Commit e2c36b46 authored by Thierry Martinez's avatar Thierry Martinez

Merged Makefile

parents dd83b3c6 b4253594
MODULES=$(shell sed -n -E 's/^- (.*\.plt?)$$/\1/p' toc.org)
MODULES=$(shell sed -n -E 's/^- (.*\.pl)$$/\1/p' toc.org)
# load_test_files/1 should make this useless, but I cannot find how to use it
TEST_MODULES=$(wildcard $(MODULES:.pl=.plt))
all: biocham biocham_debug tests doc
......@@ -17,9 +19,9 @@ tests: biocham_tests
doc: biocham
./biocham --generate-doc
biocham_tests: $(MODULES) Makefile
biocham_tests: $(MODULES) $(TEST_MODULES) Makefile
swipl -o biocham_tests \
--goal="call_cleanup((run_tests, halt(0)), halt(1))" -c $(MODULES)
--goal="call_cleanup((run_tests, halt(0)), halt(1))" -c $(MODULES) $(TEST_MODULES)
clean:
-rm -f biocham biocham_debug biocham_tests
......@@ -15,6 +15,8 @@ test(
command(add_conservation(a-a + 2*a)),
all_items([model: current_model, kind: conservation], Conservations).
%%% FIXME should test that conservations are properly used for numerical
%%% integration
test(
'delete_conservation deletes the correct conservation',
......@@ -44,7 +46,8 @@ test(
'check_conservations is ok with trivial P-invariants',
[
setup(models:clear_model),
cleanup(models:clear_model)
cleanup(models:clear_model),
blocked(not_implemented)
]
) :-
% not written 'a => b' to allow flycheck by separate compilation…
......@@ -53,6 +56,21 @@ test(
command(check_conservations).
test(
'check_conservations is unhappy with non-conserved moieties',
[
setup(models:clear_model),
cleanup(models:clear_model),
error(unproven_conservation_law([1*'a', 2*'b'])),
fixme(not_implemented)
]
) :-
% not written 'a => b' to allow flycheck by separate compilation…
command(add_rule('=>'(a, b))),
command(add_conservation(a + 2*b)),
command(check_conservations).
add_some_conservations :-
command(add_conservation(a-a + 2*a)),
command(add_conservation(b-b + 2*b)),
......
......@@ -2,16 +2,13 @@
** Overview
- doc.pl
- biocham.pl
- biocham.plt
- about.pl
** Installing and Running Biocham Locally
- commandline.pl
- util.pl
- simplify_arithmetic.pl
- formal_derivation.pl
- formal_derivation.plt
- gsl.pl
- gsl.plt
- counters.pl
** About this manual
- filename.pl
......@@ -30,44 +27,34 @@
** Loading, listing and exporting models
*** Biocham files
- models.pl
- models.plt
*** SBML files
*** ODE files
*** Graphics files
*** Other files
- nusmv.pl
- nusmv.plt
** Listing and editing rules and events
*** Rules
- rule_editor.pl
- rule_editor.plt
- ode.pl
*** Events
- events.pl
** Listing and defining initial states, molecules and locations
*** Initial state
- initial_state.pl
- initial_state.plt
** Listing and declaring parameters, macros, aliases and invariants
*** Parameters
- parameters.pl
- parameters.plt
*** Macros
- macros.pl
- macros.plt
*** Aliases
- aliases.pl
- aliases.plt
*** Algebraic invariants, conservation laws and P-invariants
- conservation_laws.pl
- conservation_laws.plt
** Simulations
*** ODE and stochastic simulations
- numerical_simulation.pl
- numerical_simulation.plt
*** Traces
- traces.pl
- traces.plt
* Index
+ index
* Bibliography
......
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