.yml
- .ci_support/environment-openmpi.yml
- .ci_support/environment-win.yml
- binder/environment.yml
- pyproject.toml
Additional comments not posted (11)
pympipool/cache/executor.py (2)
8-12: Constructor implementation looks good. It correctly sets up the cache directory and handles existing directories gracefully.
13-22: Method to set up the process is well-implemented. UsingRaisingThreadhelps in proper exception handling across threads.tests/test_cache_hdf.py (1)
19-64: Test cases are comprehensive and well-implemented. They cover various scenarios and properly clean up resources.pympipool/cache/hdf.py (3)
9-32: Thedumpfunction is well-implemented, usingcloudpicklefor serialization andh5iofor HDF5 interactions, ensuring robust data handling.
34-64: Theloadfunction is correctly implemented, handling potential missing entries gracefully and ensuring data integrity.
67-83: Theget_outputfunction is effectively implemented, correctly checking for and retrieving output from HDF5 files.tests/executables/test_cache_shared.py (1)
22-94: Test cases are comprehensive and effectively test the shared cache functionalities, including asynchronous operations usingFutureandFutureItem.tests/test_cache_file_executor.py (1)
23-105: Test cases forFileExecutorare well-implemented, effectively simulating various scenarios and properly managing resources.pympipool/cache/shared.py (1)
28-33: Ensure proper error handling inexecute_in_subprocess.This function currently lacks error handling for subprocess execution, which could lead to unmanaged subprocess failures. Consider adding a try-except block to handle potential exceptions.
pympipool/__init__.py (2)
13-13: Confirm the addition ofFileExecutorto__all__.The addition of
FileExecutorto the__all__list is consistent with the PR's objective to make it part of the public API.
3-3: Ensure that theFileExecutorimport is necessary.This verification is to ensure that the
FileExecutorimport is utilized within the file, as unused imports should be avoided to maintain clean code.Verification successful
The
FileExecutorimport is indeed used within thepympipool/__init__.pyfile.
pympipool/__init__.py: TheFileExecutoris imported and utilized within the file.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the necessity of the `FileExecutor` import. # Test: Search for `FileExecutor` usage in the file. rg --type python $'FileExecutor' pympipool/__init__.pyLength of output: 84
Script:
#!/bin/bash # Description: Verify the necessity of the `FileExecutor` import. # Test: Search for `FileExecutor` usage in the file. rg 'FileExecutor' pympipool/__init__.pyLength of output: 107
| def execute_tasks_h5(future_queue, cache_directory, execute_function): | ||
| memory_dict, process_dict, file_name_dict = {}, {}, {} | ||
| while True: | ||
| task_dict = None | ||
| try: | ||
| task_dict = future_queue.get_nowait() | ||
| except queue.Empty: | ||
| pass | ||
| if ( | ||
| task_dict is not None | ||
| and "shutdown" in task_dict.keys() | ||
| and task_dict["shutdown"] | ||
| ): | ||
| future_queue.task_done() | ||
| future_queue.join() | ||
| break | ||
| elif task_dict is not None: | ||
| task_args, task_kwargs, future_wait_key_lst = _convert_args_and_kwargs( | ||
| task_dict=task_dict, | ||
| memory_dict=memory_dict, | ||
| file_name_dict=file_name_dict, | ||
| ) | ||
| task_key, data_dict = _serialize_funct_h5( | ||
| task_dict["fn"], *task_args, **task_kwargs | ||
| ) | ||
| if task_key not in memory_dict.keys(): | ||
| if task_key + ".h5out" not in os.listdir(cache_directory): | ||
| file_name = os.path.join(cache_directory, task_key + ".h5in") | ||
| dump(file_name=file_name, data_dict=data_dict) | ||
| process_dict[task_key] = execute_function( | ||
| command=_get_execute_command(file_name=file_name), | ||
| task_dependent_lst=[ | ||
| process_dict[k] for k in future_wait_key_lst | ||
| ], | ||
| ) | ||
| file_name_dict[task_key] = os.path.join( | ||
| cache_directory, task_key + ".h5out" | ||
| ) | ||
| memory_dict[task_key] = task_dict["future"] | ||
| future_queue.task_done() | ||
| else: | ||
| memory_dict = { | ||
| key: _check_task_output( | ||
| task_key=key, future_obj=value, cache_directory=cache_directory | ||
| ) | ||
| for key, value in memory_dict.items() | ||
| if not value.done() | ||
| } |
There was a problem hiding this comment.
Refactor execute_tasks_h5 to improve readability and maintainability.
- while True:
- task_dict = None
- try:
- task_dict = future_queue.get_nowait()
- except queue.Empty:
- pass
- if (
- task_dict is not None
- and "shutdown" in task_dict.keys()
- and task_dict["shutdown"]
- ):
- future_queue.task_done()
- future_queue.join()
- break
- elif task_dict is not None:
- # processing logic
- else:
- # memory_dict processing logic
+ while not _shutdown_requested(future_queue):
+ task_dict = _try_get_task(future_queue)
+ if task_dict:
+ _process_task(task_dict, future_queue, memory_dict, file_name_dict, cache_directory, execute_function)This refactoring suggestion aims to break down the execute_tasks_h5 function into smaller, more manageable functions, improving readability and maintainability.
Committable suggestion was skipped due low confidence.
| def execute_task_in_file(file_name: str): | ||
| """ | ||
| Execute the task stored in a given HDF5 file | ||
|
|
||
| Args: | ||
| file_name (str): file name of the HDF5 file as absolute path | ||
| """ | ||
| apply_dict = load(file_name=file_name) | ||
| args = [ | ||
| arg if not isinstance(arg, FutureItem) else arg.result() | ||
| for arg in apply_dict["args"] | ||
| ] | ||
| kwargs = { | ||
| key: arg if not isinstance(arg, FutureItem) else arg.result() | ||
| for key, arg in apply_dict["kwargs"].items() | ||
| } | ||
| result = apply_dict["fn"].__call__(*args, **kwargs) | ||
| file_name_out = os.path.splitext(file_name)[0] | ||
| os.rename(file_name, file_name_out + ".h5ready") | ||
| dump(file_name=file_name_out + ".h5ready", data_dict={"output": result}) | ||
| os.rename(file_name_out + ".h5ready", file_name_out + ".h5out") |
There was a problem hiding this comment.
Consider using atomic operations or file locking mechanisms to handle file renaming to avoid issues in concurrent environments.
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Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (5)
- .ci_support/environment-mpich.yml (1 hunks)
- .ci_support/environment-openmpi.yml (1 hunks)
- binder/environment.yml (1 hunks)
- pympipool/cache/main.py (1 hunks)
- pympipool/cache/shared.py (1 hunks)
Files skipped from review due to trivial changes (1)
- pympipool/cache/main.py
Files skipped from review as they are similar to previous changes (4)
- .ci_support/environment-mpich.yml
- .ci_support/environment-openmpi.yml
- binder/environment.yml
- pympipool/cache/shared.py
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Summary by CodeRabbit
New Features
FileExecutorclass for handling file execution tasks.FileExecutor.Bug Fixes
Dependencies
h5pyversion 3.11.0 andh5ioversion 0.2.2 across various environments.Tests
FileExecutorand HDF5-related caching functionalities.Chores