vantage6 4.4.0rc3__tar.gz → 4.5.0rc3__tar.gz

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  1. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/PKG-INFO +40 -31
  2. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/setup.py +1 -1
  3. vantage6-4.5.0rc3/vantage6/cli/__init__.py +3 -0
  4. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/_version.py +1 -1
  5. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6.egg-info/PKG-INFO +40 -31
  6. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6.egg-info/requires.txt +3 -3
  7. vantage6-4.4.0rc3/vantage6/cli/__init__.py +0 -1
  8. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/setup.cfg +0 -0
  9. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/tests_cli/__init__.py +0 -0
  10. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/tests_cli/test_example.py +0 -0
  11. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/tests_cli/test_node_cli.py +0 -0
  12. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/tests_cli/test_server_cli.py +0 -0
  13. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/tests_cli/test_wizard.py +0 -0
  14. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/__build__ +0 -0
  15. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algorithm/create.py +0 -0
  16. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algorithm/update.py +0 -0
  17. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algostore/attach.py +0 -0
  18. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algostore/files.py +0 -0
  19. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algostore/list.py +0 -0
  20. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algostore/new.py +0 -0
  21. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algostore/start.py +0 -0
  22. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/algostore/stop.py +0 -0
  23. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/cli.py +0 -0
  24. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/common/decorator.py +0 -0
  25. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/common/start.py +0 -0
  26. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/common/utils.py +0 -0
  27. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/configuration_manager.py +0 -0
  28. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/configuration_wizard.py +0 -0
  29. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/context/__init__.py +0 -0
  30. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/context/algorithm_store.py +0 -0
  31. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/context/base_server.py +0 -0
  32. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/context/node.py +0 -0
  33. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/context/server.py +0 -0
  34. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/dev/create.py +0 -0
  35. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/dev/remove.py +0 -0
  36. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/dev/start.py +0 -0
  37. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/dev/stop.py +0 -0
  38. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/globals.py +0 -0
  39. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/attach.py +0 -0
  40. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/clean.py +0 -0
  41. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/common/__init__.py +0 -0
  42. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/create_private_key.py +0 -0
  43. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/files.py +0 -0
  44. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/list.py +0 -0
  45. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/new.py +0 -0
  46. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/remove.py +0 -0
  47. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/set_api_key.py +0 -0
  48. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/start.py +0 -0
  49. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/stop.py +0 -0
  50. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/node/version.py +0 -0
  51. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/rabbitmq/__init__.py +0 -0
  52. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/rabbitmq/definitions.py +0 -0
  53. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/rabbitmq/queue_manager.py +0 -0
  54. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/rabbitmq/rabbitmq.config +0 -0
  55. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/attach.py +0 -0
  56. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/common/__init__.py +0 -0
  57. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/files.py +0 -0
  58. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/import_.py +0 -0
  59. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/list.py +0 -0
  60. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/new.py +0 -0
  61. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/remove.py +0 -0
  62. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/shell.py +0 -0
  63. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/start.py +0 -0
  64. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/stop.py +0 -0
  65. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/server/version.py +0 -0
  66. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/template/node_config.j2 +0 -0
  67. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/template/server_config.j2 +0 -0
  68. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/template/server_import_config.j2 +0 -0
  69. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/test/common/diagnostic_runner.py +0 -0
  70. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/test/feature_tester.py +0 -0
  71. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/test/integration_test.py +0 -0
  72. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6/cli/utils.py +0 -0
  73. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6.egg-info/SOURCES.txt +0 -0
  74. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6.egg-info/dependency_links.txt +0 -0
  75. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6.egg-info/entry_points.txt +0 -0
  76. {vantage6-4.4.0rc3 → vantage6-4.5.0rc3}/vantage6.egg-info/top_level.txt +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: vantage6
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- Version: 4.4.0rc3
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+ Version: 4.5.0rc3
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  Summary: vantage6 command line interface
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  Home-page: https://github.com/vantage6/vantage6
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  Requires-Python: >=3.10
@@ -16,12 +16,14 @@ Provides-Extra: dev
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  <h3 align="center">
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  <!-- Badges go here-->
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  [![Release](https://github.com/vantage6/vantage6/actions/workflows/release.yml/badge.svg)](https://github.com/vantage6/vantage6/actions/workflows/release.yml)
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  [![PyPI vantage6](https://badge.fury.io/py/vantage6.svg)](https://badge.fury.io/py/vantage6)
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  [![Unittests](https://github.com/vantage6/vantage6/actions/workflows/unit_tests.yml/badge.svg)](https://github.com/vantage6/vantage6/actions/workflows/unit_tests.yml)
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  [![Coverage Status](https://coveralls.io/repos/github/vantage6/vantage6/badge.svg?branch=main)](https://coveralls.io/github/vantage6/vantage6?branch=main)
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- [![Codacy Badge](https://app.codacy.com/project/badge/Grade/2e60ac3b3f284620805f7399cba317be)](https://www.codacy.com/gh/vantage6/vantage6/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=vantage6/vantage6&amp;utm_campaign=Badge_Grade)
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- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7382602.svg)](https://doi.org/10.5281/zenodo.7382602)
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+ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/2e60ac3b3f284620805f7399cba317be)](https://app.codacy.com/gh/vantage6/vantage6/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
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+ [![DOI](https://zenodo.org/badge/492818831.svg)](https://zenodo.org/badge/latestdoi/492818831)
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  </h3>
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  <p align="center">
@@ -31,8 +33,8 @@ Provides-Extra: dev
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  <a href="#black_nib-references">References</a>
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  </p>
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+ ---
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- -----------------------------------------------------------------------------------------------------
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  This repository is contains all the **vantage6** infrastructure source code. The **vantage6** technology enables to manage and deploy privacy enhancing technologies like Federated Learning (FL) and Multi-Party Computation (MPC). Please visit our [website (vantage6.ai)](https://vantage6.ai) to learn more!
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  You can find more (user) documentation at [readthedocs (docs.vantage6.ai)](https://docs.vantage6.ai). If you have any questions, suggestions or just want to chat about federated learning: join our [Discord (https://discord.gg/yAyFf6Y)](https://discord.gg/yAyFf6Y) channel.
@@ -41,14 +43,16 @@ You can find more (user) documentation at [readthedocs (docs.vantage6.ai)](https
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  ![Vantage6 architecture overview](docs/images/overview-infrastructure.png)
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- *A High level overview of the vantage6 infrastructure. Vantage6 has both a client-server and peer-to-peer architecture. The client is used by the researcher to create (PET) computation requests. It is also used to manage users, organizations and collaborations. The server contains users, organizations, collaborations, tasks and their results. It provides a central access point for both the clients and nodes. The nodes have access to privacy sensitive data and handle computation requests retrieved from the server. Computation request are executed as separate containers on the node. These containers are connected to containers at other nodes by a VPN network.*
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+ _A High level overview of the vantage6 infrastructure. Vantage6 has both a client-server and peer-to-peer architecture. The client is used by the researcher to create (PET) computation requests. It is also used to manage users, organizations and collaborations. The server contains users, organizations, collaborations, tasks and their results. It provides a central access point for both the clients and nodes. The nodes have access to privacy sensitive data and handle computation requests retrieved from the server. Computation request are executed as separate containers on the node. These containers are connected to containers at other nodes by a VPN network._
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  ## :books: Quickstart
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  ### Requirements
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  The **vantage6** infrastructure is delivered in Docker images. To run these images, you need to have [Docker](https://docs.docker.com/get-docker/) installed. To install the latest version of the vantage6 CLI, you need to have [Python](https://www.python.org/downloads/), we recommend using an environment manager like [mini-conda](https://docs.conda.io/en/latest/miniconda.html).
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  Install the latest version of the vantage6 CLI by using:
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  ```bash
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  ```
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  From here you can use the [vantage6-client](https://pypi.org/project/vantage6-client) to interact with the server. The demo network has a pre-configured organization with the following credentials:
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  For example, you can create a new organization by running:
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@@ -110,16 +114,17 @@ You can find more (user) documentation at [readthedocs (docs.vantage6.ai)](https
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  ## Project structure
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  ### PYPI packages
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  This repository is home to 6 PyPi packages:
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- * [vantage6](https://pypi.org/project/vantage6) -> _CLI for managing node and server instances_
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- * [vantage6-client](https://pypi.org/project/vantage6-client) -> _Python client for interacting with the vantage6-server_
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- * [vantage6-algorithm-tools](https://pypi.org/project/vantage6-algorithm-tools) -> _Python tools to facilitate algorithm development_
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- * [vantage6-node](https://pypi.org/project/vantage6-node) -> _Node application package_
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- * [vantage6-server](https://pypi.org/project/vantage6-server) -> _Server application package_
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- * [vantage6-algorithm-store](https://pypi.org/project/vantage6-algorithm-store) -> _Algorithm store application package_
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- * [vantage6-common](https://pypi.org/project/vantage6-common) -> _Package with common vantage6 functions_
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- * [vantage6-backend-common](https://pypi.org/project/vantage6-backend-common) -> _Package with functions common to central server and algorithm store_
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+ - [vantage6](https://pypi.org/project/vantage6) -> _CLI for managing node and server instances_
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+ - [vantage6-client](https://pypi.org/project/vantage6-client) -> _Python client for interacting with the vantage6-server_
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+ - [vantage6-algorithm-tools](https://pypi.org/project/vantage6-algorithm-tools) -> _Python tools to facilitate algorithm development_
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+ - [vantage6-node](https://pypi.org/project/vantage6-node) -> _Node application package_
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+ - [vantage6-server](https://pypi.org/project/vantage6-server) -> _Server application package_
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+ - [vantage6-algorithm-store](https://pypi.org/project/vantage6-algorithm-store) -> _Algorithm store application package_
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+ - [vantage6-common](https://pypi.org/project/vantage6-common) -> _Package with common vantage6 functions_
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+ - [vantage6-backend-common](https://pypi.org/project/vantage6-backend-common) -> _Package with functions common to central server and algorithm store_
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  **Note that when using vantage6 you do not install the _server_ and _node_ packages. These are delivered to you in Docker images.**
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  easily.
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  ### Docker images
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  The vantage6 infrastructure is delivered in Docker images. All Docker images are stored in our private [Harbor](https://goharbor.io/) registry. The most important images are:
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- * `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
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- * `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
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- * `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
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- * `harbor2.vantage6.ai/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
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+ - `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
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+ - `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
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+ - `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
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  with `VERSION` being the full semantic version of the vantage6 infrastructure, e.g. `4.0.0` or `4.1.0rc0`.
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  Several other images are used to support the infrastructure:
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- * `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
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- * `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
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- * `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
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- * `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
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- * `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
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- * `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
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+ - `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
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+ - `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
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+ - `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
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+ - `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
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+ - `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
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+ - `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
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  And finally there are some images released for algorithm development:
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- * `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
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+ - `harbor2.vantage6.ai/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
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+ - `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
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  ## :gift_heart: Join the community!
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  We hope to continue developing, improving, and supporting **vantage6** with the help of the federated learning community. If you are interested in contributing, first of all, thank you! Second, please take a look at our [contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html)
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  </a>
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  ## :black_nib: References
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  If you are using **vantage6**, please cite this repository as well as the accompanying papers as follows:
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- > * F. Martin, M. Sieswerda, H. Alradhi, et al. vantage6. Available at https://doi.org/10.5281/zenodo.7221216. Accessed on MONTH, 20XX.
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- > * A. Moncada-Torres, F. Martin, M. Sieswerda, J. van Soest, G. Gelijnse. VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange. AMIA Annual Symposium Proceedings, 2020, p. 870-877. [[BibTeX](https://arturomoncadatorres.com/bibtex/moncada-torres2020vantage6.txt), [PDF](https://vantage6.ai/vantage6/)]
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- > * D. Smits\*, B. van Beusekom\*, F. Martin, L. Veen, G. Geleijnse, A. Moncada-Torres, An Improved Infrastructure for Privacy-Preserving Analysis of Patient Data, Proceedings of the International Conference of Informatics, Management, and Technology in Healthcare (ICIMTH), vol. 25, 2022, p. 144-147. [[BibTeX](https://arturomoncadatorres.com/bibtex/smits2022improved.txt), [PDF](https://ebooks.iospress.nl/volumearticle/60190)]
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+ > - F. Martin, M. Sieswerda, H. Alradhi, et al. vantage6. Available at https://doi.org/10.5281/zenodo.7221216. Accessed on MONTH, 20XX.
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+ > - A. Moncada-Torres, F. Martin, M. Sieswerda, J. van Soest, G. Gelijnse. VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange. AMIA Annual Symposium Proceedings, 2020, p. 870-877. [[BibTeX](https://arturomoncadatorres.com/bibtex/moncada-torres2020vantage6.txt), [PDF](https://vantage6.ai/vantage6/)]
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+ > - D. Smits\*, B. van Beusekom\*, F. Martin, L. Veen, G. Geleijnse, A. Moncada-Torres, An Improved Infrastructure for Privacy-Preserving Analysis of Patient Data, Proceedings of the International Conference of Informatics, Management, and Technology in Healthcare (ICIMTH), vol. 25, 2022, p. 144-147. [[BibTeX](https://arturomoncadatorres.com/bibtex/smits2022improved.txt), [PDF](https://ebooks.iospress.nl/volumearticle/60190)]
175
+
176
+ ---
167
177
 
168
- -----------------------------------------------------------------------------------------------------
169
178
  <p align="center">
170
179
  <a href="https://vantage6.ai">vantage6.ai</a> •
171
180
  <a href="https://discord.gg/yAyFf6Y">Discord</a> •
@@ -38,7 +38,7 @@ setup(
38
38
  "copier==9.2.0",
39
39
  "docker==6.1.2",
40
40
  "ipython==8.10.0",
41
- "jinja2==3.1.3",
41
+ "jinja2==3.1.4",
42
42
  "questionary==1.10.0",
43
43
  "rich==13.5.2",
44
44
  "schema==0.7.5",
@@ -0,0 +1,3 @@
1
+ """ Command line interface for the vantage6 infrastructure. """
2
+
3
+ from ._version import version_info, __version__ # noqa: F401
@@ -7,7 +7,7 @@ with open(os.path.join(here, "__build__")) as fp:
7
7
  __build__ = json.load(fp)
8
8
 
9
9
  # Module version
10
- version_info = (4, 4, 0, "candidate", __build__, 0)
10
+ version_info = (4, 5, 0, "candidate", __build__, 0)
11
11
 
12
12
  # Module version stage suffix map
13
13
  _specifier_ = {"alpha": "a", "beta": "b", "candidate": "rc", "final": ""}
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: vantage6
3
- Version: 4.4.0rc3
3
+ Version: 4.5.0rc3
4
4
  Summary: vantage6 command line interface
5
5
  Home-page: https://github.com/vantage6/vantage6
6
6
  Requires-Python: >=3.10
@@ -16,12 +16,14 @@ Provides-Extra: dev
16
16
  <h3 align="center">
17
17
 
18
18
  <!-- Badges go here-->
19
+
19
20
  [![Release](https://github.com/vantage6/vantage6/actions/workflows/release.yml/badge.svg)](https://github.com/vantage6/vantage6/actions/workflows/release.yml)
20
21
  [![PyPI vantage6](https://badge.fury.io/py/vantage6.svg)](https://badge.fury.io/py/vantage6)
21
22
  [![Unittests](https://github.com/vantage6/vantage6/actions/workflows/unit_tests.yml/badge.svg)](https://github.com/vantage6/vantage6/actions/workflows/unit_tests.yml)
22
23
  [![Coverage Status](https://coveralls.io/repos/github/vantage6/vantage6/badge.svg?branch=main)](https://coveralls.io/github/vantage6/vantage6?branch=main)
23
- [![Codacy Badge](https://app.codacy.com/project/badge/Grade/2e60ac3b3f284620805f7399cba317be)](https://www.codacy.com/gh/vantage6/vantage6/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=vantage6/vantage6&amp;utm_campaign=Badge_Grade)
24
- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7382602.svg)](https://doi.org/10.5281/zenodo.7382602)
24
+ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/2e60ac3b3f284620805f7399cba317be)](https://app.codacy.com/gh/vantage6/vantage6/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
25
+ [![DOI](https://zenodo.org/badge/492818831.svg)](https://zenodo.org/badge/latestdoi/492818831)
26
+
25
27
  </h3>
26
28
 
27
29
  <p align="center">
@@ -31,8 +33,8 @@ Provides-Extra: dev
31
33
  <a href="#black_nib-references">References</a>
32
34
  </p>
33
35
 
36
+ ---
34
37
 
35
- -----------------------------------------------------------------------------------------------------
36
38
  This repository is contains all the **vantage6** infrastructure source code. The **vantage6** technology enables to manage and deploy privacy enhancing technologies like Federated Learning (FL) and Multi-Party Computation (MPC). Please visit our [website (vantage6.ai)](https://vantage6.ai) to learn more!
37
39
 
38
40
  You can find more (user) documentation at [readthedocs (docs.vantage6.ai)](https://docs.vantage6.ai). If you have any questions, suggestions or just want to chat about federated learning: join our [Discord (https://discord.gg/yAyFf6Y)](https://discord.gg/yAyFf6Y) channel.
@@ -41,14 +43,16 @@ You can find more (user) documentation at [readthedocs (docs.vantage6.ai)](https
41
43
 
42
44
  ![Vantage6 architecture overview](docs/images/overview-infrastructure.png)
43
45
 
44
- *A High level overview of the vantage6 infrastructure. Vantage6 has both a client-server and peer-to-peer architecture. The client is used by the researcher to create (PET) computation requests. It is also used to manage users, organizations and collaborations. The server contains users, organizations, collaborations, tasks and their results. It provides a central access point for both the clients and nodes. The nodes have access to privacy sensitive data and handle computation requests retrieved from the server. Computation request are executed as separate containers on the node. These containers are connected to containers at other nodes by a VPN network.*
46
+ _A High level overview of the vantage6 infrastructure. Vantage6 has both a client-server and peer-to-peer architecture. The client is used by the researcher to create (PET) computation requests. It is also used to manage users, organizations and collaborations. The server contains users, organizations, collaborations, tasks and their results. It provides a central access point for both the clients and nodes. The nodes have access to privacy sensitive data and handle computation requests retrieved from the server. Computation request are executed as separate containers on the node. These containers are connected to containers at other nodes by a VPN network._
45
47
 
46
48
  ## :books: Quickstart
47
49
 
48
50
  ### Requirements
51
+
49
52
  The **vantage6** infrastructure is delivered in Docker images. To run these images, you need to have [Docker](https://docs.docker.com/get-docker/) installed. To install the latest version of the vantage6 CLI, you need to have [Python](https://www.python.org/downloads/), we recommend using an environment manager like [mini-conda](https://docs.conda.io/en/latest/miniconda.html).
50
53
 
51
54
  Install the latest version of the vantage6 CLI by using:
55
+
52
56
  ```bash
53
57
  pip install vantage6
54
58
  ```
@@ -83,8 +87,8 @@ v6 server attach
83
87
 
84
88
  From here you can use the [vantage6-client](https://pypi.org/project/vantage6-client) to interact with the server. The demo network has a pre-configured organization with the following credentials:
85
89
 
86
- * Username: `org_1-admin`
87
- * Password: `password`
90
+ - Username: `org_1-admin`
91
+ - Password: `password`
88
92
 
89
93
  For example, you can create a new organization by running:
90
94
 
@@ -110,16 +114,17 @@ You can find more (user) documentation at [readthedocs (docs.vantage6.ai)](https
110
114
  ## Project structure
111
115
 
112
116
  ### PYPI packages
117
+
113
118
  This repository is home to 6 PyPi packages:
114
119
 
115
- * [vantage6](https://pypi.org/project/vantage6) -> _CLI for managing node and server instances_
116
- * [vantage6-client](https://pypi.org/project/vantage6-client) -> _Python client for interacting with the vantage6-server_
117
- * [vantage6-algorithm-tools](https://pypi.org/project/vantage6-algorithm-tools) -> _Python tools to facilitate algorithm development_
118
- * [vantage6-node](https://pypi.org/project/vantage6-node) -> _Node application package_
119
- * [vantage6-server](https://pypi.org/project/vantage6-server) -> _Server application package_
120
- * [vantage6-algorithm-store](https://pypi.org/project/vantage6-algorithm-store) -> _Algorithm store application package_
121
- * [vantage6-common](https://pypi.org/project/vantage6-common) -> _Package with common vantage6 functions_
122
- * [vantage6-backend-common](https://pypi.org/project/vantage6-backend-common) -> _Package with functions common to central server and algorithm store_
120
+ - [vantage6](https://pypi.org/project/vantage6) -> _CLI for managing node and server instances_
121
+ - [vantage6-client](https://pypi.org/project/vantage6-client) -> _Python client for interacting with the vantage6-server_
122
+ - [vantage6-algorithm-tools](https://pypi.org/project/vantage6-algorithm-tools) -> _Python tools to facilitate algorithm development_
123
+ - [vantage6-node](https://pypi.org/project/vantage6-node) -> _Node application package_
124
+ - [vantage6-server](https://pypi.org/project/vantage6-server) -> _Server application package_
125
+ - [vantage6-algorithm-store](https://pypi.org/project/vantage6-algorithm-store) -> _Algorithm store application package_
126
+ - [vantage6-common](https://pypi.org/project/vantage6-common) -> _Package with common vantage6 functions_
127
+ - [vantage6-backend-common](https://pypi.org/project/vantage6-backend-common) -> _Package with functions common to central server and algorithm store_
123
128
 
124
129
  **Note that when using vantage6 you do not install the _server_ and _node_ packages. These are delivered to you in Docker images.**
125
130
 
@@ -128,30 +133,32 @@ is an Angular web application that can be used to interact with the vantage6 ser
128
133
  easily.
129
134
 
130
135
  ### Docker images
136
+
131
137
  The vantage6 infrastructure is delivered in Docker images. All Docker images are stored in our private [Harbor](https://goharbor.io/) registry. The most important images are:
132
138
 
133
- * `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
134
- * `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
135
- * `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
136
- * `harbor2.vantage6.ai/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
139
+ - `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
140
+ - `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
141
+ - `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
142
+ - `harbor2.vantage6.ai/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
137
143
 
138
144
  with `VERSION` being the full semantic version of the vantage6 infrastructure, e.g. `4.0.0` or `4.1.0rc0`.
139
145
 
140
146
  Several other images are used to support the infrastructure:
141
147
 
142
- * `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
143
- * `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
144
- * `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
145
- * `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
146
- * `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
147
- * `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
148
+ - `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
149
+ - `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
150
+ - `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
151
+ - `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
152
+ - `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
153
+ - `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
148
154
 
149
155
  And finally there are some images released for algorithm development:
150
156
 
151
- * `harbor2.vantage6.ai/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
152
- * `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
157
+ - `harbor2.vantage6.ai/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
158
+ - `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
153
159
 
154
160
  ## :gift_heart: Join the community!
161
+
155
162
  We hope to continue developing, improving, and supporting **vantage6** with the help of the federated learning community. If you are interested in contributing, first of all, thank you! Second, please take a look at our [contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html)
156
163
 
157
164
  <a href="https://github.com/vantage6/vantage6/graphs/contributors">
@@ -159,13 +166,15 @@ We hope to continue developing, improving, and supporting **vantage6** with the
159
166
  </a>
160
167
 
161
168
  ## :black_nib: References
169
+
162
170
  If you are using **vantage6**, please cite this repository as well as the accompanying papers as follows:
163
171
 
164
- > * F. Martin, M. Sieswerda, H. Alradhi, et al. vantage6. Available at https://doi.org/10.5281/zenodo.7221216. Accessed on MONTH, 20XX.
165
- > * A. Moncada-Torres, F. Martin, M. Sieswerda, J. van Soest, G. Gelijnse. VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange. AMIA Annual Symposium Proceedings, 2020, p. 870-877. [[BibTeX](https://arturomoncadatorres.com/bibtex/moncada-torres2020vantage6.txt), [PDF](https://vantage6.ai/vantage6/)]
166
- > * D. Smits\*, B. van Beusekom\*, F. Martin, L. Veen, G. Geleijnse, A. Moncada-Torres, An Improved Infrastructure for Privacy-Preserving Analysis of Patient Data, Proceedings of the International Conference of Informatics, Management, and Technology in Healthcare (ICIMTH), vol. 25, 2022, p. 144-147. [[BibTeX](https://arturomoncadatorres.com/bibtex/smits2022improved.txt), [PDF](https://ebooks.iospress.nl/volumearticle/60190)]
172
+ > - F. Martin, M. Sieswerda, H. Alradhi, et al. vantage6. Available at https://doi.org/10.5281/zenodo.7221216. Accessed on MONTH, 20XX.
173
+ > - A. Moncada-Torres, F. Martin, M. Sieswerda, J. van Soest, G. Gelijnse. VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange. AMIA Annual Symposium Proceedings, 2020, p. 870-877. [[BibTeX](https://arturomoncadatorres.com/bibtex/moncada-torres2020vantage6.txt), [PDF](https://vantage6.ai/vantage6/)]
174
+ > - D. Smits\*, B. van Beusekom\*, F. Martin, L. Veen, G. Geleijnse, A. Moncada-Torres, An Improved Infrastructure for Privacy-Preserving Analysis of Patient Data, Proceedings of the International Conference of Informatics, Management, and Technology in Healthcare (ICIMTH), vol. 25, 2022, p. 144-147. [[BibTeX](https://arturomoncadatorres.com/bibtex/smits2022improved.txt), [PDF](https://ebooks.iospress.nl/volumearticle/60190)]
175
+
176
+ ---
167
177
 
168
- -----------------------------------------------------------------------------------------------------
169
178
  <p align="center">
170
179
  <a href="https://vantage6.ai">vantage6.ai</a> •
171
180
  <a href="https://discord.gg/yAyFf6Y">Discord</a> •
@@ -3,13 +3,13 @@ colorama==0.4.6
3
3
  copier==9.2.0
4
4
  docker==6.1.2
5
5
  ipython==8.10.0
6
- jinja2==3.1.3
6
+ jinja2==3.1.4
7
7
  questionary==1.10.0
8
8
  rich==13.5.2
9
9
  schema==0.7.5
10
10
  SQLAlchemy==1.4.46
11
- vantage6-common==4.4.0rc3
12
- vantage6-client==4.4.0rc3
11
+ vantage6-common==4.5.0rc3
12
+ vantage6-client==4.5.0rc3
13
13
 
14
14
  [dev]
15
15
  coverage==6.4.4
@@ -1 +0,0 @@
1
- from ._version import version_info, __version__ # noqa: F401
File without changes