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release_procedure.rst

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Release procedure

This document describes how to prepare a new BIDScoin release from within the DCCN + from a local Linux VM

  1. Delete the .bidscoin config folder and manually run the tox, bidscoin, bidsmapper, bidscoiner, bids-validator and other integration tests:

    cd ~/python/bidscoin
git pull
module load bidscoin/dev
source activate tox
rm -rf ~/.bidscoin
tox
conda deactivate
source activate /opt/bidscoin
~/python/bidscoin/bidscoin/bcoin.py -t
# Perform integration tests from the commandline and PyCharm

  2. Build & test the apptainer container from GitHub in the Linux VM:

    rm -rf ~/.bidscoin
cd ~/PycharmProjects/bidscoin
vi apptainer.def    # -> pip install github
sudo apptainer build bidscoin.sif apptainer.def
xhost +
apptainer exec --cleanenv --env DISPLAY=:0 bidscoin.sif bidscoin -t
apptainer exec --cleanenv bidscoin.sif bidscoin -v
apptainer exec --cleanenv bidscoin.sif pngappend
apptainer cache clean
vi apptainer.def    # Restore pip install pypi

  3. Inspect the git history and update the CHANGELOG (including the links)

  4. Update the cli help texts and RTD files

  5. Update the version string everywhere (i.e. search without word matching) and COPYRIGHT

  6. Add and push a git version tag if everything is OK

DCCN deployment

  1. Copy the dev folder, update the bidsmaps and module:

    VERSION="4.4.0"
cp -r /opt/bidscoin/dev /opt/bidscoin/$VERSION
cd /opt/_modules/bidscoin
ln -s .common $VERSION
vi .version

  1. Run a test:

    module load bidscoin
source activate /opt/bidscoin
bidscoin -v
bidscoin -t
conda deactivate bidscoin

  2. Post a release message on the MM data management channel

GitHub

  1. Publish a new release

Pypi

  1. Temporarily remove the raw html logo markup

  2. Build and upload the new release:

    conda deactivate
source activate tox
cd ~/python/bidscoin
git checkout master
rm dist/*
python3 -m pip install --upgrade build twine
python3 -m build
python3 -m twine upload --repository testpypi dist/*
python3 -m twine upload dist/*

  3. Restore raw html logo markup

Dockerhub

  1. In the VM, build, test and push a Docker image:

    VERSION="4.4.0"
cd ~/PycharmProjects/bidscoin
sudo docker build -t marcelzwiers/bidscoin:$VERSION .
sudo docker run --rm marcelzwiers/bidscoin:$VERSION bidscoin -v
sudo docker run --rm marcelzwiers/bidscoin:$VERSION pngappend
sudo docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix marcelzwiers/bidscoin:$VERSION bidscoin -t
sudo docker push marcelzwiers/bidscoin:$VERSION
sudo docker system prune -a

Neurodesk

  1. Pull and edit the bidscoin neurocontainer in a separate release branch

  2. Build and test a neurodocker image:

    VERSION="4.4.0"
cd ~/PycharmProjects/neurocontainers/recipes/bidscoin
conda activate neurodocker
./build.sh -ds
sudo docker image list         # Checkout the TAG
sudo docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix bidscoin_${VERSION}:TAG bidscoin -t

  3. Create a neurocontainers PR from the release branch

Neurostars/X/MM

  1. Post a release message