GNU bug report logs - #43994
[PATCH] gnu: Add r-calculus.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Magali Lemes <magalilemes00 <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Magali Lemes <magalilemes00 <at> gmail.com>
Subject: [PATCH] gnu: Add r-calculus.
Date: Wed, 14 Oct 2020 16:06:09 -0300

---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 59a409f8e9..8a4f0085f6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24596,3 +24596,30 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
   Without filtering, users can perform (original) two-tailed or one-tailed
 absolute GSEA.")
     (license license:gpl2)))
+
+(define-public r-calculus
+  (package
+    (name "r-calculus")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "calculus" version))
+       (sha256
+       (base32
+        "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp"))))
+    (properties `((upstream-name . "calculus")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/emanuele-guidotti/calculus")
+    (synopsis "High Dimensional Numerical and Symbolic Calculus")
+    (description
+     "Efficient C++ optimized functions for numerical and symbolic calculus.
+It includes basic symbolic arithmetic, tensor calculus, Einstein summing
+convention, fast computation of the Levi-Civita symbol and generalized 
+Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
+accurate high-order derivatives, differential operators (Gradient, Jacobian,
+Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
+orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, 
+parabolic or user defined by custom scale factors.")
+    (license license:gpl3)))
\ No newline at end of file
-- 
2.25.1

Message #8 received at 43994 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Magali Lemes <magalilemes00 <at> gmail.com>
Cc: 43994 <at> debbugs.gnu.org
Subject: Re: [bug#43994] [PATCH] gnu: Add r-calculus.
Date: Thu, 15 Oct 2020 13:09:06 +0200

Hi,

Thank you for your contribution.  It is fine.  For the sake of the
learning process, I suggest some minor tweaks and then you can send a v2
patch.  Does it make sense?



In the commit message, it is missing:

* gnu/packages/cran.scm (r-calculus): New variable.


> ---
>  gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
>  1 file changed, 27 insertions(+)
>
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index 59a409f8e9..8a4f0085f6 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -24596,3 +24596,30 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
>    Without filtering, users can perform (original) two-tailed or one-tailed
>  absolute GSEA.")
>      (license license:gpl2)))
> +
> +(define-public r-calculus
> +  (package
> +    (name "r-calculus")
> +    (version "0.2.1")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (cran-uri "calculus" version))
> +       (sha256
> +       (base32

Here, and issue of indentation.

       (uri (cran-uri "calculus" version))
       (sha256
        (base32

Usually, with Emacs (with the correct setup “.dir-locals.el“), the
simplest is to go to the first opening parenthesis and press ‘C-M-q’.


> +        "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp"))))
> +    (properties `((upstream-name . "calculus")))
> +    (build-system r-build-system)
> +    (propagated-inputs `(("r-rcpp" ,r-rcpp)))

Usually, it is preferred to list below:

    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)))


> +    (home-page "https://github.com/emanuele-guidotti/calculus")
> +    (synopsis "High Dimensional Numerical and Symbolic Calculus")
> +    (description
> +     "Efficient C++ optimized functions for numerical and symbolic calculus.
> +It includes basic symbolic arithmetic, tensor calculus, Einstein summing
> +convention, fast computation of the Levi-Civita symbol and generalized 

End of line: extra whitespace 

> +Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
> +accurate high-order derivatives, differential operators (Gradient, Jacobian,
> +Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
> +orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, 

Idem


Again with Emacs, I personally have ’(whitespace-mode)’ with this
config and then it is really easy to spot out.

--8<---------------cut here---------------start------------->8---
(with-eval-after-load 'whitespace
  (setq whitespace-line-column nil
        whitespace-style '(face trailing lines-tail
                                space-before-tab newline
                                indentation empty space-after-tab)))

--8<---------------cut here---------------end--------------->8---

> +parabolic or user defined by custom scale factors.")
> +    (license license:gpl3)))
> \ No newline at end of file

Add RET. I guess.



Well, now you should do an “interactive rebase” and resend.  Using Emacs
(again!) and Magit , it looks like:

  r i
  edit C-c C-c
  # do your tweaks
  r r
  W c C-m b master C-m v 2 c
  ! git send-email --to=43994 <at> debbugs.gnu.org v2-0001-blabla.patch

Does it make sense?


All the best,
simon

PS:
You can use any tools you want. :-) Sorry for the Emacs’s
evangelism. ;-)

Message #11 received at 43994 <at> debbugs.gnu.org (full text, mbox):

From: Magali Lemes <magalilemes00 <at> gmail.com>
To: 43994 <at> debbugs.gnu.org
Cc: Magali Lemes <magalilemes00 <at> gmail.com>
Subject: [PATCH v2] gnu: Add r-calculus.
Date: Fri, 16 Oct 2020 15:51:07 -0300

* gnu/packages/cran.scm (r-calculus): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 252699c691..ce5ae7f64a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -30,6 +30,7 @@
 ;;; Copyright © 2020 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2020 Antoine Côté <antoine.cote <at> posteo.net>
 ;;; Copyright © 2020 Arun Isaac <arunisaac <at> systemreboot.net>
+;;; Copyright © 2020 Magali Lemes <magalilemes00 <at> gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24598,3 +24599,32 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
   Without filtering, users can perform (original) two-tailed or one-tailed
 absolute GSEA.")
     (license license:gpl2)))
+
+(define-public r-calculus
+  (package
+    (name "r-calculus")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "calculus" version))
+       (sha256
+        (base32
+         "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp"))))
+    (properties `((upstream-name . "calculus")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/emanuele-guidotti/calculus")
+    (synopsis "High Dimensional Numerical and Symbolic Calculus")
+    (description
+     "Efficient C++ optimized functions for numerical and symbolic calculus.
+It includes basic symbolic arithmetic, tensor calculus, Einstein summing
+convention, fast computation of the Levi-Civita symbol and generalized
+Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
+accurate high-order derivatives, differential operators (Gradient, Jacobian,
+Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
+orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
+parabolic or user defined by custom scale factors.")
+    (license license:gpl3)))
+
-- 
2.25.1

Message #16 received at 43994-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Magali Lemes <magalilemes00 <at> gmail.com>
Cc: 43994-done <at> debbugs.gnu.org
Subject: Re: [bug#43994] [PATCH v2] gnu: Add r-calculus.
Date: Sat, 17 Oct 2020 22:39:46 +0200

[Message part 1 (text/plain, inline)]

Hi Magali,

Magali Lemes <magalilemes00 <at> gmail.com> skribis:

> * gnu/packages/cran.scm (r-calculus): New variable.

Applied with the minor changes below (the URL change was suggested by
‘guix lint r-calculus’.)  Apart from that it’s all good.

Thanks!

Ludo’.

[Message part 2 (text/x-patch, inline)]

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ce5ae7f64a..fea560f7a1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24615,8 +24615,8 @@ absolute GSEA.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)))
-    (home-page "https://github.com/emanuele-guidotti/calculus")
-    (synopsis "High Dimensional Numerical and Symbolic Calculus")
+    (home-page "https://github.com/guidotti/calculus")
+    (synopsis "High dimensional numerical and symbolic calculus")
     (description
      "Efficient C++ optimized functions for numerical and symbolic calculus.
 It includes basic symbolic arithmetic, tensor calculus, Einstein summing

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