113 kubernetes integration by SimoneBendazzoli93 · Pull Request #130 · BrainLesion/BraTS

SimoneBendazzoli93 · 2025-11-03T19:33:26Z

fixes #113

- Introduced a new backend option for Kubernetes in the Backends enum. - Updated segmentation algorithms to accept optional keyword arguments for Kubernetes backend, enhancing flexibility for users.

…thm execution - Added a new section outlining how to configure and use the Kubernetes backend for running algorithms. - Provided examples for setting the KUBECONFIG environment variable and specifying backend options in the inference method.

- Integrated Kubernetes backend option into the BraTSAlgorithm class. - Updated methods to accept optional keyword arguments for Kubernetes, allowing for enhanced configuration during inference. - Added error handling to ensure Kubernetes kwargs are only used with the Kubernetes backend.

- Updated pyproject.toml to include the Kubernetes package with a minimum version of 34.1.0, enabling support for Kubernetes features in the project.

…Kubernetes configuration - Changed the parameter name from `mount_path` to `data_mount_path` in the documentation to accurately describe its function in the `infer_single` method for Kubernetes backend usage.

- Implemented functions for creating and managing Kubernetes jobs, including PVC creation, job execution, and output handling. - Added methods for downloading additional files from Zenodo and checking file presence in pods. - Enhanced logging for better traceability during job execution and output verification. - Integrated command execution within pods to facilitate file uploads and downloads, ensuring smooth operation of the Kubernetes backend for algorithm inference.

…_from_pod function in kubernetes.py

…ation

…rnetes.py`. Tests cover command argument building, file handling, job creation, and PVC management for different algorithm configurations.

…`local_base_dir` parameter

…hanced Kubernetes backend configuration

brainless-bot · 2025-11-03T19:33:49Z

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SimoneBendazzoli93 · 2025-11-03T19:34:17Z

/format

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Pull Request Overview

This PR adds Kubernetes backend support to the BraTS orchestrator, enabling remote algorithm execution via Kubernetes Jobs as an alternative to local Docker/Singularity containers. Key changes include:

New Kubernetes backend implementation with job orchestration, file transfer, and PVC management
Integration of Kubernetes backend into the existing algorithm inference pipeline
Support for configurable Kubernetes resources via kubernetes_kwargs parameter

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 14 comments.

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File	Description
brats/constants.py	Added KUBERNETES enum value to Backends
brats/core/kubernetes.py	New module implementing Kubernetes job execution with PVC management, file transfers, and pod lifecycle management
brats/core/brats_algorithm.py	Updated _infer_single and _infer_batch to support kubernetes_kwargs parameter and dispatch to Kubernetes backend
brats/core/segmentation_algorithms.py	Added kubernetes_kwargs parameter to infer_single and infer_batch methods for both Adult and Pediatric classes
tests/core/test_kubernetes.py	Comprehensive test suite for Kubernetes backend functionality
README.md	Added documentation for Kubernetes backend usage with configuration examples

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…new packages: `cachetools`, `durationpy`, `google-auth`, `kubernetes`, `oauthlib`, `pyasn1`, `pyasn1-modules`, `requests-oauthlib`, `rsa`, and `websocket-client`. Adjust version constraints and add optional dependencies for improved functionality.

…Lesion/BraTS into 113-kubernetes-integration

… path handling based on algorithm year, and streamline command execution logging.

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Pull Request Overview

Copilot reviewed 7 out of 8 changed files in this pull request and generated 7 comments.

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… and modify type hints in `kubernetes.py` for clarity. Enhance logging in `_download_folder_from_pod` and add TODO comments for future security context implementation. Remove commented-out code in `run_job` and adjust test cases in `test_kubernetes.py` to reflect changes.

brainless-bot · 2025-11-03T20:46:23Z

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…ntegration

… with customizable timeout and polling intervals

brainless-bot · 2026-06-14T08:02:54Z

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…rable resource retention

brainless-bot · 2026-06-14T08:19:11Z

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…py and kubernetes.py

…ython compatibility adjustments

…nd update test to reflect command output change

brainless-bot · 2026-06-14T08:37:13Z

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…adability

SimoneBendazzoli93 · 2026-06-14T08:42:31Z

Hi @neuronflow and @MarcelRosier 😄 I have pushed some fixes as suggested in the review.
Great to hear that Mehrnaz is also joining for the contribution 😄

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Pull request overview

Copilot reviewed 7 out of 8 changed files in this pull request and generated 8 comments.

neuronflow · 2026-06-14T08:56:41Z

welcome back @SimoneBendazzoli93 :) please address the above comments.

…s in pyproject.toml

…ditional block in brats_algorithm.py

…, enhancing error handling, and ensuring safe extraction of tar files

…ror handling for job completion failures

…ependencies and specify Kubernetes version constraint

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Pull request overview

Copilot reviewed 7 out of 8 changed files in this pull request and generated 8 comments.

+    core_v1_api = client.CoreV1Api()
+    logger.info(f"Waiting for Pod '{pod_name}' to be running...")
+    poll_attempts = int(timeout_seconds / poll_interval)
+    for _ in range(poll_attempts):
+        pod = core_v1_api.read_namespaced_pod(name=pod_name, namespace=namespace)
+        pod_phase = pod.status.phase
+        if pod.status.init_container_statuses:
+            exit_loop = False
+            for init_status in pod.status.init_container_statuses:
+                state = init_status.state
+                if state and state.running:
+                    logger.info(
+                        f"Pod '{pod_name}' initContainer '{init_status.name}' is running."
+                    )
+                    exit_loop = True
+                    break
+            if exit_loop:
+                break
+            if _check_pod_terminal_or_running(pod_phase, pod_name):
+                break
+        elif _check_pod_terminal_or_running(pod_phase, pod_name):
+            break
+        time.sleep(poll_interval)


neuronflow · 2026-06-15T17:10:04Z

+        base_folder_name = Path(folder_name).name
+        tarfile_path = local_base_dir / f"{base_folder_name}"
+        with open(tarfile_path, "wb") as tarfile_obj:
+            tarfile_obj.write(tar_data)


@SimoneBendazzoli93 consider using the Python tempfile storage here, this will also do automatic garbage collection etc.
https://docs.python.org/3/library/tempfile.html

+            unknown_kubernetes_kwargs = set(kubernetes_kwargs) - VALID_KUBERNETES_KWARGS
+            if unknown_kubernetes_kwargs:
+                raise ValueError(
+                    f"Unknown kubernetes_kwargs keys: {unknown_kubernetes_kwargs}"
+                )


+## Kubernetes Support
+BraTS orchestrator also supports Kubernetes to run the algorithms remotely, as an alternative to local execution with Docker or Singularity.
+To use Kubernetes for execution, the orchestrator will automatically use your kubeconfig file from the default location (`~/.kube/config`). If your kubeconfig file is not in the default location, set the `KUBECONFIG` environment variable to the location of your kubeconfig file:
+```bash
+export KUBECONFIG=/path/to/kubeconfig
+```


neuronflow · 2026-07-07T06:19:30Z

@SimoneBendazzoli93 we are approaching the end :) do you have the capacity to finish this?

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SimoneBendazzoli93 added 12 commits October 18, 2025 16:06

Add Kubernetes backend support in segmentation algorithms

46fd341

- Introduced a new backend option for Kubernetes in the Backends enum. - Updated segmentation algorithms to accept optional keyword arguments for Kubernetes backend, enhancing flexibility for users.

Add Kubernetes dependency in pyproject.toml

cead76b

- Updated pyproject.toml to include the Kubernetes package with a minimum version of 34.1.0, enabling support for Kubernetes features in the project.

Update README to reflect parameter name change for PVC mount path in …

39ccaff

…Kubernetes configuration - Changed the parameter name from `mount_path` to `data_mount_path` in the documentation to accurately describe its function in the `infer_single` method for Kubernetes backend usage.

Remove debug print statement for base folder name in _download_folder…

e99a837

…_from_pod function in kubernetes.py

Merge branch '114-singularity-integration' into 113-kubernetes-integr…

e63c443

…ation

Merge branch 'main' into 113-kubernetes-integration

ad42a55

Add comprehensive unit tests for Kubernetes integration in `test_kube…

a59b90e

…rnetes.py`. Tests cover command argument building, file handling, job creation, and PVC management for different algorithm configurations.

Update _download_folder_from_pod function to use absolute path for …

90a16c5

…`local_base_dir` parameter

Add optional kubernetes_kwargs parameter to BraTSAlgorithm for en…

cf340a2

…hanced Kubernetes backend configuration

SimoneBendazzoli93 requested review from Copilot and removed request for Copilot November 3, 2025 19:33

SimoneBendazzoli93 marked this pull request as draft November 3, 2025 19:33

Autoformat with black

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SimoneBendazzoli93 marked this pull request as ready for review November 3, 2025 19:34

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SimoneBendazzoli93 added 3 commits November 3, 2025 20:21

Merge branch '113-kubernetes-integration' of https://github.com/Brain…

bef0219

…Lesion/BraTS into 113-kubernetes-integration

Refactor Kubernetes integration: remove unused imports, adjust output…

3527cf1

… path handling based on algorithm year, and streamline command execution logging.

SimoneBendazzoli93 requested a review from Copilot November 3, 2025 20:39

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SimoneBendazzoli93 requested a review from Copilot November 3, 2025 20:46

SimoneBendazzoli93 added 3 commits June 14, 2026 09:43

docs: update README to clarify backend specification for Kubernetes i…

b56c4fe

…ntegration

feat: enhance Kubernetes backend support with validation for kwargs

38723a5

feat: enhance Kubernetes job output observation and command execution…

eba90be

… with customizable timeout and polling intervals

feat: add automatic cleanup for Kubernetes jobs and PVCs with configu…

74f3f9c

…rable resource retention

SimoneBendazzoli93 added 4 commits June 14, 2026 10:19

refactor: improve code formatting and readability in brats_algorithm.…

25abf7f

…py and kubernetes.py

chore: update poetry.lock to reflect dependency version changes and P…

4d9a030

…ython compatibility adjustments

chore: add empty lines for improved readability in pyproject.toml

6b1c7f2

refactor: streamline backend runner retrieval in brats_algorithm.py a…

bfd14bd

…nd update test to reflect command output change

refactor: improve code formatting in test_kubernetes.py for better re…

5df8f6f

…adability

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SimoneBendazzoli93 added 5 commits June 14, 2026 13:32

chore: remove specific Kubernetes version constraint from dependencie…

0de34ef

…s in pyproject.toml

refactor: move validation of kubernetes_kwargs to the appropriate con…

945d42d

…ditional block in brats_algorithm.py

refactor: update Kubernetes job handling by improving argument naming…

2e9f0f2

…, enhancing error handling, and ensuring safe extraction of tar files

refactor: update argument handling in Kubernetes job tests and add er…

c5c811c

…ror handling for job completion failures

chore: update poetry.lock and pyproject.toml to add 'dev' group for d…

200cbc8

…ependencies and specify Kubernetes version constraint

neuronflow requested a review from Copilot June 15, 2026 16:57

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neuronflow and others added 4 commits August 2, 2026 14:20

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