[bug#52408] [PATCH 0/5] gnu: Add cl-mgl-gpr.

[bug#52408] [PATCH 0/5] gnu: Add cl-mgl-gpr.

[Foo Chuan Wei]

Add MGL-GPR, a library of evolutionary algorithms.

Foo Chuan Wei (5):
  gnu: Add cl-num-utils.
  gnu: Add cl-lla.
  gnu: Add cl-rmath.
  gnu: Add cl-random.
  gnu: Add cl-mgl-gpr.

 gnu/packages/lisp-xyz.scm | 220 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 220 insertions(+)


base-commit: e1973ae74beb2880c11593155849f43e23ef620c
-- 
2.25.1

[bug#52408] [PATCH 1/5] gnu: Add cl-num-utils.

[Foo Chuan Wei]

* gnu/packages/lisp-xyz.scm (cl-num-utils, ecl-cl-num-utils,
  sbcl-cl-num-utils): New variables.
---
 gnu/packages/lisp-xyz.scm | 47 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 635f8e48cb..4925797136 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -19363,6 +19363,53 @@ command in Common Lisp.")
 (define-public ecl-which
   (sbcl-package->ecl-package sbcl-which))
 
+(define-public sbcl-cl-num-utils
+  (let ((commit "97a88cd34540acf52e872a82ebfef3da0a34fa12")
+        (revision "1"))
+    (package
+      (name "sbcl-cl-num-utils")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tpapp/cl-num-utils")
+               (commit commit)))
+         (file-name (git-file-name "cl-num-utils" version))
+         (sha256
+          (base32 "15ihsxxs76xnldmqfsbxybckqjwrxwcpphgghiwzr2mnbqjpdqkh"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("anaphora" ,sbcl-anaphora)
+         ("alexandria" ,sbcl-alexandria)
+         ("array-operations" ,sbcl-array-operations)
+         ("cl-slice" ,sbcl-cl-slice)
+         ("let-plus" ,sbcl-let-plus)))
+      (native-inputs
+       `(("clunit" ,sbcl-clunit)))
+      (home-page "https://github.com/tpapp/cl-num-utils")
+      (synopsis "Numerical utilities for Common Lisp")
+      (description
+       "@code{cl-num-utils} implements simple numerical functions for Common
+Lisp, including:
+@itemize
+@item @code{num=}, a comparison operator for floats
+@item simple arithmeric functions, like @code{sum} and @code{l2norm}
+@item elementwise operations for arrays
+@item intervals
+@item special matrices and shorthand for their input
+@item sample statistics
+@item Chebyshev polynomials
+@item univariate rootfinding
+@end itemize")
+      (license license:boost1.0))))
+
+(define-public cl-num-utils
+  (sbcl-package->cl-source-package sbcl-cl-num-utils))
+
+(define-public ecl-cl-num-utils
+  (sbcl-package->ecl-package sbcl-cl-num-utils))
+
 (define-public sbcl-cl-tld
   ;; No release.
   (let ((commit "f5014da8d831fa9481d4181d4450f10a52850c75"))
-- 
2.25.1

[bug#52408] [PATCH 2/5] gnu: Add cl-lla.

[Foo Chuan Wei]

* gnu/packages/lisp-xyz.scm (cl-lla, ecl-lla, sbcl-lla): New variables.
---
 gnu/packages/lisp-xyz.scm | 52 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 4925797136..e735ff368a 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -19410,6 +19410,58 @@ Lisp, including:
 (define-public ecl-cl-num-utils
   (sbcl-package->ecl-package sbcl-cl-num-utils))
 
+(define-public sbcl-lla
+  (let ((commit "ded805d1e9b1493e17b601116ba9bd8a3de3024f")
+        (revision "1"))
+    (package
+      (name "sbcl-lla")
+      (version (git-version "0.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tpapp/lla")
+               (commit commit)))
+         (file-name (git-file-name "cl-lla" version))
+         (sha256
+          (base32 "0n9vc7dnyjbbsv1n7rd8sylwda5fsdf8f890g4nachanyx0xps9k"))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-paths
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "src/configuration.lisp"
+                 (("\"libblas.so.3gf\"")
+                  (string-append "\"" (assoc-ref inputs "lapack")
+                                 "/lib/libblas.so\""))
+                 (("\"liblapack.so.3gf\"")
+                  (string-append "\"" (assoc-ref inputs "lapack")
+                                 "/lib/liblapack.so\""))))))))
+      (inputs
+       `(("anaphora" ,sbcl-anaphora)
+         ("alexandria" ,sbcl-alexandria)
+         ("cffi" ,sbcl-cffi)
+         ("cl-num-utils" ,sbcl-cl-num-utils)
+         ("cl-slice" ,sbcl-cl-slice)
+         ("lapack" ,lapack)
+         ("let-plus" ,sbcl-let-plus)))
+      (native-inputs
+       `(("clunit" ,sbcl-clunit)))
+      (home-page "https://github.com/tpapp/lla")
+      (synopsis "Linear algebra library for Common Lisp")
+      (description
+       "LLA is a high-level Common Lisp library built on BLAS and LAPACK, but
+providing a much more abstract interface with the purpose of freeing the user
+from low-level concerns and reducing the number of bugs in numerical code.")
+      (license license:boost1.0))))
+
+(define-public cl-lla
+  (sbcl-package->cl-source-package sbcl-lla))
+
+(define-public ecl-lla
+  (sbcl-package->ecl-package sbcl-lla))
+
 (define-public sbcl-cl-tld
   ;; No release.
   (let ((commit "f5014da8d831fa9481d4181d4450f10a52850c75"))
-- 
2.25.1

[bug#52408] [PATCH 3/5] gnu: Add cl-rmath.

[Foo Chuan Wei]

* gnu/packages/lisp-xyz.scm (cl-rmath, ecl-cl-rmath, sbcl-cl-rmath):
  New variables.
---
 gnu/packages/lisp-xyz.scm | 46 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index e735ff368a..1ee763d25f 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -93,6 +93,7 @@
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages statistics)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
@@ -19462,6 +19463,51 @@ from low-level concerns and reducing the number of bugs in numerical code.")
 (define-public ecl-lla
   (sbcl-package->ecl-package sbcl-lla))
 
+(define-public sbcl-cl-rmath
+  (let ((commit "f6add1edda31547691d08e36ccf6c17305161aca")
+        (revision "1"))
+    (package
+      (name "sbcl-cl-rmath")
+      (version (git-version "0.0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tpapp/cl-rmath")
+               (commit commit)))
+         (file-name (git-file-name "cl-rmath" version))
+         (sha256
+          (base32 "1ld8vbpy10paymx2hn0mcgd21i7cjhdrayln1jx0kayqxm12mmk4"))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-paths
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "cl-rmath.lisp"
+                 (("\\(cffi:define-foreign-library librmath" all)
+                  (string-append all "\n"
+                                 "  (:unix \""
+                                 (assoc-ref inputs "librmath")
+                                 "/lib/libRmath.so\")"))))))))
+      (inputs
+       `(("cffi" ,sbcl-cffi)
+         ("librmath" ,rmath-standalone)))
+      (home-page "https://github.com/tpapp/cl-rmath")
+      (synopsis "Common Lisp wrapper for libRmath")
+      (description
+       "@code{cl-rmath} is a simple, autogenerated foreign interface for the
+standalone R API @code{libRmath}.  There has been no effort to provide a
+high-level interface for the original library, instead, this library is meant
+to serve as a building block for such an interface.")
+      (license license:boost1.0))))
+
+(define-public cl-rmath
+  (sbcl-package->cl-source-package sbcl-cl-rmath))
+
+(define-public ecl-cl-rmath
+  (sbcl-package->ecl-package sbcl-cl-rmath))
+
 (define-public sbcl-cl-tld
   ;; No release.
   (let ((commit "f5014da8d831fa9481d4181d4450f10a52850c75"))
-- 
2.25.1

[bug#52408] [PATCH 4/5] gnu: Add cl-random.

[Foo Chuan Wei]

* gnu/packages/lisp-xyz.scm (cl-random, ecl-cl-random, sbcl-cl-random):
  New variables.
---
 gnu/packages/lisp-xyz.scm | 42 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 1ee763d25f..1477c3e091 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -19508,6 +19508,48 @@ to serve as a building block for such an interface.")
 (define-public ecl-cl-rmath
   (sbcl-package->ecl-package sbcl-cl-rmath))
 
+(define-public sbcl-cl-random
+  (let ((commit "5bb65911037f95a4260bd29a594a09df3849f4ea")
+        (revision "1"))
+    (package
+      (name "sbcl-cl-random")
+      (version (git-version "0.0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tpapp/cl-random")
+               (commit commit)))
+         (file-name (git-file-name "cl-random" version))
+         (sha256
+          (base32 "0jn80xphyvyp2v72acr6b8a2f6dw06myr5vrjfl14brsvks7wr89"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("anaphora" ,sbcl-anaphora)
+         ("array-operations" ,sbcl-array-operations)
+         ("cl-num-utils" ,sbcl-cl-num-utils)
+         ("cl-rmath" ,sbcl-cl-rmath)
+         ("cl-slice" ,sbcl-cl-slice)
+         ("gsll" ,sbcl-gsll)
+         ("let-plus" ,sbcl-let-plus)
+         ("lla" ,sbcl-lla)))
+      (native-inputs
+       `(("clunit" ,sbcl-clunit)))
+      (home-page "https://github.com/tpapp/cl-random")
+      (synopsis "Random variates for Common Lisp")
+      (description
+       "@code{cl-random} is a library for generating random draws from various
+commonly used distributions, and for calculating statistical functions, such as
+density, distribution and quantiles for these distributions.")
+      (license license:boost1.0))))
+
+(define-public cl-random
+  (sbcl-package->cl-source-package sbcl-cl-random))
+
+(define-public ecl-cl-random
+  (sbcl-package->ecl-package sbcl-cl-random))
+
 (define-public sbcl-cl-tld
   ;; No release.
   (let ((commit "f5014da8d831fa9481d4181d4450f10a52850c75"))
-- 
2.25.1

[bug#52408] [PATCH 5/5] gnu: Add cl-mgl-gpr.

[Foo Chuan Wei]

* gnu/packages/lisp-xyz.scm (cl-mgl-gpr, ecl-mgl-gpr, sbcl-mgl-gpr):
  New variables.
---
 gnu/packages/lisp-xyz.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 1477c3e091..6a1a3f9fe6 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -19550,6 +19550,39 @@ density, distribution and quantiles for these distributions.")
 (define-public ecl-cl-random
   (sbcl-package->ecl-package sbcl-cl-random))
 
+(define-public sbcl-mgl-gpr
+  (let ((commit "cb6ce51e2f87bf1d589f3703c13eea6e25780afe")
+        (revision "1"))
+    (package
+      (name "sbcl-mgl-gpr")
+      (version (git-version "0.0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/melisgl/mgl-gpr")
+               (commit commit)))
+         (file-name (git-file-name "cl-mgl-gpr" version))
+         (sha256
+          (base32 "0w51dqixh277k6sl8bqvvp1400y6kd1l5h3d9q2f40l9bpxy8gjx"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("cl-random" ,sbcl-cl-random)
+         ("mgl-pax" ,sbcl-mgl-pax)))
+      (home-page "https://melisgl.github.io/mgl-gpr")
+      (synopsis "Common Lisp library of evolutionary algorithms")
+      (description
+       "@code{MGL-GPR} is a library of evolutionary algorithms such as
+Genetic Programming (evolving typed expressions from a set of operators and
+constants) and Differential Evolution.")
+      (license license:expat))))
+
+(define-public cl-mgl-gpr
+  (sbcl-package->cl-source-package sbcl-mgl-gpr))
+
+(define-public ecl-mgl-gpr
+  (sbcl-package->ecl-package sbcl-mgl-gpr))
+
 (define-public sbcl-cl-tld
   ;; No release.
   (let ((commit "f5014da8d831fa9481d4181d4450f10a52850c75"))
-- 
2.25.1

bug#52408: [PATCH 0/5] gnu: Add cl-mgl-gpr.

[Guillaume Le Vaillant]

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Patches pushed as 163f7831c4ed7c7d877234bc208caf625afce808 and
following, with the license of cl-random fixed (expat instead of
boost1.0).
Thanks.

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