docs: sphinx website with API reference #32
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The docs look beautiful! Incredible work 👏 :
General comments:
nitpick(non-blocking): just to keep the same convention as the docs/ folder and docs commit label, we could use docs instead of doc for the makefile rule and the poetry dependency group. (would also need to be updated in the sphinx ci job)
comment(non-blocking) on some pages (e.g. cli), the navigation sidebar on the left is empty. If I understand correctly, this bar is supposed to contain sub-pages. I wondered if the CLI reference page should itself be a sub-page. We can discuss that in a future issue.
docs/tutorials/modo_arrays.md
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| modo= MODO("data/ex") | ||
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| # Generate an Array element | ||
| array_element = model.Array(id="rna1", name= "RNA raw counts", description = "RNA counts from multiple timepoints", has_sample="sample/sample1", data_format = "Zarr") |
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comment: I get
ValueError: data_path must be supplied
adding data_path with a meaningless value seems to fix it.
question: Should we open a separate issue for this? (i.e. make data_path optional)
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alternatively, we could also add a note saying that we plan to add helper functions (an array api) to simplify these operations
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Yes, very good point. I missed that - what about doing all of this:
- In this PR: Fix the docs with the "path to where we will store the array"
- In this PR: Add the note to make clear this is going to be wrapped/simplified
- Open an issue to simplify this and make the data path optional (see Add array api function to simplify adding arrays to modo #38)
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question: it would also be nice to have intersphinx mappings to modo_schema, but I'm not sure what works it implies on the modo_schema side. Do we need it to also use sphinx for this? |
Co-authored-by: Cyril Matthey-Doret <[email protected]> Co-authored-by: Cyril Matthey-Doret <[email protected]> Co-authored-by: Cyril Matthey-Doret <[email protected]>
Co-authored-by: Cyril Matthey-Doret <[email protected]> Co-authored-by: Cyril Matthey-Doret <[email protected]> Co-authored-by: Cyril Matthey-Doret <[email protected]> Co-authored-by: Cyril Matthey-Doret <[email protected]>
Co-authored-by: Cyril Matthey-Doret <[email protected]>
Aim: Setup of a basic documentation
PR elements:
ed
Ops: description of htsget slicing and streaming is missing. To be added after Feat/cram stream #31 is merged