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CHANGELOG.txt
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Changes for 'b1' beetween V1-5-6 (excluded) and V1-6-0 (included)
built by cvschangelogbuilder 2.4 (build 1.83) with option listdeltabydate.
2008-09-02
* b1@libraries/b/biochem/complex/species-type.lisp 1.54 (changed):
* b1@libraries/b/biochem/location.lisp 1.13 (changed):
* defcomplex now ensures bonds labelled with ! are unique
* added def-location-class
* b1@deliver/console.lisp 1.1 (added):
* b1@deliver/deliver.lisp 1.8 (changed):
* deliver now copies over LICENSE.txt and keeps SWANK packages in delivered binary
* added console.lisp
* [email protected] 1.4 (changed):
* [email protected] 1.8 (changed):
* [email protected] 1.1 (added):
* [email protected] 1.27 (changed):
* b1@deliver/deliver.lisp 1.7 (changed):
* [email protected] 1.6 (changed):
* [email protected] 1.6 (changed):
* [email protected] 1.10 (changed):
* b1@src/global/constants.lisp 1.10 (changed):
* updated text files
* little b console accepts command line arguments
* [email protected] 1.26 (changed):
* b1@src/reader/list-reader.lisp 1.2 (changed):
* upgraded to little b version 1.6.0 for release
* fixed reader-error to work correctly on non-lispworks on command lines
* b1@libraries/examples/custom-rates.lisp 1.2 (changed):
*** empty log message ***
* b1@libraries/examples/cell-location.lisp 1.1 (added):
* b1@libraries/examples/data-table.lisp 1.1 (added):
* b1@libraries/examples/defcomplex.lisp 1.1 (added):
* b1@libraries/examples/example1-simple.lisp 1.1 (added):
* b1@libraries/examples/example2-complexes.lisp 1.1 (added):
* b1@libraries/examples/nil-monomer.lisp 1.1 (added):
* b1@libraries/examples/receptor-ligand.lisp 1.1 (added):
* b1@libraries/examples/simple.lisp 1.1 (added):
* b1@libraries/examples/substitution-table.lisp 1.1 (added):
Added new examples
* [email protected] 1.4 (changed):
* [email protected] 1.2 (changed):
* [email protected] 1.7 (changed):
* b1@deliver/deliver.lisp 1.6 (changed):
* b1@libraries/b/biochem.lisp 1.4 (changed):
* b1@libraries/b/biochem/2-dimensional.lisp 1.2 (changed):
* b1@libraries/b/biochem/3-dimensional.lisp 1.2 (changed):
* b1@libraries/b/biochem/aggregate.lisp 1.3 (changed):
* b1@libraries/b/biochem/basic-ode-modelling.lisp 1.3 (changed):
* b1@libraries/b/biochem/complex.lisp 1.7 (changed):
* b1@libraries/b/biochem/complex/ode.lisp 1.11 (changed):
* b1@libraries/b/biochem/complex/pattern-match.lisp 1.5 (changed):
* b1@libraries/b/biochem/complex/reaction-inference.lisp 1.18 (changed):
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.26 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.55 (changed):
* b1@libraries/b/biochem/complex/test.lisp 1.3 (changed):
* b1@libraries/b/biochem/dimensionalization.lisp 1.3 (changed):
* b1@libraries/b/biochem/dimensionalization/2d.lisp 1.3 (changed):
* b1@libraries/b/biochem/dimensionalization/3d.lisp 1.3 (changed):
* b1@libraries/b/biochem/dimensionalization/null.lisp 1.3 (changed):
* b1@libraries/b/biochem/enzymatic-reaction.lisp 1.7 (changed):
* b1@libraries/b/biochem/localization.lisp 1.4 (changed):
* b1@libraries/b/biochem/location.lisp 1.14 (changed):
* b1@libraries/b/biochem/membrane-apposition.lisp 1.8 (changed):
* b1@libraries/b/biochem/multisided-cell.lisp 1.8 (changed):
* b1@libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.7 (changed):
* b1@libraries/b/biochem/multisided-cell/hex-lattice.lisp 1.2 (changed):
* b1@libraries/b/biochem/multistate-reactant.lisp 1.2 (changed):
* b1@libraries/b/biochem/non-dimensional.lisp 1.2 (changed):
* b1@libraries/b/biochem/ode.lisp 1.21 (changed):
* b1@libraries/b/biochem/reaction-inference.lisp 1.9 (changed):
* b1@libraries/b/biochem/reaction-type.lisp 1.14 (changed):
* b1@libraries/b/biochem/reaction.lisp 1.4 (changed):
* b1@libraries/b/biochem/species-type.lisp 1.5 (changed):
* b1@libraries/b/biochem/species.lisp 1.5 (changed):
* b1@libraries/b/biochem/std-rate-functions.lisp 1.8 (changed):
* b1@libraries/b/graph.lisp 1.2 (changed):
* b1@libraries/b/gui.lisp 1.2 (changed):
* b1@libraries/b/math.lisp 1.3 (changed):
* b1@libraries/b/math/defer-expression.lisp 1.3 (changed):
* b1@libraries/b/math/dimension.lisp 1.4 (changed):
* b1@libraries/b/math/dimensional-methods.lisp 1.4 (changed):
* b1@libraries/b/math/dtype.lisp 1.2 (changed):
* b1@libraries/b/math/expand.lisp 1.3 (changed):
* b1@libraries/b/math/gauss.lisp 1.3 (changed):
* b1@libraries/b/math/math-concept.lisp 1.8 (changed):
* b1@libraries/b/math/math-expression.lisp 1.2 (changed):
* b1@libraries/b/math/math-printer.lisp 1.6 (changed):
* b1@libraries/b/math/non-dimensionalize.lisp 1.3 (changed):
* b1@libraries/b/math/ode-var.lisp 1.5 (changed):
* b1@libraries/b/math/operators.lisp 1.6 (changed):
* b1@libraries/b/math/product-expression-printer.lisp 1.2 (changed):
* b1@libraries/b/math/product-expression.lisp 1.5 (changed):
* b1@libraries/b/math/quantity.lisp 1.5 (changed):
* b1@libraries/b/math/range.lisp 1.2 (changed):
* b1@libraries/b/math/reader.lisp 1.4 (changed):
* b1@libraries/b/math/sum-expression-printer.lisp 1.2 (changed):
* b1@libraries/b/math/sum-expression.lisp 1.11 (changed):
* b1@libraries/b/math/unit.lisp 1.4 (changed):
* b1@libraries/b/math/var.lisp 1.3 (changed):
* b1@libraries/b/matlab/ode-translation.lisp 1.10 (changed):
* b1@libraries/b/matlab/settings.lisp 1.2 (changed):
* b1@libraries/b/numerica/ode-translation.lisp 1.18 (changed):
* b1@libraries/b/units/dimensionalization.lisp 1.2 (changed):
* b1@libraries/b/units/null.lisp 1.2 (changed):
* b1@libraries/b/units/standard-dimensions.lisp 1.2 (changed):
* b1@libraries/b/units/standard-units.lisp 1.2 (changed):
* b1@libraries/b/units/standard.lisp 1.2 (changed):
* b1@libraries/b/units/unit-systems.lisp 1.2 (changed):
* b1@libraries/b/util.lisp 1.2 (changed):
* b1@libraries/b/util/dictionary.lisp 1.9 (changed):
* b1@libraries/examples/nil-monomer.lisp 1.2 (changed):
* b1@libraries/examples/receptor-ligand.lisp 1.2 (changed):
* [email protected] 1.9 (changed):
* b1@src/core-types/concept-class.lisp 1.8 (changed):
* b1@src/core-types/concept.lisp 1.5 (changed):
* b1@src/core-types/property-class.lisp 1.3 (changed):
* b1@src/core-types/property.lisp 1.3 (changed):
* b1@src/core-types/rule.lisp 1.2 (changed):
* b1@src/core/expose.lisp 1.4 (changed):
* b1@src/core/field-function.lisp 1.2 (changed):
* b1@src/core/field-pattern.lisp 1.3 (changed):
* b1@src/core/for-pattern.lisp 1.2 (changed):
* b1@src/core/kb.lisp 1.16 (changed):
* b1@src/core/lisa-extensions.lisp 1.3 (changed):
* b1@src/core/order.lisp 1.2 (changed):
* b1@src/core/printer.lisp 1.16 (changed):
* b1@src/core/query.lisp 1.5 (changed):
* b1@src/core/reify.lisp 1.2 (changed):
* b1@src/core/rule-patterns.lisp 1.9 (changed):
* b1@src/core/type.lisp 1.2 (changed):
* b1@src/global/constants.lisp 1.9 (changed):
* b1@src/global/error.lisp 1.6 (changed):
* b1@src/global/field.lisp 1.21 (changed):
* b1@src/global/fieldinfo.lisp 1.4 (changed):
* b1@src/global/global.lisp 1.5 (changed):
* b1@src/global/missing.lisp 1.2 (changed):
* b1@src/global/name.lisp 1.7 (changed):
* b1@src/global/object.lisp 1.10 (changed):
* b1@src/global/reader-core.lisp 1.5 (changed):
* b1@src/global/trace-filter.lisp 1.2 (changed):
* b1@src/global/trace.lisp 1.3 (changed):
* b1@src/include/clear.lisp 1.4 (changed):
* b1@src/include/compile-include-path.lisp 1.14 (changed):
* b1@src/include/edit.lisp 1.2 (changed):
* b1@src/include/include-declaration.lisp 1.2 (changed):
* b1@src/include/include-documentation.lisp 1.2 (changed):
* b1@src/include/include-path.lisp 1.8 (changed):
* b1@src/include/include.lisp 1.12 (changed):
* b1@src/include/library.lisp 1.4 (changed):
* b1@src/include/uninclude.lisp 1.2 (changed):
* b1@src/packages/mallavar-utility-pkg.lisp 1.9 (changed):
* b1@src/packages/pkgconstants.lisp 1.3 (changed):
* b1@src/packages/pkgdecl.lisp 1.24 (changed):
* b1@src/packages/portable-pkg.lisp 1.8 (changed):
* b1@src/platform/clisp.lisp 1.7 (changed):
* b1@src/platform/lispworks.lisp 1.11 (changed):
* b1@src/portable/clos.lisp 1.7 (changed):
* b1@src/portable/dspec.lisp 1.8 (changed):
* b1@src/portable/misc.lisp 1.9 (changed):
* b1@src/portable/prompt.lisp 1.2 (changed):
* b1@src/portable/windows.lisp 1.3 (changed):
* b1@src/reader/bq-reader.lisp 1.5 (changed):
* b1@src/reader/char-reader.lisp 1.2 (changed):
* b1@src/reader/field-reader.lisp 1.5 (changed):
* b1@src/reader/list-reader.lisp 1.3 (changed):
* b1@src/reader/math-reader.lisp 1.2 (changed):
* b1@src/reader/more-editor-funcs.lisp 1.2 (changed):
* b1@src/reader/object-reader.lisp 1.3 (changed):
* b1@src/reader/quote-reader.lisp 1.2 (changed):
* b1@src/reader/string-reader.lisp 1.2 (changed):
* b1@src/reader/token-reader.lisp 1.5 (changed):
* b1@src/top-level-forms/assume.lisp 1.2 (changed):
* b1@src/top-level-forms/datatable.lisp 1.3 (changed):
* b1@src/top-level-forms/def-with-fields.lisp 1.3 (changed):
* b1@src/top-level-forms/defcon.lisp 1.5 (changed):
* b1@src/top-level-forms/define.lisp 1.3 (changed):
* b1@src/top-level-forms/defplaceholder.lisp 1.3 (changed):
* b1@src/top-level-forms/defprop.lisp 1.3 (changed):
* b1@src/top-level-forms/defrule.lisp 1.8 (changed):
* b1@src/top-level-forms/initialize.lisp 1.9 (changed):
* b1@src/top-level-forms/system.lisp 1.3 (changed):
* b1@src/utility/b-utils.lisp 1.2 (changed):
* b1@src/utility/context-info.lisp 1.2 (changed):
* b1@src/utility/form-inspection.lisp 1.2 (changed):
* b1@src/utility/portable.lisp 1.2 (changed):
* b1@src/utility/predicate.lisp 1.2 (changed):
* b1@src/utility/prompt.lisp 1.2 (changed):
* b1@src/utility/trie.lisp 1.2 (changed):
* b1@src/utility/utility.lisp 1.17 (changed):
Changed to GPL license
* [email protected] 1.3 (changed):
* [email protected] 1.6 (changed):
Changelog and release notes for v1.6.0
* b1@deliver/deliver.lisp 1.5 (changed):
Deliver.lisp now copies the README CHANGELOG RELEASE and LICENSE files to the root directory
* b1@libraries/examples/defcomplex.lisp 1.2 (changed):
Fixed defcomplex example
* b1@libraries/examples/custom-rates.lisp 1.1 (added):
Initial commit of custom-rates example
* [email protected] 1.3 (changed):
Note that CLISP impl is buggy
Removed old examples
* b1@libraries/deprecated-examples/.cvsignore 1.1 (added):
* b1@libraries/deprecated-examples/_init.lisp 1.1 (added):
* b1@libraries/deprecated-examples/egfr-mapk-mkp.lisp 1.1 (added):
* b1@libraries/deprecated-examples/egfr-mapk.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example1-alternate.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example1-reversible.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example1.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example2-reversible.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example3-manual es complex.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example4-enzymatic-reaction.lisp 1.1 (added):
* b1@libraries/deprecated-examples/example5-complexes.lisp 1.1 (added):
* b1@libraries/deprecated-examples/g6pi-d.lisp 1.1 (added):
* b1@libraries/deprecated-examples/g6pi-er.lisp 1.1 (added):
* b1@libraries/deprecated-examples/g6pi.lisp 1.1 (added):
* b1@libraries/deprecated-examples/g6pi2.lisp 1.1 (added):
* b1@libraries/deprecated-examples/locations/cell.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/egf-basal-k1.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/egf-basal.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/egf-egfr.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/egfr-egf-k1.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/espx-catalysis.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/espx-deactivation.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mapk-cascade-k1.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mapk-cascade.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mkp-basal-k1.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mkp-basal-k2.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mkp-basal.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mkp-mapk-cascade-k1.lisp 1.1 (added):
* b1@libraries/deprecated-examples/reactions/mkp-mapk-cascade.lisp 1.1 (added):
* b1@libraries/deprecated-examples/species/egfr.lisp 1.1 (added):
* b1@libraries/deprecated-examples/species/mapk-cascade.lisp 1.1 (added):
* b1@libraries/deprecated-examples/species/mkp.lisp 1.1 (added):
This is a renaming of what used to be the examples library
2008-08-30
* b1@deliver/deliver.lisp 1.3 (changed):
Now using start-tty-listener in little b console application
* [email protected] 1.25 (changed):
* b1@deliver/deliver.lisp 1.4 (changed):
* b1@src/global/constants.lisp 1.8 (changed):
* b1@src/global/global.lisp 1.4 (changed):
* b1@src/global/name.lisp 1.6 (changed):
* b1@src/include/clear.lisp 1.3 (changed):
* b1@src/packages/portable-pkg.lisp 1.7 (changed):
* b1@src/platform/lispworks.lisp 1.10 (changed):
* b1@src/portable/dspec.lisp 1.7 (changed):
* b1@src/top-level-forms/datatable.lisp 1.2 (changed):
* b1@src/top-level-forms/defcon.lisp 1.4 (changed):
* b1@src/top-level-forms/defplaceholder.lisp 1.2 (changed):
* b1@src/top-level-forms/defprop.lisp 1.2 (changed):
* b1@src/top-level-forms/defrule.lisp 1.7 (changed):
* b1@src/utility/utility.lisp 1.16 (changed):
Removed requirement for lispworks EDITOR package so it can be removed when delivering the console
2008-08-29
* b1@deliver/deliver.lisp 1.1 (added):
Initial commit
* b1@deliver/deliver.lisp 1.2 (changed):
Works on linux (ubuntu 8.10)
2008-08-28
* [email protected] 1.24 (changed):
* b1@libraries/b/biochem/complex/ode.lisp 1.10 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.53 (changed):
* b1@libraries/b/biochem/ode.lisp 1.20 (changed):
* b1@libraries/b/matlab/ode-translation.lisp 1.9 (changed):
* b1@libraries/examples/example1.lisp 1.4 (changed):
* b1@src/global/field.lisp 1.20 (changed):
* b1@src/global/object.lisp 1.9 (changed):
*** empty log message ***
2008-08-25
* b1@libraries/examples/example1-reversible.lisp 1.3 (changed):
Simplified a bit
* b1@libraries/examples/example1.lisp 1.3 (changed):
Simplified example1
2008-08-22
* b1@src/global/object.lisp 1.7 (changed):
* b1@src/packages/pkgdecl.lisp 1.22 (changed):
* added define-object-macro, object-macroexpand to b package
* b1@libraries/b/biochem/complex/species-type.lisp 1.52 (changed):
* b1@src/global/object.lisp 1.8 (changed):
* b1@src/packages/pkgdecl.lisp 1.23 (changed):
* defcomplex replaces define-object-macro functionality for complex graph.
* object-macro system has been removed
2008-08-21
* b1@src/core/kb.lisp 1.15 (changed):
* b1@src/core/printer.lisp 1.14 (changed):
* b1@src/global/field.lisp 1.19 (changed):
* b1@src/include/include-path.lisp 1.6 (changed):
* b1@src/portable/dspec.lisp 1.6 (changed):
* default kb-monitor now ignores math-concepts
* clisp printer is now readable!!! (but, no pretty printing)
* without-package-lock to get defield number.terms to compile correctly on clisp
* fixed bug in include-path-compiled-signature
* allow-redefinition now contains ext:without-package-lock on clisp
* [email protected] 1.23 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.51 (changed):
* b1@libraries/b/math/math-concept.lisp 1.7 (changed):
* b1@src/core/printer.lisp 1.15 (changed):
* b1@src/include/include-path.lisp 1.7 (changed):
* fixed bug in (defield number.terms...)
* fixed clisp pprinting code - now using a fill-stream as a quick-and dirty pprinter
* added clisp-pprinter.lisp
* bug fix in complex-graph-show-dotty
2008-08-20
* b1@libraries/b/biochem/std-rate-functions.lisp 1.7 (changed):
* b1@libraries/b/math/math-concept.lisp 1.6 (changed):
* b1@libraries/b/math/sum-expression.lisp 1.9 (changed):
* b1@libraries/b/numerica/ode-translation.lisp 1.17 (changed):
* b1@src/core/kb.lisp 1.12 (changed):
* b1@src/packages/pkgdecl.lisp 1.21 (changed):
* numerica translator now ensures output directories exist
* added .terms to math-expressions and numbers
* hill-function is now just "hill"
* restructured kb-monitor system - now, a single *kb-monitor* function
* b1@src/core/kb.lisp 1.13 (changed):
* b1@src/core/printer.lisp 1.13 (changed):
* removed dead code form printer.lisp
* bug fix to kb-monitor
* b1@libraries/b/math/sum-expression.lisp 1.10 (changed):
* b1@src/core/kb.lisp 1.14 (changed):
* removed dead code form printer.lisp
* bug fix to kb-monitor
* fix clisp bug in sum-expression.terms
2008-08-19
* b1@src/global/field.lisp 1.18 (changed):
Added alpha-order
* b1@src/global/field.lisp 1.17 (changed):
Added the alpha-order field
2008-08-18
* b1@libraries/b/biochem/complex/pattern-match.lisp 1.4 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.50 (changed):
* modified gtools and files in b/biochem/complex to accomodate multibonds
* performance tests show erb/erb2 builds in approximately the same time after changes
2008-08-11
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.25 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.49 (changed):
* b1@src/core/kb.lisp 1.11 (changed):
* fixed a bug in make-difference-kb-monitor
* little b complex graph syntax no longer accepts multi-bonds
2008-08-07
* [email protected] 1.22 (changed):
* b1@src/packages/mallavar-utility-pkg.lisp 1.8 (changed):
Moved data-table to src/top-level-forms and into b packages
* b1@src/top-level-forms/datatable.lisp 1.1 (added):
* b1@src/utility/datatable.lisp 1.13 (removed):
Moved utility\datatable.lisp to top-level-forms\datatable.lisp
and added code to detect when fld-forms and non-lists are arguments to splice vars (e.g., @X)
2008-08-04
* b1@libraries/b/util/dictionary.lisp 1.8 (changed):
* b1@src/core-types/concept-class.lisp 1.7 (changed):
* b1@src/core/kb.lisp 1.10 (changed):
* b1@src/core/printer.lisp 1.12 (changed):
* b1@src/global/object.lisp 1.6 (changed):
* b1@src/packages/pkgdecl.lisp 1.20 (changed):
Now working with Allegro
2008-07-30
* b1@src/global/field.lisp 1.16 (changed):
Finalizing standard-object in field.lisp
* b1@libraries/b/biochem/complex/species-type.lisp 1.48 (changed):
Fixed port:define-dspec-class monomer bug
2008-07-29
* b1@libraries/b/biochem/complex/species-type.lisp 1.47 (changed):
Added jrsi paper
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.24 (changed):
* b1@src/core/kb.lisp 1.9 (changed):
* b1@src/utility/utility.lisp 1.15 (changed):
Squashed the remaining finally return - ansi loop compliance - bug
2008-07-21
* b1@src/core/printer.lisp 1.11 (changed):
*** empty log message ***
* b1@support/lisa3_2-inter-pattern-filter.patch 1.2 (changed):
Fixed
* [email protected] 1.21 (changed):
* b1@src/core/printer.lisp 1.10 (changed):
* b1@src/platform/clisp.lisp 1.6 (changed):
Version 1.5.10:
* clisp 2.45,2.46 workaround for defconstant/constant-warning bug
* clisp pretty-printer newline printing is suppressed
2008-07-19
* b1@libraries/b/biochem/complex/species-type.lisp 1.46 (changed):
*** empty log message ***
* b1@src/include/include.lisp 1.11 (changed):
* b1@src/packages/portable-pkg.lisp 1.6 (changed):
* b1@src/portable/dspec.lisp 1.5 (changed):
Added port:at-location to fix dspec location finding, and use it inside include.lisp during line-based include file loading
* b1@src/reader/bq-reader.lisp 1.4 (changed):
Fixed nasty bq-reader bug
* b1@libraries/b/math/operators.lisp 1.5 (changed):
Got rid of floating-point normalization - now, floats stay as floats, rationals as rationals, etc.
* b1@src/global/field.lisp 1.15 (changed):
Implemented field versions of several CL cons functions
* b1@libraries/b/numerica/ode-translation.lisp 1.16 (changed):
Removed a space from a tracing string
2008-07-18
* b1@libraries/b/biochem/complex/reaction-inference.lisp 1.17 (changed):
* b1@libraries/b/numerica/ode-translation.lisp 1.15 (changed):
* b1@src/global/reader-core.lisp 1.4 (changed):
*** empty log message ***
* [email protected] 1.20 (changed):
* b1@libraries/b/biochem/ode.lisp 1.19 (changed):
Fixed the bug where species is substituted for species-type instead of species.conc in rate eqns
* b1@libraries/b/biochem/complex/species-type.lisp 1.45 (changed):
No change
2008-05-26
* b1@libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.6 (changed):
*** empty log message ***
2008-05-21
* b1@src/core/printer.lisp 1.9 (changed):
* b1@src/global/error.lisp 1.5 (changed):
* b1@src/global/field.lisp 1.14 (changed):
* b1@src/packages/pkgdecl.lisp 1.19 (changed):
* hash-table fld method now permits ht.[key] syntax
* added with-b-error-context
* pretty printer now installs only for type T, which calls print-b-object generic function
* b1@libraries/b/biochem/complex/reaction-inference.lisp 1.16 (changed):
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.23 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.44 (changed):
* b1@libraries/b/biochem/localization.lisp 1.3 (changed):
* b1@libraries/b/biochem/membrane-apposition.lisp 1.7 (changed):
* b1@libraries/b/biochem/multisided-cell.lisp 1.7 (changed):
* b1@libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.5 (changed):
* b1@libraries/b/biochem/ode.lisp 1.18 (changed):
* b1@libraries/b/biochem/reaction-inference.lisp 1.8 (changed):
* b1@libraries/b/biochem/reaction-type.lisp 1.13 (changed):
* b1@libraries/b/biochem/reaction.lisp 1.3 (changed):
* b1@libraries/b/biochem/species-type.lisp 1.4 (changed):
* b1@libraries/b/math/ode-var.lisp 1.4 (changed):
* b1@libraries/b/math/operators.lisp 1.4 (changed):
* b1@libraries/b/math/reader.lisp 1.3 (changed):
* b1@libraries/b/matlab/ode-translation.lisp 1.8 (changed):
* improved error msgs during complex rxn inference
* introduced separate defoperator/def-macro-operator forms
* fixed value fields in wildcard monomers [* *.[:p]] for refering to a value
* added "species-type @ membrane.inner" style syntax
* fixed membrane-apposition references to .c1 and .c2 => .inner .outer
* fixed error in generation of membrane appositions in multisided-cell
* simplified the reaction-rate substituter
* def-species-types input syntax extended slightly
* implemented fast-add for fast symbolic addition
2008-05-15
* b1@src/global/field.lisp 1.13 (changed):
*** empty log message ***
2008-05-14
* b1@libraries/b/numerica/ode-translation.lisp 1.14 (changed):
Got rid of reltol/abstol
2008-05-13
* b1@libraries/b/biochem/complex/species-type.lisp 1.43 (changed):
Fixed a couple of bugs that were caught on clisp
2008-05-12
* b1@libraries/b/biochem/complex/reaction-inference.lisp 1.15 (changed):
* added check for correct localization when reaction-types are infered from complex-reaction-types
* b1@libraries/b/biochem/complex/species-type.lisp 1.42 (changed):
* b1@libraries/b/biochem/ode.lisp 1.17 (changed):
* b1@libraries/b/biochem/reaction-inference.lisp 1.7 (changed):
* b1@libraries/b/biochem/reaction-type.lisp 1.12 (changed):
* fixed clisp print bug
* rewrote code for label testing using gtools:graph-label-test-predicate
* added an error handler in make-complex-graph which reports which complex is causing an error
* reaction-type.set-rate-function now returns the reaction-type object
* error handler when reaction-types are inferred report which complex-reaction-type is causing the error
* minor alteration of the sublocations error in reaction-type.lisp
* b1@src/top-level-forms/define.lisp 1.2 (changed):
Define now accepts a list of symbols as the NAME. These are converted to a symbol where the name of each list element is separated by -. E.g., (define (a b c) 1) == (define a-b-c 1)
2008-05-09
* b1@src/core-types/concept-class.lisp 1.6 (changed):
* b1@src/core/rule-patterns.lisp 1.8 (changed):
* b1@src/global/field.lisp 1.12 (changed):
* b1@src/packages/mallavar-utility-pkg.lisp 1.7 (changed):
* b1@src/utility/utility.lisp 1.14 (changed):
* added base DOCUMENTATION methods (for T type for :fields-help :ctor-help :field-help)
* removed restriction which disallows matching CONCEPT and PROPERTY in rules
* added several new field methods
* added list-difference and related functions to mallavar-utility
2008-05-06
* b1@src/global/global.lisp 1.3 (changed):
Now clear-globals doesn't clear symbols from package B
2008-05-03
* b1@libraries/b/biochem/complex/species-type.lisp 1.41 (changed):
A few more bug fixes and improved error msgs for dealing with * monomers
2008-05-02
* b1@src/utility/datatable.lisp 1.12 (changed):
Changed error text in with-data-table (it is now comprehensible)
* b1@libraries/b/biochem/complex/species-type.lisp 1.40 (changed):
Fixed matching of wildcard patterns
2008-05-01
* b1@libraries/b/biochem/complex/species-type.lisp 1.39 (changed):
*** empty log message ***
* b1@libraries/b/biochem/complex/species-type.lisp 1.38 (changed):
Fix for problem determining location class when * and NIL monomers are present
2008-04-24
* b1@libraries/b/biochem/complex/species-type.lisp 1.36 (changed):
*** empty log message ***
* b1@libraries/b/biochem/complex/species-type.lisp 1.34 (changed):
Added NIL monomer handling - NIL monomers are ignored, and all bonds to them are deleted from final complex
* b1@libraries/b/biochem/complex/species-type.lisp 1.35 (changed):
Fixed a little bug where attempting to determine location-class for * retrieves location-class of (eval *)
* b1@libraries/b/biochem/complex/reaction-inference.lisp 1.14 (changed):
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.22 (changed):
Fixed gtools:compute-unconnected-graphs and updated code in reaction-inference.
this means that rxns where a monomer is lost now are computed correctly:
e.g., {[[a 1][ b1]] ->> [a]}
* [email protected] 1.5 (changed):
Now applies lisa inter-pattern-filter patch
* b1@libraries/b/biochem/complex/species-type.lisp 1.37 (changed):
[[m 1][nil 1]] now correctly produces a complex-pattern, rather than a complex-species-type
2008-04-08
* b1@libraries/b/numerica/ode-translation.lisp 1.13 (changed):
Got rid of a couple of minor warnings
* b1@libraries/b/numerica/ode-translation.lisp 1.12 (changed):
Rate string splitting is now optiona - turned off by setting *numerica-rate-string-max-length* to NIL
2008-04-02
* b1@libraries/b/numerica/ode-translation.lisp 1.11 (changed):
Parts as array in equation section
2008-04-01
* b1@libraries/b/numerica/ode-translation.lisp 1.9 (changed):
"partn := ..." is now in INTERMEDIATE section
* b1@libraries/b/numerica/ode-translation.lisp 1.10 (changed):
Converter writes out = 0; instead of = ; for zero rate fns.
2008-03-28
* b1@libraries/b/math/product-expression.lisp 1.4 (changed):
Fixed a bug where a ref to b/math:product-expression caused error in clisp
* b1@libraries/b/numerica/ode-translation.lisp 1.8 (changed):
Format error caught in clisp fixed
2008-03-27
* b1@libraries/b/math/quantity.lisp 1.4 (changed):
Quantity now prints float format
2008-03-26
* b1@libraries/b/numerica/ode-translation.lisp 1.6 (changed):
Added horrendous kludge to work around numerica max string-length bug
* b1@libraries/b/numerica/ode-translation.lisp 1.7 (changed):
Fixed a small bug
2008-03-07
* b1@libraries/b/biochem/complex/species-type.lisp 1.33 (changed):
* b1@libraries/b/matlab/ode-translation.lisp 1.7 (changed):
* b1@libraries/b/numerica/ode-translation.lisp 1.5 (changed):
* b1@src/packages/pkgdecl.lisp 1.18 (changed):
* b1@src/packages/portable-pkg.lisp 1.5 (changed):
* b1@src/portable/misc.lisp 1.8 (changed):
* package b now exports object-name fn
* b/numerica/ode-translation - working
* matlab & numerica ode-translation now write floats, not rationals
* portable package now contains a run-shell-command fn, which b/biochem/complex/species-type uses
instead of the asdf one
* b1@support/lisa3_2-inter-pattern-filter.patch 1.1 (added):
*** empty log message ***
2008-03-06
* b1@libraries/b/math/math-concept.lisp 1.5 (changed):
* b1@libraries/b/numerica/ode-translation.lisp 1.3 (changed):
*** empty log message ***
* b1@libraries/b/math/product-expression.lisp 1.3 (changed):
* b1@libraries/b/math/sum-expression.lisp 1.8 (changed):
Added math-expression-to-list
* b1@libraries/b/_config.lisp 1.3 (changed):
Compiles b/numerica/ode-translation now
* b1@libraries/b/numerica/ode-translation.lisp 1.4 (changed):
Produces code with erb4.lisp!
2008-03-05
* b1@libraries/b/numerica/ode-translation.lisp 1.2 (changed):
Got it to work with simple E+S -> E+P model
* b1@libraries/b/numerica/ode-translation.lisp 1.1 (added):
Initial commit
2008-02-22
* b1@libraries/b/math/ode-var.lisp 1.3 (changed):
- ode-var.rate uses (reduce #'s+ ...) rather than (apply #'s+ ...) - which fixes max arg limit problem
2008-02-14
* b1@src/core/kb.lisp 1.8 (changed):
Quiet-tracer now forces output of stdio to after each + is printed
2008-02-13
* b1@libraries/b/matlab/ode-translation.lisp 1.6 (changed):
Fixed escape-matlab-formatting-chars
2008-02-12
* b1@src/core/printer.lisp 1.8 (changed):
* b1@src/global/field.lisp 1.11 (changed):
* b1@src/platform/lispworks.lisp 1.9 (changed):
* b1@src/reader/bq-reader.lisp 1.3 (changed):
* added a printer for backquoted dotted lists
* fixed eval region in lispworks
* b1@libraries/examples/reactions/egf-basal.lisp 1.2 (changed):
* b1@libraries/examples/reactions/egf-egfr.lisp 1.2 (changed):
* b1@libraries/examples/species/egfr.lisp 1.2 (changed):
* b1@libraries/examples/species/mapk-cascade.lisp 1.2 (changed):
* b1@libraries/examples/species/mkp.lisp 1.2 (changed):
Converted examples to v1.5 notation
2008-02-02
* b1@libraries/b/biochem/complex/species-type.lisp 1.30 (changed):
*** empty log message ***
* b1@libraries/b/biochem/complex/species-type.lisp 1.31 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.32 (changed):
Fixed wildcard bindings when referencing site-by-name
2008-01-30
* [email protected] 1.19 (changed):
*** empty log message ***
2008-01-28
* b1@libraries/b/matlab/ode-translation.lisp 1.5 (changed):
* b1@src/core/rule-patterns.lisp 1.7 (changed):
* b1@src/global/fieldinfo.lisp 1.3 (changed):
* fixed the matlab printing bug
* added class-fieldinfos now throws error by default if field doesn't exist
2008-01-26
* b1@libraries/b/biochem/ode.lisp 1.16 (changed):
* b1@libraries/b/matlab/ode-translation.lisp 1.4 (changed):
* fixed ode generator -- and implemented :ode-comments-p
keyword argument to create-ode-model
2008-01-24
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.21 (changed):
Minor comment deletion
* b1@libraries/b/biochem/complex/species-type.lisp 1.29 (changed):
Site-info now has :bonds slot
2008-01-23
* [email protected] 1.8 (changed):
* b1@src/core/kb.lisp 1.7 (changed):
* b1@src/core/rule-patterns.lisp 1.5 (changed):
* b1@src/packages/pkgdecl.lisp 1.17 (changed):
* small changes to names in monitoring system
* rules now much more effient - hashing on constant tests now works rather than binding variable, then testing EQ afterwards
* removed #\. printing from graph isomorphism testing in pattern-match.lisp
* littleb.lisp now contains helper fn (delete-littleb-binaries) which clears out all asdf fasls.
* b1@src/core/rule-patterns.lisp 1.6 (changed):
* b1@src/include/include-path.lisp 1.5 (changed):
* b1@src/platform/lispworks.lisp 1.8 (changed):
* small efficiencies in lisa rule builder
* cleaned up include-path and other code leading to signals being generated during (INIT) and in lispworks' code finder
* b1@libraries/b/biochem/multisided-cell.lisp 1.6 (changed):
Fixed deprecated membrane field warnings
2008-01-22
* b1@src/core/kb.lisp 1.6 (changed):
* b1@src/packages/pkgdecl.lisp 1.16 (changed):
*kb-monitor* is now *kb-monitors*, a list
* b1@libraries/b/biochem/ode.lisp 1.15 (changed):
* b1@libraries/b/biochem/reaction-inference.lisp 1.6 (changed):
* b1@libraries/b/biochem/reaction-type.lisp 1.11 (changed):
Back to the old way of doing reaction inference :(
* [email protected] 1.18 (changed):
* b1@libraries/b/biochem/complex/species-type.lisp 1.28 (changed):
* b1@libraries/b/biochem/location.lisp 1.12 (changed):
* b1@libraries/b/biochem/membrane-apposition.lisp 1.6 (changed):
* b1@libraries/b/biochem/multisided-cell.lisp 1.5 (changed):
* b1@libraries/b/biochem/ode.lisp 1.13 (changed):
* b1@libraries/b/math/defer-expression.lisp 1.2 (changed):
* b1@libraries/b/math/ode-var.lisp 1.2 (changed):
* b1@libraries/b/math/product-expression.lisp 1.2 (changed):
* b1@libraries/b/math/quantity.lisp 1.3 (changed):
* b1@libraries/b/math/sum-expression.lisp 1.7 (changed):
* b1@libraries/b/math/unit.lisp 1.3 (changed):
* b1@libraries/b/math/var.lisp 1.2 (changed):
* b1@libraries/b/util/dictionary.lisp 1.7 (changed):
* b1@src/core-types/concept-class.lisp 1.5 (changed):
* b1@src/core/kb.lisp 1.5 (changed):
* b1@src/global/constants.lisp 1.7 (changed):
* b1@src/packages/pkgdecl.lisp 1.15 (changed):
* b1@src/top-level-forms/defcon.lisp 1.3 (changed):
* b1@src/top-level-forms/defrule.lisp 1.6 (changed):
* b1@src/top-level-forms/system.lisp 1.2 (changed):
Replaced old tracing system with *kb-monitor* approach
* b1@libraries/b/biochem/ode.lisp 1.14 (changed):
* b1@libraries/b/biochem/reaction-type.lisp 1.10 (changed):
Replaced old tracing system with *kb-monitor* approach (working)
2008-01-19
* b1@src/include/compile-include-path.lisp 1.13 (changed):
* b1@src/portable/misc.lisp 1.7 (changed):
* b1@src/portable/windows.lisp 1.2 (changed):
*** empty log message ***
2008-01-18
* b1@libraries/b/biochem/complex/species-type.lisp 1.26 (changed):
* added an upper bound on # monomers per complex: *max-monomers-per-complex*
* dot-script should not make double edges for tri bonds
* b1@libraries/b/biochem/complex/species-type.lisp 1.27 (changed):
* monomer size check now works
* b1@src/global/field.lisp 1.10 (changed):
Added fields which mirror the sequence dictionary
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.20 (changed):
Destruction of monomers bug -- fix2: a bit more efficient
2008-01-17
* b1@libraries/b/biochem/complex/species-type.lisp 1.25 (changed):
* __ default monomer argument now implemented
* added :size option to complex-species-type.show
* b1@libraries/b/biochem/reaction-type.lisp 1.7 (changed):
* b1@src/include/include.lisp 1.7 (changed):
* b1@src/utility/datatable.lisp 1.11 (changed):
* b1@src/utility/utility.lisp 1.12 (changed):
* fixed a bug in mapatoms (when nil is passed)
* prettified with-data-table destructuration errors
* b1@src/include/include.lisp 1.8 (changed):
* b1@src/packages/mallavar-utility-pkg.lisp 1.6 (changed):
* b1@src/utility/utility.lisp 1.13 (changed):
* loading source files when debugger is disabled gives nicer error messages identifying location causing error)
* added positions-if to mutils
* b1@src/include/include.lisp 1.10 (changed):
*** empty log message ***
* b1@libraries/b/biochem/complex/reaction-inference.lisp 1.13 (changed):
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.19 (changed):
Destruction of monomers bug -- initial fix
* b1@libraries/b/biochem/reaction-type.lisp 1.9 (changed):
Fixed a bug in parse-reaction-type-argments in multi-location reactions
* b1@src/include/include.lisp 1.9 (changed):
In midstream of changes
* b1@src/portable/dspec.lisp 1.4 (changed):
Initial changes toward cmucl compatibility
* b1@libraries/b/biochem/reaction-type.lisp 1.8 (changed):
Prettified error messages
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.18 (changed):
__ default monomer argument now implemented
2008-01-15
* b1@libraries/b/biochem/complex/ode.lisp 1.9 (changed):
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.17 (changed):
Added reversible complex-reaction-type
* b1@src/utility/datatable.lisp 1.10 (changed):
Changed with-data-table substitution parameters: row=>rows col=>cols data=>cells
2008-01-12
* b1@src/utility/datatable.lisp 1.9 (changed):
* b1@src/utility/utility.lisp 1.11 (changed):
* with-substitution-table, with-data-table now support @ syntax for substitution
* data-table and substitution table now correctly support single or multiple arguments
* mapatoms now takes a fn which returns 2 args, second of which indicates that
the returned value should be spliced into the returned list.
2008-01-11
* [email protected] 1.17 (changed):
* b1@src/packages/portable-pkg.lisp 1.4 (changed):
* b1@src/portable/misc.lisp 1.6 (changed):
* b1@src/portable/windows.lisp 1.1 (added):
Moved windows-specific code to portable/windows.lisp
2008-01-09
* b1@src/utility/datatable.lisp 1.7 (changed):
Comment update
* b1@src/portable/misc.lisp 1.5 (changed):
* b1@src/utility/datatable.lisp 1.8 (changed):
Fixed a couple of syntax bugs
2008-01-08
* b1@src/packages/mallavar-utility-pkg.lisp 1.5 (changed):
* b1@src/packages/pkgdecl.lisp 1.14 (changed):
* b1@src/utility/datatable.lisp 1.6 (changed):
* with-combinations now correctly computes code substitutions using combinations
* introduced with-permutations: computes code substitutions using permutations
* b1@libraries/b/biochem/complex/species-type.lisp 1.24 (changed):
.show now uses firefox rather than dotty
* b1@src/packages/portable-pkg.lisp 1.3 (changed):
* b1@src/portable/misc.lisp 1.3 (changed):
Added make-temp-file to portable
* b1@src/packages/mallavar-utility-pkg.lisp 1.4 (changed):
* b1@src/packages/pkgdecl.lisp 1.13 (changed):
* b1@src/utility/datatable.lisp 1.5 (changed):
Changed with-substituted-combinations to with-combinations
* b1@src/utility/datatable.lisp 1.4 (changed):
Datatable now accepts lists for ROW and COL
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.16 (changed):
* b1@src/portable/misc.lisp 1.4 (changed):
Destruction rxns now work
* b1@src/utility/utility.lisp 1.10 (changed):
Fixed find-and-replace
* b1@libraries/b/biochem/complex/species-type.lisp 1.23 (changed):
Just removed some comments
* [email protected] 1.16 (changed):
Updated version to 1.5.6
2008-01-07
* b1@src/utility/utility.lisp 1.9 (changed):
Fixed find-and-replace bug
2008-01-04
* b1@libraries/b/matlab/ode-translation.lisp 1.3 (changed):
Characters which cause special formatting in matlab .m files are now escaped.
* b1@libraries/b/biochem/complex/species-type.lisp 1.22 (changed):
Dot script converter added: complex-graph-concept.show demonstrates how dotty could be called
* b1@libraries/b/biochem/complex.lisp 1.6 (changed):
* b1@libraries/b/biochem/complex/reaction-type.lisp 1.15 (changed):
Remove spurious comments
2008-01-02
* b1@src/packages/mallavar-utility-pkg.lisp 1.3 (changed):
* b1@src/packages/pkgdecl.lisp 1.12 (changed):
* b1@src/platform/clisp.lisp 1.5 (changed):
* b1@src/platform/lispworks.lisp 1.7 (changed):
* b1@src/utility/utility.lisp 1.8 (changed):
Added cross-platform quit/gc to mallavar-utility: this is exported from b package
* b1@src/utility/utility.lisp 1.7 (changed):
Delete-directory fixed for sbcl
* b1@src/utility/datatable.lisp 1.3 (changed):
Fixed datatable bug: symbol empty=>ignore
2008-01-01
* b1@src/utility/utility.lisp 1.6 (changed):
Fixed assoc-val ANSI compliance bug (was incompatible with SBCL)
2007-12-29
* [email protected] 1.15 (changed):
Removed spurious comments and commented-out code in asdf PERFORM :AFTER method
2007-12-27
* [email protected] 1.7 (changed):
Cosmetic change
2007-12-24
* b1@src/reader/bq-reader.lisp 1.2 (changed):
,@ now respects *read-suppress*
* b1@libraries/b/math/non-dimensionalize.lisp 1.2 (changed):
Added ignore declaration
* b1@libraries/b/math/dimensional-methods.lisp 1.3 (changed):
Fixed def-multi-type-method ignore warning
* b1@libraries/b/biochem/enzymatic-reaction.lisp 1.6 (changed):
Fixed invalid use of parse-reaction-type-arguments in enzymatic-reaction
Get-cvs-modules scripts now cvs export lisa rather than checkout
(before this, cvs tag failed because no lisa write access)
changelog and release notes for V1-5-6
2007-12-16
* b1@src/utility/mop.lisp 1.2 (removed):
Removed mop.lisp