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datalad-tutorial-binder's Issues

Problem cloning dataset from Binder using https: `Remote origin not usable by git-annex`

Summary

Running datalad clone from a Jupyter notebook in Binder (using https) gives the following:

[INFO   ] Remote origin not usable by git-annex; setting annex-ignore 
[INFO   ] https://github.com/psychoinformatics-de/paper-remodnav.git/config download failed: Not Found

Then, running datalad get recursively fails due to an ssh connection problem.

Is this something specific to the dataset? Or should the original clone be done with ssh (i.e. the Binder git user and key should be updated?)

Full description

When running the Jupyter notebook in Binder, there is a section that clones the remodnav dataset. The original clone instruction uses ssh. For the notebook, this was changed (in the Binder session) https.

Then, running the line:

!datalad clone https://github.com/psychoinformatics-de/paper-remodnav.git

yields the following output:

Clone attempt:   0%|              | 0.00/2.00 [00:00<?, ? Candidate locations/s]
Enumerating: 0.00 Objects [00:00, ? Objects/s]
                                              
Counting:   0%|                                | 0.00/241 [00:00<?, ? Objects/s]
                                                                                
Compressing:   0%|                             | 0.00/131 [00:00<?, ? Objects/s]
                                                                                
Receiving:   0%|                             | 0.00/1.55k [00:00<?, ? Objects/s]
Receiving:  44%|█████████▋            | 682/1.55k [00:00<00:00, 2.82k Objects/s]
Receiving:  72%|██████████████▍     | 1.12k/1.55k [00:00<00:00, 2.62k Objects/s]
                                                                                
Resolving:   0%|                                | 0.00/930 [00:00<?, ? Deltas/s]
Resolving:  47%|███████████▊             | 438/930 [00:00<00:00, 3.16k Deltas/s]
Resolving:  82%|████████████████████▌    | 763/930 [00:00<00:00, 2.10k Deltas/s]
[INFO   ] Scanning for unlocked files (this may take some time)                 
[INFO   ] Remote origin not usable by git-annex; setting annex-ignore 
[INFO   ] https://github.com/psychoinformatics-de/paper-remodnav.git/config download failed: Not Found 
install(ok): /home/jovyan/code/paper-remodnav (dataset)

This then leads to an error when trying to access the subdataset files via

!datalad get --recursive --recursion-limit 2 -n .

The full output trace:

Clone attempt: 100%|███████| 3.00/3.00 [00:00<00:00, 5.49 Candidate locations/s]ssh: connect to host github.com port 22: Connection timed out
[ERROR  ] Failed to clone from any candidate source URL. Encountered errors per each url were:
| - https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav
  CommandError: 'git clone --progress https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav /home/jovyan/code/paper-remodnav/remodnav' failed with exitcode 128 [err: 'Cloning into '/home/jovyan/code/paper-remodnav/remodnav'...
remote: Not Found
fatal: repository 'https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/' not found']
- https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/.git
  CommandError: 'git clone --progress https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/.git /home/jovyan/code/paper-remodnav/remodnav' failed with exitcode 128 [err: 'Cloning into '/home/jovyan/code/paper-remodnav/remodnav'...
remote: Not Found
fatal: repository 'https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/.git/' not found']
- [email protected]:psychoinformatics-de/remodnav.git
  ConnectionOpenFailedError: 'ssh -fN -o ControlMaster=auto -o ControlPersist=15m -o ControlPath=/home/jovyan/.cache/datalad/sockets/abe403d5 [email protected]' failed with exitcode 255 [Failed to open SSH connection (could not start ControlMaster process)] [install(/home/jovyan/code/paper-remodnav/remodnav)] 
install(error): /home/jovyan/code/paper-remodnav/remodnav (dataset) [Failed to clone from any candidate source URL. Encountered errors per each url were:
- https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav
  CommandError: 'git clone --progress https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav /home/jovyan/code/paper-remodnav/remodnav' failed with exitcode 128 [err: 'Cloning into '/home/jovyan/code/paper-remodnav/remodnav'...
remote: Not Found
fatal: repository 'https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/' not found']
- https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/.git
  CommandError: 'git clone --progress https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/.git /home/jovyan/code/paper-remodnav/remodnav' failed with exitcode 128 [err: 'Cloning into '/home/jovyan/code/paper-remodnav/remodnav'...
remote: Not Found
fatal: repository 'https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav/.git/' not found']
- [email protected]:psychoinformatics-de/remodnav.git
  ConnectionOpenFailedError: 'ssh -fN -o ControlMaster=auto -o ControlPersist=15m -o ControlPath=/home/jovyan/.cache/datalad/sockets/abe403d5 [email protected]' failed with exitcode 255 [Failed to open SSH connection (could not start ControlMaster process)]]
[INFO   ] Installing Dataset(/home/jovyan/code/paper-remodnav) to get /home/jovyan/code/paper-remodnav/remodnav recursively 
Clone attempt: 100%|███████| 3.00/3.00 [00:00<00:00, 4.99 Candidate locations/s]ssh: connect to host github.com port 22: Connection timed out

Ideal scenario / next steps

Ideally, cloning operations for tutorials/snippets like these should be done via https.

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