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Yaroslav Halchenko yarikoptic
Repositories Public Activity

yarikoptic commented on issue TheChymera/mvmdna#5

mvdmlab users cannot see data or write new data because ownership is `root:con`

Hi @kleaman, sorry for the delay. Now I made `/mnt/DATA/data` world readable and made sure that your user can access it:

1 year ago

yarikoptic commented on issue TheChymera/mvmdna#5

mvdmlab users cannot see data or write new data because ownership is `root:con`

I have done JOIN on subject and text to get the meaning of "they"... accomplished the mission - "they" should be able to access it as well as anyone else, so keep that in mind - may be protect individual folders by forbidding "o"thers to access them, and share at the group level.

1 year ago

yarikoptic commented on issue TheChymera/mvmdna#2

Can neuroconv do neuropixels conversion, or do we have to wrap Spikeinterfaces ourselves?

checkout https://github.com/catalystneuro/neuroconv/blob/57100c814b44942d37ad5abd046662bb2aaf823b/docs/conversion_examples_gallery/recording/spikeglx.rst#L43

1 year ago

yarikoptic created pull request NeuralEnsemble/BEP032-examples#13

change layout, fix and extend requirements.txt, place it under git not annex (as any other code)

1 year ago

yarikoptic pushed to relayout at yarikoptic/BEP032-examples

  • 4bbb2c9dca Add pandas and scipy to code/requirements.txt
  • d590719228 fixup: fix variable name typoed before
  • b24b1bb8c2 Make code/create_rawdata.py executable and gain a shebang
  • a50e36518e [DATALAD RUNCMD] Move sourcedata/ to the top for consistency, and replace with symlink for selfsufficiency within rawdata/ If we were using git/datalad 'properly' here, sourcedata/ should have been its own dataset, so it could have been reused possibly in another BIDS dataset, where they might have had their own ideas on harmonization. And then it could have been 'installed' within a corresponding 'rawdata' dataset as 'sourcedata'. But here we are self-contained repository with examples. So for consistency we kept sourcedata/ on the top level, and symlinked into rawdata/. I was arguing against it and thought to keep sourcedata/ only under rawdata/. But I lost to Christian. Note 1: Instead of a symlink we could have relied on SourceDatasets field in dataset_description.json like it exampled in https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#source-vs-raw-vs-derived-data and overall described in https://bids-specification.readthedocs.io/en/stable/glossary.html#sourcedatasets-metadata . Note 2: datalad 0.19.3 did screw up and failed to commit the move result. We have git added symlink file manually and now --amending this commit with the rest which is already staged. === Do not change lines below === { "chain": [], "cmd": "git mv rawdata/sourcedata .; ( cd rawdata; ln -s ../sourcedata . )", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "ephys_neuropixel" } ^^^ Do not change lines above ^^^
  • 06ebc1a983 Move requirements.txt into git, and fix URLs to be git+http:// ones so pip can use them

1 year ago

yarikoptic created new branch relayout at yarikoptic/BEP032-examples

1 year ago

yarikoptic forked a repository to yarikoptic/BEP032-examples

1 year ago

yarikoptic opened issue lukko45/PROJECT_DAYS_P3_NUMBERS#1

might be containing sensitive data

3 years ago

yarikoptic opened issue NeuralEnsemble/ephy_testing_data#51

Make a versioned release and make it "registered" so would get a DOI etc

3 years ago

yarikoptic pushed to master at dandi/nwb-healthstatus-samples

3 years ago

yarikoptic created repository dandi/nwb-healthstatus-samples

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

seems to be good to me.

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

Files committed to annex as "unlocked". Pros: upon `annex get` (or `datalad get`) they will appear as real files and not as symlinks. Cons: you would have two copies (thus consuming twice more space; git status would be slower since file would might need to go through git smudge filtering to decide if modified, etc) -- one in the work tree, another under `.git/annex/objects`. Because of that some older (e.g. as of 2019/09) versions of annex might have difficulties (not getting files), but if more recent ones used, then seems to work quite fine

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

> , this still seems to grow relatively quickly when uploading via gin (e.g. from hundrets of kilobyte to a couple of MB)

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

> @yarikoptic Did you push the resulting repositories of your two recipes already somewhere on gin, so we could run some tests before converting the main repo?

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

> @yarikoptic would you be interested having direct write access on this repo ?

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

BTW, here is a relevant section in the datalad handbook on interoperability with Gin: http://handbook.datalad.org/en/latest/basics/101-139-gin.html

3 years ago

yarikoptic commented on issue NeuralEnsemble/ephy_testing_data#29

Add .gitattributes / rewrite (redo) to minimize .git/objects

> unless there are version conflicts between git annex versions used by datalad and gin.

3 years ago