Merge branch 'develop' into feature/Hybrid

Makefile

@@ -97,22 +97,23 @@ $(SWIPL): $(SWIPL).c \
 	for dir in $(SUBDIRS) ; do $(MAKE) -C $$dir ; done
 	$(CXX) $(CXXFLAGS) $^ $(LDFLAGS) $(LDLIBS) -lstdc++ -o $@
 
-doc/index.html doc/commands.js: biocham
-	./biocham --generate-doc
+doc/index.html doc/commands.js: biocham_debug
+	echo "generate_doc." | ./biocham_debug
 
 pldoc:
 	echo "doc_save(., [if(true), doc_root('doc/pldoc')])." | swipl -q > /dev/null
 
 devdoc:
-	./biocham --generate-devdoc
+	echo "generate_devdoc." | ./biocham_debug
 
 # quick ones only
 unit_tests: biocham_debug
 	echo "run_tests_and_halt." | ./biocham_debug
 
 # slow tests too
-test: biocham_debug jupyter_tests
+test: biocham_debug
 	echo "flag(slow_test, _, true), run_tests_and_halt." | ./biocham_debug
+	$(MAKE) jupyter_tests
 
 jupyter_tests: install_kernel
 	PATH=$(CURDIR):$(PATH) jupyter nbconvert --execute --stdout library/examples/cmsb_2017/sigmoids.ipynb > /dev/null

README.md

+
+[![pipeline status](https://gitlab.inria.fr/lifeware/biocham/badges/develop/pipeline.svg)](https://gitlab.inria.fr/lifeware/biocham/commits/develop)
+[![coverage report](https://gitlab.inria.fr/lifeware/biocham/badges/develop/coverage.svg)](https://gitlab.inria.fr/lifeware/biocham/commits/develop)
+[![License](https://img.shields.io/badge/license-GPLv2-orange)](https://gitlab.inria.fr/lifeware/biocham/raw/develop/LICENSE)
+
 # Biocham
 
 This README file is mostly aimed at people *contributing* to Biocham

commandline.pl

@@ -84,14 +84,6 @@ option('--trace', Arg, Arg) :-
   leash(-all),
   trace.
 
-option('--generate-doc', Arg, Arg) :-
-  generate_doc,
-  quit.
-
-option('--generate-devdoc', Arg, Arg) :-
-  generate_devdoc,
-  quit.
-
 option('--version', Arg, Arg) :-
    quit.
 
@@ -121,7 +113,7 @@ option('--list-commands', [], []) :-
 :- doc('\\texttt{biocham [file]}
 launches Biocham and optionnally loads the file given as argument.').
 
-:- doc('\\texttt{biocham --trace --generate-doc --version --list-commands} are possible options (prefixed by two dashes).').
+:- doc('\\texttt{biocham --trace --version --list-commands} are possible options (prefixed by two dashes).').
 
 :- doc('\\texttt{biocham_debug} is the command to use to launch Biocham with the Prolog toplevel.').
 

junit.pl

@@ -14,6 +14,12 @@ run_junit_tests :-
   run_junit_tests(all).
 
 
+run_junit_tests(Spec) :-
+  \+ is_list(Spec),
+  Spec \= all,
+  !,
+  run_junit_tests([Spec]).
+
 run_junit_tests(Spec) :-
   set_prolog_flag(verbose, normal),
   patch_show_coverage,
@@ -22,11 +28,7 @@ run_junit_tests(Spec) :-
   (
     Spec \= all
   ->
-    atom_concat('plunit_', Spec, TestModule),
-    module_property(TestModule, file(TestFile)),
-    atom_concat(PlFile, 't', TestFile),
-    module_property(PlModule, file(PlFile)),
-    Modules=[PlModule]
+    maplist(get_pl_module, Spec, Modules)
   ;
     Modules=[]
   ),
@@ -36,7 +38,13 @@ run_junit_tests(Spec) :-
       (
         Spec == all
       ->
-        show_coverage(run_tests, Modules)
+        (
+          flag(slow_test, true, true)
+        ->
+          show_coverage((run_tests, generate_doc))
+        ;
+          show_coverage(run_tests)
+        )
       ;
         show_coverage(run_tests(Spec), Modules)
       )
@@ -92,6 +100,12 @@ run_junit_tests(Spec) :-
   plunit:check_for_test_errors.
 
 
+get_pl_module(Spec, Module) :-
+  atom_concat('plunit_', Spec, TestModule),
+  module_property(TestModule, file(TestFile)),
+  atom_concat(PlFile, 't', TestFile),
+  module_property(Module, file(PlFile)).
+
 
 patch_show_coverage :-
   % old swi-prolog test_coverage.pl has one less argument,

pattern_reduction.pl

@@ -39,6 +39,9 @@ yesnomaybe(maybe).
 :- grammar_doc('\\emphright{Value maybe.}').
 
 
+:- dynamic(seen/1).
+
+
 pattern_reduction(Input_file, Output_file) :-
   biocham_command,
   type(Input_file, input_file),
@@ -58,8 +61,9 @@ pattern_reduction(Input_file, Output_file) :-
   Graph = [Number_vertex, Number_species, Edges, Id],
   once(construct_dict_arcs(Edges, Dict_normal_arcs, Dict_reversed_arcs)),
   debug(motif, "Edges:~w ~nNormal arcs: ~w ~nReversed arcs: ~w", [Edges, Dict_normal_arcs, Dict_reversed_arcs]),
-  open(Output_file, write, Stream),
+  retractall(seen(_)),
   assert(seen(Number_vertex)),
+  open(Output_file, write, Stream),
   (
     MM_complete = yes
   ->

pattern_reduction.plt

 :- use_module(library(plunit)).
 
-:- begin_tests(pattern).
-
 
 has_start(Start, String) :-
   atom_concat(Start, _, String).
@@ -12,86 +10,104 @@ count_start(Atom, List, Count) :-
   length(L, Count).
 
 
-test('pattern_fail') :-
-  command('pattern_reduction("library:examples/sepi/MM5.bc", "MM5_reduced.bc").'),
+:- begin_tests(pattern, [setup(command('clear_model.'))]).
+
+test('pattern_fail', [true(String = "S+E=>ES.\nES=>S+E.\nES=>P+E.\nES=>_.\n")]) :-
+  with_output_to(
+    atom(_),
+    command('pattern_reduction("library:examples/sepi/MM5.bc", "MM5_reduced.bc").')
+  ),
   read_file_to_string("MM5_reduced.bc", String, []),
-  delete_file("MM5_reduced.bc"),
-  String = "S+E=>ES.\nES=>S+E.\nES=>P+E.\nES=>_.\n".
+  delete_file("MM5_reduced.bc").
 
 
-test('pattern_success') :-
-  command('pattern_reduction("library:examples/sepi/MM1.bc", "MM1_reduced.bc").'),
+test('pattern_success', [true(String = "S+E=>P+E.\n")]) :-
+  with_output_to(
+    atom(_),
+    command('pattern_reduction("library:examples/sepi/MM1.bc", "MM1_reduced.bc").')
+  ),
   read_file_to_string("MM1_reduced.bc", String, []),
-  delete_file("MM1_reduced.bc"),
-  String = "S+E=>P+E.\n".
+  delete_file("MM1_reduced.bc").
 
 
-test('pattern_intermediary_success') :-
-  with_option([r_1: no], pattern_reduction("library:examples/sepi/MM6.bc", "MM6_reduced.bc")),
+test('pattern_intermediary_success', [true(String = "S+E=>P+E.\n")]) :-
+  with_option(
+    [r_1: no],
+  with_output_to(
+    atom(_),
+      pattern_reduction("library:examples/sepi/MM6.bc", "MM6_reduced.bc"
+  ))
+  ),
   read_file_to_string("MM6_reduced.bc", String, []),
-  delete_file("MM6_reduced.bc"),
-  String = "S+E=>P+E.\n".
+  delete_file("MM6_reduced.bc").
 
 
 test(
   'pattern_mapk1_to_mapk3',
-  [condition(flag(slow_test, true, true))]
+  [condition(flag(slow_test, true, true)), true((Count1, Count2) = (1, 1))]
 ) :-
-  command('pattern_reduction("library:examples/sepi/mapk1.bc", "mapk1_reduced.bc").'),
+  with_output_to(
+    atom(_),
+    command('pattern_reduction("library:examples/sepi/mapk1.bc", "mapk1_reduced.bc").')
+  ),
   with_output_to(
     atom(Result),
     command('search_reduction("mapk1_reduced.bc", "library:examples/sepi/mapk3.bc").')
   ),
   atomic_list_concat(Split, '\n', Result),
-  count_start('sepi', Split, 1),
+  count_start('sepi', Split, Count1),
   with_output_to(
     atom(Result2),
     command('search_reduction("library:examples/sepi/mapk3.bc", "mapk1_reduced.bc").')
   ),
   delete_file("mapk1_reduced.bc"),
   atomic_list_concat(Split2, '\n', Result2),
-  count_start('sepi', Split2, 1).
+  count_start('sepi', Split2, Count2).
 
 
 test(
   'pattern_mapk2_to_mapk3',
-  [condition(flag(slow_test, true, true))]
+  [condition(flag(slow_test, true, true)), true((Count1, Count2) = (1, 1))]
 ) :-
-  with_option([r_1: no], pattern_reduction("library:examples/sepi/mapk2.bc", "mapk2_reduced.bc")),
+  with_option(
+    [r_1: no],
+    pattern_reduction("library:examples/sepi/mapk2.bc", "mapk2_reduced.bc")
+  ),
   with_output_to(
     atom(Result),
     command('search_reduction("mapk2_reduced.bc", "library:examples/sepi/mapk3.bc").')
   ),
   atomic_list_concat(Split, '\n', Result),
-  count_start('sepi', Split, 1),
+  count_start('sepi', Split, Count1),
   with_output_to(
     atom(Result2),
     command('search_reduction("library:examples/sepi/mapk3.bc", "mapk2_reduced.bc").')
   ),
   delete_file("mapk2_reduced.bc"),
   atomic_list_concat(Split2, '\n', Result2),
-  count_start('sepi', Split2, 1).
+  count_start('sepi', Split2, Count2).
 
 
-test('pattern_R-2_EP') :-
+test('pattern_R-2_EP', [true(Output = '\nNumber of Michaelis Menten patterns: 2\n')]) :-
   with_output_to(
     atom(Output),
     command('pattern_reduction("library:examples/sepi/mapk26.bc", "mapk26_reduced.bc").')
   ),
-  delete_file("mapk26_reduced.bc"),
-  Output = '\nNumber of Michaelis Menten patterns: 2\n'.
+  delete_file("mapk26_reduced.bc").
 
 
-test('maybe_option') :-
+test('maybe_option', [true(Output = '\nNumber of Michaelis Menten patterns: 4\n')]) :-
   with_output_to(
     atom(Output),
-    with_option([r_1: maybe, r_2: maybe, ep: maybe], pattern_reduction("library:examples/sepi/mapk26.bc", "mapk26_reduced.bc"))
+    with_option(
+      [r_1: maybe, r_2: maybe, ep: maybe],
+      pattern_reduction("library:examples/sepi/mapk26.bc", "mapk26_reduced.bc")
+    )
   ),
-  delete_file("mapk26_reduced.bc"),
-  Output = '\nNumber of Michaelis Menten patterns: 4\n'.
+  delete_file("mapk26_reduced.bc").
 
 
-test('hill_reaction') :-
+test('hill_reaction', [true(Output3 = '\nNumber of Hill patterns: 0\n')]) :-
   with_output_to(
     atom(Output),
     with_option([michaelis_menten: no, hill_reaction: yes], pattern_reduction("library:examples/sepi/MM_variants/MM_SES.bc", "MM_SES_reduced.bc"))
@@ -108,11 +124,10 @@ test('hill_reaction') :-
     atom(Output3),
     with_option([michaelis_menten: no, hill_reaction: yes], pattern_reduction("library:examples/sepi/MM_variants/MM_SES_false.bc", "MM_SES_reduced.bc"))
   ),
-  delete_file("MM_SES_reduced.bc"),
-  Output3 = '\nNumber of Hill patterns: 0\n'.
+  delete_file("MM_SES_reduced.bc").
 
 
-test('partial_hill_reaction') :-
+test('partial_hill_reaction', [true(Output3 = '\nNumber of partial Hill patterns: 0\n')]) :-
   with_output_to(
     atom(Output),
     with_option([michaelis_menten: no, partial_hill_reaction: yes], pattern_reduction("library:examples/sepi/MM_variants/MM_ESS.bc", "MM_ESS_reduced.bc"))
@@ -129,11 +144,10 @@ test('partial_hill_reaction') :-
     atom(Output3),
     with_option([michaelis_menten: no, partial_hill_reaction: yes], pattern_reduction("library:examples/sepi/MM_variants/MM_ESS_false.bc", "MM_ESS_reduced.bc"))
   ),
-  delete_file("MM_ESS_reduced.bc"),
-  Output3 = '\nNumber of partial Hill patterns: 0\n'.
+  delete_file("MM_ESS_reduced.bc").
 
 
-test('double_michaelis_menten') :-
+test('double_michaelis_menten', [true(Output3 = '\nNumber of double Michaelis Menten: 0\n')]) :-
   with_output_to(
     atom(Output),
     with_option([michaelis_menten: no, double_michaelis_menten: yes], pattern_reduction("library:examples/sepi/MM_variants/MM_SEE.bc", "MM_SEE_reduced.bc"))
@@ -150,13 +164,21 @@ test('double_michaelis_menten') :-
     atom(Output3),
     with_option([michaelis_menten: no, double_michaelis_menten: yes], pattern_reduction("library:examples/sepi/MM_variants/MM_SEE_false.bc", "MM_SEE_reduced.bc"))
   ),
-  delete_file("MM_SEE_reduced.bc"),
-  Output3 = '\nNumber of double Michaelis Menten: 0\n'.
+  delete_file("MM_SEE_reduced.bc").
 
 
-test('expansion') :-
-  command('pattern_reduction("library:examples/sepi/MM1.bc", "MM1_reduced.bc").'),
-  with_option([michaelis_menten: no, michaelis_menten_expansion: yes], pattern_reduction("MM1_reduced.bc", "MM1_expanded.bc")),
+test('expansion', [true(Count = 1)]) :-
+  with_output_to(
+    atom(_),
+    command('pattern_reduction("library:examples/sepi/MM1.bc", "MM1_reduced.bc").')
+  ),
+  with_output_to(
+    atom(_),
+    with_option(
+      [michaelis_menten: no, michaelis_menten_expansion: yes],
+      pattern_reduction("MM1_reduced.bc", "MM1_expanded.bc")
+    )
+  ),
   with_output_to(
     atom(Result),
     command('search_reduction("MM1_expanded.bc", "library:examples/sepi/MM1.bc").')
@@ -170,6 +192,6 @@ test('expansion') :-
   delete_file("MM1_reduced.bc"),
   delete_file("MM1_expanded.bc"),
   atomic_list_concat(Split2, '\n', Result2),
-  count_start('sepi', Split2, 1).
+  count_start('sepi', Split2, Count).
 
 :- end_tests(pattern).

tmpnb/lifeware_biocham/Dockerfile

-FROM jupyter/minimal-notebook
+FROM jupyter/minimal-notebook:702d2f6a3eaa
 LABEL Author="Sylvain Soliman <Sylvain.Soliman@inria.fr>"
 LABEL Maintainer="Biocham team <biocham@inria.fr>"