Upload PAM50 registered labels from Yehuda Warszawer #23
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| name: BIDS Validator | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.7 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: before_install | |
| run: | | |
| # install spine-generic for acquisition parameters check | |
| pip install spinegeneric@git+https://github.com/spine-generic/[email protected] | |
| # use conda's git-annex, because it's the most up to date; | |
| # Debian's is very behind, and even neurodebian's is behind | |
| # by a year, and is currently incompatible with the format of this repo. | |
| wget -O/tmp/Miniconda3-latest-Linux-x86_64.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -f | |
| source ~/miniconda3/bin/activate # careful! after this we're no longer in GH action's python, we're in conda's! | |
| conda install -y -c conda-forge git-annex | |
| # install proper NodeJS for bids-validator | |
| sudo rm -rf ~/.nvm | |
| curl -sL https://deb.nodesource.com/setup_current.x | sudo -E bash - | |
| sudo apt-get install -y nodejs | |
| sudo npm install -g bids-validator | |
| - name: Include miniconda in PATH | |
| run: | | |
| echo "$HOME/miniconda3/bin" >> $GITHUB_PATH | |
| echo "$HOME/miniconda3/Scripts" >> $GITHUB_PATH | |
| git config --global user.name "gh-actions" | |
| git config --global user.email "gh-actions" | |
| - name: setup | |
| run: | | |
| # download the data content | |
| git fetch origin git-annex:git-annex # Travis does a shallow checkout, so it is missing this important branch | |
| git annex init | |
| - name: download data | |
| run: | | |
| echo -e "\e[1m \e[4m \e[34mDownloading dataset; this will take a while. \n" | |
| # this is -q because git-annex doesn't have a short progress bar like git | |
| # and the download log is overwhelming and not interesting and might trip over | |
| # https://docs.travis-ci.com/user/common-build-problems/#log-length-exceeded. | |
| # but -q might instead trip over | |
| # https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received | |
| # so it's a balancing act. | |
| git annex get -J8 | |
| - name: script | |
| run: | | |
| echo -e "\e[1m \e[4m \e[34mRunning BIDS-validator \n" | |
| bids-validator ./ | |
| echo -e "\e[1m \e[4m \e[34mChecking acquisition parameters \n" | |
| sg_params_checker -path-in ./ | |
| echo -e "\e[1m \e[4m \e[34mChecking data consistency \n" | |
| sg_check_data_consistency -path-in ./ |