[cl-sbml-cvs] CVS cl-sbml
CVS User mantoniotti
mantoniotti at common-lisp.net
Fri Feb 1 11:41:36 UTC 2013
Update of /project/cl-sbml/cvsroot/cl-sbml
In directory tiger.common-lisp.net:/tmp/cvs-serv11586
Modified Files:
COPYING build-model.lisp cl-sbml-package.lisp cl-sbml.system
species-reference.lisp species.lisp unit-kind.lisp
Log Message:
Fixed a few glitches that made the system not loadable (some bit-rot).
Copyright Notice also updated.
--- /project/cl-sbml/cvsroot/cl-sbml/COPYING 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/COPYING 2013/02/01 11:41:36 1.2
@@ -1,5 +1,7 @@
-Copyright (c) 2004-2005 Marco Antoniotti, Bioinformatics Group, Courant
-Institute of Mathematical Sciences, New York University
+Copyright (c) 2004-2013 Marco Antoniotti, Bioinformatics Group, Courant
+Institute of Mathematical Sciences, New York University, New York, USA and
+Dipartimento di Informatica, Sistemistica e Comunicazione, Universita`
+degli Studi di Milano Bicocca, Milan, Italy.
All rights reserved.
Permission is hereby granted, without written agreement and without
@@ -9,19 +11,22 @@
copies of this software.
IN NO EVENT SHALL THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT
-INSTITUTE OF MATHEMATICAL SCIENCES, OR NEW YORK UNIVERSITY BE LIABLE
-TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR
-CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
-DOCUMENTATION, EVEN IF THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE
-COURANT INSTITUTE OF MATHEMATICAL SCIENCES, OR NEW YORK UNIVERSITY
-HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT INSTITUTE OF
-MATHEMATICAL SCIENCES, AND NEW YORK UNIVERSITY SPECIFICALLY DISCLAIMS
-ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
-PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE AUTHOR(S), THE
+INSTITUTE OF MATHEMATICAL SCIENCES, NEW YORK UNIVERSITY, DIPARTIMENTO
+DI INFORMATICA, SISTEMISTICA E COMUNICAZIONE, OR UNIVERSITA` DEGLI STUDI
+DI MILANO BICOCCA, BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
+SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE
+OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE AUTHOR(S), THE
BIOINFORMATICS GROUP, THE COURANT INSTITUTE OF MATHEMATICAL SCIENCES,
-OR NEW YORK UNIVERSITY HAVE NO OBLIGATION TO PROVIDE MAINTENANCE,
-SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+OR NEW YORK UNIVERSITY HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT INSTITUTE OF
+MATHEMATICAL SCIENCES, NEW YORK UNIVERSITY, DIPARTIMENTO DI
+INFORMATICA, SISTEMISTICA E COMUNICAZIONE, AND UNIVERSITA` DEGLI STUDI
+DI MILANO BICOCCA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING,
+BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS
+ON AN "AS IS" BASIS, AND THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE
+COURANT INSTITUTE OF MATHEMATICAL SCIENCES, OR NEW YORK UNIVERSITY
+HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
+ENHANCEMENTS, OR MODIFICATIONS.
--- /project/cl-sbml/cvsroot/cl-sbml/build-model.lisp 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/build-model.lisp 2013/02/01 11:41:36 1.2
@@ -1,9 +1,7 @@
-;;;
+;;;; -*- Mode: Emacs -*-
(in-package "CL-SBML")
-(use-package "CL-XML-EXT")
-
;;;===========================================================================
;;; System dependencies.
@@ -23,7 +21,7 @@
#+(and lispworks win32)
(eval-when (:load-toplevel :execute)
(warn "Automatic and silent stack group extension not implemented ~@
- for LWW. INFIX may not work rpoperly.")
+ for LWW. INFIX may not work properly.")
(setf sys::*stack-overflow-behaviour* nil))
--- /project/cl-sbml/cvsroot/cl-sbml/cl-sbml-package.lisp 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/cl-sbml-package.lisp 2013/02/01 11:41:36 1.2
@@ -1,6 +1,6 @@
;;; -*- Mode: Lisp -*-
-(defpackage "EDU.NYU.BIOINFORMATICS.MARCOXA.CL-SBML" (:use "COMMON-LISP")
+(defpackage "EDU.NYU.BIOINFORMATICS.MARCOXA.CL-SBML" (:use "COMMON-LISP" "CL-XML-EXT")
(:nicknames "CL-SBML")
(:documentation "The CL-SBML Package.")
--- /project/cl-sbml/cvsroot/cl-sbml/cl-sbml.system 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/cl-sbml.system 2013/02/01 11:41:36 1.2
@@ -74,10 +74,11 @@
"build-model"
"sbml-writer"
))
- #+lispworks
+ #| #+lispworks
(:module "gui"
:components ("cl-sbml-interface")
:depends-on ("base"))
+ |#
)
:depends-on ("cl-xml-ext" "cl-mathml"))
--- /project/cl-sbml/cvsroot/cl-sbml/species-reference.lisp 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/species-reference.lisp 2013/02/01 11:41:36 1.2
@@ -2,7 +2,7 @@
(defstruct (species-reference (:include simple-species-reference))
"The SBML Species Reference Structure Class."
- (stoichiometry 0.0d0 :type double)
+ (stoichiometry 0.0d0 :type double-float)
(stoichiometry-math () :type (or null cons stoichiometry-math))
)
--- /project/cl-sbml/cvsroot/cl-sbml/species.lisp 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/species.lisp 2013/02/01 11:41:36 1.2
@@ -14,7 +14,7 @@
(has-only-substance-units-p nil :type boolean)
- (boundary-condition-p nil :type boolean)
+ (boundary-condition nil :type boolean)
(charge 0 :type fixnum)
(constant-p nil :type boolean)
)
--- /project/cl-sbml/cvsroot/cl-sbml/unit-kind.lisp 2005/05/12 17:21:30 1.1
+++ /project/cl-sbml/cvsroot/cl-sbml/unit-kind.lisp 2013/02/01 11:41:36 1.2
@@ -1,44 +1,45 @@
(in-package "CL-SBML")
-(defconstant +unit-kinds+
- '(
- :AMPERE
- :BECQUEREL
- :CANDELA
- :CELSIUS
- :COULOMB
- :DIMENSIONLESS
- :FARAD
- :GRAM
- :GRAY
- :HENRY
- :HERTZ
- :ITEM
- :JOULE
- :KATAL
- :KELVIN
- :KILOGRAM
- :LITER
- :LITRE
- :LUMEN
- :LUX
- :METER
- :METRE
- :MOLE
- :NEWTON
- :OHM
- :PASCAL
- :RADIAN
- :SECOND
- :SIEMENS
- :SIEVERT
- :STERADIAN
- :TESLA
- :VOLT
- :WATT
- :WEBER
- :INVALID)
- )
+(eval-when (:load-toplevel :compile-toplevel :execute)
+ (defconstant +unit-kinds+
+ '(
+ :AMPERE
+ :BECQUEREL
+ :CANDELA
+ :CELSIUS
+ :COULOMB
+ :DIMENSIONLESS
+ :FARAD
+ :GRAM
+ :GRAY
+ :HENRY
+ :HERTZ
+ :ITEM
+ :JOULE
+ :KATAL
+ :KELVIN
+ :KILOGRAM
+ :LITER
+ :LITRE
+ :LUMEN
+ :LUX
+ :METER
+ :METRE
+ :MOLE
+ :NEWTON
+ :OHM
+ :PASCAL
+ :RADIAN
+ :SECOND
+ :SIEMENS
+ :SIEVERT
+ :STERADIAN
+ :TESLA
+ :VOLT
+ :WATT
+ :WEBER
+ :INVALID)
+ ))
(deftype unit-kind ()
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