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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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QMP example data #470 #597

Closed ShadmanIshraq closed 1 week ago

antagomir commented 1 week ago

Can you also save code that was used to create the R data from original source files - that can be put in inst/scripts/

antagomir commented 1 week ago

The colData(tse) has sampleID on the rows; it would be good to have this also as its own column, see e.g.

data(GlobalPatterns)
names(colData(GlobalPatterns))
[1] "X.SampleID"               "Primer"                  
[3] "Final_Barcode"            "Barcode_truncated_plus_T"
[5] "Barcode_full_length"      "SampleType"              
[7] "Description"
antagomir commented 1 week ago

I suggest to replace periods "." in the rowData species names with "_". The periods occasionally cause problems in some systems.

ShadmanIshraq commented 1 week ago

Can you also save code that was used to create the R data from original source files - that can be put in inst/scripts/

antagomir commented 1 week ago

Just curious, why this was closed? Another option would be to fix the suggested points and add new commits on the existing PR?

ShadmanIshraq commented 1 week ago

Shall I put the coldata, rowdata and assaydata also with the R code in inst/scripts/ ?

antagomir commented 1 week ago

Shall I put the coldata, rowdata and assaydata also with the R code in inst/scripts/ ?

That's usually not done but it would be helpful if had these source files available.

You could add here (as a PR): https://github.com/microbiome/data

Remember to cite the original publication very clearly in the relevant README

antagomir commented 1 week ago

@ShadmanIshraq could you resolve the comments that you have fixed already?

antagomir commented 1 week ago

@TuomasBorman this is good to go for me, not sure why the GHA error?

TuomasBorman commented 1 week ago

Every manual page should be listed in pkgdown/pkgdown.yml to be added to the manual. The new page about this new dataset was not added there which caused the error.

TuomasBorman commented 1 week ago

Now the error is caused by permission issues "remote: Permission to microbiome/mia.git denied to github-actions[bot]". This should be fixed when pushed to devel branch.

antagomir commented 1 week ago

Ok - could @ShadmanIshraq do that?

TuomasBorman commented 1 week ago

Pushing to devel without checks passing requires bypassing branch rules (which can only be done by admins)