Commit 576e2846 authored by SOLIMAN Sylvain's avatar SOLIMAN Sylvain
Browse files

Unblock slow tests, fix diagnosis.out, fixme

parent 72712dea
......@@ -53,8 +53,7 @@ KERNEL_DIR=$(JUPYTER_DIR)/kernel/biocham_kernel
WORKFLOWS_DIR=$(JUPYTER_DIR)/guinbextension/src/config/workflows
# NOTEBOOKS=$(shell find . -type f -name '*.ipynb' -print)
# NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb library/examples/doctor_in_the_cell/diagnosis.ipynb
NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb
NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb library/examples/doctor_in_the_cell/diagnosis.ipynb
REFDIR=nbrefs
all: biocham biocham_debug quick doc/index.html pldoc install_kernel install_gui
......
......@@ -88,25 +88,31 @@ Cf3+Cfa2+Cia2+Cib1+Cib2+Cio3+HRP2+NADH+NADN+glucose+glucoseext+isopropanol+2*Cf4
m=0/\M=67383000
T>287.057
0.946074
[duck:15427] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 206
[duck:15425] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 206
[duck:15438] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 206
[duck:15437] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 206
<img src="plot-1.csv" alt="Simulation results">
T>88.2305
acetone_p*glucose_p for glucose_p+acetone_p=>resorufin_p+glucose_p+acetone_p.
acetone_n*glucose_n for glucose_n+acetone_n=>resorufin_p+glucose_n+acetone_n.
[duck:15459] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 206
[duck:15458] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 206
acetone_p*glucose_p for acetone_p+glucose_p=>acetone_p+glucose_p+resorufin_p.
acetone_n*glucose_n for acetone_n+glucose_n=>acetone_n+glucose_n+resorufin_p.
MA(1) for resorufin_p=>_.
acetone_p*glucose_n for glucose_n+acetone_p=>resorufin_n+glucose_n+acetone_p.
acetone_n*glucose_p for glucose_p+acetone_n=>resorufin_n+glucose_p+acetone_n.
acetone_p*glucose_n for acetone_p+glucose_n=>acetone_p+glucose_n+resorufin_n.
acetone_n*glucose_p for acetone_n+glucose_p=>acetone_n+glucose_p+resorufin_n.
MA(1) for resorufin_n=>_.
MA(1) for _=>temp2_p.
MA(1) for acetone_n=>temp2_p+acetone_n.
MA(1) for acetone_n=>acetone_n+temp2_p.
MA(1) for temp2_p=>_.
0 for _=>temp2_n.
MA(1) for acetone_p=>temp2_n+acetone_p.
MA(1) for acetone_p=>acetone_p+temp2_n.
MA(1) for temp2_n=>_.
glucose_p*temp2_p for temp2_p+glucose_p=>NADH_p+temp2_p+glucose_p.
glucose_n*temp2_n for temp2_n+glucose_n=>NADH_p+temp2_n+glucose_n.
glucose_p*temp2_p for glucose_p+temp2_p=>NADH_p+glucose_p+temp2_p.
glucose_n*temp2_n for glucose_n+temp2_n=>NADH_p+glucose_n+temp2_n.
MA(1) for NADH_p=>_.
glucose_p*temp2_n for temp2_n+glucose_p=>NADH_n+temp2_n+glucose_p.
glucose_n*temp2_p for temp2_p+glucose_n=>NADH_n+temp2_p+glucose_n.
glucose_p*temp2_n for glucose_p+temp2_n=>NADH_n+glucose_p+temp2_n.
glucose_n*temp2_p for glucose_n+temp2_p=>NADH_n+glucose_n+temp2_p.
MA(1) for NADH_n=>_.
fast*resorufin_p*resorufin_n for resorufin_n+resorufin_p=>_.
fast*temp2_p*temp2_n for temp2_n+temp2_p=>_.
......@@ -136,10 +142,10 @@ parameter(
MA(1) for _=>x_p.
0 for _=>x_n+z_n.
MA(1) for x_p=>y_p.
MA(1) for z_n=>y_p+x_n.
MA(1) for z_n=>x_n+y_p.
MA(1) for y_p=>_.
MA(1) for x_n=>y_n.
MA(1) for z_p=>y_n+x_p.
MA(1) for z_p=>x_p+y_n.
MA(1) for y_n=>_.
fast*x_p*x_n for x_n+x_p=>_.
fast*z_p*z_n for z_n+z_p=>_.
......
......@@ -30,6 +30,7 @@ test('Max', [setup(max_model), cleanup(clear_model)]) :-
atom_concat('The model is rate independent', _, Result).
test('everything', [
fixme('Work in progress'),
condition(flag(slow_test, true, true)),
forall((expand_file_name('./library/examples/tests/rate_independence_*.bc', FileList), member(File, FileList))),
setup((with_output_to(atom(ExpectedLong), command(load(File))), sub_string(ExpectedLong, 0, 9, _, Expected))),
......
......@@ -2,7 +2,7 @@
% not necessary, except for separate compilation
:- use_module(reaction_rules).
:- begin_tests(reduce, [blocked(francois), setup((clear_model, reset_options))]).
:- begin_tests(reduce, [setup((clear_model, reset_options))]).
test(
'reduce_3_inhibitions',
......
......@@ -3,7 +3,7 @@
:- use_module(reaction_rules).
:- begin_tests(revision, [condition(flag(slow_test, true, true)),
blocked(francois), setup((clear_model, reset_options))]).
setup((clear_model, reset_options))]).
test(
'categorize_query',
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment