scripts and doc re-organisation

[jburel]

• Re-organise the documentation. The original file has now be broken in several files
• Migrate with history groovy script from training-scripts repo
• Include code snippets
• Provide python script similar to notebook

This should make it easier to include example and doc using zarr files. The "tracking mitosis" file will be reviewed in an other PR and replace if possible with a notebook using IDR cc @pwalczysko

[pwalczysko]

I think we have to unify the order of the parts Setup and Resources. There are both cases in the different Ilastik guide chapters, Setup before Resoureces and also Setup after Resources (e.g. Getting started with ilastik API ... and Use ilastik as a Fiji plugin... have different order)

[jburel]

order swapped

[pwalczysko]

conda env update -n ilastik --file binder/environment.yml
....
UnsatisfiableError: The following specifications were found                     
to be incompatible with the existing python installation in your environment:

Specifications:

  - ilastik-meta -> python[version='>=3.7,<3.8.0a0']
  - omero-py -> python[version='2.7.*|3.5.*|3.7.*']
  - omero-py -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.8,<3.9.0a0']
  - pip -> python=3.7

Your python: python=3.6
...

When following

[jburel]

I copied this section from CP, this won't work since few more things need to happen

[pwalczysko]

The other fixes look good. The https://github.com/ome/omero-guide-ilastik/pull/10#issuecomment-618435274 needs to be checked. Mybinder was also failing for me now to build the notebook, but will come to that later.

[jburel]

@pwalczysko https://github.com/ome/omero-guide-ilastik/pull/10#issuecomment-618435274 should be fixed

[jburel]

I have checked on mybinder again this morning and it works Did you use the correct repo and branch?

[pwalczysko]

I have checked on mybinder again this morning and it works Did you use the correct repo and branch?

Sorry, did not understand about the branches. Tried again with this repo here and the branch scripts. Binder worked fine, saved 2 probability images ot OMERO (connection failed after that)

It seems to work.

[jburel]

are you happy with the current state? Still some work to be done on the mitosis front, but that will happen in another PR

[pwalczysko]

Sorry, still cannot find this bit in the code The part below is very abrupt - I installed my ilastik and omero-py into the conda env as instructed. Instead of telling me what comes next, it says: Alternatively, do repo2docker. And after that, only the repo2docker story line is followed. Some conclusion would be good, like "now start using the ilastik API using the other chapter in this section ?".

[jburel]

I guess the "bit" you indicating is the command in binder/postBuild

[pwalczysko]

Where is binder/postBuild ? - actually, sorry about the blue highlight in my screenshot, this is irrelevant - by bit I mean the whole page, including the whole section in the screenshot

[jburel]

there is a folder named binder and you will a file postBuild in the omero-guide-ilastik directory

[pwalczysko]

The new Options in the installation instructions look fine.

Also, did the install of ilastik locally and then ran the pixel_slassification.py script from the local environment. It gives some error messages at the start, but it works as expected, the probabilities image was saved to OMERO.

Running repo2docker . now

[pwalczysko]

repo2docker works as expected too. I think this gives us a nice range of use cases. Thanks Ready to merge fmpov.

[jburel]

Thanks @pwalczysko for the review and the feedback I will merge so we have the new doc updated