Laboratory for Predictive Neuroimaging - University Hospital Essen, Germany

git clone [email protected]:pni-lab/PUMI.git

• pull the docker image:
  • pnilab/pumi-slim:latest: for a slim image containing the latest PUMI version and only the exact dependencies it needs
  • pnilab/pumi:latest: for the full image, containing all dependnecies but no PUMI source code (useful when integrating new tools, but takes long to download). To work in the full image:

  • - run it: `docker run -ti pnilab/pumi bash`
    - get the latest PUMI source by `git clone http://github.com/pni-lab/PUMI.git`
    - install PUMI: `cd /PUMI; pip install .`
    - 
    

• set up your IDE to work within the container

• FSL
• AFNI
• ANTs
• Freesurfer

cd data_in
export WEBDAV_USERNAME=XXXX
export WEBDAV_PASSWORD=XXXX-XXXX-XXXX-XXXX
datalad install -s [email protected]:pni-data/pumi_test_data.git pumi_test_data
datalad siblings -d pumi_test_data enable -s sciebo.sfb289
datalad get pumi_test_data/*

Contact the developers for webdav credentials.

• name of workflow is the same as the name of the variable that holds it

• name of node is the same as the name of the variable that holds it

• qc nodes's name defines the subdir in qc; it should be: <base_wf>_qc

• avoid "batch-connects" in @PumiPipeline funcions: it is preferred that right after node (or workflow) definition all possible connect statements corresponding to the node are specified

• for readibility, we use the signature: connect(source_node, source_field, dest_node, dest_field)

• except, in case there are multiple connections between the same pair of nodes, batch-connect should be used

• @PumiPipeline funcions' first connect statement(s) is (are) connecting to the inputspec

• @PumiPipeline funcions' last connect statement(s) is (are) connecting to the outputspec

• @PumiPipeline funcions' are minimalistic and do NO "housekeeping".

• increment major if:
  • reverse-compatibility is broken
  • a substantial set of new features are added or a grand milestone is reached in the development
• increment minor if:
  • the running environment must be changed, i.e. when the docker image pnilab/pumi has been changed
  • new feature is added (e.g. a new preprocessing step is integrated)
• increment patch for smaller patches, e.g.:
  • changes in existing behavior (new parameter, params renamed)
  • bugfixes
  • typically after merging a pull request

Reverse compatibility will not be guaranteed until the major version reaches 1

• commit the changes
• tag the commit, deploy the new full docker image locally, push the tag:

git tag <MAJOR>.<MINOR>.<PATCH>
./deploy_full.sh # creates the new full docker image
git push --tag

• push to your branch
• open PR A github action automatically creates the new slim docker image.

• commit the changes
• tag the commit, push the tag

git tag <MAJOR>.<MINOR>.<PATCH>
git push --tag

• push to your branch
• open PR A github action automatically creates the new slim docker image.

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