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‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: bug
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**To Reproduce**
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Steps to reproduce the behavior:
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**Computational environment**
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- OS: [e.g., Windows 10]
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- Python version [e.g., 3.8]
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- DendroPy version [e.g., 4.6.1]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: enhancement
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is.
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/workflows/ci.yaml

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name: ci
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on: [push, pull_request]
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on: [push, pull_request, workflow_dispatch]
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jobs:
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examples:
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Refresh Package Sources
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run: |
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal main restricted universe multiverse" > /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-updates main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-security main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-backports main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.canonical.com/ubuntu focal partner" >> /etc/apt/sources.list'
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sudo apt-get update -y
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- name: Install dependencies
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run: |
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sudo apt-get install libpython2.7 # required by paup
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sudo apt-get install aptitude
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sudo aptitude install -y gcc-7 g++-7 gfortran-7
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sudo apt-get install -y libpython2.7 # required by paup
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python -m pip install --upgrade pip
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- name: Install paup
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run: |
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temp_dir=$(mktemp -d)
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wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz
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gunzip ${temp_dir}/paup4a168_ubuntu64.gz
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chmod +x ${temp_dir}/paup4a168_ubuntu64
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sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup
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wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
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gunzip ${temp_dir}/paup4a169_ubuntu64.gz
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chmod +x ${temp_dir}/paup4a169_ubuntu64
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sudo mv ${temp_dir}/paup4a169_ubuntu64 /usr/local/bin/paup
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echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
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- name: Install dendropy
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run: |
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fail-fast: False
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matrix:
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python-version:
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- "2.7"
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- "3.5"
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- "3.6"
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- "3.7"
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- "3.8"
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continue-on-error: true
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with:
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python-version: ${{ matrix.python-version }}
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- name: Refresh Package Sources
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run: |
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal main restricted universe multiverse" > /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-updates main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-security main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-backports main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.canonical.com/ubuntu focal partner" >> /etc/apt/sources.list'
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sudo apt-get update -y
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt-get install python2 libpython2.7 # required by paup
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sudo apt-get install aptitude
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sudo aptitude install -y gcc-7 g++-7 gfortran-7
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sudo apt-get install -y libpython2.7 # required by paup
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python -m pip install --upgrade pip
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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if [ -f .github/workflows/requirements.txt ]; then pip install -r .github/workflows/requirements.txt; fi
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- name: Install paup
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run: |
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temp_dir=$(mktemp -d)
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wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz
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gunzip ${temp_dir}/paup4a168_ubuntu64.gz
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chmod +x ${temp_dir}/paup4a168_ubuntu64
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sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup
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wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
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gunzip ${temp_dir}/paup4a169_ubuntu64.gz
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chmod +x ${temp_dir}/paup4a169_ubuntu64
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sudo mv ${temp_dir}/paup4a169_ubuntu64 /usr/local/bin/paup
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echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
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- name: Python2 compatibility workaround # TODO remove when Python2 compatibility dropped
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if: matrix.python-version == '2.7'
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- name: Unit tests with setup.py
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run: |
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python setup.py pytest --addopts '-m "not smoke"'
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- name: Smoke tests with setup.py
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run: |
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python setup.py pytest --addopts "-m smoke"
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entrypoints:
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runs-on: ubuntu-20.04
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strategy:
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fail-fast: False
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matrix:
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python-version:
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- "3.6"
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- "3.7"
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- "3.8"
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- "3.9"
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- "3.10"
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- "3.11"
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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@v4
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continue-on-error: true
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with:
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python-version: ${{ matrix.python-version }}
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- name: Refresh Package Sources
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run: |
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rm tests/dendropy
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curl --silent --show-error --retry 5 https://bootstrap.pypa.io/pip/2.7/get-pip.py | sudo python2
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python2 -m pip install setuptools --upgrade
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python2 setup.py test
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- name: Test with setup.py
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if: matrix.python-version != '2.7'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal main restricted universe multiverse" > /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-updates main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-security main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-backports main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.canonical.com/ubuntu focal partner" >> /etc/apt/sources.list'
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sudo apt-get update -y
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- name: Install dependencies
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run: |
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python setup.py test
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sudo apt-get install aptitude
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sudo aptitude install -y gcc-7 g++-7 gfortran-7
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sudo apt-get install libpython2.7 # required by paup
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python -m pip install --upgrade pip
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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python -m pip install .
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- name: Test sumtrees
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run: |
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which sumtrees
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sumtrees --help
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sumtrees 2>&1 | grep sumtrees || exit 1
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- name: Test sumlabels
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run: |
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which sumlabels
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sumlabels --help
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sumlabels 2>&1 | grep sumlabels || exit 1
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- name: Test dendropy-format
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run: |
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which dendropy-format
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dendropy-format --help
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dendropy-format 2>&1 | grep dendropy-format || exit 1
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- name: Test deprecated entrypoints
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run: |
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which sumtrees.py
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sumtrees.py --help
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sumtrees.py 2>&1 | grep sumtrees.py || exit 1
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which sumlabels.py
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sumlabels.py --help
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sumlabels.py 2>&1 | grep sumlabels.py || exit 1
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coverage:
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runs-on: ubuntu-20.04
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steps:
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uses: actions/setup-python@master
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python-version: 3.8
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- name: Install paup
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- name: Refresh Package Sources
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run: |
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sudo apt-get install libpython2.7 # required by paup
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal main restricted universe multiverse" > /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-updates main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-security main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.ubuntu.com/ubuntu focal-backports main restricted universe multiverse" >> /etc/apt/sources.list'
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sudo sh -c 'echo "deb http://archive.canonical.com/ubuntu focal partner" >> /etc/apt/sources.list'
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sudo apt-get update -y
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- name: Install dependencies
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run: |
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sudo apt-get install aptitude
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sudo aptitude install -y gcc-7 g++-7 gfortran-7
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sudo apt-get install -y libpython2.7 # required by paup
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python -m pip install --upgrade pip
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temp_dir=$(mktemp -d)
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wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz
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gunzip ${temp_dir}/paup4a168_ubuntu64.gz
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chmod +x ${temp_dir}/paup4a168_ubuntu64
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sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup
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wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
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gunzip ${temp_dir}/paup4a169_ubuntu64.gz
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chmod +x ${temp_dir}/paup4a169_ubuntu64
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sudo mv ${temp_dir}/paup4a169_ubuntu64 /usr/local/bin/paup
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echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
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- name: Install coverage dependencies
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run: |
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python3 -m pip install pytest
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python3 -m pip install pytest-cov
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- name: Generate coverage report
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run: |
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python3 -m pytest tests --cov=tests/dendropy --cov-report=xml
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- uses: codecov/codecov-action@v3
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python3 -m pytest tests/unittests --cov=tests --cov-report=xml
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- uses: codecov/codecov-action@v4
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with:
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token: ae13d715-bae4-4e6d-9dce-f47e7d7c7c01
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flags: unittests # optional
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fail_ci_if_error: true # optional (default = false)
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verbose: true # optional (default = false)
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run: |
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find . -type f -name '*.py' -exec rm {} \;
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python3 -c "import dendropy; print(dendropy.__version__)"
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docs:
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permissions:
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contents: write
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Set up Python 3.9
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uses: actions/setup-python@v4
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continue-on-error: true
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with:
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python-version: 3.9
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- name: Upgrade pip
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run: python3 -m pip install pip --upgrade
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- name: Install from source
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run: python3 -m pip install .
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- name: Install documentation build dependencies
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run: python3 -m pip install -r docs/requirements.txt
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- name: Build documentation
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run: make -C docs html
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- name: Deploy docs
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if: github.ref == 'refs/heads/main'
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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folder: docs/build/html # The folder the action should deploy.
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# uses: jsmrcaga/[email protected]
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# with:
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# NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
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# NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
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# NETLIFY_DEPLOY_MESSAGE: "Prod deploy v${{ github.ref }}"
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# NETLIFY_DEPLOY_TO_PROD: true
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# install_command: "echo Skipping installing the dependencies"
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# build_command: "echo Skipping building the web files"
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# build_directory: docs/build/html
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deploy:
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/v')
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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paper:
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runs-on: ubuntu-latest
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: joss/paper.md
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- name: Upload
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uses: actions/upload-artifact@v4
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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path: joss/paper.pdf

‎.github/workflows/requirements.in

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pytest==7.0.1
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iniconfig==1.1.1
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pluggy==1.0.0
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packaging==21.3
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tomli==1.2.3
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importlib-metadata==4.8.3
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typing-extensions==4.1.1
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zipp==3.6.0

‎.github/workflows/requirements.txt

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#
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# This file is autogenerated by pip-compile
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# To update, run:
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#
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# pip-compile --output-file requirements.txt requirements.in
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#
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attrs==22.2.0 # via pytest
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importlib-metadata==4.8.3
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iniconfig==1.1.1
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packaging==21.3
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pluggy==1.0.0
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py==1.11.0 # via pytest
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pyparsing==3.1.1 # via packaging
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pytest==7.0.1
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tomli==1.2.3
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typing-extensions==4.1.1
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zipp==3.6.0

‎.github/workflows/requirements37.in

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pytest

‎.github/workflows/requirements37.txt

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#
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# This file is autogenerated by pip-compile with Python 3.7
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# by the following command:
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#
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# pip-compile requirements.in
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#
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exceptiongroup==1.1.3
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# via pytest
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importlib-metadata==6.7.0
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# via
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# pluggy
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# pytest
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iniconfig==2.0.0
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# via pytest
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packaging==23.2
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# via pytest
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pluggy==1.2.0
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# via pytest
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pytest==7.4.3
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# via -r requirements.in
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tomli==2.0.1
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# via pytest
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typing-extensions==4.7.1
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# via importlib-metadata
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zipp==3.15.0
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# via importlib-metadata

‎.gitignore

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setup.cfg
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setuptools-*.egg
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__pycache__
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.eggs
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# PyCharm
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**/.idea

‎AUTHORS.rst

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Jeet Sukumaran <[email protected]>
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Mark T. Holder <[email protected]>
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- Jeet Sukumaran <[email protected]>
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- Mark T. Holder <[email protected]>
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- Matthew Andres Moreno <[email protected]>
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Find a comprehensive, up-to-date listing of project contributors `here <https://github.com/jeetsukumaran/DendroPy/graphs/contributors>`_.

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