Initial commit of personalized algorithm template

.copier-answers.yml

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+# DO NOT MODIFY THIS FILE MANUALLY.
+# This file contains the answers to the questions asked by the
+# v6-algorithm-template-creator (using the Copier package). The answers will
+# be updated if you re-run the template creator. Also, the answers in this file
+# may be used to submit your algorithm to a vantage6 algorithm store.
+_commit: 4.3.4
+_src_path: gh:vantage6/v6-algorithm-template.git
+advanced: true
+algorithm_description: Create a summary of the data (mean, range, variance, length,
+    ...)
+algorithm_name: v6-summary-py
+author: B. van Beusekom, H. Alradhi, F.C. Martin
+central_args:
+- columns
+- organizations_to_include
+central_function_client: true
+central_function_data: false
+central_function_name: summary
+copyright: IKNL, 2024
+docker_image: harbor2.vantage6.ai/algorithms/v6-summary-py
+docker_registry: harbor2.vantage6.ai
+has_central_function: true
+has_docs: true
+has_gh_pipeline: true
+has_partial_function: true
+open_source_license: mit
+partial_args:
+- columns
+partial_function_client: false
+partial_function_data: true
+partial_function_name: summary_per_data_station
+partial_function_number_databases: 1
+private_registry: true
+project_name: v6-summary-py
+use_vpn: false

.github/workflows/release.yaml

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+name: Create Release
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+    create-docker-image:
+        runs-on: ubuntu-latest
+
+        steps:
+        - name: Checkout Repository
+          uses: actions/checkout@v4
+
+        - name: Login to Docker registry
+          uses: docker/login-action@v3
+          with:
+            registry: harbor2.vantage6.ai
+            username: ${{ secrets.DOCKER_USER }}
+            password: ${{ secrets.DOCKER_PASSWORD }}
+
+        - name: Run Makefile Rule
+          run: docker build -t harbor2.vantage6.ai/algorithms/v6-summary-py .
+
+        - name: Push Docker image
+          run: |
+            docker push harbor2.vantage6.ai/algorithms/v6-summary-py

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+.vscode/

Dockerfile

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+# basic python3 image as base
+FROM harbor2.vantage6.ai/infrastructure/algorithm-base
+
+# This is a placeholder that should be overloaded by invoking
+# docker build with '--build-arg PKG_NAME=...'
+ARG PKG_NAME="v6-summary-py"
+
+# install federated algorithm
+COPY . /app
+RUN pip install /app
+
+
+# Set environment variable to make name of the package available within the
+# docker image.
+ENV PKG_NAME=${PKG_NAME}
+
+# Tell docker to execute `wrap_algorithm()` when the image is run. This function
+# will ensure that the algorithm method is called properly.
+CMD python -c "from vantage6.algorithm.tools.wrap import wrap_algorithm; wrap_algorithm()"

LICENSE

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+MIT License
+
+Copyright (c)  
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+
+# v6-summary-py
+
+Create a summary of the data (mean, range, variance, length, ...)
+
+This algorithm is designed to be run with the [vantage6](https://vantage6.ai)
+infrastructure for distributed analysis and learning.
+
+The base code for this algorithm has been created via the
+[v6-algorithm-template](https://github.com/vantage6/v6-algorithm-template)
+template generator.
+
+### Checklist
+
+Note that the template generator does not create a completely ready-to-use
+algorithm yet. There are still a number of things you have to do yourself.
+Please ensure to execute the following steps. The steps are also indicated with
+TODO statements in the generated code - so you can also simply search the
+code for TODO instead of following the checklist below.
+
+- [ ] Include a URL to your code repository in setup.py.
+- [ ] Implement your algorithm functions.
+  - [ ] You are free to add more arguments to the functions. Be sure to add them
+    *after* the `client` and dataframe arguments.
+  - [ ] When adding new arguments, if you run the `test/test.py` script, be sure
+    to include values for these arguments in the `client.task.create()` calls
+    that are available there.
+- [ ] If you are using Python packages that are not in the standard library, add
+  them to the `requirements.txt` and `setup.py` file.
+- [ ] Fill in the documentation template. This will help others to understand your
+  algorithm, be able to use it safely, and to contribute to it.
+- [ ] If you want to submit your algorithm to a vantage6 algorithm store, be sure
+  to fill in everything in ``algorithm_store.json`` (and be sure to update
+  it if you change function names, arguments, etc.).
+- [ ] Create a ``DOCKER_USER`` and ``DOCKER_PASSWORD`` secret in the GitHub repository
+  settings. This will be used to push the Docker image to the registry in the github
+  pipeline.
+- [ ] Finally, remove this checklist section to keep the README clean.
+
+### Dockerizing your algorithm
+
+To finally run your algorithm on the vantage6 infrastructure, you need to
+create a Docker image of your algorithm.
+
+#### Automatically
+
+The easiest way to create a Docker image is to use the GitHub Actions pipeline to
+automatically build and push the Docker image. All that you need to do is push a
+commit to the ``main`` branch.
+
+#### Manually
+
+A Docker image can be created by executing the following command in the root of your
+algorithm directory:
+
+```bash
+docker build -t [my_docker_image_name] .
+```
+
+where you should provide a sensible value for the Docker image name. The
+`docker build` command will create a Docker image that contains your algorithm.
+You can create an additional tag for it by running
+
+```bash
+docker tag [my_docker_image_name] [another_image_name]
+```
+
+This way, you can e.g. do
+`docker tag local_average_algorithm harbor2.vantage6.ai/algorithms/average` to
+make the algorithm available on a remote Docker registry (in this case
+`harbor2.vantage6.ai`).
+
+Finally, you need to push the image to the Docker registry. This can be done
+by running
+
+```bash
+docker push [my_docker_image_name]
+```
+
+Note that you need to be logged in to the Docker registry before you can push
+the image. You can do this by running `docker login` and providing your
+credentials. Check [this page](https://docs.docker.com/get-started/04_sharing_app/)
+For more details on sharing images on Docker Hub. If you are using a different
+Docker registry, check the documentation of that registry and be sure that you
+have sufficient permissions.

algorithm_store.json

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+{
+  "name": "v6-summary-py",
+  "image": "harbor2.vantage6.ai/algorithms/v6-summary-py",
+  "vantage6_version": "4.3",
+  "partitioning": "horizontal",
+  "functions": [
+    {
+      "name": "summary",
+      "description": "Create a summary of the data (mean, range, variance, length, ...)",
+      "type": "central",
+      "databases": [],
+      "arguments": [
+        {
+          "name": "columns",
+          "type": "",
+          "description": ""
+        },
+        {
+          "name": "organizations_to_include",
+          "type": "",
+          "description": ""
+        }
+      ]
+    },
+    {
+      "name": "summary_per_data_station",
+      "description": "",
+      "type": "federated",
+      "databases": [
+        {
+          "name": "Database 1"
+        }
+      ],
+      "arguments": [
+        {
+          "name": "columns",
+          "type": "",
+          "description": ""
+        }
+      ]
+    }
+  ]
+}

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+livehtml:
+	sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

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+# Documentation of v6-summary-py
+
+### How to run this documentation locally
+
+```bash
+
+# Install the required packages
+pip install -r requirements.txt
+
+# Build the documentation
+make html
+
+# Run a local service to view the documentation that updates when you make changes
+make livehtml
+```
+
+### How to publish the documentation
+
+View the instructions from [Sphinx](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/read-the-docs.html)