Unblock slow tests, fix diagnosis.out, fixme

Makefile

@@ -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

nbrefs/diagnosis.out.ref

@@ -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=>_.

rate_independence.plt

@@ -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))),

reduce.plt

@@ -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',

revision.plt

@@ -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',