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[DOC] Update documentation #65

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merged 15 commits into from
Dec 21, 2020

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@sebastientourbier sebastientourbier commented Dec 15, 2020

List of changes:

  • Update the documentation to explain how to install and use singularity and the new wrapper (Fix Update documentation to explain how to run on cluster and uses the singularity image #64)
  • Rename the container image to be simply mialsuperresolutiontoolkit
  • Use Nipype sphinx extension for generation of the documentation of the interfaces
  • Review all docstrings and the desc= argument of all nipype input and output class attributes for correct rendering using the new nipype sphinx extension, that uses directly the desc= argument of all the input and output class attributes so that we do not have to describe the attributes again.

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sebastientourbier commented Dec 15, 2020

@pdedumast @hamzake Should be ready to merge this PR, waiting all tests pass and your review. In particular it includes:

List of changes:

* Update the documentation to explain how to install and use singularity and the new wrapper (Fix #64)

* Rename the container image to be simply `mialsuperresolutiontoolkit`

* Use Nipype sphinx extension for generation of the documentation of the interfaces

* Review all docstrings and the `desc=` argument of all nipype input and output class attributes for correct rendering using the new nipype sphinx extension, that uses directly the `desc=` argument of all the input and output class attributes so that we do not have to describe the attributes again.

We are now using the nipype sphinx extension to generate the doc of the interfaces such that it is really important to use the argument desc= for each input/output class attributes. The good news is that we do not need to write dozen of lines of docstrings for these classes.

Note also another important thing with the desc= argument for InputMultiPath and OutputMultiPath attribute type should not be in File(), i.e.:

input_images = InputMultiPath(File(), desc='Input images')

Otherwise the nipype sphinx extension is not happy and the correct rendering of interface inputs and outputs breaks.

Doc is rendered at https://mialsrtk.readthedocs.io/en/64_doc_singularity_v2.0.1-dev.

By merging this PR and then PR #63, we will be ready to release the new version.

@sebastientourbier sebastientourbier added documentation Improvements or additions to documentation maintenance mid-effort labels Dec 15, 2020
@sebastientourbier sebastientourbier added this to the v2.0.1 milestone Dec 15, 2020
@sebastientourbier sebastientourbier changed the title [DOC] Update documentation to explain how to run on cluster and uses the singularity image [DOC] Update documentation Dec 17, 2020
@sebastientourbier sebastientourbier merged commit a6fbea4 into v2.0.1-dev Dec 21, 2020
@sebastientourbier sebastientourbier deleted the 64_doc_singularity_v2.0.1-dev branch December 21, 2020 07:01
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Update documentation to explain how to run on cluster and uses the singularity image
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