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mantheymanthey
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Move to Girder 3.
Move HistomicsTK server components to this repo. The default ui has moved from /histomicstk to /histomics. Individual deployments can mount this at other locations. Because we now use the girder-3 branch of slicer_cli_web, the cli access settings are no longer necessary. The docker cli endpoints are only present in slicer_cli_web. Where appropriate, references have been changed from HistomicsTK to Digital Slide Archive. This removes the options to ingest from tcga-data.nci.nih.gov, as that has not been served in a compatible manner in a long time. Still needed: - Add a test that includes using a docker CLI. This will require appropriate infrastructure for starting girder_worker and running docker containers. - Add a test to ensure that local paths are used within the CLI test. - Add deployment to pypi on successful builds - Migrate appropriate docs from HistomicsTK
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‎.circleci/config.yml‎

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version: 2
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jobs:
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build:
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working_directory: ~/project
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docker:
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- image: zachmullen/tox-and-node
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- image: memcached
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- image: circleci/mongo:4.0-ram
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- image: rabbitmq
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steps:
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- checkout
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- run:
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name: Preinstall phantomjs to work around an npm permission issue
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command: npm install -g phantomjs-prebuilt --unsafe-perm
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- run:
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name: Run tests via tox
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# Piping through cat does less buffering of the output but can
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# consume the exit code
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command: tox | cat; test ${PIPESTATUS[0]} -eq 0
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- run:
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name: Install Codecov client
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command: pip install codecov
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- run:
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name: Upload coverage
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# Retry as codecov can be flaky
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command: for i in $(seq 1 10); do [ %i -gt 1 ] && echo "retrying $i" && sleep 5; codecov --required --disable search pycov gcov --root project --file build/test/coverage/py_coverage.xml build/test/coverage/cobertura-coverage.xml && s=0 && break || s=$?; done; (exit $s)
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release:
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docker:
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- image: circleci/python:3.7
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steps:
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- checkout
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- deploy:
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name: Run tests via tox
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# Piping through cat does less buffering of the output but can
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# consume the exit code
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command: tox -e release | cat; test ${PIPESTATUS[0]} -eq 0
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workflows:
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version: 2
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ci:
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jobs:
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- build:
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filters:
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tags:
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only: /^v.*/
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- release:
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requires:
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- build
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filters:
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tags:
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only: /^v.*/
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branches:
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only: master

‎.editorconfig‎

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root = true
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[*]
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indent_style = space
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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charset = utf-8
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[*.py]
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indent_size = 4
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max_line_length = 100
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[*.js]
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indent_size = 4
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[*.json]
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indent_size = 4
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[*.pug]
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indent_size = 2
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[*.styl]
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indent_size = 2
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[*.yml]
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indent_size = 2

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# pyenv
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.python-version
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# dotenv
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.env
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# virtualenv
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.venv
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venv/
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ENV/
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node_modules/
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tests/externaldata

‎.travis.yml‎

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sudo: false
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dist: xenial
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language: python
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python:
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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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services:
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- mongodb
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install:
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- pip install --upgrade pip
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- pip install --upgrade virtualenv
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- pip install tox-travis
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script:
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# Piping through cat does less buffering of the output but can consume the
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# exit code
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# Deselect the test_conversion tests, as the virtualenv travis uses fails
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# to import pyvips with an error
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# "OSError: dlopen: cannot load any more object with static TLS"
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- tox | cat; test ${PIPESTATUS[0]} -eq 0
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after_success:
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- pip install codecov
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- codecov --disable search pycov gcov --file .tox/coverage/py_coverage.xml build/test/coverage/cobertura-coverage.xml

‎LICENSE‎

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Apache Software License 2.0
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Copyright (c) 2019, Kitware, Inc.
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.

‎MANIFEST.in‎

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include LICENSE
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include README.rst
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include setup.py
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graft histomicsui
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graft docs
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prune test
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global-exclude *.py[co] *.cmake __pycache__ node_modules

‎README.rst‎

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===========
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HistomicsUI
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===========
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Organize, visualize, and analyze histology images.
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`HistomicsUI`_ organizes and managed whole slide image (WSI) files using Girder_. It has a dedicated interface to select WSI, add annotations manually, and to run analysis and algorithms on all or parts of images.
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Girder provides authentication, access control, and diverse storage options, including using local file systems and Amazon S2. WSI images are read and displayed via the large_image_ module. Algorithms are containerized using Docker_ and are run using the slicer_cli_web_ Girder plugin. These can be run on multiple worker machines via `Girder Worker`_ and celery_.
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A set of common algorithms are provided by HistomicsTK_.
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Installation
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------------
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Linux
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=====
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In linux with Python 2.7, Python 3.5, 3.6, or 3.7:
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Prerequisites:
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- MongoDB must be installed and running.
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- An appropriate version of Python must be installed.
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.. code-block:: bash
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pip install histomicsui --find-links https://girder.github.io/large_image_wheels
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girder build
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girder serve
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To use Girder Worker:
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.. code-block:: bash
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pip install girder_slicer_cli_web[worker]
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GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1
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The first time you start HistomicsUI, you'll also need to configure Girder with at least one user and one assetstore (see the Girder_ documentation). Additionally, it is recommended that you install the HistomicsTK_ algorithms. This can be done going to the Admin Console, Plugins, Slicer CLI Web settings. Set a default task upload folder, then import the `dsarchive/histomicstk:latest` docker image.
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Reference Deployment
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====================
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The standard deployment of HistomicsUI is the `Digital Slide Archive`_. The associated repository has tools for readily installing via Docker, VirtualBox, or shell scripts on Ubuntu.
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Funding
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-------
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This work is funded in part by the NIH grant U24-CA194362-01_.
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.. _HistomicsUI: https://github.com/DigitalSlideArchive/HistomicsUI
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.. _Docker: https://www.docker.com/
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.. _Kitware: https://www.kitware.com/
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.. _U24-CA194362-01: http://grantome.com/grant/NIH/U24-CA194362-01
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.. _Girder: http://girder.readthedocs.io/en/latest/
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.. _Girder Worker: https://girder-worker.readthedocs.io/en/latest/
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.. _large_image: https://github.com/girder/large_image
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.. _slicer_cli_web: https://github.com/girder/slicer_cli_web
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.. _slicer execution model: https://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
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.. _Discourse forum: https://discourse.girder.org/c/histomicstk
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.. _Gitter Chatroom: https://gitter.im/DigitalSlideArchive/HistomicsTK?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
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.. _celery: http://www.celeryproject.org/
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.. _HistomicsTK: https://github.com/DigitalSlideArchive/HistomicsTK
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.. _Digital Slide Archive: https://github.com/DigitalSlideArchive/digital_slide_archive
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‎codecov.yml‎

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comment: false
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coverage:
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status:
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# We have some variation in tests due to variations in the test runs. We
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# want to ignore these changes, but not let code coverage slip too much.
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project:
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default:
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threshold: 1
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# This applies to the changed code. We allow it to be much less covered
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# than the main code, since we use the project threshold for that.
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patch:
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default:
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threshold: 25
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only_pulls: true
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