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🔖 Release v0.5.0 (#33)
2 parents 9be16ca + 9d4191f commit 7957098

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‎.github/workflows/pythonpublish.yml

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on:
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release:
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types: [created, edited, published, released]
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types: [published]
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jobs:
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deploy:

‎.github/workflows/test_cpac.yml

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strategy:
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matrix:
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platform: [docker, singularity]
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tag: [latest, dev-v1.8]
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platform: [docker]
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tag: [latest, nightly]
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go: [1.14]
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python: [3.6, 3.7, 3.8]
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python: [3.7, 3.8, 3.9, "3.10"]
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singularity: [3.6.4]
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steps:
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run: python -m pip install --upgrade pip setuptools wheel
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- name: Set up Singularity
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if: ${{ matrix.platform == 'singularity' }}
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uses: eWaterCycle/setup-singularity@v5
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uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: ${{ matrix.singularity }}
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- name: Prepare Singularity cache and tmp directories
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if: ${{ matrix.platform == 'singularity' }}
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run: mkdir -p ${SINGULARITY_CACHEDIR} && mkdir -p ${SINGULARITY_TMPDIR}
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- name: Install dependencies
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run: |
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sudo apt-get install libarchive-dev \
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libffi-dev \
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flawfinder \
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libgpgme11-dev \
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libseccomp-dev \
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squashfs-tools \
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libssl1.1 libssl-dev \
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libuuid1 uuid-dev
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sudo apt-get install libffi-dev \
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flawfinder \
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libgpgme11-dev \
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libseccomp-dev \
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squashfs-tools \
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libssl1.1 libssl-dev \
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libuuid1 uuid-dev
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pip install -r requirements.txt
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pip install -r requirements-dev.txt
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pip install coverage coveralls nipype
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- name: Install cpac
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run: cd $GITHUB_WORKSPACE && pip install -e .
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- name: Test cpac, platform and tag specified
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run: |
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coverage run --append -m pytest --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
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coverage report -m
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- name: Test cpac, platform specified, tag unspecified
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if: ${{ matrix.tag == 'latest' }}
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run: |
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coverage run --append -m pytest --doctest-modules --platform ${{ matrix.platform }} .
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} .
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coverage report -m
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- name: Test cpac, platform unspecified, tag specified
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if: ${{ matrix.platform == 'docker' }}
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run: |
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coverage run --append -m pytest --doctest-modules --tag ${{ matrix.tag }} .
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --tag ${{ matrix.tag }} .
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coverage report -m
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- name: Test cpac, platform and tag unspecified
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if: ${{ matrix.platform == 'docker' }} && ${{ matrix.tag }} == 'latest'
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run: |
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coverage run --append -m pytest --doctest-modules .
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules .
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coverage report -m
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- name: Report coverage
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uses: AndreMiras/coveralls-python-action@v20201129
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Install cpac
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run: cd $GITHUB_WORKSPACE && pip install .
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- name: Configure Git credentials

‎.gitignore

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.cache/*
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.*.swp
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*/.ipynb_checkpoints/*
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tmp
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# Project files
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.ropeproject
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.venv*/
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# Singularity Images
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**/*.simg
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**/*.simg
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**/*.sif

‎CHANGELOG.rst

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=========
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Changelog
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=========
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`Version 0.5.0: Parse Resources <https://github.com/FCP-INDI/cpac/releases/tag/v0.5.0>`_
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================================================================================================
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* 🧮 Evaluates memory usage for specific nodes from ``callback.log`` files
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* ✨ Adds ``enter`` command to enter a container's ``BASH``
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* ✨ Adds ``version`` command to give version of in-container C-PAC
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* ✨ Adds ``parse-resources`` command to parse resources from ``callback.log``
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* 🐛 Fixes issue where ``--version`` command was not working
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* 🐛 Fixes issue where custom pipeline configurations were not binding to temporary container prior to checking for bind paths
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* ✅ Updates for tests that were failing
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* 📝 Add known issues to usage string
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* ⬆ Require Python ≥ 3.7 (for typing annotations)
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* 📝 Documents support for Singularity 3
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`Version 0.4.0: Goodbye Singularity Hub <https://github.com/FCP-INDI/cpac/releases/tag/v0.4.0>`_
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================================================================================================
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* 👽 Drop call to now-deprecated Singularity Hub

‎README.rst

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Dependencies
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============
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* `Python <https://www.python.org>`_ ≥3.6
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* `Python <https://www.python.org>`_ ≥3.7
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* `pip <https://pip.pypa.io>`_
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* At least one of:
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* `Docker <https://www.docker.com>`_
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* `Singularity <https://sylabs.io/singularity>`_ ≥2.5&≤3.0
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* `Singularity <https://sylabs.io/singularity>`_ ≥2.5
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Usage
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=====
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usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
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[--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
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[--working_dir PATH] [-v] [-vv]
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{run,group,utils,pull,upgrade,crash} ...
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{run,utils,version,group,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
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...
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cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images.
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cpac run --help
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Known issues:
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- Some Docker containers unexpectedly persist after cpac finishes. To clear them, run
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1. `docker ps` to list the containers
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For each C-PAC conatainer that persists, run
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2. `docker attach <container_name>`
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3. `exit`
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- https://github.com/FCP-INDI/cpac/issues
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positional arguments:
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{run,group,utils,pull,upgrade,crash}
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{run,utils,version,group,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
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run Run C-PAC. See
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"cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] run --help"
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for more information.
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utils Run C-PAC commandline utilities. See
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"cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] utils --help"
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for more information.
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version Print the version of C-PAC that cpac is using.
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group Run a group level analysis in C-PAC. See
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"cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] group --help"
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for more information.
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pull (upgrade) Upgrade your local C-PAC version to the latest version
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by pulling from Docker Hub or other repository.
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Use with "--image" and/or "--tag" to specify an image
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other than the default "fcpindi/c-pac:latest" to pull.
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enter (bash, shell)
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Enter a new C-PAC container via BASH.
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parse-resources (parse_resources)
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When provided with a `callback.log` file, this utility can sort through
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the memory `runtime` usage, `estimate`, and associated `efficiency`, to
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identify the `n` tasks with the `highest` or `lowest` of each of these
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categories.
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"parse-resources" is intended to be run outside a C-PAC container.
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See "cpac parse-resources --help" for more information.
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crash Convert a crash pickle to plain text (C-PAC < 1.8.0).
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optional arguments:
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-h, --help show this help message and exit

‎requirements.txt

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docker >= 4.2.1
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dockerpty
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docker-pycreds
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pandas >= 0.23.4
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pyyaml
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setuptools
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spython >= 0.0.81
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tabulate >= 0.8.6
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tornado
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websocket-client
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websocket-client
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rich

‎setup.cfg

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Operating System :: OS Independent
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Programming Language :: Python :: 3
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Topic :: Scientific/Engineering :: Bio-Informatics
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version = 0.4.0
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version = 0.5.0
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[options]
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zip_safe = False
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pyyaml
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install_requires =
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docker
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dockerpty
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docker-pycreds
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pandas >= 0.23.4
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spython >= 0.0.81
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pyyaml
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rich
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tabulate >= 0.8.6
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tornado
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websocket-client
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python_requires = >=3.6
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python_requires = >=3.7
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[options.packages.find]
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where = src

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