ENH: run: Move the image from inputs to extra_inputs

[kyleam]

containers-run builds on run, augmenting the input list with a
Singularity image. This means that if a user then puts "{inputs}" in
their command, the image file is included too. This is almost
certainly surprising to the user because the user has not explicitly
specified the image with --input and is probably not aware that
containers-run adds it. Avoid this by using run_command's recently
added extra_inputs argument.

This depends on datalad/datalad#3038.

Closes #38.

[yarikoptic]

We shouldn't forget to boost version dependency on datalad before releasing this one

[yarikoptic]

FWIW #3038 is merged. I thought we merged this one as well and thought to use it.

[codecov]

Codecov Report

Merging #60 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master      #60   +/-   ##
=======================================
  Coverage   85.48%   85.48%           
=======================================
  Files          14       14           
  Lines         627      627           
=======================================
  Hits          536      536           
  Misses         91       91

Impacted Files	Coverage Δ
datalad_container/containers_run.py	86.79% <100%> (ø)	⬆️

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[yarikoptic]

I think I ran into this issue again, forgot that I probably installed from your PR branch, then upgraded to current master, and kaboom ... took some time to arrive back to this PR to recall details - downgraded to your PR branch and now it works again.
we should definitely finish up/merge this PR asap, restarted travis builds

[kyleam]

we should definitely finish up/merge this PR asap, restarted travis builds

I'll leave merging up to you.

I'm hesitant to merge it because that means it might be released, along with the required datalad version bump, before there is a fix for datalad/datalad#3087 (fallout from datalad/datalad#3009), which breaks the "dhub://" prefix. It looks like the current plan for 3087 is to wait for revolution pr to be merged (datalad/datalad#3106), though IMO 3087 is a bigger issue than original issues addressed by 3009, and it'd be better to revert the changes from 3009 while we wait for the revolution pr.

[yarikoptic]

oh right -- good analysis, thanks! I should get back to the datalad/datalad#3106 and see what could be done, especially given @mih 's feedback. Any help would be most welcome!

[yarikoptic]

although i failed to fix that datalad/datalad#3087 yet (may be revolution would just fix it all!) is this change anyhow directly demands it? if not, I would say we should merge -- I keep needing this fix, and haven't used dhub:// yet -- all images I use are singularity.

[kyleam]

is this change anyhow directly demands it?

I don't have anything to add to what I said above.

[kyleam]

Rebased and bumped DataLad dependency in setup.py.

range-diff

1:  70fe020 ! 1:  d2dd8d7 RF: run: Use run_command()
    @@ -17,7 +17,7 @@
     +from datalad.interface.run import run_command
      from datalad.interface.run import get_command_pwds
      from datalad.interface.run import normalize_command
    - from datalad_container.containers_list import ContainersList
    + from datalad_container.find_container import find_container
     @@
              inputs = (inputs or []) + [image_path]
      
    @@ -25,7 +25,7 @@
     -        for r in Run.__call__(
     +        for r in run_command(
                      cmd=cmd,
    -                 dataset=ds,
    +                 dataset=dataset or (ds if ds.path == pwd else None),
                      inputs=inputs,
     @@
                      message=message,
2:  7e03c5e ! 2:  89e9f03 ENH: run: Move the image from inputs to extra_inputs
    @@ -26,7 +26,7 @@
              # fire!
              for r in run_command(
                      cmd=cmd,
    -                 dataset=ds,
    +                 dataset=dataset or (ds if ds.path == pwd else None),
                      inputs=inputs,
     +                extra_inputs=[image_path],
                      outputs=outputs,
-:  ------- > 3:  2036812 MNT: setup.py: Bump require DataLad version for extra_inputs

[yarikoptic]

datalad/datalad#3106 is ready for review to address the issue with adding directories. Unless some show stopped is found, it should make it into datalad 0.11.5

[yarikoptic]

I kicked 0.11.5 out -- so after conflicts resolved we could merge/release!

[kyleam]

Didn't realize there was yet another round of conflicts. Will update.