Publisher

[glatard]

bosh-publish finds valid Boutiques descriptors in a local Git repository and generate OWL objects to be added to the Neurolinks index. It could be extended using PyGihub to automatically PR in Neurolinks.

[coveralls]

Coverage increased (+1.9%) to 78.511% when pulling 4c744ba on glatard:publisher into bcdd421 on boutiques:develop.

[gkiar]

I'm in the process of migrating neurolinks to using json files - I'm not great at javascript so it'll take some time, but I'll comment back here with a template for how we should produce entries once that is complete (hopefully after this weekend).

In the mean time, we'll keep this open.

[gkiar]

nl:neurodocker was specific for a certain tool - we want to set a unique identifier of nl:..... for each new tool, and ensure that it is unique

[gkiar]

no semi-colon after this line, and I'm not sure about the : between has_boutiques and true, either... it didn't work at first attempt but I changed this and the above simultaneously so don't know what did the trick. I think this is a problem though.

[glatard]

sounds good! I'll wait for the JSON implementation.

[gkiar]

Updated JSON implementation for neurolinks, as described here

[coveralls]

Coverage decreased (-3.7%) to 72.934% when pulling c7af2a5 on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-3.6%) to 73.032% when pulling ae5f8d9 on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-3.6%) to 73.032% when pulling 37dc21f on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-3.6%) to 73.032% when pulling f6efe05 on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-3.6%) to 73.032% when pulling 77fdfe9 on glatard:publisher into bcdd421 on boutiques:develop.

[gkiar]

Currently this is my situation when installing from your fork:

$ virtualenv myenv -p python3.6 & source myenv/bin/activate
$ pip install -e .
$ cd /gitrepo/with/boutiques/descriptors
$ bosh-publish
Traceback (most recent call last):
  File "/Users/greg/code/gkiar/boutiques/tools/python/env/boutiques3.6/bin/bosh-publish", line 11, in <module>
    load_entry_point('boutiques', 'console_scripts', 'bosh-publish')()
  File "/Users/greg/code/gkiar/boutiques/tools/python/boutiques/publisher.py", line 364, in main
    results.github_login, results.github_password, results.no_github).publish()
  File "/Users/greg/code/gkiar/boutiques/tools/python/boutiques/publisher.py", line 78, in __init__
    self.fix_github_credentials()
  File "/Users/greg/code/gkiar/boutiques/tools/python/boutiques/publisher.py", line 112, in fix_github_credentials
    username = self.get_from_stdin("GitHub login")
  File "/Users/greg/code/gkiar/boutiques/tools/python/boutiques/publisher.py", line 166, in get_from_stdin
    answer = raw_input(prompt)
NameError: name 'raw_input' is not defined

I get the same error when running from an unrelated dir and passing the location with the -b flag. For reference, I'm using this repo: https://github.com/neurodata/boutiques-tools/

(dismissing out of date review)

[coveralls]

Coverage decreased (-3.8%) to 72.834% when pulling 95b0b97 on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-3.8%) to 72.834% when pulling 95b0b97 on glatard:publisher into bcdd421 on boutiques:develop.

[glatard]

@gkiar, thanks for the review, it should be fixed now!

[coveralls]

Coverage increased (+5.0%) to 81.593% when pulling c4b6f0d on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-2.3%) to 74.361% when pulling 09ae1bf on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-2.3%) to 74.361% when pulling 09ae1bf on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage decreased (-2.3%) to 74.361% when pulling 09ae1bf on glatard:publisher into bcdd421 on boutiques:develop.

[coveralls]

Coverage increased (+5.0%) to 81.593% when pulling c4b6f0d on glatard:publisher into bcdd421 on boutiques:develop.