Add neurodesk singularity containers to the collection

yarikoptic commented 2 years ago

they are all made available from https://objectstorage.us-ashburn-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/ .
- we might or might not redistribute copies (falkor server space is tight due to hosting archive of good old shub)
singularity containers are likely produced from docker containers which are built/uploaded using workflows such as https://github.com/NeuroDesk/neurocontainers/blob/7c10e7c930cb7b1d8f287447832ec6c50b4671ee/.github/workflows/convert3D.yml
https://neurodesk.github.io/docs/neurocontainers/ has two (besides docker) items : 1. CVMFS - Neurodesk Singularity Containers on CVMFS; 2. Singularity - Neurodesk Singularity Containers . I am not yet sure what the difference is and either we need both
Thought to place under images/neurodesk/ and just map image filenames to match what we have for others

Just FYI @stebo85 - the Mr. NeuroDesk

stebo85 commented 2 years ago

Dear @yarikoptic,

This would be amazing and super useful! Happy to help with this after the holidays :)

Correct, we build docker containers using the github actions you identified. Then we store them in the gihub container registry and in the docker registry. Another action converts these docker images to singularity and uploads them to the object storage in Ashburn. Since I live at the other side of the internet (Australia :p) this object storage is then mirrored to other locations (Frankfurt, Sydney, Brisbane). We then pull these singularity files using aria2c from all locations simultaneously so that everyone gets a good download speed no matter where they are.

container_pull="aria2c https://objectstorage.us-ashburn-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/$container https://objectstorage.eu-frankfurt-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/$container https://objectstorage.ap-sydney-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/$container https://swift.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/$container"

To avoid people having to download the whole singularity container we do another trick: We unpack the singularity images in a sandbox and store these on a CVMFS Stratum 0 Server hosted in Brisbane. This server then mirrors to Stratum 1 Servers distributed in the US, Canada, Europe and Australia and people can directly mount this in user space and directly access all containers :)

Have a wonderful holiday season and very much looking forward to help getting our containers in datalad run :)

Cheers Steffen

stebo85 commented 2 years ago

Dear @yarikoptic,

Just wondering what I can do to help get to get our containers into datalad :) Can datalad map the different download sources of our containers and download them from multiple sources or would it help to have one domain that get routed based on DNS to the closest download location?

Cheers Steffen

yarikoptic commented 1 year ago

Hi @stebo85 , thanks for the great talk you gave yesterday -- exciting to see how many "moving parts" are in place and your live-demo gods favor you so much that it all went so smooth. I think it is ripe time to get back to this little subproject, and may be @asmacdo would also join to help eventually. Meanwhile let me answer your question:

Can datalad map the different download sources of our containers and download them from multiple sources

yes, git-annex (used by datalad) can add arbitrary number of URLs for any given file. Since recent version we can also give priorities to different sources (ref: https://git-annex.branchable.com/todo/Allow_for_URLs_prioritization_WITHIN___40__web__41___remote/#comment-3ed32f70bcdd682c3d3d41f5541f9593 and therein, sample repos with such setting: https://github.com/dandisets/).

or would it help to have one domain that get routed based on DNS to the closest download location?

wouldn't hurt since would make it dynamic (no need to hardassign costs) but not required.

What would help me to get started is probably get a pointer to some datastructure listing all singularity containers with some urls on where to get them from.

As for docker -- we never figured a way to store images with references to individual layers: https://github.com/datalad/datalad-container/issues/98 . may be should look into it again at some point.

stebo85 commented 1 year ago

Dear @yarikoptic,

Thank you :) I am very excited to make progress on this - would be so cool to have our containers available through datalad =)

Then let's start simple:

This list contains all current and tested container releases (automatically updated by our CD): https://github.com/NeuroDesk/neurocommand/blob/main/cvmfs/log.txt (we also added the categories, because we use this file to build our application search: https://www.neurodesk.org/applications/)

so for example the first entry is: container=afni_21.2.00_20210714

The container name from the list then only needs an ".simg" attached and the URL for the 3 main mirror servers in APAC, EUROPE, AMERICAS becomes: https://objectstorage.us-ashburn-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg https://objectstorage.eu-frankfurt-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg https://objectstorage.ap-sydney-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg

so, for example this URL should get you the fastest way to download our singularity container in the US: https://objectstorage.us-ashburn-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/afni_21.2.00_20210714.simg

That should be good to automate on your end, right? Would you need anything else?

Thank you so much :) Steffen

yarikoptic commented 1 year ago

ok, pushed them all in a branch to my fork (with git-annex branch being pushed to), if interested to have a pick/check: https://github.com/yarikoptic/containers/tree/enh-neurodesk-preview (images under https://github.com/yarikoptic/containers/tree/enh-neurodesk-preview/images/neurodesk). TODOs:

[ ] annotate to not re-distribute the copy for now (we are getting tight on space there with mirroring after-life of singularity-hub)
[ ] merge/push and it would become a part of the cron job

I didn't bother about metadata annotations at all yet :-/

stebo85 commented 1 year ago

Dear @yarikoptic,

That's great :)

one thing I noticed is that the versioning of the containers seems to be truncated: e.g.

neurodesk-qsmxt--1.1.simg neurodesk-qsmxt--1.3.simg

These are actually 4 containers:

qsmxt_1.1.9_20211219 categories:phase processing, quantitative imaging,structural imaging,workflows, qsmxt_1.1.10_20220302 categories:phase processing, quantitative imaging,structural imaging,workflows, qsmxt_1.1.13_20221018 categories:phase processing, quantitative imaging,structural imaging,workflows, qsmxt_1.3.2_20230204 categories:phase processing,quantitative imaging,structural imaging, workflows,

But it looks like it is truncated after the first 4 characters and therefore 1.1.9 1.1.10 and 1.1.13 are collapsed to neurodesk-qsmxt--1.1.simg

could that be or am I misunderstanding the versioning in datalad?

spinalcordtoolbox is affected by this as well: neurodesk-spinalcordtoolbox--5.simg

should be: spinalcordtoolbox_5.4_20211208 categories:spine, spinalcordtoolbox_5.5_20220419 categories:spine, spinalcordtoolbox_5.6_20220503 categories:spine, spinalcordtoolbox_5.7_20220803 categories:spine, spinalcordtoolbox_5.8_20230117 categories: spine,

it looks like all toolboxes with multiple versions where the version string is 3 digits are affected?

yarikoptic commented 1 year ago

wow, that is a fun bug! the culprit is this line: https://github.com/ReproNim/containers/blob/master/scripts/create_singularities#L164 and in particular use of pathlib.Path's .with_suffix - which now obvious in hindsight would take last number as the suffix (extension) and replace with .simg. Yikes, so I screwed up pretty much all containers, uff... Let's redo ;) the easiest way for me would really be just to fix and redo so do not mind another 300GB of downloads ;) I will update here whenever it is done

stebo85 commented 1 year ago

ok, glad we spotted this early on :)

yarikoptic commented 1 year ago

yeap -- thanks for the review. Lesson to myself: I am too old to code late in the evening ;) pushed now fixed state with various fixes.

An overall diff from old invalid state to current

```diff diff --git a/.datalad/config b/.datalad/config index b4ab204..834af5f 100644 --- a/.datalad/config +++ b/.datalad/config @@ -219,157 +219,157 @@ image = images/bids/bids-fitlins--0.11.0.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-vesselapp"] - image = images/neurodesk/neurodesk-vesselapp--0.3.simg + image = images/neurodesk/neurodesk-vesselapp--0.3.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-trackvis"] - image = images/neurodesk/neurodesk-trackvis--0.6.simg + image = images/neurodesk/neurodesk-trackvis--0.6.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-tgvqsm"] - image = images/neurodesk/neurodesk-tgvqsm--1.0.simg + image = images/neurodesk/neurodesk-tgvqsm--1.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-surfice"] - image = images/neurodesk/neurodesk-surfice--1.0.simg + image = images/neurodesk/neurodesk-surfice--1.0.20210730.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-spm12"] image = images/neurodesk/neurodesk-spm12--r7771.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-spinalcordtoolbox"] - image = images/neurodesk/neurodesk-spinalcordtoolbox--5.simg + image = images/neurodesk/neurodesk-spinalcordtoolbox--5.8.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-sovabids"] - image = images/neurodesk/neurodesk-sovabids--0.3.simg + image = images/neurodesk/neurodesk-sovabids--0.3.1a0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-slicersalt"] - image = images/neurodesk/neurodesk-slicersalt--3.0.simg + image = images/neurodesk/neurodesk-slicersalt--3.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-slicer"] - image = images/neurodesk/neurodesk-slicer--4.11.simg + image = images/neurodesk/neurodesk-slicer--5.0.3.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-sigviewer"] - image = images/neurodesk/neurodesk-sigviewer--0.6.simg + image = images/neurodesk/neurodesk-sigviewer--0.6.4.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-rstudio"] - image = images/neurodesk/neurodesk-rstudio--1.4.simg + image = images/neurodesk/neurodesk-rstudio--2022.07.2.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-root"] - image = images/neurodesk/neurodesk-root--6.22.simg + image = images/neurodesk/neurodesk-root--6.22.02.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-romeo"] - image = images/neurodesk/neurodesk-romeo--3.2.simg + image = images/neurodesk/neurodesk-romeo--3.2.8.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-rabies"] - image = images/neurodesk/neurodesk-rabies--0.3.simg + image = images/neurodesk/neurodesk-rabies--0.3.5.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-qsmxt"] - image = images/neurodesk/neurodesk-qsmxt--1.1.simg + image = images/neurodesk/neurodesk-qsmxt--1.3.2.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-physio"] - image = images/neurodesk/neurodesk-physio--r7771.simg + image = images/neurodesk/neurodesk-physio--r2021a.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-palm"] image = images/neurodesk/neurodesk-palm--alpha119.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-oshyx"] - image = images/neurodesk/neurodesk-oshyx--0.simg + image = images/neurodesk/neurodesk-oshyx--0.4.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-nipype"] - image = images/neurodesk/neurodesk-nipype--1.8.simg + image = images/neurodesk/neurodesk-nipype--1.8.3.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-niistat"] - image = images/neurodesk/neurodesk-niistat--1.0.simg + image = images/neurodesk/neurodesk-niistat--1.0.20191216.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-niftyreg"] - image = images/neurodesk/neurodesk-niftyreg--1.4.simg + image = images/neurodesk/neurodesk-niftyreg--1.4.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mrtrix3tissue"] - image = images/neurodesk/neurodesk-mrtrix3tissue--5.2.simg + image = images/neurodesk/neurodesk-mrtrix3tissue--5.2.8.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mrtrix3"] - image = images/neurodesk/neurodesk-mrtrix3--3.0.simg + image = images/neurodesk/neurodesk-mrtrix3--3.0.3.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mrsiproc"] - image = images/neurodesk/neurodesk-mrsiproc--0.0.simg + image = images/neurodesk/neurodesk-mrsiproc--0.0.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mritools"] - image = images/neurodesk/neurodesk-mritools--3.3.simg + image = images/neurodesk/neurodesk-mritools--3.3.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mriqc"] - image = images/neurodesk/neurodesk-mriqc--0.16.simg + image = images/neurodesk/neurodesk-mriqc--0.16.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mricron"] - image = images/neurodesk/neurodesk-mricron--1.0.simg + image = images/neurodesk/neurodesk-mricron--1.0.20190902.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mricrogl"] - image = images/neurodesk/neurodesk-mricrogl--1.2.simg + image = images/neurodesk/neurodesk-mricrogl--1.2.20211006.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mneextended"] - image = images/neurodesk/neurodesk-mneextended--1.1.simg + image = images/neurodesk/neurodesk-mneextended--1.1.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mne"] - image = images/neurodesk/neurodesk-mne--0.23.simg + image = images/neurodesk/neurodesk-mne--1.1.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-minc"] - image = images/neurodesk/neurodesk-minc--1.9.simg + image = images/neurodesk/neurodesk-minc--1.9.18.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-matlab"] image = images/neurodesk/neurodesk-matlab--2022a.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-lcmodel"] - image = images/neurodesk/neurodesk-lcmodel--6.simg + image = images/neurodesk/neurodesk-lcmodel--6.3.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-laynii"] - image = images/neurodesk/neurodesk-laynii--2.2.simg + image = images/neurodesk/neurodesk-laynii--2.2.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-lashis"] - image = images/neurodesk/neurodesk-lashis--1.simg + image = images/neurodesk/neurodesk-lashis--2.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-julia"] - image = images/neurodesk/neurodesk-julia--1.4.simg + image = images/neurodesk/neurodesk-julia--1.4.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-itksnap"] - image = images/neurodesk/neurodesk-itksnap--3.8.simg + image = images/neurodesk/neurodesk-itksnap--3.8.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-hdbet"] - image = images/neurodesk/neurodesk-hdbet--1.0.simg + image = images/neurodesk/neurodesk-hdbet--1.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-gimp"] - image = images/neurodesk/neurodesk-gimp--2.10.simg + image = images/neurodesk/neurodesk-gimp--2.10.18.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fsl"] - image = images/neurodesk/neurodesk-fsl--6.0.simg + image = images/neurodesk/neurodesk-fsl--6.0.5.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-freesurfer"] - image = images/neurodesk/neurodesk-freesurfer--7.1.simg + image = images/neurodesk/neurodesk-freesurfer--7.3.2.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fmriprep"] - image = images/neurodesk/neurodesk-fmriprep--20.1.simg + image = images/neurodesk/neurodesk-fmriprep--21.0.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fieldtrip"] - image = images/neurodesk/neurodesk-fieldtrip--20211114.simg + image = images/neurodesk/neurodesk-fieldtrip--20220617.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fatsegnet"] - image = images/neurodesk/neurodesk-fatsegnet--1.0.simg + image = images/neurodesk/neurodesk-fatsegnet--1.0.gpu.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-eeglab"] - image = images/neurodesk/neurodesk-eeglab--2020.simg + image = images/neurodesk/neurodesk-eeglab--2020.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-dsistudio"] - image = images/neurodesk/neurodesk-dsistudio--2020.simg + image = images/neurodesk/neurodesk-dsistudio--2020.10.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-diffusiontoolkit"] - image = images/neurodesk/neurodesk-diffusiontoolkit--0.6.4.simg + image = images/neurodesk/neurodesk-diffusiontoolkit--0.6.4.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-delphi"] - image = images/neurodesk/neurodesk-delphi--0.0.simg + image = images/neurodesk/neurodesk-delphi--0.0.2.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-deepretinotopy"] - image = images/neurodesk/neurodesk-deepretinotopy--1.0.simg + image = images/neurodesk/neurodesk-deepretinotopy--1.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-convert3d"] - image = images/neurodesk/neurodesk-convert3d--1.0.simg + image = images/neurodesk/neurodesk-convert3d--1.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-connectomeworkbench"] - image = images/neurodesk/neurodesk-connectomeworkbench--1.4.simg + image = images/neurodesk/neurodesk-connectomeworkbench--1.5.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-conn"] image = images/neurodesk/neurodesk-conn--20b.simg @@ -378,35 +378,35 @@ image = images/neurodesk/neurodesk-code--220114.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-clearswi"] - image = images/neurodesk/neurodesk-clearswi--1.0.simg + image = images/neurodesk/neurodesk-clearswi--1.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-cat12"] image = images/neurodesk/neurodesk-cat12--r1933.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-brainstorm"] - image = images/neurodesk/neurodesk-brainstorm--3.simg + image = images/neurodesk/neurodesk-brainstorm--3.211130.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-bidstools"] - image = images/neurodesk/neurodesk-bidstools--1.0.simg + image = images/neurodesk/neurodesk-bidstools--1.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-bidscoin"] - image = images/neurodesk/neurodesk-bidscoin--3.7.simg + image = images/neurodesk/neurodesk-bidscoin--3.7.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-bart"] - image = images/neurodesk/neurodesk-bart--0.7.simg + image = images/neurodesk/neurodesk-bart--0.7.00.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-ashs"] - image = images/neurodesk/neurodesk-ashs--2.0.simg + image = images/neurodesk/neurodesk-ashs--2.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-aslprep"] - image = images/neurodesk/neurodesk-aslprep--0.2.simg + image = images/neurodesk/neurodesk-aslprep--0.2.7.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-ants"] - image = images/neurodesk/neurodesk-ants--2.3.simg + image = images/neurodesk/neurodesk-ants--2.3.5.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-aidamri"] - image = images/neurodesk/neurodesk-aidamri--1.simg + image = images/neurodesk/neurodesk-aidamri--1.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-afni"] - image = images/neurodesk/neurodesk-afni--21.2.simg + image = images/neurodesk/neurodesk-afni--23.0.00.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} diff --git a/images/neurodesk/neurodesk-afni--21.2.00.simg b/images/neurodesk/neurodesk-afni--21.2.00.simg new file mode 120000 index 0000000..043ea30 --- /dev/null +++ b/images/neurodesk/neurodesk-afni--21.2.00.simg @@ -0,0 +1 @@ +../../.git/annex/objects/xX/q7/MD5E-s2278383647--284c304cd70ff5e3f4e1270a2afcded2.00.simg/MD5E-s2278383647--284c304cd70ff5e3f4e1270a2afcded2.00.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--21.2.simg b/images/neurodesk/neurodesk-afni--21.2.simg deleted file mode 120000 index 6b7b01d..0000000 --- a/images/neurodesk/neurodesk-afni--21.2.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/WG/FZ/MD5E-s2278383647--284c304cd70ff5e3f4e1270a2afcded2.2.simg/MD5E-s2278383647--284c304cd70ff5e3f4e1270a2afcded2.2.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--22.1.14.simg b/images/neurodesk/neurodesk-afni--22.1.14.simg new file mode 120000 index 0000000..5a72b39 --- /dev/null +++ b/images/neurodesk/neurodesk-afni--22.1.14.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Xx/Mp/MD5E-s2502078495--a39ce5018752585cf0c07cd89e662aad.14.simg/MD5E-s2502078495--a39ce5018752585cf0c07cd89e662aad.14.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--22.1.simg b/images/neurodesk/neurodesk-afni--22.1.simg deleted file mode 120000 index 1d349d0..0000000 --- a/images/neurodesk/neurodesk-afni--22.1.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/ww/VP/MD5E-s2502078495--a39ce5018752585cf0c07cd89e662aad.1.simg/MD5E-s2502078495--a39ce5018752585cf0c07cd89e662aad.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--22.3.06.simg b/images/neurodesk/neurodesk-afni--22.3.06.simg new file mode 120000 index 0000000..9beeaca --- /dev/null +++ b/images/neurodesk/neurodesk-afni--22.3.06.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Z6/Xm/MD5E-s2229780511--4844a374ea162ba9ed116cda5163ad2a.06.simg/MD5E-s2229780511--4844a374ea162ba9ed116cda5163ad2a.06.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--22.3.07.simg b/images/neurodesk/neurodesk-afni--22.3.07.simg new file mode 120000 index 0000000..9315351 --- /dev/null +++ b/images/neurodesk/neurodesk-afni--22.3.07.simg @@ -0,0 +1 @@ +../../.git/annex/objects/9z/Gx/MD5E-s8663834655--a525bf693e5a6a92019b05aabe072cc8.07.simg/MD5E-s8663834655--a525bf693e5a6a92019b05aabe072cc8.07.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--22.3.simg b/images/neurodesk/neurodesk-afni--22.3.simg deleted file mode 120000 index 6edc86a..0000000 --- a/images/neurodesk/neurodesk-afni--22.3.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/VV/G6/MD5E-s8663834655--a525bf693e5a6a92019b05aabe072cc8.3.simg/MD5E-s8663834655--a525bf693e5a6a92019b05aabe072cc8.3.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--23.0.00.simg b/images/neurodesk/neurodesk-afni--23.0.00.simg new file mode 120000 index 0000000..37af168 --- /dev/null +++ b/images/neurodesk/neurodesk-afni--23.0.00.simg @@ -0,0 +1 @@ +../../.git/annex/objects/kZ/28/MD5E-s8608391199--98b305f5ccc068faa6b0e25566855acf.00.simg/MD5E-s8608391199--98b305f5ccc068faa6b0e25566855acf.00.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--23.0.simg b/images/neurodesk/neurodesk-afni--23.0.simg deleted file mode 120000 index 4446a2b..0000000 --- a/images/neurodesk/neurodesk-afni--23.0.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/4G/kw/MD5E-s8608391199--98b305f5ccc068faa6b0e25566855acf.0.simg/MD5E-s8608391199--98b305f5ccc068faa6b0e25566855acf.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-aidamri--1.1.simg b/images/neurodesk/neurodesk-aidamri--1.1.simg new file mode 120000 index 0000000..722e426 --- /dev/null +++ b/images/neurodesk/neurodesk-aidamri--1.1.simg @@ -0,0 +1 @@ +../../.git/annex/objects/F6/fW/MD5E-s3488174111--2f6714db274e2530223cec0e566a5ed5.1.simg/MD5E-s3488174111--2f6714db274e2530223cec0e566a5ed5.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-aidamri--1.simg b/images/neurodesk/neurodesk-aidamri--1.simg deleted file mode 120000 index aa7d224..0000000 --- a/images/neurodesk/neurodesk-aidamri--1.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/25/fv/MD5E-s3488174111--2f6714db274e2530223cec0e566a5ed5.simg/MD5E-s3488174111--2f6714db274e2530223cec0e566a5ed5.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-ants--2.3.1.simg b/images/neurodesk/neurodesk-ants--2.3.1.simg new file mode 120000 index 0000000..7a84303 --- /dev/null +++ b/images/neurodesk/neurodesk-ants--2.3.1.simg @@ -0,0 +1 @@ +../../.git/annex/objects/vQ/16/MD5E-s623202335--bf91169b847dddc05cb6e25171d11422.1.simg/MD5E-s623202335--bf91169b847dddc05cb6e25171d11422.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-ants--2.3.4.simg b/images/neurodesk/neurodesk-ants--2.3.4.simg new file mode 120000 index 0000000..fdb2d3f --- /dev/null +++ b/images/neurodesk/neurodesk-ants--2.3.4.simg @@ -0,0 +1 @@ +../../.git/annex/objects/3m/qj/MD5E-s210243615--b3a201d8a8952626008a40bb11580a43.4.simg/MD5E-s210243615--b3a201d8a8952626008a40bb11580a43.4.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-ants--2.3.5.simg b/images/neurodesk/neurodesk-ants--2.3.5.simg new file mode 120000 index 0000000..c73559c --- /dev/null +++ b/images/neurodesk/neurodesk-ants--2.3.5.simg @@ -0,0 +1 @@ +../../.git/annex/objects/2k/wm/MD5E-s211628063--1f3a86d35e676f7b7913fff3b751e58a.5.simg/MD5E-s211628063--1f3a86d35e676f7b7913fff3b751e58a.5.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-ants--2.3.simg b/images/neurodesk/neurodesk-ants--2.3.simg deleted file mode 120000 index 1fa49c1..0000000 --- a/images/neurodesk/neurodesk-ants--2.3.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/Wg/m0/MD5E-s211628063--1f3a86d35e676f7b7913fff3b751e58a.3.simg/MD5E-s211628063--1f3a86d35e676f7b7913fff3b751e58a.3.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-ashs--2.0.simg b/images/neurodesk/neurodesk-ashs--2.0.0.simg similarity index 100% rename from images/neurodesk/neurodesk-ashs--2.0.simg rename to images/neurodesk/neurodesk-ashs--2.0.0.simg diff --git a/images/neurodesk/neurodesk-aslprep--0.2.7.simg b/images/neurodesk/neurodesk-aslprep--0.2.7.simg new file mode 120000 index 0000000..74afe19 --- /dev/null +++ b/images/neurodesk/neurodesk-aslprep--0.2.7.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Qq/zj/MD5E-s9435635743--fb08c1441d57686b30ea08317ef83275.7.simg/MD5E-s9435635743--fb08c1441d57686b30ea08317ef83275.7.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-aslprep--0.2.simg b/images/neurodesk/neurodesk-aslprep--0.2.simg deleted file mode 120000 index 3c21b33..0000000 --- a/images/neurodesk/neurodesk-aslprep--0.2.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/GX/P0/MD5E-s9435635743--fb08c1441d57686b30ea08317ef83275.2.simg/MD5E-s9435635743--fb08c1441d57686b30ea08317ef83275.2.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-bart--0.7.00.simg b/images/neurodesk/neurodesk-bart--0.7.00.simg new file mode 120000 index 0000000..1f7ef02 --- /dev/null +++ b/images/neurodesk/neurodesk-bart--0.7.00.simg @@ -0,0 +1 @@ +../../.git/annex/objects/vK/9M/MD5E-s129302559--9e14f314e9b2b89fb6f0135d492414b1.00.simg/MD5E-s129302559--9e14f314e9b2b89fb6f0135d492414b1.00.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-bart--0.7.simg b/images/neurodesk/neurodesk-bart--0.7.simg deleted file mode 120000 index 2f7d29f..0000000 --- a/images/neurodesk/neurodesk-bart--0.7.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/G5/6Q/MD5E-s129302559--9e14f314e9b2b89fb6f0135d492414b1.7.simg/MD5E-s129302559--9e14f314e9b2b89fb6f0135d492414b1.7.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-bidscoin--3.7.0.simg b/images/neurodesk/neurodesk-bidscoin--3.7.0.simg new file mode 120000 index 0000000..2a84003 --- /dev/null +++ b/images/neurodesk/neurodesk-bidscoin--3.7.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Jq/Zx/MD5E-s601649183--4644631e969263055c1f681f3b0190bc.0.simg/MD5E-s601649183--4644631e969263055c1f681f3b0190bc.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-bidscoin--3.7.simg b/images/neurodesk/neurodesk-bidscoin--3.7.simg deleted file mode 120000 index da361b9..0000000 --- a/images/neurodesk/neurodesk-bidscoin--3.7.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/mz/Kq/MD5E-s601649183--4644631e969263055c1f681f3b0190bc.7.simg/MD5E-s601649183--4644631e969263055c1f681f3b0190bc.7.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-bidstools--1.0.simg b/images/neurodesk/neurodesk-bidstools--1.0.0.simg similarity index 100% rename from images/neurodesk/neurodesk-bidstools--1.0.simg rename to images/neurodesk/neurodesk-bidstools--1.0.0.simg diff --git a/images/neurodesk/neurodesk-brainstorm--3.simg b/images/neurodesk/neurodesk-brainstorm--3.211130.simg similarity index 100% rename from images/neurodesk/neurodesk-brainstorm--3.simg rename to images/neurodesk/neurodesk-brainstorm--3.211130.simg diff --git a/images/neurodesk/neurodesk-clearswi--1.0.simg b/images/neurodesk/neurodesk-clearswi--1.0.0.simg similarity index 100% rename from images/neurodesk/neurodesk-clearswi--1.0.simg rename to images/neurodesk/neurodesk-clearswi--1.0.0.simg diff --git a/images/neurodesk/neurodesk-connectomeworkbench--1.4.2.simg b/images/neurodesk/neurodesk-connectomeworkbench--1.4.2.simg new file mode 120000 index 0000000..1a00b52 --- /dev/null +++ b/images/neurodesk/neurodesk-connectomeworkbench--1.4.2.simg @@ -0,0 +1 @@ +../../.git/annex/objects/jz/XK/MD5E-s190287903--23a77a3498d7167c7efc94becab31bbb.2.simg/MD5E-s190287903--23a77a3498d7167c7efc94becab31bbb.2.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-connectomeworkbench--1.4.simg b/images/neurodesk/neurodesk-connectomeworkbench--1.4.simg deleted file mode 120000 index eb476a9..0000000 --- a/images/neurodesk/neurodesk-connectomeworkbench--1.4.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/ZM/4K/MD5E-s190287903--23a77a3498d7167c7efc94becab31bbb.4.simg/MD5E-s190287903--23a77a3498d7167c7efc94becab31bbb.4.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-connectomeworkbench--1.5.0.simg b/images/neurodesk/neurodesk-connectomeworkbench--1.5.0.simg new file mode 120000 index 0000000..75cec58 --- /dev/null +++ b/images/neurodesk/neurodesk-connectomeworkbench--1.5.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/fW/j3/MD5E-s2554990623--f3fd4db7699137839aa4cb2918cccfb1.0.simg/MD5E-s2554990623--f3fd4db7699137839aa4cb2918cccfb1.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-connectomeworkbench--1.5.simg b/images/neurodesk/neurodesk-connectomeworkbench--1.5.simg deleted file mode 120000 index e206258..0000000 --- a/images/neurodesk/neurodesk-connectomeworkbench--1.5.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/QZ/0V/MD5E-s2554990623--f3fd4db7699137839aa4cb2918cccfb1.5.simg/MD5E-s2554990623--f3fd4db7699137839aa4cb2918cccfb1.5.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-convert3d--1.0.simg b/images/neurodesk/neurodesk-convert3d--1.0.0.simg similarity index 100% rename from images/neurodesk/neurodesk-convert3d--1.0.simg rename to images/neurodesk/neurodesk-convert3d--1.0.0.simg diff --git a/images/neurodesk/neurodesk-deepretinotopy--1.0.simg b/images/neurodesk/neurodesk-deepretinotopy--1.0.0.simg similarity index 100% rename from images/neurodesk/neurodesk-deepretinotopy--1.0.simg rename to images/neurodesk/neurodesk-deepretinotopy--1.0.0.simg diff --git a/images/neurodesk/neurodesk-delphi--0.0.1.simg b/images/neurodesk/neurodesk-delphi--0.0.1.simg new file mode 120000 index 0000000..9cd3cac --- /dev/null +++ b/images/neurodesk/neurodesk-delphi--0.0.1.simg @@ -0,0 +1 @@ +../../.git/annex/objects/73/83/MD5E-s3810111519--79a3e7049fe886c9ce2673246a015611.1.simg/MD5E-s3810111519--79a3e7049fe886c9ce2673246a015611.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-delphi--0.0.2.simg b/images/neurodesk/neurodesk-delphi--0.0.2.simg new file mode 120000 index 0000000..b77c7cc --- /dev/null +++ b/images/neurodesk/neurodesk-delphi--0.0.2.simg @@ -0,0 +1 @@ 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+../../.git/annex/objects/Qg/Jf/MD5E-s2749784095--9d99ca1801ddb3ccd0135b9d165939c1.7.simg/MD5E-s2749784095--9d99ca1801ddb3ccd0135b9d165939c1.7.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-spinalcordtoolbox--5.8.simg b/images/neurodesk/neurodesk-spinalcordtoolbox--5.8.simg new file mode 120000 index 0000000..01b025b --- /dev/null +++ b/images/neurodesk/neurodesk-spinalcordtoolbox--5.8.simg @@ -0,0 +1 @@ +../../.git/annex/objects/MZ/W5/MD5E-s2672267295--0d9c368fcd759aaa2beea3f40bc5fa8e.8.simg/MD5E-s2672267295--0d9c368fcd759aaa2beea3f40bc5fa8e.8.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-spinalcordtoolbox--5.simg b/images/neurodesk/neurodesk-spinalcordtoolbox--5.simg deleted file mode 120000 index 2a1a6b9..0000000 --- a/images/neurodesk/neurodesk-spinalcordtoolbox--5.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/7f/p3/MD5E-s2672267295--0d9c368fcd759aaa2beea3f40bc5fa8e.simg/MD5E-s2672267295--0d9c368fcd759aaa2beea3f40bc5fa8e.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-surfice--1.0.20210730.simg b/images/neurodesk/neurodesk-surfice--1.0.20210730.simg new file mode 120000 index 0000000..dafb3cc --- /dev/null +++ b/images/neurodesk/neurodesk-surfice--1.0.20210730.simg @@ -0,0 +1 @@ +../../.git/annex/objects/7P/FG/MD5E-s213975071--45e075d92da4ec91e80c30dfa44bd316.simg/MD5E-s213975071--45e075d92da4ec91e80c30dfa44bd316.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-surfice--1.0.simg b/images/neurodesk/neurodesk-surfice--1.0.simg deleted file mode 120000 index 79af787..0000000 --- a/images/neurodesk/neurodesk-surfice--1.0.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/Pg/0x/MD5E-s213975071--45e075d92da4ec91e80c30dfa44bd316.0.simg/MD5E-s213975071--45e075d92da4ec91e80c30dfa44bd316.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-tgvqsm--1.0.simg b/images/neurodesk/neurodesk-tgvqsm--1.0.0.simg similarity index 100% rename from images/neurodesk/neurodesk-tgvqsm--1.0.simg rename to images/neurodesk/neurodesk-tgvqsm--1.0.0.simg diff --git a/images/neurodesk/neurodesk-trackvis--0.6.1.simg b/images/neurodesk/neurodesk-trackvis--0.6.1.simg new file mode 120000 index 0000000..9e94d64 --- /dev/null +++ b/images/neurodesk/neurodesk-trackvis--0.6.1.simg @@ -0,0 +1 @@ +../../.git/annex/objects/8G/WK/MD5E-s103469087--45d6299d7a11236ce078f247d88a3b88.1.simg/MD5E-s103469087--45d6299d7a11236ce078f247d88a3b88.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-trackvis--0.6.simg b/images/neurodesk/neurodesk-trackvis--0.6.simg deleted file mode 120000 index f8f0ebb..0000000 --- a/images/neurodesk/neurodesk-trackvis--0.6.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/Z7/45/MD5E-s103469087--45d6299d7a11236ce078f247d88a3b88.6.simg/MD5E-s103469087--45d6299d7a11236ce078f247d88a3b88.6.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-vesselapp--0.3.1.simg b/images/neurodesk/neurodesk-vesselapp--0.3.1.simg new file mode 120000 index 0000000..892e15a --- /dev/null +++ b/images/neurodesk/neurodesk-vesselapp--0.3.1.simg @@ -0,0 +1 @@ +../../.git/annex/objects/36/J4/MD5E-s4394446879--1e3088b4e47624f6f439244cb8a5670f.1.simg/MD5E-s4394446879--1e3088b4e47624f6f439244cb8a5670f.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-vesselapp--0.3.simg b/images/neurodesk/neurodesk-vesselapp--0.3.simg deleted file mode 120000 index d0899e0..0000000 --- a/images/neurodesk/neurodesk-vesselapp--0.3.simg +++ /dev/null @@ -1 +0,0 @@ -../../.git/annex/objects/qJ/Qk/MD5E-s4394446879--1e3088b4e47624f6f439244cb8a5670f.3.simg/MD5E-s4394446879--1e3088b4e47624f6f439244cb8a5670f.3.simg \ No newline at end of file diff --git a/scripts/create_singularities b/scripts/create_singularities index 4d6f0ae..6eaa193 100755 --- a/scripts/create_singularities +++ b/scripts/create_singularities @@ -161,8 +161,8 @@ class Builder: prior_img = None added, registered = [], 0 for img in all_imgs: - imagefile = (outdir / get_imagename(img.name, 'neurodesk', img.version)).with_suffix(".simg") - if not imagefile.exists(): + imagefile = Path(str(outdir / get_imagename(img.name, 'neurodesk', img.version)) + ".simg") + if not (imagefile.exists() or imagefile.is_symlink()): log.info("%s <- singularity %s", 'neurodesk', img.container) out = dl.download_url( img.urls[0], @@ -176,19 +176,20 @@ class Builder: key, url ) added.append(str(imagefile)) - if img.name != prior_img: - registered += 1 - log.info(" <- register %s %s", img.name, img.version) - self.runcmd( - "datalad", - "containers-add", - get_familyname(img.name, 'neurodesk'), - "-i", - str(imagefile), - "--update", - "--call-fmt", - "{img_dspath}/scripts/singularity_cmd run {img} {cmd}", - ) + if img.name != prior_img: + prior_img = img.name + registered += 1 + log.info(" <- register %s %s", img.name, img.version) + self.runcmd( + "datalad", + "containers-add", + get_familyname(img.name, 'neurodesk'), + "-i", + str(imagefile), + "--update", + "--call-fmt", + "{img_dspath}/scripts/singularity_cmd run {img} {cmd}", + ) if added: ds.repo.set_metadata(files=added, add={'distribution-restrictions': 'out-of-space'}) ds.save(path=added, @@ -392,9 +393,6 @@ def main() -> None: log.error("singularity is 'too new'") sys.exit(1) - builder.add_neurodesk_singularity_images() - return - r = requests.get( "https://raw.githubusercontent.com/BIDS-Apps/bids-apps.github.io/master/_config.yml" ) ```

please have another look

stebo85 commented 1 year ago

Dear @yarikoptic,

quick question: where are we with this? Is it all working and can I document this on the Neurodesk website? Does it need anything from me where I can help?

Kind regards Steffen

yarikoptic commented 1 year ago

oh, right -- totally forgot this one opened. I think "we are done" and we are getting "upgrades" like d3486762991b265cbd6d2e141c207f670c61762c . I would assume that it is all working to the degree it could work here. Would be nice to get some example to solidify it all. Could you point me to some prototypical analysis using one of the containers ?

meanwhile the issue I think could be closed really.

stebo85 commented 1 year ago

Dear @yarikoptic,

I tried using a container with datalad containers-run

datalad containers-run -n neurodesk-bart
[INFO   ] Making sure inputs are available (this may take some time) 
get(error): images/neurodesk/neurodesk-bart--0.7.00.simg (file) [not available; (Note that these git remotes have annex-ignore set: origin)]                                                                                                                                                                                                        
[INFO   ] == Command start (output follows) ===== 
ERROR  : Unknown image format/type: images/neurodesk/neurodesk-bart--0.7.00.simg
ABORT  : Retval = 255
[INFO   ] == Command exit (modification check follows) ===== 
run(error): /home/jovyan/test/containers (dataset) [./scripts/singularity_cmd run images/neu...]
action summary:                                                                                                                                                                                                                                                                                                                                     
  get (error: 1)
  run (error: 1)
  save (notneeded: 1)

other containers work - but the neurodesk containers through this error. Any idea :?

yarikoptic commented 1 year ago

Maaan, you are even a bigger bug magnet than I am! Thank you for that ;)

There is indeed only a handful (21) of neurodesk images which have URLs assigned

```shell $> git annex find --in web | nl 1 images/neurodesk/neurodesk-ashs--2.0.0.simg 2 images/neurodesk/neurodesk-bidstools--1.0.0.simg 3 images/neurodesk/neurodesk-brainstorm--3.211130.simg 4 images/neurodesk/neurodesk-cat12--r1933.simg 5 images/neurodesk/neurodesk-clearswi--1.0.0.simg 6 images/neurodesk/neurodesk-code--220114.simg 7 images/neurodesk/neurodesk-conn--20b.simg 8 images/neurodesk/neurodesk-convert3d--1.0.0.simg 9 images/neurodesk/neurodesk-deepretinotopy--1.0.0.simg 10 images/neurodesk/neurodesk-fieldtrip--20211114.simg 11 images/neurodesk/neurodesk-fieldtrip--20220617.simg 12 images/neurodesk/neurodesk-freesurfer--7.1.1.simg 13 images/neurodesk/neurodesk-hdbet--1.0.0.simg 14 images/neurodesk/neurodesk-matlab--2022a.simg 15 images/neurodesk/neurodesk-mne--1.1.1.simg 16 images/neurodesk/neurodesk-palm--alpha119.simg 17 images/neurodesk/neurodesk-physio--r2021a.simg 18 images/neurodesk/neurodesk-physio--r7771.simg 19 images/neurodesk/neurodesk-slicersalt--3.0.0.simg 20 images/neurodesk/neurodesk-spm12--r7771.simg 21 images/neurodesk/neurodesk-tgvqsm--1.0.0.simg ```

whenever most do not have ANY!

```shell $> git annex find --not --in web | grep neurodesk | nl 1 images/neurodesk/neurodesk-afni--21.2.00.simg 2 images/neurodesk/neurodesk-afni--22.1.14.simg 3 images/neurodesk/neurodesk-afni--22.3.06.simg 4 images/neurodesk/neurodesk-afni--22.3.07.simg 5 images/neurodesk/neurodesk-afni--23.0.00.simg 6 images/neurodesk/neurodesk-afni--23.0.04.simg 7 images/neurodesk/neurodesk-afni--23.0.07.simg 8 images/neurodesk/neurodesk-aidamri--1.1.simg 9 images/neurodesk/neurodesk-ants--2.3.1.simg 10 images/neurodesk/neurodesk-ants--2.3.4.simg 11 images/neurodesk/neurodesk-ants--2.3.5.simg 12 images/neurodesk/neurodesk-aslprep--0.2.7.simg 13 images/neurodesk/neurodesk-bart--0.7.00.simg 14 images/neurodesk/neurodesk-bidscoin--3.7.0.simg 15 images/neurodesk/neurodesk-code--230315.simg 16 images/neurodesk/neurodesk-connectomeworkbench--1.4.2.simg 17 images/neurodesk/neurodesk-connectomeworkbench--1.5.0.simg 18 images/neurodesk/neurodesk-delphi--0.0.1.simg 19 images/neurodesk/neurodesk-delphi--0.0.2.simg 20 images/neurodesk/neurodesk-diffusiontoolkit--0.6.4.1.simg 21 images/neurodesk/neurodesk-dsistudio--2020.10.simg 22 images/neurodesk/neurodesk-eeglab--2020.0.simg 23 images/neurodesk/neurodesk-fatsegnet--1.0.gpu.simg 24 images/neurodesk/neurodesk-fmriprep--20.1.3.simg 25 images/neurodesk/neurodesk-fmriprep--20.2.3.simg 26 images/neurodesk/neurodesk-fmriprep--20.2.6.simg 27 images/neurodesk/neurodesk-fmriprep--21.0.1.simg 28 images/neurodesk/neurodesk-fmriprep--22.1.1.simg 29 images/neurodesk/neurodesk-fmriprep--23.0.0.simg 30 images/neurodesk/neurodesk-freesurfer--7.2.0.simg 31 images/neurodesk/neurodesk-freesurfer--7.3.2.simg 32 images/neurodesk/neurodesk-fsl--6.0.3.simg 33 images/neurodesk/neurodesk-fsl--6.0.4.simg 34 images/neurodesk/neurodesk-fsl--6.0.5.1.simg 35 images/neurodesk/neurodesk-gimp--2.10.18.simg 36 images/neurodesk/neurodesk-itksnap--3.8.0.simg 37 images/neurodesk/neurodesk-julia--1.4.1.simg 38 images/neurodesk/neurodesk-lashis--1.0.simg 39 images/neurodesk/neurodesk-lashis--2.0.simg 40 images/neurodesk/neurodesk-laynii--2.2.1.simg 41 images/neurodesk/neurodesk-lcmodel--6.3.simg 42 images/neurodesk/neurodesk-mfcsc--1.0.simg 43 images/neurodesk/neurodesk-mfcsc--1.1.simg 44 images/neurodesk/neurodesk-mgltools--1.5.7.simg 45 images/neurodesk/neurodesk-minc--1.9.17.simg 46 images/neurodesk/neurodesk-minc--1.9.18.simg 47 images/neurodesk/neurodesk-mne--0.23.4.simg 48 images/neurodesk/neurodesk-mne--1.0.0.simg 49 images/neurodesk/neurodesk-mne--1.0.3.simg 50 images/neurodesk/neurodesk-mneextended--1.1.0.simg 51 images/neurodesk/neurodesk-mricrogl--1.2.20211006.simg 52 images/neurodesk/neurodesk-mricron--1.0.20190902.simg 53 images/neurodesk/neurodesk-mriqc--0.16.1.simg 54 images/neurodesk/neurodesk-mriqc--22.0.6.simg 55 images/neurodesk/neurodesk-mritools--3.3.0.simg 56 images/neurodesk/neurodesk-mrsiproc--0.0.1.simg 57 images/neurodesk/neurodesk-mrtrix3--3.0.1.simg 58 images/neurodesk/neurodesk-mrtrix3--3.0.2.simg 59 images/neurodesk/neurodesk-mrtrix3--3.0.3.simg 60 images/neurodesk/neurodesk-mrtrix3tissue--5.2.8.simg 61 images/neurodesk/neurodesk-niftyreg--1.4.0.simg 62 images/neurodesk/neurodesk-niistat--1.0.20191216.simg 63 images/neurodesk/neurodesk-nipype--1.8.3.simg 64 images/neurodesk/neurodesk-oshyx--0.3.simg 65 images/neurodesk/neurodesk-oshyx--0.4.simg 66 images/neurodesk/neurodesk-qsmxt--1.1.10.simg 67 images/neurodesk/neurodesk-qsmxt--1.1.13.simg 68 images/neurodesk/neurodesk-qsmxt--1.1.9.simg 69 images/neurodesk/neurodesk-qsmxt--1.3.2.simg 70 images/neurodesk/neurodesk-qsmxt--1.3.3.simg 71 images/neurodesk/neurodesk-qsmxt--1.3.4.simg 72 images/neurodesk/neurodesk-qsmxt--1.3.5.simg 73 images/neurodesk/neurodesk-rabies--0.3.5.simg 74 images/neurodesk/neurodesk-romeo--3.2.4.simg 75 images/neurodesk/neurodesk-romeo--3.2.7.simg 76 images/neurodesk/neurodesk-romeo--3.2.8.simg 77 images/neurodesk/neurodesk-root--6.22.02.simg 78 images/neurodesk/neurodesk-rstudio--1.4.1106.simg 79 images/neurodesk/neurodesk-rstudio--2022.07.2.simg 80 images/neurodesk/neurodesk-sigviewer--0.6.4.simg 81 images/neurodesk/neurodesk-slicer--4.11.20200930.simg 82 images/neurodesk/neurodesk-slicer--5.0.3.simg 83 images/neurodesk/neurodesk-sovabids--0.3.1a0.simg 84 images/neurodesk/neurodesk-spinalcordtoolbox--5.4.simg 85 images/neurodesk/neurodesk-spinalcordtoolbox--5.5.simg 86 images/neurodesk/neurodesk-spinalcordtoolbox--5.6.simg 87 images/neurodesk/neurodesk-spinalcordtoolbox--5.7.simg 88 images/neurodesk/neurodesk-spinalcordtoolbox--5.8.simg 89 images/neurodesk/neurodesk-surfice--1.0.20210730.simg 90 images/neurodesk/neurodesk-trackvis--0.6.1.simg 91 images/neurodesk/neurodesk-vesselapp--0.3.1.simg 92 images/neurodesk/neurodesk-vina--1.2.3.simg ```

I am staring at the code which should have added URLs -- https://github.com/ReproNim/containers/blob/master/scripts/create_singularities#L125 -- and do not get (without debugging) how that could have happened, besides (just thinking aloud) that git-annex managed to skip some (invalid?) ones somehow... I will debug, and might add it as a test of some kind

yarikoptic commented 1 year ago

uff -- long friday, filed an issue against git-annex -- https://git-annex.branchable.com/bugs/registerurl_does_not_register_if_external_remote/?updated

stebo85 commented 1 year ago

wow - what a bug :/ Sorry to have attracted that one - it looks difficult to debug because to me there is currently no logical pattern why some work and some don't. I hope someone can point us to the root cause of this or any pointers in the right direction.

yarikoptic commented 1 year ago

never enough tests... and here is there is none for availability...

ok -- worked around via actions performed in https://github.com/ReproNim/containers/blob/HEAD/scripts/utils/get-rid-of-datalad-remote.sh which should mitigate this issue.

Now I get an empty

$> git annex find  --not --in web --and --not --in datalad-public

which I now made into a "test" within f406b16e84a68d94ba143e019198915aede3e4a4

Please check again if all is kosher now on a fresh clone, or just after smth like datalad update

stebo85 commented 1 year ago

Dear @yarikoptic,

That works perfectly now :) Thank you so much for fixing that!

One little question before I document this on the neurodesk website:

Currently it only seems possible to pull the latest version of each container.

Running:

datalad containers-run -n neurodesk-afni

downloads images/neurodesk/neurodesk-afni--23.0.07.simg

but it doesn't seem possible to run something like:

datalad containers-run -n images/neurodesk/neurodesk-afni--22.3.07.simg

How would a user access a specific version?

Thank you Steffen

yarikoptic commented 1 year ago

Currently it only seems possible to pull the latest version of each container.

this is just a default behavior ;)

User can

create a new definition of a container they like either directly in their clone of the repo, e.g. smth like neurodesk-afni-22.3.05 which would have a copy of that original definition but pointing to that other version image. Just look into .datalad/config where those definitions are - we hope it is kinda self-explanatory ;)
use the helper we have https://github.com/ReproNim/containers/blob/master/scripts/freeze_versions to "freeze" existing container definition to some version (see more doc in the header of that file... eh -- need to make it a little more proper)
with that helper they can actually follow a recently introduced "more proper" way described in https://github.com/ReproNim/containers#runnable-script (and yet to be adjusted in detailed explanation, #90 ) -- to copy that definition into superdataset which would contain this containers dataset.

I hope this is clear'ish enough. Feedback (and contributions) are always welcome to improve things.

stebo85 commented 1 year ago

Dear @yarikoptic

cool - that default behavior makes a lot of sense :) And it's great versions can be changed in addition (and frozen!)

I tested the freez_versions script and found a little bug (sorry - but I think you are right about that bug magnet hypothesis):

scripts/freeze_versions neurodesk-romeo=3.2.4
topd_rel: 
I: neurodesk-romeo -> 3.2.4
ERROR:  There is no ./images/neurodesk/neurodesk-romeo--3.2.4.sing .  Available images for the app are:
  ./images/neurodesk/neurodesk-romeo--3.2.4.simg
  ./images/neurodesk/neurodesk-romeo--3.2.7.simg
  ./images/neurodesk/neurodesk-romeo--3.2.8.simg

It assumes .sing as file ending?

However, changing the versions in .datalad/config worked like a charm and I now documented that on our website: https://www.neurodesk.org/docs/neurocontainers/datalad/

Thank you Steffen

stebo85 commented 1 year ago

Dear @yarikoptic,

Your freeze_versions fix is perfect :) It works nicely now to change the versions

scripts/freeze_versions neurodesk-romeo=3.2.4
topd_rel: 
I: neurodesk-romeo -> 3.2.4

I documented this option as well on our website: https://www.neurodesk.org/docs/neurocontainers/datalad/#option-2-change-version-using-freeze_versions-script

Thank you Steffen

yarikoptic commented 1 year ago

Great, thank you for the feedback! Let's again consider this overall issue addressed ;-)

ReproNim / containers

Add neurodesk singularity containers to the collection #64