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Peeter/docstring clean new#3225

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Apr 22, 2025
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Peeter/docstring clean new#3225
ppiegaze merged 20 commits into
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peeter/docstring-clean-new

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@ppiegaze ppiegaze commented Apr 11, 2025

Tracking issue

NA

Why are the changes needed?

What changes were proposed in this pull request?

Update the docstring format

How was this patch tested?

Setup process

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  • I updated the documentation accordingly.
  • All new and existing tests passed.
  • All commits are signed-off.

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Summary by Bito

This PR modernizes documentation across Flytekit modules by converting legacy reST formatting to markdown syntax, enhancing readability and standardizing code examples. It adds explicit type annotations and detailed parameter descriptions to docstrings, particularly in the webhook task module, while addressing bug fixes in critical code paths, especially in the entrypoint and Slurm connector modules to improve error handling and command execution reliability.

Unit tests added: False

Estimated effort to review (1-5, lower is better): 5

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flyte-bot commented Apr 11, 2025

Code Review Agent Run #087561

Actionable Suggestions - 1
  • plugins/flytekit-slurm/flytekitplugins/slurm/function/connector.py - 1
    • JSON parsing error after format change · Line 85-85
Review Details
  • Files reviewed - 70 · Commit Range: f79cd03..83bd484
    • flytekit/__init__.py
    • flytekit/bin/entrypoint.py
    • flytekit/clients/auth_helper.py
    • flytekit/clients/friendly.py
    • flytekit/clients/raw.py
    • flytekit/clis/sdk_in_container/serialize.py
    • flytekit/configuration/__init__.py
    • flytekit/configuration/file.py
    • flytekit/core/annotation.py
    • flytekit/core/array_node_map_task.py
    • flytekit/core/base_sql_task.py
    • flytekit/core/base_task.py
    • flytekit/core/checkpointer.py
    • flytekit/core/condition.py
    • flytekit/core/context_manager.py
    • flytekit/core/data_persistence.py
    • flytekit/core/dynamic_workflow_task.py
    • flytekit/core/launch_plan.py
    • flytekit/core/legacy_map_task.py
    • flytekit/core/local_fsspec.py
    • flytekit/core/notification.py
    • flytekit/core/promise.py
    • flytekit/core/python_auto_container.py
    • flytekit/core/python_customized_container_task.py
    • flytekit/core/python_function_task.py
    • flytekit/core/reference.py
    • flytekit/core/resources.py
    • flytekit/core/schedule.py
    • flytekit/core/shim_task.py
    • flytekit/core/task.py
    • flytekit/core/testing.py
    • flytekit/core/tracker.py
    • flytekit/core/type_engine.py
    • flytekit/core/workflow.py
    • flytekit/deck/__init__.py
    • flytekit/deck/deck.py
    • flytekit/exceptions/eager.py
    • flytekit/extend/__init__.py
    • flytekit/extras/accelerators.py
    • flytekit/extras/sqlite3/task.py
    • flytekit/extras/tasks/shell.py
    • flytekit/extras/webhook/task.py
    • flytekit/lazy_import/lazy_module.py
    • flytekit/models/core/execution.py
    • flytekit/models/literals.py
    • flytekit/models/security.py
    • flytekit/remote/__init__.py
    • flytekit/remote/backfill.py
    • flytekit/remote/remote.py
    • flytekit/tools/module_loader.py
    • flytekit/tools/repo.py
    • flytekit/types/directory/__init__.py
    • flytekit/types/directory/types.py
    • flytekit/types/error/__init__.py
    • flytekit/types/file/__init__.py
    • flytekit/types/file/file.py
    • flytekit/types/iterator/__init__.py
    • flytekit/types/pickle/__init__.py
    • flytekit/types/structured/__init__.py
    • plugins/flytekit-geopandas/flytekitplugins/geopandas/gdf_transformers.py
    • plugins/flytekit-geopandas/tests/test_geopandas_plugin.py
    • plugins/flytekit-hive/flytekitplugins/hive/task.py
    • plugins/flytekit-kf-mpi/flytekitplugins/kfmpi/task.py
    • plugins/flytekit-kf-pytorch/flytekitplugins/kfpytorch/task.py
    • plugins/flytekit-kf-tensorflow/flytekitplugins/kftensorflow/task.py
    • plugins/flytekit-papermill/flytekitplugins/papermill/task.py
    • plugins/flytekit-slurm/flytekitplugins/slurm/function/connector.py
    • plugins/flytekit-slurm/flytekitplugins/slurm/script/connector.py
    • tests/flytekit/integration/remote/workflows/basic/basic_workflow.py
    • tests/flytekit/integration/remote/workflows/basic/hello_world.py
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flyte-bot commented Apr 11, 2025

Changelist by Bito

This pull request implements the following key changes.

Key Change Files Impacted
Documentation - Docstring and Documentation Modernization

__init__.py - Modernized remote module docstrings and code examples to use markdown formatting, replacing obsolete reST sections with clear markdown syntax.

backfill.py - Updated backfill module documentation by converting code-block directives to markdown admonitions for notes and warnings.

remote.py - Replaced the reST note block with a markdown styled note, enhancing clarity in parameter descriptions.

__init__.py - Adjusted testing module docstrings to align with updated markdown formatting and improved module clarity.

module_loader.py - Refined TODO comment formatting by removing redundant comment symbols to clarify future enhancements.

repo.py - Converted reST references to markdown inline links in repository utilities, ensuring consistency in documentation.

__init__.py - Modernized directory type module documentation to markdown style with updated tables and section headers.

types.py - Replaced reST directives with markdown admonitions and warnings, clarifying usage and caveats in directory handling.

__init__.py - Cleaned up the error module by removing redundant documentation, resulting in a leaner docstring.

__init__.py - Updated file type documentation to reflect markdown styling improvements and a streamlined module overview.

file.py - Enhanced file handling function comments by replacing reST code-blocks with markdown formatting for better readability.

__init__.py - Performed minor adjustments on iterator module docstrings, shifting from reST to a minimalist markdown format.

__init__.py - Simplified pickle module docstring structures by adopting a concise markdown style.

__init__.py - Removed obsolete reST formatting in structured dataset documentation to provide a cleaner markdown presentation.

__init__.py - Updated in previous run – streamlined module-level documentation and modernized markdown formatting across client modules.

pydoclint-errors-baseline.txt - Updated baseline to remove obsolete docstring error codes in the core workflow module.

basic_workflow.py - Modernized inline documentation and converted reST links to markdown references in workflow comments.

hello_world.py - Replaced reST link syntax with markdown formatting in workflow documentation.

)
job_res = await conn.run(f"scontrol --json show job {resource_meta.job_id}", check=True)
job_info = json.loads(job_res.stdout)["jobs"][0]
job_res = await conn.run(f"scontrol show job {resource_meta.job_id}", check=True)
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JSON parsing error after format change

The --json flag was removed from the scontrol show job command, but the code still tries to parse the output as JSON on line 88. This will cause a runtime error since the output format has changed.

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Check the AI-generated fix before applying
Suggested change
job_res = await conn.run(f"scontrol show job {resource_meta.job_id}", check=True)
job_res = await conn.run(f"scontrol --json show job {resource_meta.job_id}", check=True)
job_info = json.loads(job_res.stdout)["jobs"][0]

Code Review Run #087561


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@ppiegaze ppiegaze force-pushed the peeter/docstring-clean-new branch from 9288172 to 72f239e Compare April 16, 2025 13:33
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flyte-bot commented Apr 16, 2025

Code Review Agent Run #c0739b

Actionable Suggestions - 2
  • plugins/flytekit-slurm/flytekitplugins/slurm/function/connector.py - 1
    • Reference to undefined variable job_info · Line 88-88
  • plugins/flytekit-geopandas/flytekitplugins/geopandas/gdf_transformers.py - 1
    • Incorrect directory creation logic for local paths · Line 46-47
Additional Suggestions - 10
  • flytekit/bin/entrypoint.py - 2
  • flytekit/core/local_fsspec.py - 1
  • flytekit/core/notification.py - 1
    • Deprecated typing import needs updating · Line 11-11
  • flytekit/extras/tasks/shell.py - 1
    • Exception with string literal in ValueError · Line 243-243
  • flytekit/lazy_import/lazy_module.py - 1
    • Docstring formatting issues need correction · Line 31-31
  • flytekit/tools/module_loader.py - 1
    • Replace Any with specific return type · Line 44-44
  • flytekit/tools/repo.py - 1
    • Boolean positional argument in function definition · Line 55-55
  • flytekit/types/iterator/__init__.py - 1
    • Empty module docstring needs content · Line 1-1
  • flytekit/types/pickle/__init__.py - 1
    • Empty module docstring needs content · Line 1-1
Review Details
  • Files reviewed - 79 · Commit Range: cfdad78..0682305
    • flytekit/__init__.py
    • flytekit/bin/entrypoint.py
    • flytekit/clients/auth_helper.py
    • flytekit/clients/friendly.py
    • flytekit/clients/raw.py
    • flytekit/configuration/__init__.py
    • flytekit/configuration/file.py
    • flytekit/core/annotation.py
    • flytekit/core/array_node_map_task.py
    • flytekit/core/base_sql_task.py
    • flytekit/core/base_task.py
    • flytekit/core/checkpointer.py
    • flytekit/core/condition.py
    • flytekit/core/context_manager.py
    • flytekit/core/dynamic_workflow_task.py
    • flytekit/core/launch_plan.py
    • flytekit/core/legacy_map_task.py
    • flytekit/core/notification.py
    • flytekit/core/python_function_task.py
    • flytekit/core/resources.py
    • flytekit/core/schedule.py
    • flytekit/core/task.py
    • flytekit/core/testing.py
    • flytekit/tools/module_loader.py
    • flytekit/core/shim_task.py
    • flytekit/core/tracker.py
    • flytekit/core/type_engine.py
    • flytekit/deck/deck.py
    • flytekit/exceptions/eager.py
    • flytekit/extras/accelerators.py
    • flytekit/extras/sqlite3/task.py
    • flytekit/extras/tasks/shell.py
    • flytekit/lazy_import/lazy_module.py
    • flytekit/remote/__init__.py
    • flytekit/remote/backfill.py
    • flytekit/remote/remote.py
    • flytekit/types/directory/types.py
    • flytekit/types/file/file.py
    • flytekit/core/data_persistence.py
    • flytekit/core/local_fsspec.py
    • flytekit/core/python_auto_container.py
    • flytekit/core/python_customized_container_task.py
    • flytekit/deck/__init__.py
    • flytekit/extend/__init__.py
    • flytekit/types/directory/__init__.py
    • flytekit/types/error/__init__.py
    • flytekit/types/iterator/__init__.py
    • flytekit/types/pickle/__init__.py
    • flytekit/types/structured/__init__.py
    • plugins/flytekit-hive/flytekitplugins/hive/task.py
    • plugins/flytekit-kf-mpi/flytekitplugins/kfmpi/task.py
    • plugins/flytekit-kf-pytorch/flytekitplugins/kfpytorch/task.py
    • plugins/flytekit-kf-tensorflow/flytekitplugins/kftensorflow/task.py
    • tests/flytekit/integration/remote/workflows/basic/basic_workflow.py
    • plugins/flytekit-geopandas/flytekitplugins/geopandas/gdf_transformers.py
    • plugins/flytekit-geopandas/tests/test_geopandas_plugin.py
    • plugins/flytekit-slurm/flytekitplugins/slurm/function/connector.py
    • plugins/flytekit-slurm/flytekitplugins/slurm/script/connector.py
    • flytekit/extras/webhook/task.py
    • flytekit/clis/sdk_in_container/serialize.py
    • flytekit/core/reference.py
    • flytekit/core/workflow.py
    • flytekit/core/promise.py
    • flytekit/models/core/execution.py
    • flytekit/models/literals.py
    • flytekit/models/security.py
    • flytekit/tools/repo.py
    • flytekit/types/file/__init__.py
    • plugins/flytekit-papermill/flytekitplugins/papermill/task.py
    • tests/flytekit/integration/remote/workflows/basic/hello_world.py
    • flytekit/clients/__init__.py
    • flytekit/extras/pytorch/__init__.py
    • flytekit/extras/sklearn/__init__.py
    • flytekit/extras/sqlite3/__init__.py
    • flytekit/extras/tasks/__init__.py
    • flytekit/extras/tensorflow/__init__.py
    • flytekit/image_spec/__init__.py
    • flytekit/interactive/__init__.py
    • flytekit/testing/__init__.py
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job_res = await conn.run(f"scontrol show job {resource_meta.job_id}", check=True)

# Determine the current flyte phase from Slurm job state
job_state = job_info["job_state"][0].strip().lower()
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Reference to undefined variable job_info

The variable job_info is used but not defined anywhere in the code. This will cause a runtime error. You need to define job_info before using it, likely by parsing the output from job_res.

Code suggestion
Check the AI-generated fix before applying
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job_state = job_info["job_state"][0].strip().lower()
# Parse job information from job_res
job_info = parse_job_output(job_res.stdout)
job_state = job_info["job_state"][0].strip().lower()

Code Review Run #c0739b


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Comment on lines +46 to +47
Path(uri).mkdir(parents=True, exist_ok=True)
uri = str(Path(uri) / "data.parquet")
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Incorrect directory creation logic for local paths

The code creates a directory path but doesn't ensure the parent directory exists before creating the file. When uri is a remote path, Path(uri).mkdir() is called but only after checking if it's remote, which is incorrect.

Code suggestion
Check the AI-generated fix before applying
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Path(uri).mkdir(parents=True, exist_ok=True)
uri = str(Path(uri) / "data.parquet")
parent_dir = Path(uri)
parent_dir.mkdir(parents=True, exist_ok=True)
uri = str(parent_dir / "data.parquet")
else:
uri = str(Path(uri) / "data.parquet")

Code Review Run #c0739b


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make fmt not working, will take a look.

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Code Review Agent Run #439111

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    • flytekit/extras/webhook/task.py
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 77.91%. Comparing base (8abecfe) to head (c772027).
Report is 3 commits behind head on master.

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@@             Coverage Diff             @@
##           master    #3225       +/-   ##
===========================================
- Coverage   89.81%   77.91%   -11.91%     
===========================================
  Files         136      237      +101     
  Lines        6599    23451    +16852     
  Branches        0     2927     +2927     
===========================================
+ Hits         5927    18271    +12344     
- Misses        672     4328     +3656     
- Partials        0      852      +852     

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Code Review Agent Run #8ac766

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chmod77 added 8 commits April 21, 2025 14:40
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
chmod77 and others added 9 commits April 21, 2025 14:40
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
@ppiegaze ppiegaze force-pushed the peeter/docstring-clean-new branch from b9b844d to be44c36 Compare April 21, 2025 12:40
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@wild-endeavor This still appears stuck. Any ideas?

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flyte-bot commented Apr 21, 2025

Code Review Agent Run #6053ce

Actionable Suggestions - 1
  • flytekit/core/legacy_map_task.py - 1
Additional Suggestions - 10
  • flytekit/bin/entrypoint.py - 3
  • flytekit/core/local_fsspec.py - 1
  • flytekit/core/notification.py - 1
    • Deprecated typing.List import usage · Line 11-11
  • flytekit/exceptions/eager.py - 1
    • Exception name missing Error suffix · Line 1-1
  • flytekit/extras/tasks/shell.py - 1
    • Exception with string literal in ValueError · Line 243-243
  • flytekit/tools/repo.py - 1
    • Boolean positional argument in function definition · Line 55-55
  • flytekit/types/iterator/__init__.py - 1
    • Empty docstring in module init file · Line 1-1
  • flytekit/types/pickle/__init__.py - 1
    • Empty docstring in module needs content · Line 1-1
Review Details
  • Files reviewed - 79 · Commit Range: b9b844d..be44c36
    • flytekit/__init__.py
    • flytekit/bin/entrypoint.py
    • flytekit/clients/auth_helper.py
    • flytekit/clients/friendly.py
    • flytekit/clients/raw.py
    • flytekit/configuration/__init__.py
    • flytekit/configuration/file.py
    • flytekit/core/annotation.py
    • flytekit/core/array_node_map_task.py
    • flytekit/core/base_sql_task.py
    • flytekit/core/base_task.py
    • flytekit/core/checkpointer.py
    • flytekit/core/condition.py
    • flytekit/core/context_manager.py
    • flytekit/core/dynamic_workflow_task.py
    • flytekit/core/launch_plan.py
    • flytekit/core/legacy_map_task.py
    • flytekit/core/notification.py
    • flytekit/core/python_function_task.py
    • flytekit/core/resources.py
    • flytekit/core/schedule.py
    • flytekit/core/task.py
    • flytekit/core/testing.py
    • flytekit/tools/module_loader.py
    • flytekit/core/shim_task.py
    • flytekit/core/tracker.py
    • flytekit/core/type_engine.py
    • flytekit/deck/deck.py
    • flytekit/exceptions/eager.py
    • flytekit/extras/accelerators.py
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Comment thread flytekit/core/legacy_map_task.py
Signed-off-by: Kevin Su <pingsutw@apache.org>
Signed-off-by: Kevin Su <pingsutw@apache.org>
pingsutw
pingsutw previously approved these changes Apr 22, 2025
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Code Review Agent Run #bd05ad

Actionable Suggestions - 0
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  • flytekit/bin/entrypoint.py - 6
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    • Empty module docstring needs content · Line 1-1
  • flytekit/types/directory/types.py - 1
  • flytekit/types/iterator/__init__.py - 1
    • Empty module docstring needs content · Line 1-1
  • flytekit/types/pickle/__init__.py - 1
    • Empty docstring needs meaningful content · Line 1-1
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  • Files reviewed - 19 · Commit Range: be44c36..0620664
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@pingsutw pingsutw closed this Apr 22, 2025
@pingsutw pingsutw reopened this Apr 22, 2025
Signed-off-by: Kevin Su <pingsutw@apache.org>
@ppiegaze ppiegaze merged commit e72fbde into master Apr 22, 2025
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@ppiegaze ppiegaze deleted the peeter/docstring-clean-new branch April 22, 2025 14:19
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Atharva1723 pushed a commit to Atharva1723/flytekit that referenced this pull request Oct 5, 2025
* chore: docstring cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: docstring cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: cleanup docstrings

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: fix merge conflicts

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: fix merge conflicts

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: fix merge conflicts

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: further cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: further cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: further docstring cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: further docstring cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* chore: further docstring cleanup

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* feat: replace sphinx directives with relevant shortcodes

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* Cleanup docstrings

Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* fix missing code block delimiter

Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* empty

Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* Remove unneeded param in docstring

Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* try fixing docstring again

Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>

* fix tests

Signed-off-by: Kevin Su <pingsutw@apache.org>

* nit

Signed-off-by: Kevin Su <pingsutw@apache.org>

* disable monodoc

Signed-off-by: Kevin Su <pingsutw@apache.org>

---------

Signed-off-by: chmod77 <chmod777.ke@gmail.com>
Signed-off-by: Peeter Piegaze <1153481+ppiegaze@users.noreply.github.com>
Signed-off-by: Kevin Su <pingsutw@apache.org>
Co-authored-by: chmod77 <chmod777.ke@gmail.com>
Co-authored-by: Yee Hing Tong <wild-endeavor@users.noreply.github.com>
Co-authored-by: Kevin Su <pingsutw@apache.org>
Signed-off-by: Atharva <atharvakulkarni172003@gmail.com>
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