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Merge branch 'testing' of https://github.com/miguelmarco/kenzo into testing

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This commit is contained in:
Ana Romero 2019-06-27 17:35:22 +02:00
commit 804813be71
6 changed files with 238 additions and 94 deletions
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142
kenzo.asd
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@ -1,71 +1,71 @@
;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10 -* ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10 -*
(in-package :cl-user) (in-package :cl-user)
(defpackage :kenzo-asd (defpackage :kenzo-asd
(:use :cl :asdf)) (:use :cl :asdf))
(in-package :kenzo-asd) (in-package :kenzo-asd)
(asdf:defsystem #:kenzo (asdf:defsystem #:kenzo
:description "A Symbolic Software for Effective Homology Computation by Francis Sergeraert" :description "A Symbolic Software for Effective Homology Computation by Francis Sergeraert"
:version "1.1.7" :version "1.1.7"
:author "Francis Sergeraert <Francis.Sergeraert@ujf-grenoble.fr>" :author "Francis Sergeraert <Francis.Sergeraert@ujf-grenoble.fr>"
:license "GPLv3" :license "GPLv3"
:serial t :serial t
:components :components
((:file "package") ((:file "package")
(:module "src" (:module "src"
:components :components
( (
(:file "kenzo") (:file "kenzo")
(:file "abbreviations") (:file "abbreviations")
(:file "macros") (:file "macros")
(:file "various") (:file "various")
(:file "classes") (:file "classes")
(:file "combinations") (:file "combinations")
(:file "chain-complexes") (:file "chain-complexes")
(:file "chcm-elementary-op") (:file "chcm-elementary-op")
(:file "effective-homology") (:file "effective-homology")
(:file "homology-groups") (:file "homology-groups")
(:file "searching-homology") (:file "searching-homology")
(:file "cones") (:file "cones")
(:file "bicones") (:file "bicones")
(:file "tensor-products") (:file "tensor-products")
(:file "coalgebras") (:file "coalgebras")
(:file "cobar") (:file "cobar")
(:file "algebras") (:file "algebras")
(:file "bar") (:file "bar")
(:file "simplicial-sets") (:file "simplicial-sets")
(:file "simplicial-mrphs") (:file "simplicial-mrphs")
(:file "delta") (:file "delta")
(:file "special-smsts") (:file "special-smsts")
(:file "suspensions") (:file "suspensions")
(:file "disk-pasting") (:file "disk-pasting")
(:file "cartesian-products") (:file "cartesian-products")
(:file "eilenberg-zilber") (:file "eilenberg-zilber")
(:file "kan") (:file "kan")
(:file "simplicial-groups") (:file "simplicial-groups")
(:file "fibrations") (:file "fibrations")
(:file "loop-spaces") (:file "loop-spaces")
(:file "ls-twisted-products") (:file "ls-twisted-products")
(:file "lp-space-efhm") (:file "lp-space-efhm")
(:file "classifying-spaces") (:file "classifying-spaces")
(:file "k-pi-n") (:file "k-pi-n")
(:file "serre") (:file "serre")
(:file "cs-twisted-products") (:file "cs-twisted-products")
(:file "cl-space-efhm") (:file "cl-space-efhm")
(:file "whitehead") (:file "whitehead")
(:file "smith") (:file "smith")
(:file "sage-interface") (:file "sage-interface")
(:module "anromero" (:module "anromero"
:components :components
((:file "resolutions") ((:file "resolutions")
(:file "cylinders") (:file "cylinders")
(:file "fundamental-classes") (:file "fundamental-classes")
(:file "homotopy") (:file "homotopy")
(:file "bicomplexes") (:file "bicomplexes")
(:file "filtered-complexes") (:file "filtered-complexes")
(:file "spectral-sequences") (:file "spectral-sequences")
(:file "persistent-homology") (:file "persistent-homology")
)))))) ))))))

15
run-kenzo-test.lisp
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@ -2,9 +2,18 @@
(DECLAIM (OPTIMIZE (speed 3) (space 0) (debug 3))) (DECLAIM (OPTIMIZE (speed 3) (space 0) (debug 3)))
(require 'asdf) (require :asdf)
(require :kenzo)
(asdf:operate 'asdf:load-op 'kenzo-test) (require :ecl-quicklisp)
(ql:quickload "fiveam")
(push #P"./" asdf:*central-registry*)
(require :kenzo-test)
(setf fiveam:*debug-on-error* t
fiveam:*debug-on-failure* t)
(setf *debugger-hook*
(lambda (c h)
(declare (ignore c h))
(uiop:quit -1)))
(fiveam:run! :kenzo) (fiveam:run! :kenzo)
#+(or ecl ccl) (quit) #+(or ecl ccl) (quit)

12
src/anromero/homotopy.lisp
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@ -119,15 +119,21 @@
(cond ((equal (car list) 1) (let* ((ch (chml-clss chcm indx)) (cond ((equal (car list) 1) (let* ((ch (chml-clss chcm indx))
(fib (z-whitehead chcm ch)) (fib (z-whitehead chcm ch))
(ft (fibration-total fib))) (ft (fibration-total fib)))
(construct-space-iterative ft (cdr list) indx))) (progn
(kill-epis ft 1 indx)
(construct-space-iterative ft (cdr list) indx))))
((equal (car list) 2) (let* ((ch (chml-clss chcm indx)) ((equal (car list) 2) (let* ((ch (chml-clss chcm indx))
(fib (z2-whitehead chcm ch)) (fib (z2-whitehead chcm ch))
(ft (fibration-total fib))) (ft (fibration-total fib)))
(construct-space-iterative ft (cdr list) indx))) (progn
(kill-epis ft 1 indx)
(construct-space-iterative ft (cdr list) indx))))
(t (let* ((ch (chml-clss chcm indx)) (t (let* ((ch (chml-clss chcm indx))
(fib (zp-whitehead (car list) chcm ch)) (fib (zp-whitehead (car list) chcm ch))
(ft (fibration-total fib))) (ft (fibration-total fib)))
(construct-space-iterative ft (cdr list) indx))) (progn
(kill-epis ft 1 indx)
(construct-space-iterative ft (cdr list) indx))))
))) )))

89
src/sage-interface.lisp
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@ -8,8 +8,10 @@
(DEFVAR *ASCII-NUM-START* 48) ;;;;; Chain complexes ;;;;;
(DEFVAR *ASCII-NUM-START* 48)
(DEFVAR *ASCII-NUM-END* 57) (DEFVAR *ASCII-NUM-END* 57)
@ -33,7 +35,6 @@
(return (format nil "~{~a~}" (nreverse result)))))) (return (format nil "~{~a~}" (nreverse result))))))
(DEFUN STRCAT (&rest strings) (apply 'concatenate 'string strings)) (DEFUN STRCAT (&rest strings) (apply 'concatenate 'string strings))
@ -41,8 +42,8 @@
`(read-from-string (strcat "G" (itoa ,num1) "G" (itoa ,num2)))) `(read-from-string (strcat "G" (itoa ,num1) "G" (itoa ,num2))))
(DEFUN KBASIS (schcm) (DEFUN KBASIS (schcm)
#| Provide the slot :basis of the KenzoSimplicialSet obtained by applying the function 'KChainComplex' to 'schcm' |#
(flet ((rslt (dim) (flet ((rslt (dim)
(let ((pair (assoc dim schcm))) (let ((pair (assoc dim schcm)))
(if (null pair) (if (null pair)
@ -52,8 +53,8 @@
(the basis #'rslt))) (the basis #'rslt)))
(DEFUN KDFFR (schcm) (DEFUN KDFFR (schcm)
#| Provide the slot :intr-dffr of the KenzoSimplicialSet obtained by applying the function 'KChainComplex' to 'schcm' |#
(flet ((frslt (dim gnr) (flet ((frslt (dim gnr)
(let* ((sep (1+ (position #\G (subseq (write-to-string gnr) 1)))) (let* ((sep (1+ (position #\G (subseq (write-to-string gnr) 1))))
(dim_gnr (read-from-string (subseq (write-to-string gnr) 1 sep))) (dim_gnr (read-from-string (subseq (write-to-string gnr) 1 sep)))
@ -75,8 +76,8 @@
#'frslt)) #'frslt))
(DEFUN G-CMPR (GnGm1 GnGm2) (DEFUN G-CMPR (GnGm1 GnGm2)
#| Provide the slot :cmpr of the KenzoSimplicialSet obtained by applying the function 'KChainComplex' to 'schcm' |#
(let* ((sep (1+ (position #\G (subseq (write-to-string GnGm1) 1)))) (let* ((sep (1+ (position #\G (subseq (write-to-string GnGm1) 1))))
(m1 (read-from-string (subseq (write-to-string GnGm1) (1+ sep)))) (m1 (read-from-string (subseq (write-to-string GnGm1) (1+ sep))))
(m2 (read-from-string (subseq (write-to-string GnGm2) (1+ sep))))) (m2 (read-from-string (subseq (write-to-string GnGm2) (1+ sep)))))
@ -89,8 +90,16 @@
:greater))))) :greater)))))
(DEFUN ENTRY (mat i j)
#| Provide the entry in row 'i' and column 'j' of the matrice 'mat' |#
(let ((p (left (chercher-hor (baselig mat i) j))))
(if (= j (icol p))
(val p)
0)))
(DEFUN CONVERTMATRICE (matrice) (DEFUN CONVERTMATRICE (matrice)
#| Convert a matrix of type matrice to an array |#
(let* ((numfil (nlig matrice)) (let* ((numfil (nlig matrice))
(numcol (ncol matrice)) (numcol (ncol matrice))
(rslt (make-array (list numfil numcol) :initial-element 0))) (rslt (make-array (list numfil numcol) :initial-element 0)))
@ -102,16 +111,8 @@
rslt)) rslt))
(DEFUN ENTRY (mat i j)
(let ((p (left (chercher-hor (baselig mat i) j))))
(if (= j (icol p))
(val p)
0)))
(DEFUN CHCM-MAT2 (chcm n) (DEFUN CHCM-MAT2 (chcm n)
#| The same 'chcm-mat' function but it does not print on screen intermediate computations |#
(declare (declare
(type chain-complex chcm) (type chain-complex chcm)
(type fixnum n)) (type fixnum n))
@ -145,8 +146,51 @@
mat))) mat)))
(DEFUN MAKE-ARRAY-TO-LISTS (array)
#| Convert an array to a list formed by the array's rows |#
(loop for i below (array-dimension array 0)
collect (loop for j below (array-dimension array 1)
collect (aref array i j))))
(DEFUN MAKE-ARRAY-FROM-LISTS (nrows ncols list)
#| Construct an array from a list formed by the array's rows |#
(make-array (list nrows ncols) :initial-contents list))
(DEFUN BASIS_AUX1 (kchcm dim)
(basis kchcm dim))
(DEFUN ORGN_AUX1 (kchcm)
(orgn kchcm))
(DEFUN DFFR_AUX1(kchcm dim cmbn_list)
#| Differential of a comb with dimension 'dim' and 'cmbn_list' as its cmbn-list |#
(let ((comb (cmbn dim)))
(setf (cmbn-list comb) cmbn_list)
(dffr kchcm comb)))
(DEFUN KCHAINCOMPLEX_AUX1 (chcm str_orgn)
#| Construct a chain complex in Kenzo from the information of the assoc list 'chcm' constructed from a dictionary whose values are matrices |#
(build-chcm :cmpr #'G-CMPR
:strt :GNRT
:basis (kbasis chcm)
:intr-dffr (kdffr chcm)
:orgn `(KChainComplex ,str_orgn)))
;;;;; Simplicial Sets ;;;;;
(DEFUN KABSTRACTSIMPLEX_AUX1 (degeneracies name)
(absm (dgop-ext-int degeneracies) name))
(DEFUN BUILD-FINITE-SS2 (list) (DEFUN BUILD-FINITE-SS2 (list)
#| The same 'build-finite-ss' function but it does not check the face relations of the simplices in 'list' ('check-smst' omitted) |#
(declare (list list)) (declare (list list))
(let ((bspn (first list)) (let ((bspn (first list))
(table (finite-ss-table list)) (table (finite-ss-table list))
@ -166,5 +210,18 @@
(setf (symbol-value ind-smst) rslt) (setf (symbol-value ind-smst) rslt)
rslt))) rslt)))
(DEFUN MAKE-ARRAY-FROM-LISTS (list)
(make-array (list (length list) (length (first list))) :initial-contents list)) (DEFUN SFINITESIMPLICIALSET_AUX1 (finitess limit)
#| Construct a list (L0 L1 ... Lm), with m <= 'limit', where each list Lk is formed by lists of the form (S (a0 ... ak)), where each aj is a face of the k-simplex S |#
(let ((rslt NIL))
(do ((k 1 (1+ k))) ((> k limit))
(let ((dimk NIL))
(dolist (simplex (basis finitess k))
(let ((faces NIL))
(do ((i k (1- i))) ((< i 0))
(push (face finitess i k simplex) faces))
(push (cons simplex faces) dimk)))
(push dimk rslt)))
(reverse rslt)))

4
src/smith.lisp
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@ -644,7 +644,9 @@
(if (and (symbolp gnrt1) (if (and (symbolp gnrt1)
(eq (symbol-package gnrt1) (eq (symbol-package gnrt1)
+gnrts-pckg+)) +gnrts-pckg+))
(s-cmpr gnrt1 gnrt2) ;;(s-cmpr gnrt1 gnrt2)
(f-cmpr (parse-integer (subseq (string gnrt1) 3))
(parse-integer (subseq (string gnrt2) 3)))
(funcall cmpr gnrt1 gnrt2))) (funcall cmpr gnrt1 gnrt2)))
:basis #'(lambda (degr) :basis #'(lambda (degr)
(declare (fixnum degr)) (declare (fixnum degr))

70
test/homotopy-test.lisp Normal file
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@ -0,0 +1,70 @@
;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10 -*
(in-package :kenzo-test)
(in-suite :kenzo)
(test homotopy-s2
(cat:cat-init)
(let* ((s2 (cat:sphere 2))
)
(is (equalp (cat:homotopy-list s2 2 '(1))))
(is (equalp (cat:homotopy-list s2 3 '(1))))
(is (equalp (cat:homotopy-list s2 4 '(2))))
(is (equalp (cat:homotopy-list s2 5 '(2))))
(is (equalp (cat:homotopy-list s2 6 '(12))))
))
(test homotopy-s3
(cat:cat-init)
(let* ((s3 (cat:sphere 3))
)
(is (equalp (cat:homotopy-list s3 2 nil)))
(is (equalp (cat:homotopy-list s3 3 '(1))))
(is (equalp (cat:homotopy-list s3 4 '(2))))
(is (equalp (cat:homotopy-list s3 5 '(2))))
(is (equalp (cat:homotopy-list s3 6 '(12))))
))
(test homotopy-s4
(cat:cat-init)
(let* ((s4 (cat:sphere 4))
)
(is (equalp (cat:homotopy-list s4 2 nil)))
(is (equalp (cat:homotopy-list s4 3 nil)))
(is (equalp (cat:homotopy-list s4 4 '(1))))
(is (equalp (cat:homotopy-list s4 5 '(2))))
(is (equalp (cat:homotopy-list s4 6 '(2))))
(is (equalp (cat:homotopy-list s4 7 '(12 1))))
))
(test homotopy-s5
(cat:cat-init)
(let* ((s5 (cat:sphere 5))
)
(is (equalp (cat:homotopy-list s5 2 nil)))
(is (equalp (cat:homotopy-list s5 3 nil)))
(is (equalp (cat:homotopy-list s5 4 nil)))
(is (equalp (cat:homotopy-list s5 5 '(1))))
(is (equalp (cat:homotopy-list s5 6 '(2))))
(is (equalp (cat:homotopy-list s5 7 '(2))))
(is (equalp (cat:homotopy-list s5 8 '(24))))
))
(test homotopy-s6
(cat:cat-init)
(let* ((s6 (cat:sphere 6))
)
(is (equalp (cat:homotopy-list s6 2 nil)))
(is (equalp (cat:homotopy-list s6 3 nil)))
(is (equalp (cat:homotopy-list s6 4 nil)))
(is (equalp (cat:homotopy-list s6 5 nil)))
(is (equalp (cat:homotopy-list s6 6 '(1))))
(is (equalp (cat:homotopy-list s6 7 '(2))))
(is (equalp (cat:homotopy-list s6 8 '(2))))
(is (equalp (cat:homotopy-list s6 9 '(24))))
))