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View Code? Open in Web Editor NEWPortable neuroimaging pipelines that understand BIDS datasets
Home Page: https://bids-apps.neuroimaging.io/
License: Other
Portable neuroimaging pipelines that understand BIDS datasets
Home Page: https://bids-apps.neuroimaging.io/
License: Other
Hey BIDS apps team! It looks like a column of badges are 404-ing on https://bids-apps.neuroimaging.io/apps/:
I suspect a circle workflow was removed, changed, or something along those lines, it looks like the Circle URL that is linked to is 404 along with the badge. https://circleci.com/gh/BIDS-Apps/aa.svg?style=shield
Just wanted to let you know!
Looking through a lot of the CI tests we have, many apps are tested against at least 2 datasets:
I would say that this should be a requirement in the test suite that new bids apps must have.
Of course only if relevant.
ref: datalad/datalad-container#157 (attn @m-petersen)
apparently only good old fmriprep is listed
$> git grep mriprep
_config.yml: - gh: 'nipreps/fmriprep'
_config.yml: dh: 'nipreps/fmriprep'
and none of the other nipreps bids-apps. Would be nice to see them added. context: I use this listing to populate/update (well -- yet to account for shub:// going read-only, so outdated ATM) https://github.com/ReproNim/containers/
Possibly split example and snake bids example into a different subsection.
useful for creating lists of apps in other repo with a blurb of what each app does
similar to: https://github.com/bids-standard/
but note #47 (needs to be done first, perhaps)
I had a some bit of trouble with figuring out the appropriate paths that would be available to the Singularity container. Do you think that adding a bit more text after the example to explain that, when running the Singularity container version, the paths to the data and the output need to be determined specifically for the cluster being used, but that using paths from /home/
are a good bet?
As you note, different folders will be accessible in different places, and I got confused about which to use.
I can write some text and submit via PR if this seems a good idea.
Describe how one can contribute to this repository (the bids-apps.neuroimaging.io website)
https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution
https://github.com/emdupre/me-ica/blob/py3/CONTRIBUTING.md
Given a "raw" BIDS dataset, but which was not defaced yet, should deface anatomicals for all subjects/sessions, and move non-defaced under sourcedata/
. Could be any of the https://open-brain-consent.readthedocs.io/en/stable/anon_tools.html#faces-dental-stripping but probably ideally the one used by OpenNeuro folks themselves. Note also that the https://github.com/mih/mridefacer/blob/master/mridefacer also has "datalad support" in that it takes care about annotating non-defaced anatomicals as having distribution restrictions.
tags to add: good for a hackathon
The only CI check we currently have (recently migrated from Travis to GH actions) is a quick "build test": https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/.github/workflows/ruby_tests.yml#L1
I think it'd be cool to extend this by uploading the html artifacts for inspection. Doing this on GH Actions is slightly inconvenient, because one always has to download a zip file and then look at it.
With circleci and https://github.com/larsoner/circleci-artifacts-redirector, this can be made much more convenient (just click on the check, and view artifacts in the browser)
Currently we can only show CI badges on our app page if the app runs its CI on circle-CI.
This is too restrictive.
We should probably allow apps to run their CI anywhere and adapt how those badges are grabbed for each case.
We could cover:
god knows why it cannot checkout the repo...
No response
Would defo help me at the moment at least.
I'm running tests on CircleCI for BrainSuite BIDS App and I have been running into this error:
test: print version
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#!/bin/bash -eo pipefail
docker load -i /tmp/workspace/docker/image.tar
docker run -ti --rm --read-only \
-v /tmp/workspace/data/ds114_test1:/bids_dataset \
-v ${HOME}/outputs02:/outputs \
bids/${CIRCLE_PROJECT_REPONAME,,} \
/bids_dataset \
/outputs participant --version
Loaded image: bids-apps/brainsuite:latest
Unable to find image 'bids/brainsuite:latest' locally
latest: Pulling from bids/brainsuite
Image docker.io/bids/brainsuite:latest uses outdated schema1 manifest format. Please upgrade to a schema2 image for better future compatibility. More information at https://docs.docker.com/registry/spec/deprecated-schema-v1/
beaf4746: Pulling fs layer
f24b2f04: Pulling fs layer
ad169b64: Pulling fs layer
c6d5adc7: Pulling fs layer
ab9f2a29: Pulling fs layer
4b4059e9: Pulling fs layer
1a21da73: Pulling fs layer
95caeb02: Pulling fs layer
e5bc09e8: Pulling fs layer
3589680c: Pulling fs layer
bba3cada: Pulling fs layer
f6521379: Pulling fs layer
e4a4baa8: Pulling fs layer
cfbeee3a: Pulling fs layer
03d7defc: Pulling fs layer
dc8e2ad7: Pulling fs layer
db59422b: Pulling fs layer
Digest: sha256:8487b132383863d077361f0c31030efbce31eecdea77933f9908ef7c2c86eebe
Status: Downloaded newer image for bids/brainsuite:latest
^@^@Traceback (most recent call last):
File "./qc-system/run.py", line 9, in <module>
import nibabel
File "/opt/conda/lib/python2.7/site-packages/nibabel/__init__.py", line 45, in <module>
from .loadsave import load, save
File "/opt/conda/lib/python2.7/site-packages/nibabel/loadsave.py", line 18, in <module>
from .imageclasses import all_image_classes
File "/opt/conda/lib/python2.7/site-packages/nibabel/imageclasses.py", line 15, in <module>
from .minc2 import Minc2Image
File "/opt/conda/lib/python2.7/site-packages/nibabel/minc2.py", line 31, in <module>
h5py, have_h5py, setup_module = optional_package('h5py')
File "/opt/conda/lib/python2.7/site-packages/nibabel/optpkg.py", line 98, in optional_package
pkg = __import__(name, fromlist=fromlist)
File "/opt/conda/lib/python2.7/site-packages/h5py/__init__.py", line 60, in <module>
from .tests import run_tests
File "/opt/conda/lib/python2.7/site-packages/h5py/tests/__init__.py", line 13, in <module>
from .common import ut
File "/opt/conda/lib/python2.7/site-packages/h5py/tests/common.py", line 40, in <module>
testfile, fname = tempfile.mkstemp(unichr(0x03b7))
File "/opt/conda/lib/python2.7/tempfile.py", line 307, in mkstemp
dir = gettempdir()
File "/opt/conda/lib/python2.7/tempfile.py", line 275, in gettempdir
tempdir = _get_default_tempdir()
File "/opt/conda/lib/python2.7/tempfile.py", line 217, in _get_default_tempdir
("No usable temporary directory found in %s" % dirlist))
IOError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
I believe it can't find the /tmp directory inside the CircleCI container (not the bids app container). Do you have any suggestions? Current config.yml is located in bids-apps/BrainSuite/.circleci/config.yml (https://github.com/bids-apps/BrainSuite/blob/master/.circleci/config.yml).
I hope this is the correct place to post this issue, but if not, please let me know where the appropriate place is would be to post CircleCI testing issues for bids apps.
Thank you!
When the website is finalized.
Not sure if this document may be incorporated here on the BIDS apps website or maybe better in the bids starter kit. I cannot decide.
similar to how it's currently done in bids-standard/bids-website#261
knowing when an app was last updated gives an indication of how actively it is developed, as a heuristic for reliability and whether or not it's worth looking into.
I don't we need this file: https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/Gemfile.lock#L1
do we? This just contains the "fixed" versions that are to be installed when deploying to GH pages ... but for a simple setup such as this one (or bids-website), just the Gemfile should be enough: https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/Gemfile#L1
I think that removing the lock file will also get rid of the security warning.
I didn't find a link to either of those two important resources:
There is currently this logo for the BIDS-Apps organization:
I wonder where it comes from, how it is licensed, and whether we should change it to just the BIDS logo.
Furthermore, there is currently this background image on the website:
I think we can probably do without it -- it's okay to have it, but it's not really related to "anything BIDS-Apps".
Was getting some awkward behavior on my phone.
Nav bar was hard to locate.
any idea where this could be coming from?
I have not looked into it yet. Just in case you have a better hunch than me.
Hi folks,
I just noticed that the BIDS Apps
logo doesn't show up on all but the landing page. The working logo points to
https://bids-apps.neuroimaging.io/images/BIDS_apps_logo_black.jpg, while the non-working one points to https://bids-apps.neuroimaging.io/dev_faq/images/BIDS_apps_logo_black.jpg. Happy to submit a small PR for this if no one else wants to/is on it.
Cheers, Peer
Inspired by
which broke our cron job in https://github.com/ReproNim/containers . So would be nice if _config.yml records were checked for presence on gh/dh. For dh it is just https://registry.hub.docker.com/v2/repositories/bids/{dh} away AFAIK.
The license currently says:
And the author currently says:
I think we should:
bids contributors
, the website template belongs to josh gerdes
bids contributors
, given that more people than Chris G have contributed by now (and -- more importantly -- will do so in the future)What are your opinions?
#25 was a first pass at our contributing guide. During the process, we found additional headings that would helpful to add to the contributing guide. Please feel free to suggest more topics on this issue!
might be related to #2
please invite me to the organization ;-)
so it would be easier to find it to discuss/file generic issues
At then moment the names of each app may not be transparent enough to know what the app does.
Should at least be added to the yml for each app:
The badges for build success and issue count do not appear to be updating. CPAC now has no issues and several passed circleCI tests, but it still says that its build is a failure and that there is an issue. Do I need to do something to trigger the web page to be rebuilt or something?
- gh: "cpp-lln-lab/bidsMReye"
dh: "cpplab/bidsmreye"
ci: "gh"
branch: "main"
workflow: "test"
ds_type:
- raw
datatype:
- func
I fear some change I made broke things! The beautiful formatting is gone.
- gh: "cpp-lln-lab/bidspm"
dh: "cpplab/bidspm"
ci: "gh"
branch: "main"
workflow: "test"
ds_type:
- raw
- derivative
datatype:
- anat
- func
The title says what I'd like to do. What are your opinions? Can you think of potential caveats that we need to check first?
Hi @Remi-Gau
I made a new release today of BrainSuite BIDS App (with CircleCI tests passed) but I still only see the unstable tag on DockerHub. Could you let me know any additional steps I should take in order to push the "stable" tag version?
To clarify - I've tried making a git tag (v21a in this case) and pushing the tag with new commits to trigger the circleci tests. I don't know how the $CIRCLE_TAG variable gets set in https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/push_docker.sh.
Thank you!
I'm not sure why it's not on there, but we would love to be part of the board!
Originally posted by @yeunkim in #95 (comment)
Hello!
I am hoping to have a new app added to the list? Please let me know if there is anything I need do to, it is already set up on circleci.
Docker: khanlab/hippunfold:v0.4.1
Docs: https://hippunfold.readthedocs.io/en/latest/
Github: https://github.com/khanlab/hippunfold
Thanks!
Ali
I'd find it reasonable to move the BIDS Apps website away from the "blog feeling" with the DISQUS widget for making comments. Instead, we should explicitly advise people to use one of our "standard" communication channels:
WDYT?
Note that apart from our standard mailing list (called "bids-discussion"), there is another mailing list: https://groups.google.com/g/bids-apps-dev (last post 2018?)
Personally, I'd like to discontinue that one and re-direct people towards "bids-discussion" or the other channels named above.
again: WDYT?
I think there may be some files in this repository that:
Candidates for 1.
OHBM2017_poster.afdesign
--> this should rather be a PDF on Zenodo or similarCandidates for 2.
Is everyone fine with removing these files? If somebody really needs the poster, it'll be in the git history.
For example:
https://app.circleci.com/pipelines/github/bids-apps/BROCCOLI
No response
In light of
bids-apps/maintenance-tools#7
it seems that it maybe be more useful to have our dashboard show the status of how the latest version of an app is running rather than the status of the default branch of the repo.
We could keep those on a separate page that could more useful for us or anyone who would like to try the bleeding edge version of an app.
Hi @Remi-Gau
Sorry for the barrage of requests. One more thing - could you add "- func" to the datatype in the _config.yml (line 137) for brainsuite?
Thank you!
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