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JoostJMJoostJM
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Merge pull request #788 from JoostJM/circle-ci-mac-os
Fix errors in continuous integration
2 parents 06bea71 + d2f8102 commit 8017bdb

24 files changed

+353
-420
lines changed

‎.circleci/config.yml‎

Lines changed: 164 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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# docker pull circleci/picard
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# docker run -it --rm -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):$(pwd) -v ~/.circleci/:/root/.circleci --workdir $(pwd) circleci/picard circleci build
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5-
version: 2
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version: 2.1
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jobs:
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test-notebooks:
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working_directory: /pyradiomics
@@ -32,10 +32,72 @@ jobs:
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command: |
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jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute notebooks/helloRadiomics.ipynb notebooks/helloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb
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build-3.5: &build_template
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build-mac-37: &build_mac_template
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working_directory: ~/pyradiomics
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macos:
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xcode: 12.5.1
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environment:
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PYTHON_VERSION: 3.7.10
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PYTHON_SHORT_VERSION: 3.7
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steps:
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- run:
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name: Setup MAC OS environment
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# Workaround the following error occurring because python installation is cached but gettext dependency is not
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# dyld: Library not loaded: /usr/local/opt/gettext/lib/libintl.8.dylib
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# Referenced from: /Users/travis/.pyenv/versions/3.7.2/bin/python
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# Reason: Incompatible library version: python requires version 11.0.0 or later, but libintl.8.dylib provides version 10.0.0
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# See https://github.com/scikit-build/cmake-python-distributions/issues/112 and
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# https://github.com/scikit-build/cmake-python-distributions/pull/113
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command: |
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echo "HOMEBREW_NO_AUTO_UPDATE=1" >> $BASH_ENV
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brew install gettext
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brew install pyenv
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echo 'export PATH=$HOME/.pyenv/versions/$PYTHON_VERSION/bin:$HOME/bin:$PATH' >> $BASH_ENV
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mkdir -p $HOME/bin
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ln -s $(which pip3) $HOME/bin/pip
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ln -s $(which python3) $HOME/bin/python
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pyenv install --list
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pyenv install $PYTHON_VERSION
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- run:
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name: Setup SciKit-CI
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command: |
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pip install scikit-ci scikit-ci-addons
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ci_addons --install ../addons
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- run:
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name: Setup PyEnv
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command: python ../addons/travis/install_pyenv.py
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- checkout
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- attach_workspace:
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at: ~/pyradiomics
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- run:
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name: Install
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command: ci install
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- run:
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name: Test
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command: ci test
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- run:
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name: Build Distribution
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command: ci after_test
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- persist_to_workspace:
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root: .
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paths: [dist]
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build-mac-38:
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<<: *build_mac_template
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environment:
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PYTHON_VERSION: 3.8.10
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PYTHON_SHORT_VERSION: 3.7
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build-mac-39:
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<<: *build_mac_template
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environment:
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PYTHON_VERSION: 3.9.5
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PYTHON_SHORT_VERSION: 3.9
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build-37: &build_template
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working_directory: /pyradiomics
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docker:
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- image: circleci/python:3.5-jessie
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- image: cimg/python:3.7
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user: root
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steps:
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- checkout
@@ -57,43 +119,89 @@ jobs:
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command: ci after_test
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- persist_to_workspace:
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root: .
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paths: dist
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paths: [dist]
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build-3.6:
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build-38:
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<<: *build_template
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docker:
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- image: circleci/python:3.6-jessie
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- image: cimg/python:3.8
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user: root
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build-3.7:
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build-39:
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<<: *build_template
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docker:
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- image: circleci/python:3.7
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user: root
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- image: cimg/python:3.9
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user: root
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test_deploy:
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working_directory: /pyradiomics
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docker:
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- image: cimg/python:3.8
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user: root
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steps:
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- run:
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name: Check Repo User
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command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi
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- checkout
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- run:
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name: Setup SciKit-CI
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command: |
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pip install scikit-ci scikit-ci-addons
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ci_addons --install ../addons
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- run:
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name: Install
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command: ci install
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- run:
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name: Install patchelf auditwheel, twine
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command: |
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apt update
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apt-get install patchelf # needed to run auditwheel
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python -m pip install "auditwheel<3.2.0"
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python -m pip install twine
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# only attach the workspace at this point to prevent the removal of source distributions
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- attach_workspace:
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at: /pyradiomics
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- run:
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name: Create sdist
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command: python setup.py sdist
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- run:
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name: Fix Distribution Wheels
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command: |
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ls ./dist/*-linux_$(uname -m).whl # This will prevent further deployment if no wheels are found
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# Since there are no external shared libraries to bundle into the wheels
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# this step will fixup the wheel switching from 'linux' to 'manylinux1' tag
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for whl in $(ls ./dist/*-linux_$(uname -m).whl); do
174+
python -m auditwheel repair $whl -w ./dist/
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rm $whl
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done
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- run:
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name: Deploy source and linux wheels
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command: python -m twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_TEST_USER -p $PYPI_TEST_PASSWORD -r testpypi
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deploy:
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working_directory: /pyradiomics
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docker:
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- image: circleci/python:3.6-jessie
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- image: cimg/python:3.6
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user: root
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steps:
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- run:
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name: Check Repo User
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command: if [[ $CIRCLE_PROJECT_USERNAME != "Radiomics" ]]; then circleci step halt; fi
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command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi
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- checkout
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- run:
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name: Setup SciKit-CI
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command: |
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pip install scikit-ci==0.13.0 scikit-ci-addons==0.11.0
194+
pip install scikit-ci scikit-ci-addons
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ci_addons --install ../addons
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- run:
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name: Install
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command: ci install
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- run:
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name: Install patchelf auditwheel, twine
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command: |
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apt update
95203
apt-get install patchelf # needed to run auditwheel
96-
python -m pip install auditwheel
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python -m pip install "auditwheel<3.2.0"
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python -m pip install twine
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# only attach the workspace at this point to prevent the removal of source distributions
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- attach_workspace:
@@ -108,22 +216,22 @@ jobs:
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# Since there are no external shared libraries to bundle into the wheels
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# this step will fixup the wheel switching from 'linux' to 'manylinux1' tag
110218
for whl in $(ls ./dist/*-linux_$(uname -m).whl); do
111-
auditwheel repair $whl -w ./dist/
219+
python -m auditwheel repair $whl -w ./dist/
112220
rm $whl
113221
done
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- run:
115223
name: Deploy source and linux wheels
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command: twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_USER -p $PYPI_PASSWORD
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command: python -m twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_USER -p $PYPI_PASSWORD
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deploy_conda:
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working_directory: /pyradiomics
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docker:
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- image: circleci/python:3.6-jessie
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- image: cimg/python:3.8
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user: root
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steps:
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- run:
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name: Check Repo User
126-
command: if [[ $CIRCLE_PROJECT_USERNAME != "Radiomics" ]]; then circleci step halt; fi
234+
command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi
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- checkout
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- run:
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name: Install Miniconda
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name: Build Conda packages
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command: |
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mkdir /conda-bld
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conda build ./conda --python=3.5 --croot /conda-bld
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conda build ./conda --python=3.6 --croot /conda-bld
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conda build ./conda --python=3.7 --croot /conda-bld
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conda build ./conda --python=3.8 --croot /conda-bld
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conda build ./conda --python=3.9 --croot /conda-bld
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- run:
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name: Deploy Conda packages
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command: |
@@ -153,31 +262,53 @@ workflows:
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version: 2
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build_and_deploy:
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jobs:
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- build-3.5: &build_job_template
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- build-mac-37: &build_job_template
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filters:
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tags:
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only:
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- /^v?[0-9]+(\.[0-9]+)*(rc[0-9]+)?/
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- build-3.6:
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- /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?/
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- build-mac-38:
162271
<<: *build_job_template
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- build-3.7:
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- build-mac-39:
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<<: *build_job_template
165-
- test-notebooks:
166-
requires:
167-
- build-3.5
168-
- build-3.6
169-
- build-3.7
170-
- deploy: &deploy_template
274+
- build-37:
275+
<<: *build_job_template
276+
- build-38:
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<<: *build_job_template
278+
- build-39:
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<<: *build_job_template
280+
- test-notebooks: &requires_template
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requires:
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- build-3.5
173-
- build-3.6
174-
- build-3.7
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- build-37
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- build-38
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- build-39
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- build-mac-37
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- build-mac-38
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- build-mac-39
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- test_deploy:
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<<: *requires_template
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filters:
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branches:
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ignore:
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- /.*/
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tags:
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only:
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- /^v?[0-9]+(\.[0-9]+)*(rc[0-9]+)?/
296+
- /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)/
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- deploy:
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<<: *requires_template
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filters:
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branches:
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ignore:
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- /.*/
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tags:
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only:
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- /^v?[0-9]+(\.[0-9]+)*/
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- deploy_conda:
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<<: *deploy_template
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<<: *requires_template
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filters:
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branches:
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ignore:
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- /.*/
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tags:
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only:
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- /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?/

‎.travis.yml‎

Lines changed: 0 additions & 88 deletions
This file was deleted.

‎MANIFEST.in‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ include requirements-dev.txt
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include requirements-setup.txt
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include versioneer.py
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recursive-include radiomics *
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recursive-include src/radiomics *
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1111
recursive-include data/baseline *
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recursive-include data *_image.nrrd
@@ -24,4 +24,3 @@ recursive-include bin *.py
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recursive-exclude * __pycache__
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recursive-exclude * *.py[cod]
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recursive-exclude * nosetests.xml

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