Re: [External] Re: New outreachy participant introduction

[Gábor Boskovits]

Hello Nardos,

We have not heard from you for a while. Should you need any help, please feel free to reach out to us.

Asfaw, Nardos <address@hidden> ezt írta (időpont: 2019. okt. 13., Vas 2:41):

Thank you Zimon.

This has been very helpful.
________________________________________
From: zimoun <address@hidden>
Sent: Tuesday, October 8, 2019 9:24 AM
To: Christopher Baines
Cc: Asfaw, Nardos; Guix Devel
Subject: Re: [External] Re: New outreachy participant introduction

Hi Nardos,

Welcome ! :-)


On Tue, 8 Oct 2019 at 08:48, Christopher Baines <address@hidden> wrote:

> One good starting point would be an importer, there are a set of
> importers included in Guix that take a package definition from somewhere
> else (like the Python package index, or Rubygems) and try to generate a
> Guix package definition. If you're familiar with some packages from one
> of the collections with a corresponding importer, that might be a good
> place to start.

As an example, let consider packages from BioConductor [1] (mainly R
packages used in bioinformatics field). If I have right, then 2002
packages are still missing in Guix, so there is materials. ;-)

Well, let's pick one which is not packaged yet: zinbwave [2]. Then it is easy:

  guix import cran -r -a bioconductor zinbwave

This will download TAR archives and automatically compute the hash. It
corresponds to the manual:

  guix download
https://bioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0.tar.gz


[1] https://bioconductor.org/
[2] https://bioconductor.org/packages/release/bioc/html/zinbwave.html


Moreover, the importer provides the definition of the package:

--8<---------------cut here---------------start------------->8---
(define-public r-zinbwave
  (package
    (name "r-zinbwave")
    (version "1.6.0")
    (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
          (base32
            "187r7l9jf2q74qaqx63df5zx6iphmvl817448balvfv9vqyhrp2j"))))
    (properties `((upstream-name . "zinbwave")))
    (build-system r-build-system)
    (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-copula" ,r-copula)
        ("r-edger" ,r-edger)
        ("r-genefilter" ,r-genefilter)
        ("r-glmnet" ,r-glmnet)
        ("r-matrix" ,r-matrix)
        ("r-singlecellexperiment"
         ,r-singlecellexperiment)
        ("r-softimpute" ,r-softimpute)
        ("r-summarizedexperiment"
         ,r-summarizedexperiment)))
    (home-page
      "https://bioconductor.org/packages/zinbwave")
    (synopsis
      "Zero-Inflated Negative Binomial Model for RNA-Seq Data")
    (description
      " Implements a general and flexible zero-inflated negative
binomial model that can be used to provide a low-dimensional
representations of single-cell RNA-seq data.  The model accounts for
zero inflation (dropouts), over-dispersion, and the count nature of
the data.  The model also accounts for the difference in library sizes
and optionally for batch effects and/or other covariates, avoiding the
need for pre-normalize the data.")
    (license artistic2.0)))
--8<---------------cut here---------------end--------------->8---

In the propagated input, you can see the package `r-copula` which is
not yet packaged neither. But, the nice option --recursive does the
job for you and it also gives you the package definition.

Now, let add them to the Guix source. Clone the repo and go in the
folder. The command:

  guix environment guix

will download the dependencies to build Guix and setup all the
variables correctly. Well, refer to the documentation to compile Guix
from source. Basically:

  ./bootstrap
  ./configure --localstatedir=/var
  make

Now, you can run this version with ./pre-inst-env, for example:

   ./pre-inst-env guix describe


Well, ready to add one package! For example, add `r-copula` to the
file gnu/package/cran.scm then recompile with make. Check if it is ok:

  ./pre-inst-env guile show r-copula

Ouch! `r-psline` is missing so let also add it (the definition was
provided by the importer), run make again. Now "./pre-inst-env guix
show r-copula" should work.
Add the package definition of zinbwave to the file gnu/package/bioconductor.scm.

Let build them:

  ./pre-inst-env guix build r-zinbwave

and time to breath. ;-)


If something fails, try to investigate by yourself and do not hesitate
to ask advices or help.
If everything is ok, the package still needs some polishing: synopsis,
description, indentation, etc and really important: check the license
field.

The next step is to commit the changes. In this case, three commits
(one per package) seem nice. Give a look to previous commits as
example of commit message (ChangeLog format, etc.). Now, it is time to
prepare the submission:

  git format-patch --cover-letter - o patches master

this will create the 3 patches in the folder patches/ and one cover
letter. Edit the cover letter to describe what the patches are about
then submit it to the bug tracker:

  git send-email --to=address@hidden patches/0000-cover-letter.patch

Wait the answer to the bug tracker.
You should receive an email (if your .gitconfig is ok) with the bug
number. Last submit the patches:

  git send-email --to=address@hidden patches/000{1,2,3}-*

where ABCDEF is the bug number.



Well, if you need some inspiration to find unpackaged tools from BioConductor:

  wget https://git.bioconductor.org -qO - | sed -ne
'/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest
  ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_manifest

where the file `missing-bioconductor.scm` is given by:

--8<---------------cut here---------------start------------->8---
(use-modules ((guix import utils) #:select (guix-name))
             (gnu packages)
             (srfi srfi-1)  ;lists
             (ice-9 textual-ports))

(define (fetch-names manifest)
  "Return a list of strings, each corresponding to a name from the
input file MANIFEST."
  (call-with-input-file manifest
    (lambda (port)
      (let loop ((lines '())
                 (line (get-line port)))
        (if (eof-object? line)
            (reverse lines)
            (loop (cons line lines)
                  (get-line port)))))))

;;; Start!

(map (lambda (name)
       (when (null? (find-packages-by-name (guix-name "r-" name)))
         (begin
           (display name)
           (newline))))
     (fetch-names (cadr (command-line))))

;; wget https://git.bioconductor.org -qO - | sed -ne
'/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest
;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_manifest
--8<---------------cut here---------------end--------------->8---


Hope that help.

All the best,
simon