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MetaCell / geppetto-scidash

Geppetto scidash extension
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missing dependency #511

Open zsinnema opened 3 years ago

zsinnema commented 3 years ago

hi @rgerkin

I'm trying to setup my dev env on my computer.

I get this error when I try to install neuronunit

(venv) zoran@zoran-XPS-15-9560:/opt/projects/metacell/scidash/scidash$ pip install git+git://github.com/scidash/neuronunit@metacell#egg=neuronunit
Collecting neuronunit
  Cloning git://github.com/scidash/neuronunit (to revision metacell) to /tmp/pip-install-kxue2wgg/neuronunit
  Running command git clone -q git://github.com/scidash/neuronunit /tmp/pip-install-kxue2wgg/neuronunit
  Running command git checkout -b metacell --track origin/metacell
  Switched to a new branch 'metacell'
  Branch 'metacell' set up to track remote branch 'metacell' from 'origin'.
  Running command git submodule update --init --recursive -q
Collecting allensdk==0.14.5
  Using cached allensdk-0.14.5.tar.gz (494 kB)
Collecting bluepyopt@ git+https://github.com/russelljjarvis/BluePyOpt@scidash#egg=bluepyopt-9999
  Cloning https://github.com/russelljjarvis/BluePyOpt (to revision scidash) to /tmp/pip-install-kxue2wgg/bluepyopt
  Running command git clone -q https://github.com/russelljjarvis/BluePyOpt /tmp/pip-install-kxue2wgg/bluepyopt
  WARNING: Did not find branch or tag 'scidash', assuming revision or ref.
  Running command git checkout -q scidash
  error: pathspec 'scidash' did not match any file(s) known to git
ERROR: Command errored out with exit status 1: git checkout -q scidash Check the logs for full command output.

I've checked the repo https://github.com/russelljjarvis/BluePyOptBU and it seems that there is no scidash branch/tag there

zsinnema commented 3 years ago

can I use another branch? e.g. master

rgerkin commented 3 years ago

You can use master. But I also just simplified the requirements a bit in metacell branch. Try installing again from metacell branch and see if it works.

rgerkin commented 3 years ago

Metacell branch still doesn't work. I'll let you know here when I have something that builds successfully in Travis. pip always makes breaking changes.

zsinnema commented 3 years ago

thanks @rgerkin please keep me posted on the progress

rgerkin commented 3 years ago

@zsinnema OK it builds now: https://travis-ci.org/github/scidash/neuronunit/jobs/767745905

zsinnema commented 3 years ago

perfect! thanks