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Löffler, Hannes
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Release 0.7.1
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‎.github/pull_request_template.md‎

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### Description
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### Checklist
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If you're providing a new node for maize, please make sure of the following:
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- [ ] My node has been placed in an appropriate subfolder, and exposed in the corresponding `__init__.py` file
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- [ ] My node has tests (using `TestRig`, and testing a variety of inputs and parameters)
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- [ ] My node is fully documented using [ReST syntax](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html) and references if neccessary
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- [ ] My code passes type-checking using `mypy --strict --explicit-package-bases`
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- [ ] My code lints correctly
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- [ ] My code has been formatted with `black`, using a `line-length` of 100

‎.github/workflows/mypy.yml‎

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name: Mypy
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on: [push, workflow_dispatch]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
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bash -s -- --batch
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conda env create -f env-dev.yml
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conda run --name maize-dev pip install --no-deps .
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conda run --name maize-dev pip install types-PyYAML types-toml
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- name: Analysing the code with mypy
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run: |
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conda run --name maize-dev mypy --strict --explicit-package-bases maize/steps maize/utilities

‎.github/workflows/pylint.yml‎

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name: Pylint
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on: [push, workflow_dispatch]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
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bash -s -- --batch
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conda env create -f env-dev.yml
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conda run --name maize-dev pip install --no-deps .
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- name: Analysing the code with pylint
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run: |
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conda run --name maize-dev pylint --exit-zero maize/steps maize/utilities

‎.github/workflows/singularity.yml‎

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name: singularity
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on:
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push:
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# Edit the branches here if you want to change deploy behavior
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branches:
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- main
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- master
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# Do the builds on all pull requests (to test them)
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pull_request: []
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jobs:
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build-test-containers:
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runs-on: ubuntu-latest
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strategy:
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# Keep going on other deployments if anything bloops
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fail-fast: false
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matrix:
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changed_file:
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- devtools/singularity.def
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singularity_version:
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- '3.8.1'
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container:
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image: quay.io/singularity/singularity:v${{ matrix.singularity_version }}
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options: --privileged
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name: check
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steps:
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- name: Check out code for the container builds
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uses: actions/checkout@v2
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- name: Continue if Singularity Recipe
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run: |
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# Continue if we have a changed Singularity recipe
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if [[ "${{ matrix.changed_file }}" = *Singularity* ]]; then
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echo "keepgoing=true" >> $GITHUB_ENV
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fi
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- name: Build Container
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if: ${{ env.keepgoing == 'true' }}
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env:
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recipe: ${{ matrix.changed_file }}
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run: |
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ls
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sudo -E singularity build maize.sif devtools/singularity.def
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tag=$(echo "${recipe/Singularity\./}")
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if [ "$tag" == "Singularity" ]; then
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tag=latest
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fi
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# Build the container and name by tag
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echo "Tag is $tag."
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echo "tag=$tag" >> $GITHUB_ENV
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- name: Login and Deploy Container
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if: (github.event_name != 'pull_request')
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env:
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keepgoing: ${{ env.keepgoing }}
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run: |
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if [[ "${keepgoing}" == "true" ]]; then
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echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
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singularity push maize.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${tag}
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fi

‎.github/workflows/sonar-scan.yml‎

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name: sonarqube
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on: [push, workflow_dispatch]
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jobs:
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sonar_setup:
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uses: azu-enterprise/action-sonar-auto-enrol/.github/workflows/sonar-auto-enrol.yml@main
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with:
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project_key: ${{ github.event.repository.name }}
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sonarqube_url: "https://sonarqube.astrazeneca.com"
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secrets:
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sq_token: ${{ secrets.SQ_TOKEN }}

‎.github/workflows/test-docking.yml‎

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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name: Test-docking
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on:
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push:
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branches: [ "master" ]
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pull_request:
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branches: [ "master" ]
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
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bash -s -- --batch
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conda env create -v -f env-dev.yml
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conda run --name maize-dev pip install --no-deps .
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conda run --name maize-dev ./devtools/install_test_deps.sh
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- name: Run docking test with pytest
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run: |
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conda run --name maize-dev pytest tests/test_docking.py

‎.gitignore‎

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.ipynb_checkpoints
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.VSCodeCounter
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__pycache__
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*.egg-info
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.coverage
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.vscode
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.pylintrc
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.env
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.*_cache
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*_autosummary
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coverage
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docs/_build
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docs/_static
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docs/autosummary
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docs/Makefile
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docs/make.bat
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/test-config.toml
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test
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testing.ipynb
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deplicenses.txt
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build

‎.sonarlint/connectedMode.json‎

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{
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"sonarQubeUri": "https://sonarqube.astrazeneca.com",
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"projectKey": "maize-contrib"
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}

‎AUTHORS.md‎

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Primary Authors
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===============
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- [Thomas Löhr](https://github.com/tlhr)
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- Marco Klähn
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Contributing Authors
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====================
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- Michele Assante
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- Lili Cao
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- Michael Dodds
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- Jon Paul Janet
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- Mikhail Kabeshov
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- Alessandro Tibo

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