[bug#64400] [PATCH 0/5] Add ocaml-owl and ocaml-toml.

[bug#64400] [PATCH 0/5] Add ocaml-owl and ocaml-toml.

[Anders Ågren Thuné]

Hello,

This patch series adds the OCaml packages owl and toml, and their
dependencies.  These packages are used for scientific computing and handling
toml files, respectively.

Anders Ågren Thuné (5):
  gnu: Add ocaml-ISO8601.
  gnu: Add ocaml-ocb.
  gnu: Add ocaml-npy.
  gnu: Add ocaml-toml.
  gnu: Add ocaml-owl.

 gnu/packages/ocaml.scm | 126 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 126 insertions(+)


base-commit: 8af22b493199a17f46351c2f3d9f6ee759e48564
-- 
2.40.1

[bug#64400] [PATCH 1/5] gnu: Add ocaml-ISO8601.

[Anders Ågren Thuné]

* gnu/packages/ocaml.scm (ocaml-ISO8601): New variable.
---
 gnu/packages/ocaml.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index ab0aa0574a..abdf09bdc1 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -29,6 +29,7 @@
 ;;; Copyright © 2022 Garek Dyszel <garekdyszel@disroot.org>
 ;;; Copyright © 2023 Csepp <raingloom@riseup.net>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
+;;; Copyright © 2023 Anders Ågren Thuné <anders@aathn.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2699,6 +2700,32 @@ (define-public ocaml-ppx-tools
 syntactic tools.")
     (license license:expat)))
 
+(define-public ocaml-ISO8601
+  ;; NOTE: Using commit from master branch as 0.2.6 uses the Pervasives
+  ;; module in its tests, which is incompatible with OCaml 5.0.
+  (let ((revision "0")
+        (commit "ad50cb01061405623c834608c26f1ef2d44f8340"))
+    (package
+      (name "ocaml-ISO8601")
+      (version (git-version "0.2.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ocaml-community/ISO8601.ml")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1lvjrxz66b7dv40cbl8xyfv3x8nmwj0m5ipfvxc37mjaaf3xrr5g"))))
+      (build-system dune-build-system)
+      (propagated-inputs (list ocaml-odoc))
+      (native-inputs (list ocaml-ounit))
+      (home-page "https://github.com/ocaml-community/ISO8601.ml/")
+      (synopsis "ISO 8601 and RFC 3339 date parsing for OCaml")
+      (description
+       "OCaml parser and printer for date-times in ISO8601 and RFC 3339")
+      (license license:expat))))
+
 (define-public ocaml-parmap
   (package
     (name "ocaml-parmap")
-- 
2.40.1

[bug#64400] [PATCH 2/5] gnu: Add ocaml-ocb.

[Anders Ågren Thuné]

* gnu/packages/ocaml.scm (ocaml-ocb): New variable.
---
 gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index abdf09bdc1..f2170a3060 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2726,6 +2726,28 @@ (define-public ocaml-ISO8601
        "OCaml parser and printer for date-times in ISO8601 and RFC 3339")
       (license license:expat))))
 
+(define-public ocaml-ocb
+  (package
+    (name "ocaml-ocb")
+    (version "0.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/OCamlPro/ocb")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nk90jax91ld8qd36qi408mll8a7w1d60fa2qdsnff7cldwixc1d"))))
+    (build-system dune-build-system)
+    (propagated-inputs (list ocaml-odoc))
+    (home-page "https://ocamlpro.github.io/ocb/")
+    (synopsis "SVG badge generator")
+    (description
+     "An OCaml library for SVG badge generation.  There's also a command-line tool
+provided.")
+    (license license:isc)))
+
 (define-public ocaml-parmap
   (package
     (name "ocaml-parmap")
-- 
2.40.1

[bug#64400] [PATCH 3/5] gnu: Add ocaml-npy.

[Anders Ågren Thuné]

* gnu/packages/ocaml.scm (ocaml-npy): New variable.
---
 gnu/packages/ocaml.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index f2170a3060..083c1aca99 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2748,6 +2748,30 @@ (define-public ocaml-ocb
 provided.")
     (license license:isc)))
 
+(define-public ocaml-npy
+  (package
+    (name "ocaml-npy")
+    (version "0.0.9")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/LaurentMazare/npy-ocaml")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1fryglkm20h6kdqjl55b7065b34bdg3g3p6j0jv33zvd1m5888m1"))))
+    (build-system dune-build-system)
+    (native-inputs (list zlib python-wrapper python-numpy))
+    (propagated-inputs (list camlzip))
+    (home-page "https://github.com/LaurentMazare/npy-ocaml")
+    (synopsis "Numpy npy file format reading/writing for OCaml")
+    (description
+     "A library providing simple read/write function using the numpy npy/npz
+file formats.  These can be used to save a bigarray to disk and then load it
+from python using numpy.")
+    (license license:asl2.0)))
+
 (define-public ocaml-parmap
   (package
     (name "ocaml-parmap")
-- 
2.40.1

[bug#64400] [PATCH 4/5] gnu: Add ocaml-toml.

[Anders Ågren Thuné]

* gnu/packages/ocaml.scm (ocaml-toml): New variable.
---
 gnu/packages/ocaml.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 083c1aca99..83077addb0 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2772,6 +2772,31 @@ (define-public ocaml-npy
 from python using numpy.")
     (license license:asl2.0)))
 
+(define-public ocaml-toml
+  (package
+    (name "ocaml-toml")
+    (version "7.1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ocaml-toml/to.ml")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0z2873mj3i6h9cg8zlkipcjab8jympa4c4avhk4l04755qzphkds"))))
+    (build-system dune-build-system)
+    (propagated-inputs (list ocaml-odoc ocaml-ISO8601))
+    (native-inputs
+     (list ocaml-menhir ocaml-ounit2 ocaml-mdx ocaml-bisect-ppx ocaml-ocb))
+    (home-page "https://ocaml-toml.github.io/To.ml/")
+    (synopsis "Library for TOML with a parser, a serializer and a printer")
+    (description
+     "toml is an OCaml library providing a parser, a serializer and a printer for
+TOML, a minimal configuration file format.  Helpful getters to retrieve data as
+OCaml primitive types are also supplied.")
+    (license license:lgpl3)))
+
 (define-public ocaml-parmap
   (package
     (name "ocaml-parmap")
-- 
2.40.1

[bug#64400] [PATCH 5/5] gnu: Add ocaml-owl.

[Anders Ågren Thuné]

* gnu/packages/ocaml.scm (ocaml-owl): New variable.
---
 gnu/packages/ocaml.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 83077addb0..f118c1289e 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2797,6 +2797,34 @@ (define-public ocaml-toml
 OCaml primitive types are also supplied.")
     (license license:lgpl3)))
 
+(define-public ocaml-owl
+  (package
+    (name "ocaml-owl")
+    (version "1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/owlbarn/owl")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "08jvgf1fd7d28cxxjifx4ikmwcbfbiyw0sivw3xy4vdzvbyc9xw9"))))
+    (build-system dune-build-system)
+    (propagated-inputs (list openblas zlib ocaml-ctypes ocaml-npy ocaml-compiler-libs))
+    (native-inputs (list ocaml-alcotest ocaml-base ocaml-stdio))
+    (home-page "https://github.com/owlbarn/owl")
+    (synopsis "OCaml Scientific and Engineering Computing")
+    (description
+     "Owl is an OCaml numerical library.  It supports N-dimensional
+arrays, both dense and sparse matrix operations, linear algebra,
+regressions, fast Fourier transforms, and many advanced mathematical
+and statistical functions (such as Markov chain Monte Carlo methods).
+Recently, Owl has implemented algorithmic differentiation which
+simplifies developing machine learning and neural network
+algorithms.")
+    (license license:expat)))
+
 (define-public ocaml-parmap
   (package
     (name "ocaml-parmap")
-- 
2.40.1

[bug#64400] [PATCH 1/5] gnu: Add ocaml-ISO8601.

[Liliana Marie Prikler]

Am Samstag, dem 01.07.2023 um 17:43 +0000 schrieb Anders Ågren Thuné:
> * gnu/packages/ocaml.scm (ocaml-ISO8601): New variable.
> ---
>  gnu/packages/ocaml.scm | 27 +++++++++++++++++++++++++++
>  1 file changed, 27 insertions(+)
> 
> diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
> index ab0aa0574a..abdf09bdc1 100644
> --- a/gnu/packages/ocaml.scm
> +++ b/gnu/packages/ocaml.scm
> @@ -29,6 +29,7 @@
>  ;;; Copyright © 2022 Garek Dyszel <garekdyszel@disroot.org>
>  ;;; Copyright © 2023 Csepp <raingloom@riseup.net>
>  ;;; Copyright © 2023 Foundation Devices, Inc.
> <hello@foundationdevices.com>
> +;;; Copyright © 2023 Anders Ågren Thuné <anders@aathn.org>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -2699,6 +2700,32 @@ (define-public ocaml-ppx-tools
>  syntactic tools.")
>      (license license:expat)))
>  
> +(define-public ocaml-ISO8601
> +  ;; NOTE: Using commit from master branch as 0.2.6 uses the
> Pervasives
> +  ;; module in its tests, which is incompatible with OCaml 5.0.
> +  (let ((revision "0")
> +        (commit "ad50cb01061405623c834608c26f1ef2d44f8340"))
> +    (package
> +      (name "ocaml-ISO8601")
> +      (version (git-version "0.2.6" revision commit))
> +      (source (origin
> +                (method git-fetch)
> +                (uri (git-reference
> +                      (url
> "https://github.com/ocaml-community/ISO8601.ml")
> +                      (commit commit)))
> +                (file-name (git-file-name name version))
> +                (sha256
> +                 (base32
> +                 
> "1lvjrxz66b7dv40cbl8xyfv3x8nmwj0m5ipfvxc37mjaaf3xrr5g"))))
> +      (build-system dune-build-system)
> +      (propagated-inputs (list ocaml-odoc))
> +      (native-inputs (list ocaml-ounit))
> +      (home-page "https://github.com/ocaml-community/ISO8601.ml/")
> +      (synopsis "ISO 8601 and RFC 3339 date parsing for OCaml")
Can probably be shortened to "OCaml date parsing"
> +      (description
> +       "OCaml parser and printer for date-times in ISO8601 and RFC
> 3339")
The description should consist at least of one complete sentence.  The
typical go to pattern here if information is scarce is "this package
provides…" as in "This package provides an OCaml library with parsers
and printers for date times in ISO 8601 and RFC 3339 formats."

Cheers

[bug#64400] [PATCH 2/5] gnu: Add ocaml-ocb.

[Liliana Marie Prikler]

Am Samstag, dem 01.07.2023 um 17:43 +0000 schrieb Anders Ågren Thuné:
> * gnu/packages/ocaml.scm (ocaml-ocb): New variable.
> ---
>  gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++
>  1 file changed, 22 insertions(+)
> 
> diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
> index abdf09bdc1..f2170a3060 100644
> --- a/gnu/packages/ocaml.scm
> +++ b/gnu/packages/ocaml.scm
> @@ -2726,6 +2726,28 @@ (define-public ocaml-ISO8601
>         "OCaml parser and printer for date-times in ISO8601 and RFC
> 3339")
>        (license license:expat))))
>  
> +(define-public ocaml-ocb
> +  (package
> +    (name "ocaml-ocb")
> +    (version "0.2")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/OCamlPro/ocb")
> +                    (commit version)))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "1nk90jax91ld8qd36qi408mll8a7w1d60fa2qdsnff7cldwixc1d"))))
> +    (build-system dune-build-system)
> +    (propagated-inputs (list ocaml-odoc))
> +    (home-page "https://ocamlpro.github.io/ocb/")
> +    (synopsis "SVG badge generator")
> +    (description
> +     "An OCaml library for SVG badge generation.  There's also a
> command-line tool
> +provided.")
"This package provides an OCaml library and command-line tool for
creating SVG badges" :)

[bug#64400] [PATCH 5/5] gnu: Add ocaml-owl.

[Liliana Marie Prikler]

Am Samstag, dem 01.07.2023 um 17:43 +0000 schrieb Anders Ågren Thuné:
> * gnu/packages/ocaml.scm (ocaml-owl): New variable.
> ---
>  gnu/packages/ocaml.scm | 28 ++++++++++++++++++++++++++++
>  1 file changed, 28 insertions(+)
> 
> diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
> index 83077addb0..f118c1289e 100644
> --- a/gnu/packages/ocaml.scm
> +++ b/gnu/packages/ocaml.scm
> @@ -2797,6 +2797,34 @@ (define-public ocaml-toml
>  OCaml primitive types are also supplied.")
>      (license license:lgpl3)))
>  
> +(define-public ocaml-owl
> +  (package
> +    (name "ocaml-owl")
> +    (version "1.1")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/owlbarn/owl")
> +                    (commit version)))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "08jvgf1fd7d28cxxjifx4ikmwcbfbiyw0sivw3xy4vdzvbyc9xw9"))))
> +    (build-system dune-build-system)
> +    (propagated-inputs (list openblas zlib ocaml-ctypes ocaml-npy
> ocaml-compiler-libs))
I'm pretty sure some of those inputs shouldn't be propagated.
> +    (native-inputs (list ocaml-alcotest ocaml-base ocaml-stdio))
> +    (home-page "https://github.com/owlbarn/owl")
> +    (synopsis "OCaml Scientific and Engineering Computing")
> +    (description
> +     "Owl is an OCaml numerical library.  It supports N-dimensional
> +arrays, both dense and sparse matrix operations, linear algebra,
> +regressions, fast Fourier transforms, and many advanced mathematical
> +and statistical functions (such as Markov chain Monte Carlo
> methods).
> +Recently, Owl has implemented algorithmic differentiation which
> +simplifies developing machine learning and neural network
> +algorithms.")
> +    (license license:expat)))
This package sadly fails to build on aarch64 and probably also has
issues on other architectures, as it assumes some build flags specific
to x86_64 (see the CI build logs).  These should be stripped in a
patch, snippet or pre-build phase.  If these flags are there for
performance reasons, you should instead mark the package as tunable.

Cheers