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[REL] Latest updates + New CI : Merge pull request #141 from FenTechSolutions/circleci-project-setup
[REL] Latest updates + New CI
2 parents e43d8ff + d244668 commit aac9661

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‎.circleci/bumpversion.sh‎

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#!/bin/bash
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VERSION=$(cat setup.py| grep version | cut -c 20- | rev | cut -c 3- | rev)
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COMMIT_MESSAGE="$(git log --format=%B -n 1)"
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git config --global user.email "[email protected]"
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git config --global user.name "CircleCI Bumpversion"
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git config --global push.default simple
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pip install bumpversion
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if [[ $COMMIT_MESSAGE == *"[NV]"* ]] || [[ $COMMIT_MESSAGE == *"[DOC]"* ]];
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then echo "No version update";
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elif [[ $COMMIT_MESSAGE == *"[REL]"* ]];
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then bumpversion --current-version $VERSION minor setup.py README.md docs/index.rst docs/conf.py cdt/__init__.py;
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elif [[ $COMMIT_MESSAGE == *"[MREL]"* ]];
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then bumpversion --current-version $VERSION major setup.py README.md docs/index.rst docs/conf.py cdt/__init__.py;
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else bumpversion --current-version $VERSION patch setup.py README.md docs/index.rst docs/conf.py cdt/__init__.py;
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fi

‎.circleci/config.yml‎

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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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jobs:
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build-test:
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# Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
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# See: https://circleci.com/docs/2.0/configuration-reference/#docker-machine-macos-windows-executor
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docker:
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- image: docker:17.05.0-ce-git
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auth:
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username: $DOCKER_USER
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password: $DOCKER_PASS
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# Add steps to the job
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# See: https://circleci.com/docs/2.0/configuration-reference/#steps
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steps:
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- checkout
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- setup_remote_docker
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- run:
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name: "Build test image"
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command: |
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docker pull fentechai/cdt-base:latest
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docker build -t fentechai/cdt-test:$CIRCLE_BRANCH .
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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docker push fentechai/cdt-test:$CIRCLE_BRANCH
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test-image:
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docker:
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- image: fentechai/cdt-test:$CIRCLE_BRANCH
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auth:
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username: $DOCKER_USER
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password: $DOCKER_PASS
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steps:
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- checkout
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- setup_remote_docker
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- run:
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name: Test CDT installation
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no_output_timeout: 40m
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command: |
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cd /CDT && pip3 uninstall cdt -y
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python3 setup.py install develop --user
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pytest --cov-report=xml --cov=./cdt
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codecov --token $CODECOV_TOKEN
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bumpversion:
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docker:
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- image: docker:17.05.0-ce-git
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auth:
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username: $DOCKER_USER
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password: $DOCKER_PASS
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steps:
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- checkout
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- setup_remote_docker
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- run:
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name: Install dependencies
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command: |
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apk add --no-cache \
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py-pip=9.0.0-r1
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apk add --no-cache bash
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- add_ssh_keys:
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fingerprints:
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- "94:dc:75:8a:05:8e:b6:ef:bc:34:01:ed:7d:6b:86:ee"
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- when:
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condition:
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equal: [ master, << pipeline.git.branch >> ]
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steps:
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- run:
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name: Bumpversion
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command: |
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bash ./.circleci/bumpversion.sh
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git config --global user.email "[email protected]"
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git config --global user.name "CircleCI Bumpversion"
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git config --global push.default simple
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git remote add deploy [email protected]:FenTechSolutions/CausalDiscoveryToolbox.git
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git add -u
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VERSION_NEW=$(cat setup.py| grep version | cut -c 20- | rev | cut -c 3- | rev)
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git commit -m "[DEPLOY] $VERSION_NEW [skip ci]"
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git push deploy HEAD:master
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build-push-docker-images:
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parameters:
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base-image:
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type: string
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target-image:
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type: string
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dockerfile:
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type: string
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docker:
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- image: docker:17.05.0-ce-git
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auth:
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username: $DOCKER_USER
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password: $DOCKER_PASS
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steps:
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- checkout
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- setup_remote_docker
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- run:
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name: Define run environment variables
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command: |
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echo 'export COMMIT_MESSAGE="$(git log --format=%B -n 1)"' >> $BASH_ENV
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echo 'export SUFFIX=$SUFFIX' >> $BASH_ENV
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echo 'Defined VARS: SUFFIX:$SUFFIX COMMIT_MESSAGE:$COMMIT_MESSAGE'
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source $BASH_ENV
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- when:
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condition:
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equal: [ master, << pipeline.git.branch >> ]
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steps:
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- run:
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name: Push Docker image
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command: |
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source $BASH_ENV
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git pull origin master
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VERSION_NEW=$(cat setup.py| grep version | cut -c 20- | rev | cut -c 3- | rev)
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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docker pull << parameters.base-image>>:latest
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docker build -f << parameters.dockerfile >> -t << parameters.target-image >>$SUFFIX:$VERSION_NEW .
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docker push << parameters.target-image >>$SUFFIX:$VERSION_NEW
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docker tag << parameters.target-image >>$SUFFIX:$VERSION_NEW << parameters.target-image >>$SUFFIX:latest
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docker push << parameters.target-image >>$SUFFIX:latest
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deploy-pypi:
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docker:
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- image: docker:17.05.0-ce-git
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auth:
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username: $DOCKER_USER
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password: $DOCKER_PASS
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steps:
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- checkout
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- setup_remote_docker
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- when:
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condition:
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equal: [ master, << pipeline.git.branch >> ]
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steps:
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- run:
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name: Push to PyPi
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command: |
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git pull origin master
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VERSION_NEW=$(cat setup.py| grep version | cut -c 20- | rev | cut -c 3- | rev)
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docker pull fentechai/cdt:$VERSION_NEW
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docker run -e PYPI_PASSWORD=$PYPI_PASSWORD --rm fentechai/cdt:$VERSION_NEW /bin/sh -c "cd /CDT && pip3 install --upgrade keyrings.alt && pip3 install twine wheel && python3 setup.py sdist bdist_wheel && twine upload -u divkal -p '$PYPI_PASSWORD' dist/*"
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build-docs:
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docker:
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- image: fentechai/cdt:latest
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auth:
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username: $DOCKER_USER
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password: $DOCKER_PASS
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steps:
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- checkout
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- setup_remote_docker
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- add_ssh_keys:
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fingerprints:
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- "94:dc:75:8a:05:8e:b6:ef:bc:34:01:ed:7d:6b:86:ee"
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- when:
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condition:
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equal: [ master, << pipeline.git.branch >> ]
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steps:
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- run:
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name: Build Docs and Push to GitHub
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command: |
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cd /CDT
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git pull origin master
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VERSION_NEW=$(cat setup.py| grep version | cut -c 20- | rev | cut -c 3- | rev)
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# docker pull fentechai/cdt:$VERSION_NEW
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git config --global user.email "[email protected]"
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git config --global user.name "Circle CI Docs"
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git config --global push.default simple
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# docker run -v $(pwd):/cdtlib --rm fentechai/cdt:$VERSION_NEW /bin/sh -c 'cd /cdtlib && pip3 uninstall cdt -y && pip3 install . && pip3 install sphinx recommonmark sphinxcontrib-napoleon sphinx_rtd_theme && cd docs && sphinx-build -Eab html . html'
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pip3 install sphinx recommonmark sphinxcontrib-napoleon sphinx_rtd_theme
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cd docs
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sphinx-build -Eab html . html
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git remote add deploy [email protected]:FenTechSolutions/CausalDiscoveryToolbox.git
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cd ..
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git add ./docs
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git commit -m "[DEPLOY] Docs $VERSION_NEW [skip ci]"
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git push deploy HEAD:master
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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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default:
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jobs:
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- build-test:
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name: build-test-image
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- test-image:
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name: test-image
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requires: [build-test-image]
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- bumpversion:
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requires: [test-image]
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filters:
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branches:
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only:
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- master
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- build-push-docker-images:
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name: build-cpu-image
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base-image: fentechai/cdt-base
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target-image: fentechai/cdt
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dockerfile: Dockerfile
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requires: [bumpversion]
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- build-push-docker-images:
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name: build-gpu-image
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base-image: fentechai/nv-cdt-base
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target-image: fentechai/nv-cdt
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dockerfile: nv-Dockerfile
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requires: [bumpversion]
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- deploy-pypi:
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requires: [build-cpu-image]
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- build-docs:
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requires: [build-cpu-image]

‎.travis.yml‎

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- docker pull fentechai/nv-cdt-env-base:21.01
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- docker build --build-arg python=3.6 --build-arg spy=36 -t fentechai/cdt-dev .
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- if [[ $TRAVIS_PULL_REQUEST == "false" ]]; then
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docker run -e CODECOV_TOKEN --rm fentechai/cdt-dev /bin/sh -c 'cd /CDT && pip3 uninstall cdt -y && python3 setup.py install develop --user && pytest --cov-report= --cov=./cdt && codecov --token $CODECOV_TOKEN';
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docker run -e CODECOV_TOKEN --rm fentechai/cdt-dev /bin/sh -c 'cd /CDT && pip3 uninstall cdt -y && python3 setup.py install develop --user && pytest --cov-report=xml --cov=./cdt && codecov --token $CODECOV_TOKEN';
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echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin;
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docker push fentechai/cdt-dev;
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docker build -f nv-Dockerfile -t fentechai/nv-cdt-dev .;

‎Dockerfile‎

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FROM fentechai/cdt-env-base:22.02
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FROM fentechai/cdt-base:latest
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MAINTAINER Diviyan Kalainathan <[email protected]>
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LABEL description="Docker image for the Causal Discovery Toolbox"
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ARG python
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ARG spy
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RUN mkdir -p /CDT
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COPY . /CDT
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RUN cd /CDT && \
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add-apt-repository ppa:deadsnakes/ppa -y && \
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apt-get update --allow-unauthenticated && \
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apt-get -q install "python${python}" "python${python}-dev" python3-pip python3-setuptools -y && \
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rm /usr/bin/python3 && ln -s /usr/bin/python${python} /usr/bin/python3 && \
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python3 -m pip install -r requirements.txt && \
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python3 -m pip install -r docker-requirements.txt && \
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python3 -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu && \
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python3 -m pip install pytest pytest-cov && \
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python3 -m pip install codecov && \
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python3 setup.py install

‎README.md‎

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[![Dev Status](https://travis-ci.org/FenTechSolutions/CausalDiscoveryToolbox.svg?branch=dev)](https://travis-ci.org/FenTechSolutions/CausalDiscoveryToolbox)
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[![codecov](https://codecov.io/gh/FenTechSolutions/CausalDiscoveryToolbox/branch/master/graph/badge.svg)](https://codecov.io/gh/FenTechSolutions/CausalDiscoveryToolbox)
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[![Hex.pm](https://img.shields.io/badge/License-MIT-blue.svg?maxAge=259200)](https://raw.githubusercontent.com/FenTechSolutions/CausalDiscoveryToolbox/master/LICENSE.md)
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[![version](https://img.shields.io/badge/version-0.5.23-yellow.svg?maxAge=259200)](#)
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[![version](https://img.shields.io/badge/version-0.5.24-yellow.svg?maxAge=259200)](#)
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![PyPI - Downloads](https://img.shields.io/pypi/dm/cdt.svg)
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It implements lots of algorithms for graph structure recovery (including algorithms from the __bnlearn__, __pcalg__ packages), mainly based out of observational data.
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| Branch | master | dev |
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|:----------------:|:--------------------------------------------------------------------------------------------------------------------------------------:|:------------------------------------------------------------------------------------------------------------------------------------:|
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| Python 3.6 - CPU | [![d36cpu](https://img.shields.io/badge/docker-0.5.23-0db7ed.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/cdt/) | [![d36cpudev](https://img.shields.io/badge/docker-latest-0db7ed.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/cdt-dev) |
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| Python 3.6 - GPU | [![d36gpu](https://img.shields.io/badge/nvidia--docker-0.5.23-76b900.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/nv-cdt/) | [![d36gpudev](https://img.shields.io/badge/nvidia--docker-latest-76b900.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/nv-cdt-dev) |
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| Python 3.6 - CPU | [![d36cpu](https://img.shields.io/badge/docker-0.5.24-0db7ed.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/cdt/) | [![d36cpudev](https://img.shields.io/badge/docker-latest-0db7ed.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/cdt-dev) |
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| Python 3.6 - GPU | [![d36gpu](https://img.shields.io/badge/nvidia--docker-0.5.24-76b900.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/nv-cdt/) | [![d36gpudev](https://img.shields.io/badge/nvidia--docker-latest-76b900.svg?maxAge=259200)](https://hub.docker.com/r/fentechai/nv-cdt-dev) |
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## Installation
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‎cdt/__init__.py‎

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from cdt.utils import loss
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from cdt.utils.Settings import SETTINGS
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from cdt.utils.R import RPackages
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__version__ = '0.5.23'
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__version__ = '0.5.24'

‎cdt/causality/pairwise/Jarfo_model/estimator.py‎

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import numpy as np
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from sklearn import pipeline
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from sklearn.base import BaseEstimator
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from sklearn.ensemble import GradientBoostingClassifier
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from multiprocessing import Pool
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try:
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# For latest versions of scikit-learn
17+
from sklearn.ensemble import HistGradientBoostingClassifier as GradBoostClassifier
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extra_params = None
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except ImportError:
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from sklearn.ensemble import GradientBoostingClassifier as GradBoostClassifier
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extra_params = {'n_estimators': 500,
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'subsample': 1.0,
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'min_samples_split': 8,
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'loss':'deviance',
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}
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gbc_params = {
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'loss':'deviance',
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'learning_rate': 0.1,
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'n_estimators': 500,
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'subsample': 1.0,
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'min_samples_split': 8,
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'min_samples_leaf': 1,
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'max_depth': 9,
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'init': None,
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'random_state': 1,
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'max_features': None,
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'verbose': 0
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}
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if extra_params is not None:
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gbc_params.update(extra_params)
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selected_features = [
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'Adjusted Mutual Information[A,A type,B,B type]',
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265273
CauseEffectEstimatorID(
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features_direction=self.features,
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features_independence=self.features,
268-
regressor=GradientBoostingClassifier,
276+
regressor=GradBoostClassifier,
269277
params=gbc_params,
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symmetrize=symmetrize),
271279
CauseEffectEstimatorSymmetric(
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features=self.features,
273-
regressor=GradientBoostingClassifier,
281+
regressor=GradBoostClassifier,
274282
params=gbc_params,
275283
symmetrize=symmetrize),
276284
CauseEffectEstimatorOneStep(
277285
features=self.features,
278-
regressor=GradientBoostingClassifier,
286+
regressor=GradBoostClassifier,
279287
params=gbc_params,
280288
symmetrize=symmetrize),
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]

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