GNU bug report logs - #62579
[PATCH 0/3] *** Package targets and tarchetypes ***

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

From: kyle <kyle <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: rekado=@elephly.net, Kyle Andrews <kyle <at> posteo.net>
Subject: [PATCH 0/3] *** Package targets and tarchetypes ***
Date: Sat, 01 Apr 2023 04:48:54 +0000

From: Kyle Andrews <kyle <at> posteo.net>

*** these packages implement an R-native scientific workflow system ***

Kyle Andrews (3):
  gnu: Add r-targets package
  gnu: Add r-future-callr
  gnu: Add r-tarchetypes

 gnu/packages/cran.scm | 109 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 109 insertions(+)


base-commit: 47ea688fd27d0ce0c8ea5481f1f94d0ebc3e37eb
-- 
2.39.2

Message #8 received at 62579 <at> debbugs.gnu.org (full text, mbox):

From: kyle <kyle <at> posteo.net>
To: 62579 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net, Kyle Andrews <kyle <at> posteo.net>
Subject: [PATCH 1/3] gnu: Add r-targets package
Date: Sat, 01 Apr 2023 04:57:00 +0000

From: Kyle Andrews <kyle <at> posteo.net>

---
 gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f2bdd750ca..3e8ec429e1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14456,6 +14456,47 @@ (define-public r-tab
 handle data from simple random samples as well as complex surveys.")
     (license license:gpl3+)))
 
+(define-public r-targets
+  (package
+    (name "r-targets")
+    (version "0.14.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "targets" version))
+              (sha256
+               (base32
+		"0mhwvlbxnb4w054pjiw2smss28i90sg52w8v040y7sqy6gq2c8n6"))))
+    (properties `((upstream-name . "targets")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-base64url
+                             r-callr
+                             r-cli
+                             r-codetools
+                             r-data-table
+                             r-digest
+                             r-igraph
+                             r-knitr
+                             r-r6
+                             r-rlang
+                             r-tibble
+                             r-tidyselect
+                             r-vctrs
+                             r-withr
+                             r-yaml))
+    (native-inputs (list r-knitr))
+    (home-page "https://docs.ropensci.org/targets/")
+    (synopsis "Dynamic Function-Oriented 'Make'-Like Declarative Pipelines")
+    (description
+     "This package provides a pipeline toolkit for Statistics and data science in R,
+the targets package brings function-oriented programming to Make'-like
+declarative pipelines.  targets orchestrates a pipeline as a graph of
+dependencies, skips steps that are already up to date, runs the necessary
+computation with optional parallel workers, abstracts files as R objects, and
+provides tangible evidence that the results are reproducible given the
+underlying code and data.  The methodology in this package borrows from GNU Make
+(2015, ISBN:978-9881443519) and drake (2018, <doi:10.21105/joss.00550>).")
+    (license license:expat)))
+
 (define-public r-dvmisc
   (package
     (name "r-dvmisc")
-- 
2.39.2

Message #11 received at 62579 <at> debbugs.gnu.org (full text, mbox):

From: kyle <kyle <at> posteo.net>
To: 62579 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net, Kyle Andrews <kyle <at> posteo.net>
Subject: [PATCH 2/3] gnu: Add r-future-callr
Date: Sat, 01 Apr 2023 04:57:01 +0000

From: Kyle Andrews <kyle <at> posteo.net>

---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3e8ec429e1..d2036b0629 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19309,6 +19309,37 @@ (define-public r-future-apply
 machine or distributed on a compute cluster.")
     (license license:gpl2+)))
 
+(define-public r-future-callr
+  (package
+    (name "r-future-callr")
+    (version "0.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "future.callr" version))
+              (sha256
+               (base32
+		"1w7wq2nrvj65a25nsb5h99258p9565qwnlvcc07nyc21gm5zrg9k"))))
+    (properties `((upstream-name . "future.callr")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-HOME
+            (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs (list r-callr r-future))
+    (native-inputs (list r-r-rsp))
+    (home-page "https://future.callr.futureverse.org")
+    (synopsis "Future API for Parallel Processing using 'callr'")
+    (description
+     "Implementation of the Future API on top of the callr package.  This allows you
+to process futures, as defined by the future package, in parallel out of the
+box, on your local (Linux, macOS, Windows, ...) machine.  Contrary to backends
+relying on the parallel package (e.g. future::multisession') and socket
+connections, the callr backend provided here can run more than 125 parallel R
+processes.")
+    (license license:lgpl2.1+)))
+
 (define-public r-rsvd
   (package
     (name "r-rsvd")
-- 
2.39.2

Message #14 received at 62579 <at> debbugs.gnu.org (full text, mbox):

From: kyle <kyle <at> posteo.net>
To: 62579 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net, Kyle Andrews <kyle <at> posteo.net>
Subject: [PATCH 3/3] gnu: Add r-tarchetypes
Date: Sat, 01 Apr 2023 04:57:02 +0000

From: Kyle Andrews <kyle <at> posteo.net>

---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d2036b0629..56dcf705db 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14456,6 +14456,43 @@ (define-public r-tab
 handle data from simple random samples as well as complex surveys.")
     (license license:gpl3+)))
 
+
+(define-public r-tarchetypes
+  (package
+    (name "r-tarchetypes")
+    (version "0.7.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "tarchetypes" version))
+              (sha256
+               (base32
+		"05yhq8xnrpk37x7fq0yjw4m527ji28s16dskfmljrbrzb064nw2g"))))
+    (properties `((upstream-name . "tarchetypes")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-digest
+                             r-dplyr
+                             r-fs
+                             r-furrr
+                             r-future
+                             r-future-callr
+                             r-rlang
+                             r-targets
+                             r-tibble
+                             r-tidyselect
+                             r-vctrs
+                             r-withr))
+    (home-page "https://docs.ropensci.org/tarchetypes/")
+    (synopsis "Archetypes for Targets")
+    (description
+     "Function-oriented Make-like declarative pipelines for Statistics and data
+science are supported in the targets R package.  As an extension to targets',
+the tarchetypes package provides convenient user-side functions to make targets
+easier to use.  By establishing reusable archetypes for common kinds of targets
+and pipelines, these functions help express complicated reproducible pipelines
+concisely and compactly.  The methods in this package were influenced by the
+drake R package by Will Landau (2018) <doi:10.21105/joss.00550>.")
+    (license license:expat)))
+
 (define-public r-targets
   (package
     (name "r-targets")
-- 
2.39.2

Message #19 received at 62579-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: kyle <kyle <at> posteo.net>
Cc: 62579-done <at> debbugs.gnu.org
Subject: Re: [PATCH 1/3] gnu: Add r-targets package
Date: Tue, 04 Apr 2023 19:46:43 +0200

Hi Kyle,

thank you for the patches!  I applied them with the commits ending with
4d313b918ec6d2ed05dd16030a860c162e63d8a0.

I slightly adjusted descriptions and indentation (each of the patches
had tabs on the hash line) and added r-markdown where the vignette
builder needed it.

-- 
Ricardo

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