Update BIDScoin from 3.7.0 to 4.2.0

[marcelzwiers]

Hello all,

I noticed that the BIDScoin app in neurodesk is outdated and that a few of BIDScoin's entry points (bidsapps and other utilities) are missing / need updating. Also, the Ubuntu base image of your container doesn't need a backport to Qt5, you can simply pip install from pypi (and include the extras, e.g. pip install bidscoin[all]). I'm happy to assist if you have any questions.

Best,
Marcel (I'm the main BIDScoin developer)

[karl-koschutnig]

Hello,
An update would be very much appreciated!

Best, Karl

[stebo85]

Dear @marcelzwiers , that would be wonderful :) could you directly propose the changes here through a pull request?

https://github.com/NeuroDesk/neurocontainers/recipes/bidscoin/build.sh

thank you so much
Steffen

[marcelzwiers]

The relevant parts from the pyproject.toml file:

[project.optional-dependencies]
dcm2niix2bids    = ['dcm2niix']
spec2nii2bids    = ['spec2nii >= 0.6.1']
deface           = ['pydeface', 'drmaa']
pet2bids         = ['pypet2bids >= 1.0.12']
# phys2bidscoin    = ['bioread >= 1.0.5', 'pymatreader >= 0.0.24', 'duecredit', 'phys2bids >= 2.0.0, < 3.0.0']
all              = ['bidscoin[dcm2niix2bids,spec2nii2bids,deface,pet2bids]']    # + phys2bidscoin
dev              = ['bidscoin[spec2nii2bids,deface,pet2bids]', 'tox', 'pytest', 'sphinx-rtd-theme', 'myst-parser'] # + phys2bidscoin

[project.scripts]
bidscoin         = 'bidscoin.bcoin:main'
bidseditor       = 'bidscoin.bidseditor:main'
bidsmapper       = 'bidscoin.bidsmapper:main'
bidscoiner       = 'bidscoin.bidscoiner:main'
echocombine      = 'bidscoin.bidsapps.echocombine:main'
deface           = 'bidscoin.bidsapps.deface:main'
medeface         = 'bidscoin.bidsapps.medeface:main'
skullstrip       = 'bidscoin.bidsapps.skullstrip:main'
slicereport      = 'bidscoin.bidsapps.slicereport:main'
dicomsort        = 'bidscoin.utilities.dicomsort:main'
bidsparticipants = 'bidscoin.utilities.bidsparticipants:main'
rawmapper        = 'bidscoin.utilities.rawmapper:main'
physio2tsv       = 'bidscoin.utilities.physio2tsv:main'
plotphysio       = 'bidscoin.utilities.plotphysio:main'

And for the relevant part of the container, this is what is needed for a python:3.10-slim base image:

# First install pyqt5 as Debian package to solve dependencies issues occurring when installed with pip
# Then install the latest stable BIDScoin Qt5 release from Github (install the normal Qt6 branch from PyPi when using recent base images such as Ubuntu:22.04)
ENV PIP_NO_CACHE_DIR=off
RUN apt update && apt -y --no-install-recommends install pigz curl python3-pyqt5 python3-pyqt5.qtx11extras git && apt clean; \
    pip install --upgrade pip; \
    pip install bidscoin[spec2nii2bids,deface,pet2bids]@git+https://github.com/Donders-Institute/[email protected]+qt5

So if you have an Ubuntu:22.04 base image (as I think you do) then the Qt5 part can be skipped and simply be replaced with something like:

ENV PIP_NO_CACHE_DIR=off
RUN apt update && apt -y --no-install-recommends install pigz curl && apt clean; \
    pip install --upgrade pip; \
    pip install bidscoin[spec2nii2bids,deface,dcm2niix]

[marcelzwiers]

I can do a PR, but a little guidance would be helpful (I don't know neurodesk very well). Is the build recipe (btw, your link is dead) the only file I need to adapt? Because when I search for "BIDScoin" I find 19 files...

p.s. The new BIDScoin version 4.2.0 is an important update for containerized BIDScoin usage, because the templates are now stored outside the container (in the user home directory) -- which makes them user-editable

[marcelzwiers]

I see that inside the neurocontainers repository there are two build scripts that include BIDScoin:

https://github.com/NeuroDesk/neurocontainers/blob/master/recipes/bidscoin/build.sh
https://github.com/NeuroDesk/neurocontainers/blob/master/recipes/bidstools/build.sh

I suppose that will do?

[stebo85]

Yes, I had forgotten that we also included it in the bidstools container - if you could propose the changes to both that would be wonderful. Thank you so much!

[marcelzwiers]

Are you sure that's it? Outside the neurocontainers repo I see for instance also stuff like:

NeuroDesk/CharacterisationVL-Software · bidscoin/Singularity.bidscoin_3

 APPLICATION_NAME BIDSCOIN
 APPLICATION_VERSION latest
 echo #### Install bidscoin ####
 apt install -y python3-pyqt5

And

NeuroDesk/neurocommand · neurodesk/apps.json

    },
    "bidscoin": {
        "apps": {
            "bidscoin 3.7.0": {
                "version": "20220329",
                "exec": ""
            }
        },
        "categories": ["data organisation"]
    },

[stebo85]

Yes, the two links to the recipes is what we currently use in Neurodesk. The Characterization virtual laboratory is an old repository we are not using anymore.

The references to bidscoin in the apps.json file will be updated to the latest container versions once it is built and tested. The apps.json file controls what is exposed to users in neurodesk.

Thank you
Steffen

[marcelzwiers]

And there is much more...

[marcelzwiers]

NeuroDesk/neurocontainers#497