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smoiasmoia
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Merge pull request #39 from kristinazvolanek/switch_ci
Update CircleCI configuration, add pre-commit
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‎.circleci/config.yml‎

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# Python CircleCI 2.1 configuration file
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#
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#
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#
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# Use the latest 2.1 version of CircleCI pipeline process engine.
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# See: https://circleci.com/docs/2.0/configuration-reference
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version: 2.1
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orbs:
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codecov: codecov/[email protected]
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jobs:
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makeenv_37:
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docker:
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- image: continuumio/miniconda3
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working_directory: /tmp/src/phys2denoise
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steps:
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- checkout
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- persist_to_workspace:
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root: /tmp
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paths:
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- src/phys2denoise
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- restore_cache:
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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- run:
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name: Generate environment
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command: |
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if [[ -e /opt/conda/envs/py36_env ]]; then
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echo "Restoring environment from cache"
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source activate phys2denoise_py37
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else
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conda create -yq -n phys2denoise_py37 python=3.7
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source activate phys2denoise_py37
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pip install -e ".[test,doc]"
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fi
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- save_cache:
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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paths:
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- /opt/conda/envs/phys2denoise_py37
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unittest_36:
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docker:
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- image: continuumio/miniconda3
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working_directory: /tmp/src/phys2denoise
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steps:
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- checkout
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- restore_cache:
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key: conda-py36-v1-{{ checksum "setup.cfg" }}
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- run:
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name: Generate environment
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command: |
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apt-get install -yqq make
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if [ ! -d /opt/conda/envs/phys2denoise_py36 ]; then
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conda create -yq -n phys2denoise_py36 python=3.6
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source activate phys2denoise_py36
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pip install -e ".[test]"
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fi
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- run:
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name: Running unit tests
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command: |
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source activate phys2denoise_py36
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make unittest
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mkdir /tmp/src/coverage
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mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.py36
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- save_cache:
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key: conda-py36-v1-{{ checksum "setup.cfg" }}
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paths:
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- /opt/conda/envs/phys2denoise_py36
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- persist_to_workspace:
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root: /tmp
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paths:
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- src/coverage/.coverage.py36
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unittest_37:
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docker:
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- image: continuumio/miniconda3
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working_directory: /tmp/src/phys2denoise
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steps:
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- checkout
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- restore_cache:
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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- run:
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name: Running unit tests
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command: |
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apt-get install -y make
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source activate phys2denoise_py37 # depends on makeenv_37
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make unittest
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mkdir /tmp/src/coverage
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mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.py37
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- persist_to_workspace:
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root: /tmp
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paths:
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- src/coverage/.coverage.py37
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# Orbs are reusable packages of CircleCI configuration that you may share across projects, enabling you to create encapsulated, parameterized commands, jobs, and executors that can be used across multiple projects.
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# See: https://circleci.com/docs/2.0/orb-intro/
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orbs:
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# The python orb contains a set of prepackaged CircleCI configuration you can use repeatedly in your configuration files
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# Orb commands and jobs help you with common scripting around a language/tool
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# so you dont have to copy and paste it everywhere.
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# See the orb documentation here: https://circleci.com/developer/orbs/orb/circleci/python
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python: circleci/[email protected]
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codecov: codecov/[email protected]
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integrationtest_36:
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# Define a job to be invoked later in a workflow.
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# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
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jobs:
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test37: # This is the name of the job, feel free to change it to better match what you're trying to do!
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# These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/
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# You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub
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# A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
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# The executor is the environment in which the steps below will be executed - below will use a python 3.6.14 container
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# Change the version below to your required version of python
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docker:
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- image: continuumio/miniconda3
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- image: cimg/python:3.7
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working_directory: /tmp/src/phys2denoise
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resource_class: medium
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# Checkout the code as the first step. This is a dedicated CircleCI step.
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# The python orb's install-packages step will install the dependencies from a Pipfile via Pipenv by default.
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# Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
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# Then run your tests!
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# CircleCI will report the results back to your VCS provider.
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steps:
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- checkout
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- restore_cache:
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key: conda-py36-v1-{{ checksum "setup.cfg" }}
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# Install Pillow first to avoid jpsg and zlib issues
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- python/install-packages:
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path-args: .[test]
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pypi-cache: false
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venv-cache: false
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pkg-manager: pip-dist
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# app-dir: ~/project/package-directory/ # If you're requirements.txt isn't in the root directory.
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# pip-dependency-file: test-requirements.txt # if you have a different name for your requirements file, maybe one that combines your runtime and test requirements.
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- run:
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name: Generate environment
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name: Run tests
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# This assumes pytest is installed via the install-package step above
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command: |
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apt-get install -yqq make
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if [ ! -d /opt/conda/envs/phys2denoise_py36 ]; then
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conda create -yq -n phys2denoise_py36 python=3.6
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source activate phys2denoise_py36
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pip install -e ".[test]"
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fi
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- run:
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name: Run integration tests
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no_output_timeout: 10m
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command: |
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source activate phys2denoise_py36
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make integration
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pytest --cov=./phys2denoise
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mkdir /tmp/src/coverage
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mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.integration36
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mv ./.coverage /tmp/src/coverage/.coverage.py37
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- store_artifacts:
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path: /tmp/data
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path: /tmp/src/coverage
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# Persist the specified paths (workspace/echo-output) into the workspace for use in downstream job.
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- persist_to_workspace:
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# Must be an absolute path, or relative path from working_directory. This is a directory on the container which is
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# taken to be the root directory of the workspace.
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root: /tmp
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# Must be relative path from root
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paths:
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- src/coverage/.coverage.integration36
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- src/coverage/.coverage.py37
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integrationtest_37:
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test310:
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docker:
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- image: continuumio/miniconda3
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- image: cimg/python:3.10
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working_directory: /tmp/src/phys2denoise
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resource_class: medium
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steps:
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- checkout
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- restore_cache:
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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- python/install-packages:
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path-args: .[test]
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pypi-cache: false
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venv-cache: false
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pkg-manager: pip-dist
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- run:
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name: Run integration tests
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no_output_timeout: 10m
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name: Run tests
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command: |
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apt-get install -yqq make
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source activate phys2denoise_py37 # depends on makeenv_37
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make integration
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pytest --cov=./phys2denoise
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mkdir /tmp/src/coverage
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mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.integration37
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mv ./.coverage /tmp/src/coverage/.coverage.py310
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- store_artifacts:
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path: /tmp/data
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path: /tmp/src/coverage
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- persist_to_workspace:
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root: /tmp
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paths:
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- src/coverage/.coverage.integration37
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- src/coverage/.coverage.py310
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style_check:
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docker:
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- image: continuumio/miniconda3
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- image: cimg/python:3.7
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working_directory: /tmp/src/phys2denoise
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resource_class: small
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steps:
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- checkout
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- restore_cache:
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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- python/install-packages:
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path-args: .[style]
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pypi-cache: false
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venv-cache: false
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pkg-manager: pip-dist
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- run:
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name: Style check
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command: |
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apt-get install -yqq make
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source activate phys2denoise_py37 # depends on makeenv37
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make lint
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- store_artifacts:
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path: /tmp/data/lint
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build_docs:
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working_directory: /tmp/src/phys2denoise
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docker:
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- image: continuumio/miniconda3
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steps:
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- attach_workspace: # get phys2denoise
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at: /tmp
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- restore_cache: # load environment
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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- run:
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name: Build documentation
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command: |
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apt-get install -yqq make
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source activate phys2denoise_py37 # depends on makeenv_37
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make -C docs html
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- store_artifacts:
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path: /tmp/src/phys2denoise/docs/_build/html
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name: Check style
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command: echo "Skipping for now" # |
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# isort --check .
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# black --check phys2denoise
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# flake8 ./phys2denoise
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merge_coverage:
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working_directory: /tmp/src/phys2denoise
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docker:
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- image: continuumio/miniconda3
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- image: cimg/python:3.10
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resource_class: small
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steps:
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- attach_workspace:
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at: /tmp
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- checkout
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- restore_cache:
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key: conda-py37-v1-{{ checksum "setup.cfg" }}
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- python/install-packages:
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args: coverage
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pkg-manager: pip-dist
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- run:
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name: Merge coverage files
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command: |
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apt-get install -yqq curl
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source activate phys2denoise_py37 # depends on makeenv37
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sudo apt update && sudo apt install curl
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cd /tmp/src/coverage/
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coverage combine
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coverage xml
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- codecov/upload:
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file: /tmp/src/coverage/coverage.xml
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# Invoke jobs via workflows
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# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
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workflows:
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version: 2.1
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build_test:
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build_test: # This is the name of the workflow, feel free to change it to better match your workflow.
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# Inside the workflow, you define the jobs you want to run.
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jobs:
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- makeenv_37
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- style_check:
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- style_check
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- test37:
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requires:
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- makeenv_37
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- merge_coverage:
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- style_check
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- test310:
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requires:
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- style_check
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- merge_coverage:
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requires:
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- test37
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- test310

‎.coveragerc‎

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[run]
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omit =
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docs/*
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tests/*
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_version.py
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__init__.py
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**/__init__.py
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due.py
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.*rc
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versioneer.py
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setup.py
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phys2denoise/tests/*
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phys2denoise/_version.py
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phys2denoise/__init__.py
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phys2denoise/**/__init__.py
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phys2denoise/due.py
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phys2denoise/.*rc
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phys2denoise/versioneer.py
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phys2denoise/setup.py

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- id: check-case-conflict
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- id: check-merge-conflict
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- repo: https://github.com/psf/black
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rev: 22.10.0
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hooks:
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- id: black
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- repo: https://github.com/pycqa/isort
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rev: 5.10.1
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hooks:
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- id: isort
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- repo: https://github.com/pycqa/flake8
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rev: 6.0.0
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hooks:
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- id: flake8
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- repo: https://github.com/pycqa/pydocstyle
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rev: 6.1.1
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hooks:
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- id: pydocstyle
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- repo: https://github.com/pre-commit/pygrep-hooks
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rev: v1.9.0
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hooks:
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- id: rst-backticks
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- id: rst-directive-colons
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- id: rst-inline-touching-normal

‎.readthedocs.yml‎

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# Required
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version: 2
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build:
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os: "ubuntu-20.04"
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tools:
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python: "3.7"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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python:
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version: 3.7
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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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- doc
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system_packages: true
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system_packages: true

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