Commit 42a0316a authored by FAGES Francois's avatar FAGES Francois
Browse files

merging

Merge branch 'develop' of gitlab.inria.fr:lifeware/biocham into develop
parents 4801fd65 c78b39c9
......@@ -12,7 +12,7 @@ ifndef $(PREFIX)
PREFIX=/usr/local
endif
$(foreach var, CC PLBASE PLARCH PLLIB PLCFLAGS PLLDFLAGS PLSOEXT PLVERSION, \
$(foreach var, CC PLBASE PLARCH PLLIB PLLIBDIR PLCFLAGS PLLDFLAGS PLSOEXT PLVERSION, \
$(eval \
$(shell \
swipl --dump-runtime-variables | \
......@@ -37,7 +37,8 @@ endif
CFLAGS=$(addprefix -I, $(INCLUDEDIRS)) $(PLCFLAGS)
CXXFLAGS=$(CFLAGS) -std=c++11 `pkg-config --cflags libgvc`
LDFLAGS=$(PLLDFLAGS) $(RPATH) $(addprefix -L, $(PLBASE)/lib/$(PLARCH)/)
# FIXME PLLDFLAGS always empty?
LDFLAGS=$(PLLDFLAGS) $(RPATH) -L $(PLLIBDIR)
LIBSBML=$(shell pkg-config --silence-errors --libs libsbml)
ifeq ($(strip $(LIBSBML)),)
......
......@@ -48,6 +48,7 @@ then
sudo apt-get -qy install software-properties-common
sudo apt-add-repository -y ppa:swi-prolog/stable
sudo apt-get -qy install swi-prolog libsbml5-dev
sudo cp /usr/lib/swi-prolog/lib/x86-64-linux/libswipl.* /usr/lib/
if [[ $release == "bionic" ]]
then
sudo apt-get -qy install zlib1g-dev
......
:- module(partialfraction, [
partial_fraction/5
]).
degree/2,
partial_fraction/5
]).
% :- use_foreign_library(foreign(roots)).
......@@ -15,11 +16,9 @@ small(A) :-
% calculates the degree of a polynomial
% with the null polynomial being of degree -1 instead of -infinity.
degree([], -1).
degree([_|A_next], D) :-
degree(A_next, D_next),
D is D_next + 1.
degree(Polynomial, Degree) :-
length(Polynomial, N),
Degree is N - 1.
% calculates the oppisite polynomial, i.e. -P.
opposite([], []).
......
......@@ -97,9 +97,9 @@ delete_reaction_prefixed(Prefix):-
find_reaction_prefixed(Prefix,Name):-
biocham_command,
type(Prefix, name),
type(Name, name),
%% biocham_command,
%% type(Prefix, name),
%% type(Name, name),
devdoc('
Name is the name of a reaction prefixed by Prefix.
'),
......
:- module(
search,
[
% grammar
search_condition/1,
% commands
search_parameters/3,
search_parameters/2,
robustness/3
......@@ -12,6 +15,11 @@
:- use_module(objects).
:- use_module(biocham).
search_condition((Formula, Event, Objective)) :-
foltl(Formula),
list(parameter_name=number, Event),
list(variable_objective, Objective).
:- doc('The continuous satisfaction degree of an FO-LTL(Rlin) in a given trace with respect to the objective values for the free variables can be used to compute parameter sensitivity indices and robustness measures with respect to parameter perturbation according to normal distributions, and to search parameter values for satisfying an FO-LTL(Rlin) formula \\cite{RBFS11tcs} or even maximizing the margins and the robustness \\cite{FS18cmsb}.').
:- initial('option(robustness_samples: 100)').
......@@ -179,7 +187,7 @@ biocham: search_parameters(G(Time < T => a > b), [0 <= k <= 2], [T -> 5], cmaes_
search_parameters(Parameters, Conditions) :-
biocham_command,
type(Parameters, [parameter_between_interval]),
% type(Conditions, [(foltl, *(parameter_name=number), [variable_objective])]),
type(Conditions, [search_condition]),
option(time, time, _Time, 'time horizon of the numerical integration'),
option(method, method, _Method, 'method for the numerical solver'),
option(
......
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