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gnu: Add clml.

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* gnu/packages/lisp-xyz.scm (cl-clml, sbcl-clml): New variables.
* gnu/packages/patches/sbcl-clml-fix-types.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
This commit is contained in:
Guillaume Le Vaillant 2020-12-01 10:13:19 +01:00
parent c3e459d266
commit 0809e4a4fa
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GPG key ID: 6BE8208ADF21FE3F
3 changed files with 321 additions and 0 deletions
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1
gnu/local.mk
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@ -1591,6 +1591,7 @@ dist_patch_DATA = \
%D%/packages/patches/rust-reproducible-builds.patch \ %D%/packages/patches/rust-reproducible-builds.patch \
%D%/packages/patches/rust-openssl-sys-no-vendor.patch \ %D%/packages/patches/rust-openssl-sys-no-vendor.patch \
%D%/packages/patches/rxvt-unicode-escape-sequences.patch \ %D%/packages/patches/rxvt-unicode-escape-sequences.patch \
%D%/packages/patches/sbcl-clml-fix-types.patch \
%D%/packages/patches/sbcl-geco-fix-organism-class.patch \ %D%/packages/patches/sbcl-geco-fix-organism-class.patch \
%D%/packages/patches/scalapack-blacs-mpi-deprecations.patch \ %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch \
%D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scheme48-tests.patch \

40
gnu/packages/lisp-xyz.scm
View file

@ -11699,3 +11699,43 @@ Common Lisp arrays and performing numerical calculations with them.")
(define-public ecl-array-operations (define-public ecl-array-operations
(sbcl-package->ecl-package sbcl-array-operations)) (sbcl-package->ecl-package sbcl-array-operations))
(define-public sbcl-clml
(let ((commit "95505b54c8c7b4b27f500c3be97fa5732f4b51a8")
(revision "0"))
(package
(name "sbcl-clml")
(version (git-version "0.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mmaul/clml")
(commit commit)))
(file-name (git-file-name "clml" version))
(sha256
(base32 "006pii59nmpc61n7p7h8ha5vjg6x0dya327i58z0rnvxs249h345"))
;; TODO: Remove this when the patch has been merged upstream.
(patches (search-patches "sbcl-clml-fix-types.patch"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("alexandia" ,sbcl-alexandria)
("array-operations" ,sbcl-array-operations)
("cl-fad" ,sbcl-cl-fad)
("cl-ppcre" ,sbcl-cl-ppcre)
("drakma" ,sbcl-drakma)
("introspect-environment" ,sbcl-introspect-environment)
("iterate" ,sbcl-iterate)
("lparallel" ,sbcl-lparallel)
("parse-number" ,sbcl-parse-number)
("split-sequence" ,sbcl-split-sequence)
("trivial-garbage" ,sbcl-trivial-garbage)))
(synopsis "Common Lisp machine learning library")
(description
"CLML (Common Lisp Machine Learning) is a high performance and large
scale statistical machine learning package")
(home-page "https://mmaul.github.io/clml/")
(license license:llgpl))))
(define-public cl-clml
(sbcl-package->cl-source-package sbcl-clml))

280
gnu/packages/patches/sbcl-clml-fix-types.patch Normal file
View file

@ -0,0 +1,280 @@
commit 9920bf86604b536c735b6478488a3cb89413e000
Author: Guillaume Le Vaillant <glv@posteo.net>
Date: Tue Dec 1 09:38:41 2020 +0100
Fix some type declarations
This allows compiling with SBCL 2.0.11 which is less tolerant with wrong type
declarations.
diff --git a/som/src/lvq_pak.lisp b/som/src/lvq_pak.lisp
index 1a062cc..4006ed6 100644
--- a/som/src/lvq_pak.lisp
+++ b/som/src/lvq_pak.lisp
@@ -53,7 +53,7 @@
(current :accessor entries-current :initarg :current :initform 0
:documentation "index of current data-entry inside data-entries")
(entries :accessor entries-entries :initarg :entries :initform nil
- :type #-ccl cons #+ccl list
+ :type #-ccl (or null cons) #+ccl list
:documentation "list of data-entries")
(num-loaded :accessor entries-num-loaded :initarg :num-loaded :initform nil
:documentation "number of lines loaded in entries list")
diff --git a/statistics/src/rand/rand.lisp b/statistics/src/rand/rand.lisp
index 3cd806a..c8f9952 100644
--- a/statistics/src/rand/rand.lisp
+++ b/statistics/src/rand/rand.lisp
@@ -154,7 +154,7 @@
(xn (make-array (1+ n) :element-type 'double-float)))
(declare (type double-float r v d)
(type fixnum k n n-minus-1)
- (type (vector double-float *) xn))
+ (type (simple-array double-float (*)) xn))
;; build xn
(setf (aref xn n) (* v (exp (/ (* r r) 2))))
(setf (aref xn (1- n)) r)
@@ -233,8 +233,8 @@
(base (expt 2 (- +bit-operation-m+ k 1))))
(declare (type double-float r v d)
(type fixnum k n n-minus-1 base)
- (type (vector double-float *) wn fn)
- (type (vector fixnum *) kn))
+ (type (simple-array double-float (*)) wn fn)
+ (type (simple-array fixnum (*)) kn))
;; build arrays
(setf (aref wn (- n 1)) (/ (* v (exp (/ (* r r) 2))) base))
(setf (aref wn (- n 2)) (/ r base))
@@ -347,8 +347,8 @@
(base (expt 2 (- +bit-operation-m+ k))))
(declare (type double-float r v d)
(type fixnum k n n-minus-1 base)
- (type (vector double-float *) wn fn)
- (type (vector fixnum *) kn))
+ (type (simple-array double-float (*)) wn fn)
+ (type (simple-array fixnum (*)) kn))
;; build arrays
(setf (aref wn (- n 1)) (/ (* v (exp (/ (* r r) 2))) base))
(setf (aref wn (- n 2)) (/ r base))
@@ -546,8 +546,8 @@
(base (expt 2 (- +bit-operation-m+ k 1))))
(declare (type double-float r v tr1 tr2)
(type fixnum k n n-minus-1 base)
- (type (vector double-float *) wn fn)
- (type (vector fixnum *) kn))
+ (type (simple-array double-float (*)) wn fn)
+ (type (simple-array fixnum (*)) kn))
;; build arrays
(setf (aref wn (- n 1)) (/ (* v (+ 1 (* r r))) base))
(setf (aref wn (- n 2)) (/ r base))
@@ -663,8 +663,8 @@
(base (expt 2 (- +bit-operation-m+ k))))
(declare (type double-float r v)
(type fixnum k n n-minus-1 base)
- (type (vector double-float *) wn fn)
- (type (vector fixnum *) kn))
+ (type (simple-array double-float (*)) wn fn)
+ (type (simple-array fixnum (*)) kn))
;; build arrays
(setf (aref wn (- n 1)) (/ (* v (exp r)) base))
(setf (aref wn (- n 2)) (/ r base))
@@ -804,8 +804,8 @@
(base (expt 2 (- +bit-operation-m+ k 1))))
(declare (type double-float r v)
(type fixnum k n n-minus-1 base)
- (type (vector double-float *) wn fn)
- (type (vector fixnum *) kn))
+ (type (simple-array double-float (*)) wn fn)
+ (type (simple-array fixnum (*)) kn))
;; build arrays
(setf (aref wn (- n 1)) (/ (* v (exp r)) base))
(setf (aref wn (- n 2)) (/ r base))
@@ -2083,8 +2083,8 @@
(base (expt 2 (- +bit-operation-m+ k 1))))
(declare (type double-float r v tr)
(type fixnum k n n-minus-1 base)
- (type (vector double-float *) wn fn)
- (type (vector fixnum *) kn))
+ (type (simple-array double-float (*)) wn fn)
+ (type (simple-array fixnum (*)) kn))
;; build arrays
(setf (aref wn (- n 1)) (/ (* (expt (+ 1d0 tr) 2) v) tr base))
(setf (aref wn (- n 2)) (/ r base))
@@ -2383,7 +2383,7 @@
ans)))
(declare (type double-float s a d)
(type vector tix)
- (type (vector fixnum *) si))
+ (type (simple-array fixnum (*)) si))
(values tix si)))
(defun binomial-table-lookup (tix si)
@@ -2415,7 +2415,7 @@
(b (expt 2 k)))
(declare (type double-float s a)
(type fixnum nsq k b)
- (type (vector double-float *) pbins))
+ (type (simple-array double-float (*)) pbins))
;; build pbins
(setf (aref pbins 0) (int-power (- 1d0 probability) size))
(loop for i from 1 to size do
@@ -2438,7 +2438,7 @@
do (incf j tx)) :initial-element -1 :element-type 'fixnum))
(thetan 0d0))
(declare (type double-float w thetan)
- (type (vector fixnum *) table))
+ (type (simple-array fixnum (*)) table))
(loop with j = 0
for x from 0
for pbin across pbins
@@ -2454,8 +2454,8 @@
(vi (make-array nsq :element-type 'double-float
:initial-contents (loop for i from 0 to size collect (dfloat (/ (+ i 1) nsq)))))
(c (dfloat (/ nsq))))
- (declare (type (vector fixnum *) ki)
- (type (vector double-float *) vi)
+ (declare (type (simple-array fixnum (*)) ki)
+ (type (simple-array double-float (*)) vi)
(type double-float c))
(loop repeat size do
(let ((maxp 0)
@@ -2658,7 +2658,7 @@
(thetan 0d0)
(sum 0d0))
(declare (type double-float w thetan sum)
- (type (vector fixnum *) table))
+ (type (simple-array fixnum (*)) table))
(loop with j = 0
for x from 0
for pgeo across pgeos
@@ -2675,8 +2675,8 @@
(vi (make-array nsq :element-type 'double-float
:initial-contents (loop for i from 0 below nsq collect (dfloat (/ (+ i 1) nsq)))))
(c (dfloat (/ nsq))))
- (declare (type (vector fixnum *) ki)
- (type (vector double-float *) vi)
+ (declare (type (simple-array fixnum (*)) ki)
+ (type (simple-array double-float (*)) vi)
(type double-float c))
(loop repeat (1- nsq) do
(let ((maxp 0)
@@ -2911,7 +2911,7 @@
(sum 0d0))
(declare (type double-float w thetan sum pl pu)
(type fixnum nsq d)
- (type (vector fixnum *) table))
+ (type (simple-array fixnum (*)) table))
(unless (= xl 0)
(setf pps (subseq pps xl)))
(loop with j = 0
@@ -2930,8 +2930,8 @@
(vi (make-array nsq :element-type 'double-float
:initial-contents (loop for i from 0 below nsq collect (dfloat (/ (+ i 1) nsq)))))
(c (dfloat (/ nsq))))
- (declare (type (vector fixnum *) ki)
- (type (vector double-float *) vi)
+ (declare (type (simple-array fixnum (*)) ki)
+ (type (simple-array double-float (*)) vi)
(type double-float c))
(loop repeat (1- nsq) do
(let ((maxp 0)
@@ -3174,7 +3174,7 @@
(k 7)
(b (expt 2 k)))
(declare (type fixnum a1 a2 nsq k b)
- (type (vector double-float *) phs))
+ (type (simple-array double-float (*)) phs))
;; build phs
(setf (aref phs 0)
(/ (dfloat (the fixnum (* (combination successes a1) (combination (- elements successes) (- samples a1)))))
@@ -3200,7 +3200,7 @@
(table (make-array b :initial-element -1 :element-type 'fixnum))
(thetan 0d0))
(declare (type double-float w thetan)
- (type (vector fixnum *) table))
+ (type (simple-array fixnum (*)) table))
(loop with j = 0
for x from a1
for i from 0
@@ -3217,8 +3217,8 @@
(vi (make-array nsq :element-type 'double-float
:initial-contents (loop for i from 0 below nsq collect (dfloat (/ (+ i 1) nsq)))))
(c (dfloat (/ nsq))))
- (declare (type (vector fixnum *) ki)
- (type (vector double-float *) vi)
+ (declare (type (simple-array fixnum (*)) ki)
+ (type (simple-array double-float (*)) vi)
(type double-float c))
(loop repeat (1- nsq) do
(let ((maxp 0)
@@ -3442,7 +3442,7 @@
(sum 0d0))
(declare (type double-float w thetan sum pl pu)
(type fixnum nsq d)
- (type (vector fixnum *) table))
+ (type (simple-array fixnum (*)) table))
(unless (= xl 0)
(setf pnbs (subseq pnbs xl)))
(loop with j = 0
@@ -3461,8 +3461,8 @@
(vi (make-array nsq :element-type 'double-float
:initial-contents (loop for i from 0 below nsq collect (dfloat (/ (+ i 1) nsq)))))
(c (dfloat (/ nsq))))
- (declare (type (vector fixnum *) ki)
- (type (vector double-float *) vi)
+ (declare (type (simple-array fixnum (*)) ki)
+ (type (simple-array double-float (*)) vi)
(type double-float c))
(loop repeat (1- nsq) do
(let ((maxp 0)
diff --git a/time-series/src/ts-read-data.lisp b/time-series/src/ts-read-data.lisp
index 09ad933..a692514 100644
--- a/time-series/src/ts-read-data.lisp
+++ b/time-series/src/ts-read-data.lisp
@@ -5,7 +5,7 @@
((frequency :initarg :frequency
:accessor ts-freq
:initform nil
- :type number)
+ :type (or null number))
(start :initarg :start :accessor ts-start :initform nil)
(end :initarg :end :accessor ts-end :initform nil)
(ts-type :initarg :ts-type :accessor ts-type :initform nil)
diff --git a/time-series/src/ts-state-space-model.lisp b/time-series/src/ts-state-space-model.lisp
index 4dbf56a..ad9e5cc 100644
--- a/time-series/src/ts-state-space-model.lisp
+++ b/time-series/src/ts-state-space-model.lisp
@@ -348,8 +348,8 @@
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(eval-when (:execute :compile-toplevel :load-toplevel)
(defclass trend-model (gaussian-stsp-model)
- ((diff-k :initarg :diff-k :initform nil :type integer :accessor diff-k)
- (tau^2 :initarg :tau^2 :initform nil :type number :accessor tau^2)
+ ((diff-k :initarg :diff-k :initform nil :type (or null integer) :accessor diff-k)
+ (tau^2 :initarg :tau^2 :initform nil :type (or null number) :accessor tau^2)
(aic :initarg :aic :initform +nan+ :type number))
(:documentation "- parent: gaussian-stsp-model
- accessors:
@@ -492,9 +492,9 @@
; seasonal model ;
;;;;;;;;;;;;;;;;;;
(defclass seasonal-model (gaussian-stsp-model)
- ((s-deg :initarg :s-deg :initform nil :type fixnum :accessor s-deg)
- (s-freq :initarg :s-freq :initform nil :type fixnum :accessor s-freq)
- (tau^2 :initarg :tau^2 :initform nil :type number :accessor tau^2))
+ ((s-deg :initarg :s-deg :initform nil :type (or null fixnum) :accessor s-deg)
+ (s-freq :initarg :s-freq :initform nil :type (or null fixnum) :accessor s-freq)
+ (tau^2 :initarg :tau^2 :initform nil :type (or null number) :accessor tau^2))
(:documentation "- parent: gaussian-stsp-model
- accessors
- s-deg : Degree for seasonal model
@@ -593,8 +593,8 @@
; seasonal-adjustment-model ;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(defclass seasonal-adjustment-model (gaussian-stsp-model)
- ((trend :initarg :trend :initform nil :type trend-model :accessor trend-model)
- (seasonal :initarg :seasonal :initform nil :type seasonal-model :accessor seasonal-model))
+ ((trend :initarg :trend :initform nil :type (or null trend-model) :accessor trend-model)
+ (seasonal :initarg :seasonal :initform nil :type (or null seasonal-model) :accessor seasonal-model))
(:documentation "Standard seasonal adjustment model ( Trend + Seasonal )
- parent: gaussian-stsp-model
- accessors