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Merge pull request #108 from KohlbacherLab/develop
Release 4.0.0
2 parents 5a3a2c8 + b1cd7fe commit b694fd1

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‎.github/workflows/claude-code-review.yml‎

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name: Claude Code Review
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on:
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pull_request:
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types: [opened, synchronize, ready_for_review, reopened]
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# Optional: Only run on specific file changes
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# paths:
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# - "src/**/*.ts"
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# - "src/**/*.tsx"
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# - "src/**/*.js"
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# - "src/**/*.jsx"
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jobs:
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claude-review:
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# Optional: Filter by PR author
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# if: |
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# github.event.pull_request.user.login == 'external-contributor' ||
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# github.event.pull_request.user.login == 'new-developer' ||
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# github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
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runs-on: ubuntu-latest
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permissions:
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contents: read
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pull-requests: read
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issues: read
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id-token: write
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env:
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HAS_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN != '' }}
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steps:
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- name: Checkout repository
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if: env.HAS_TOKEN == 'true'
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uses: actions/checkout@v4
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with:
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fetch-depth: 1
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- name: Run Claude Code Review
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if: env.HAS_TOKEN == 'true'
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id: claude-review
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uses: anthropics/claude-code-action@v1
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with:
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claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
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plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
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plugins: 'code-review@claude-code-plugins'
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prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
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‎.github/workflows/claude.yml‎

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name: Claude Code
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on:
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issue_comment:
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types: [created]
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pull_request_review_comment:
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types: [created]
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issues:
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types: [opened, assigned]
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pull_request_review:
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types: [submitted]
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jobs:
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claude:
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if: |
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(github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
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(github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
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(github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
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(github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
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runs-on: ubuntu-latest
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permissions:
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contents: read
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pull-requests: read
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issues: read
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id-token: write
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actions: read # Required for Claude to read CI results on PRs
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 1
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- name: Run Claude Code
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id: claude
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uses: anthropics/claude-code-action@v1
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with:
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claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
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# This is an optional setting that allows Claude to read CI results on PRs
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additional_permissions: |
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actions: read
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# Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
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# prompt: 'Update the pull request description to include a summary of changes.'
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# Optional: Add claude_args to customize behavior and configuration
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# See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
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# or https://code.claude.com/docs/en/cli-reference for available options
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# claude_args: '--allowed-tools Bash(gh pr:*)'
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‎.github/workflows/pypi-publish.yml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.7
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uses: actions/setup-python@v4
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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python-version: 3.7
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python-version: '3.11'
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- name: Install pypa/build
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run: >-
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python -m

‎.github/workflows/python-test-conda-external.yml‎

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name: Unit tests external tools
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on:
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push:
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branches: [ main, develop ]
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pull_request:
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branches: [ main, develop ]
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branches: [ main, master ]
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jobs:
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tests-external:
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strategy:
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matrix:
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platform: [ubuntu-latest]
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python-version: [3.7]
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python-version: ['3.11', '3.12']
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runs-on: ${{ matrix.platform }}
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steps:
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working-directory: ./epytope-tools/
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run: |
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./post.runner
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- name: Set conda package directory
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run: |
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mkdir /tmp/condapkgs
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echo "CONDA_PKGS_DIRS=/tmp/condapkgs" >> $GITHUB_ENV
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- name: Activate epytope-tools
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run: |
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echo "$PWD/epytope-tools/bin" >> $GITHUB_PATH
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echo "PATH=$PATH"
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- name: Set up Python ${{ matrix.python-version }}
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run: |
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$CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" protobuf"<=3.20.1"
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- name: Activate conda environment
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run: |
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echo "/tmp/condaenv/bin" >> $GITHUB_PATH
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export PATH="/tmp/condaenv/bin:$PATH"
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: ${{ matrix.python-version }}
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activate-environment: test
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auto-activate-base: false
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- name: Install epytope
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shell: bash -el {0}
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run: |
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pip install ./epytope/
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- name: Set up test environment
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shell: bash -el {0}
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run: |
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conda install -p /tmp/condaenv -c conda-forge -c bioconda nose
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pip install pytest
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- name: Run Tests - Cleavage Prediction
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working-directory: ./epytope/
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shell: bash -el {0}
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continue-on-error: true
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run: nosetests -v epytope/test/external/TestExternalCleavagePrediction.py || echo "Cleavage Prediction" >> FAILED_TESTS
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run: pytest -v epytope/test/external/TestExternalCleavagePrediction.py || echo "Cleavage Prediction" >> FAILED_TESTS
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- name: Run Tests - Epitope Prediction
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working-directory: ./epytope/
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run: nosetests -v epytope/test/external/TestExternalEpitopePrediction.py || echo "Epitope Prediction" >> FAILED_TESTS
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shell: bash -el {0}
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run: pytest -v epytope/test/external/TestExternalEpitopePrediction.py || echo "Epitope Prediction" >> FAILED_TESTS
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- name: Validate Test Results
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working-directory: ./epytope/
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run: |

‎.github/workflows/python-test-conda.yml‎

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strategy:
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matrix:
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platform: [ubuntu-latest, macos-latest]
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python-version: [3.7]
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python-version: ['3.11', '3.12']
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runs-on: ${{ matrix.platform }}
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steps:
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- uses: actions/checkout@v4
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- name: Set conda package directory
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run: |
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mkdir /tmp/condapkgs
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echo "CONDA_PKGS_DIRS=/tmp/condapkgs" >> $GITHUB_ENV
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- name: Set up Python ${{ matrix.python-version }}
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run: |
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$CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" protobuf"<=3.20.1"
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- name: Activate conda environment
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run: |
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echo "/tmp/condaenv/bin" >> $GITHUB_PATH
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export PATH="/tmp/condaenv/bin:$PATH"
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: ${{ matrix.python-version }}
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activate-environment: test
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auto-activate-base: false
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- name: Install epytope
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shell: bash -el {0}
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run: |
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pip install .
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- name: Install Test dependencies
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run: conda install -p /tmp/condaenv -c conda-forge -c bioconda nose nose-exclude glpk
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shell: bash -el {0}
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run: |
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pip install pytest
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conda install -c conda-forge glpk
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- name: Run Tests
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run: nosetests --exclude-dir=epytope/test/external epytope
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shell: bash -el {0}
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run: pytest epytope/test/ --ignore=epytope/test/external -v

‎.readthedocs.yaml‎

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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.11"
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sphinx:
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configuration: epytope/doc/conf.py
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- docs

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v4.0.0 - Unreleased
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### `Added`
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- [#107](https://github.com/KohlbacherLab/epytope/pull/107) Added `EnsemblRESTAdapter` and `PyEnsemblAdapter` as drop-in replacements for `MartsAdapter` [#103](https://github.com/KohlbacherLab/epytope/issues/103) [#106](https://github.com/KohlbacherLab/epytope/issues/106)
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- Added MHCFlurry 2.0 predictor class
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### `Changed`
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- **BREAKING**: Minimum Python version raised to 3.11, build via `pyproject.toml`
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- **BREAKING**: Removed `mhcnuggets` predictors; `mhcflurry` is now optional (`pip install epytope[mhcflurry]`)
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- Full pandas 3.0 compatibility
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- Migrated CI to `pytest` with Python 3.11/3.12 matrix
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- [#107](https://github.com/KohlbacherLab/epytope/pull/107) Switched CI tests from `MartsAdapter` (BioMart) to `EnsemblRESTAdapter` (REST API) to eliminate flaky BioMart failures
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- [#107](https://github.com/KohlbacherLab/epytope/pull/107) Restricted external tool CI tests to PRs targeting `main`/`master` only
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### `Fixed`
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- Fixed `MartsAdapter` `KeyError` caused by inconsistent BioMart display-name headers
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- Fixed nondeterministic OptiTope results due to unordered set inputs to Pyomo
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## v3.4.0 - 2024-01-10
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### `Added`
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- [#93](https://github.com/KohlbacherLab/epytope/pull/93) Added NetMHCIIpan version 4.2 interface [#92](https://github.com/KohlbacherLab/epytope/issues/92)
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- [#96](https://github.com/KohlbacherLab/epytope/pull/96) Added NetMHCIIpan version 4.3 interface [#95](https://github.com/KohlbacherLab/epytope/issues/95)
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### `Changed`
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### `Fixed`
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- [#93](https://github.com/KohlbacherLab/epytope/pull/93) Fixed length restriction of NetMHCIIpan interfaces [#91](https://github.com/KohlbacherLab/epytope/issues/91)

‎README.md‎

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### Python Packages
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- pandas
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- pandas>=2.1
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- pyomo>=4.0
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- svmlight
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- PyMySQL
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- biopython
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- pyVCF
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- h5py<=2.10.0
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- PyVCF3
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- requests
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- beautifulsoup4
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### Third-Party Software (not installed through pip)
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- Assembly with spacers by [Schubert et al.](https://pubmed.ncbi.nlm.nih.gov/26813686/)
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- Epitope Prediction
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- [SYFPEITHI](https://link.springer.com/article/10.1007/s002510050595)
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- [MHCNuggets](https://pubmed.ncbi.nlm.nih.gov/31871119/) 2.0, 2.3.2
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- [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/29960884/) 1.2.2, 1.4.3
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- [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/29960884/) 1.2.2, 1.4.3, 2.0 (optional: `pip install epytope[mhcflurry]`)
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- [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0
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- [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3
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- [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1

‎epytope/CleavagePrediction/PSSM.py‎

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:return: Returns a :class:`~epytope.Core.Result.CleavageSitePredictionResult` object
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:rtype: :class:`~epytope.Core.Result.CleavageSitePredictionResult`
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"""
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return super(PCM, self).predict(peptides, lenght=length, **kwargs)
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return super().predict(peptides, lenght=length, **kwargs)
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class ProteaSMMConsecutive(APSSMCleavageSitePredictor):
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:return: Returns a :class:`~epytope.Core.Result.CleavageSitePredictionResult` object
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"""
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return super(ProteaSMMConsecutive, self).predict(peptides, length=length, **kwargs)
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return super().predict(peptides, length=length, **kwargs)
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class ProteaSMMImmuno(APSSMCleavageSitePredictor):
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"""
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return super(ProteaSMMImmuno, self).predict(peptides, length=length, **kwargs)
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return super().predict(peptides, length=length, **kwargs)
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class APSSMCleavageFragmentPredictor(ACleavageFragmentPrediction):
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Implements predict functionality
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"""
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@abc.abstractproperty
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@property
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@abc.abstractmethod
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def trailingN(self):
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"""
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The number of trailing residues at the N-terminal of the peptide used for prediction
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"""
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raise NotImplementedError
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@abc.abstractproperty
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@property
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@abc.abstractmethod
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def tralingC(self):
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"""
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