{"id":24562631,"url":"https://github.com/humanbrainproject/cortical-voluba","last_synced_at":"2026-08-05T08:34:43.660Z","repository":{"id":73403227,"uuid":"192695117","full_name":"HumanBrainProject/cortical-voluba","owner":"HumanBrainProject","description":"VoluBA backend for non-linear depth-informed alignment of cortical patches","archived":false,"fork":false,"pushed_at":"2020-06-09T11:57:34.000Z","size":133,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-10-10T21:13:57.853Z","etag":null,"topics":["cortex","neuroimaging"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/HumanBrainProject.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-06-19T08:51:07.000Z","updated_at":"2020-06-09T11:57:36.000Z","dependencies_parsed_at":"2023-03-02T05:16:39.900Z","dependency_job_id":null,"html_url":"https://github.com/HumanBrainProject/cortical-voluba","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/HumanBrainProject/cortical-voluba","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HumanBrainProject%2Fcortical-voluba","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HumanBrainProject%2Fcortical-voluba/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HumanBrainProject%2Fcortical-voluba/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HumanBrainProject%2Fcortical-voluba/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HumanBrainProject","download_url":"https://codeload.github.com/HumanBrainProject/cortical-voluba/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HumanBrainProject%2Fcortical-voluba/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":36305528,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-07-20T02:08:10.276Z","status":"online","status_checked_at":"2026-08-05T02:00:06.619Z","response_time":104,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cortex","neuroimaging"],"created_at":"2025-01-23T09:16:37.077Z","updated_at":"2026-08-05T08:34:43.650Z","avatar_url":"https://github.com/HumanBrainProject.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"VoluBA backend for non-linear depth-informed alignment of cortical patches\n\n.. image:: https://api.travis-ci.com/HumanBrainProject/cortical-voluba.svg?branch=master\n   :target: https://travis-ci.com/HumanBrainProject/cortical-voluba\n   :alt: Travis Build Status\n\n.. image:: https://codecov.io/gh/HumanBrainProject/cortical-voluba/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/HumanBrainProject/cortical-voluba\n   :alt: Coverage Status\n\n.. image:: https://img.shields.io/swagger/valid/3.0?label=OpenAPI\u0026specUrl=https%3A%2F%2Fcortical-voluba.apps-dev.hbp.eu%2Fopenapi.json\n   :target: https://cortical-voluba.apps-dev.hbp.eu/redoc\n   :alt: Swagger Validator\n\n\nPublic deployments\n==================\n\nA test deployment (following the ``dev`` branch) is deployed on https://cortical-voluba.apps-dev.hbp.eu. |uptime-dev|  The corresponding front-end is https://voluba-dev.apps-dev.hbp.eu/.\n\nThe public deployments are managed by OpenShift clusters, the relevant configuration is described in `\u003copenshift-deployment/\u003e`_.\n\n\nDocumentation\n=============\n\nThe API is documented using the OpenAPI standard (a.k.a. Swagger): see `the ReDoc-generated documentation \u003chttps://cortical-voluba.apps-dev.hbp.eu/redoc\u003e`_. `A Swagger UI page \u003chttps://cortical-voluba.apps-dev.hbp.eu/swagger-ui\u003e`_ is also available for trying out the API.\n\n\nDevelopment\n===========\n\nThe backend uses `highres-cortex`_ and `ANTs`_, both of which must be available the ``PATH``. You can use `\u003cdocker-highres-cortex/script.sh\u003e`_ to build a Docker image containing highres-cortex (a pre-built image is available on Docker Hub: `ylep/highres-cortex \u003chttps://hub.docker.com/r/ylep/highres-cortex\u003e`_). You can use `\u003cdocker-highres-cortex-ants/Dockerfile\u003e`_ to add the relevant ANTs tools (a pre-built image is available on Docker Hub: `ylep/highres-cortex-ants \u003chttps://hub.docker.com/r/ylep/highres-cortex-ants\u003e`_).\n\nThe compute-intensive alignment runs on a task queue that uses `Celery \u003chttp://www.celeryproject.org/\u003e`_. It needs to be configured with a broker (Redis was tested successfully), see `First steps with Celery`_. The queue runner needs to be started separately::\n\nUseful commands for development:\n\n.. code-block:: shell\n\n  git clone https://github.com/HumanBrainProject/cortical-voluba.git\n\n  # Install in a virtual environment\n  cd cortical-voluba\n  python3 -m venv venv/\n  . venv/bin/activate\n  pip install -e .[dev]\n\n  export FLASK_APP=hbp_spatial_backend\n  flask run  # run a local development server\n  celery --app=cortical_voluba worker --loglevel=info  # run the task queue\n\n  # Tests\n  pytest  # run tests\n  pytest --cov=hbp_spatial_backend --cov-report=html  # detailed test coverage report\n  tox  # run tests under all supported Python versions\n\n  # Please install pre-commit if you intend to contribute\n  pip install pre-commit\n  pre-commit install  # install the pre-commit hook\n\n\nContributing\n============\n\nThis repository uses `pre-commit`_ to ensure that all committed code follows minimal quality standards. Please install it and configure it to run as a pre-commit hook in your local repository (see above).\n\n\n.. |uptime-dev| image:: https://img.shields.io/uptimerobot/ratio/7/m783468854-2ce9835116702e502b149972?style=flat-square\n   :alt: Weekly uptime ratio of the development instance\n.. _highres-cortex: https://github.com/neurospin/highres-cortex\n.. _ANTs: http://stnava.github.io/ANTs/\n.. _Celery: http://www.celeryproject.org/\n.. _`First steps with Celery`: http://docs.celeryproject.org/en/latest/getting-started/first-steps-with-celery.html\n.. _pre-commit: https://pre-commit.com/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhumanbrainproject%2Fcortical-voluba","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhumanbrainproject%2Fcortical-voluba","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhumanbrainproject%2Fcortical-voluba/lists"}