Merge branch 'develop' of...

Merge branch 'develop' of https://scm.gforge.inria.fr/authscm/dcoudrin/git/biocham/biocham into develop

LICENSE

+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
\ No newline at end of file

Makefile

@@ -6,7 +6,10 @@ MODULES=$(shell sed -n -E 's/^[+-] (.*\.pl)$$/\1/p' toc.org) \
   $(ADDITIONAL_MODULES)
 # load_test_files/1 should make this useless, but I cannot find how to use it
 TEST_MODULES=$(wildcard $(MODULES:.pl=.plt)) junit.pl
-VERSION=4.0.$(shell date +%Y%m%d)
+
+ifndef $(PREFIX)
+  PREFIX=/usr/local
+endif
 
 $(foreach var, CC PLBASE PLARCH PLLIB PLCFLAGS PLLDFLAGS PLSOEXT, \
   $(eval \
@@ -21,10 +24,14 @@ SUBDIRS=$(dir $(wildcard modules/*/Makefile))
 INCLUDEDIRS=$(PLBASE)/include $(SUBDIRS) \
   modules/glucose/glucose-syrup modules/glucose/glucose-syrup/core
 
+RPATH=
+ifneq ($(LD_RUN_PATH),)
+  RPATH=-Wl,-rpath=$(LD_RUN_PATH)
+endif
 CFLAGS=$(addprefix -I, $(INCLUDEDIRS)) $(PLCFLAGS)
 CXXFLAGS=$(CFLAGS) -Wno-logical-op-parentheses `pkg-config --cflags libgvc`
 
-LDFLAGS=$(PLLDFLAGS) $(addprefix -L, $(PLBASE)/lib/$(PLARCH)/)
+LDFLAGS=$(PLLDFLAGS) $(RPATH) $(addprefix -L, $(PLBASE)/lib/$(PLARCH)/)
 
 LIBSBML=$(shell pkg-config --silence-errors --libs libsbml)
 ifeq ($(strip $(LIBSBML)),)
@@ -41,7 +48,18 @@ all: biocham biocham_debug test doc/index.html jupyter
 quick: unit_tests
 
 .PHONY: all slow test unit_tests clean web cabernet cabernet_restart \
-  jupyter gadagne gadagne_restart jupyter_tests
+  jupyter gadagne gadagne_restart jupyter_tests install pldoc
+
+# should we depend on jupyter target?
+install: biocham biocham_debug
+	mkdir -p $(PREFIX)/bin
+	mkdir -p $(PREFIX)/share/biocham
+	cp $? $(PREFIX)/share/biocham/
+	ln -fs $(PREFIX)/share/biocham/biocham $(PREFIX)/bin/biocham
+	ln -fs $(PREFIX)/share/biocham/biocham_debug $(PREFIX)/bin/biocham_debug
+	cp -r library $(PREFIX)/share/biocham/
+	cp -r doc $(PREFIX)/share/biocham/
+	cp -r biocham_kernel $(PREFIX)/share/biocham/
 
 biocham: $(SWIPL) $(MODULES) toc.org $(CMAES_LIB) \
 	library/gsl_solver.o library/cmaes.o library/csv_reader.o Makefile
@@ -49,7 +67,7 @@ biocham: $(SWIPL) $(MODULES) toc.org $(CMAES_LIB) \
 		--goal="\
 			set_prolog_flag(verbose, normal), \
 			start" \
-		--toplevel=toplevel --stand_alone=true -O --foreign=save -c $(MODULES)
+		--toplevel=toplevel --stand_alone=true -O -c $(MODULES)
 
 biocham_debug: $(SWIPL) $(MODULES) $(TEST_MODULES) toc.org \
 	library/gsl_solver.o Makefile
@@ -74,9 +92,12 @@ modules/glucose/glucose-syrup/core/Solver.cc: modules/glucose/Solver.patch
 	rm -f glucose-syrup.tgz
 	patch $@ < $<
 
-doc/index.html doc/commands.js: biocham
+doc/index.html doc/commands.js: biocham pldoc
 	./biocham --generate-doc
 
+pldoc:
+	echo "doc_save(., [if(true), doc_root('doc/pldoc')])." | swipl -q
+
 # quick ones only
 unit_tests: biocham_debug
 	echo "run_tests_and_halt." | ./biocham_debug

c_compiler.pl

@@ -39,14 +39,31 @@ compile_cpp_program(SourceFiles, Options, ExecutableFilename) :-
   ).
 
 
-gsl_compile_options(['-lgsl', '-lgslcblas', '-lm']).
+%% TODO 
+%%  - robust parsing (w.r.t. spaces for instance)
+%%  - error handling (unknown library)
+pkg_compile_options(PkgName, Options) :-
+  format(string(Command), "pkg-config --libs --cflags ~w", [PkgName]),
+  open(pipe(Command), read, Fd),
+  read_string(Fd, "", "\n", _, OptionString),
+  split_string(OptionString, " ", "", Options).
 
 
+gsl_compile_options(Options) :-
+  pkg_compile_options('gsl', Options).
+
 ppl_compile_options(['-lppl_c', '-lppl', '-lgmpxx', '-lgmp']).
 
 
 % Private predicates
 
+callp(P,E,O) :-
+  is_absolute_file_name(P),
+  !,
+  call_subprocess(P,E,O).
+
+callp(P,E,O) :-
+  call_subprocess(path(P),E,O).
 
 compile_program(Compiler, SourceFiles, Options, ExecutableFilename) :-
   library_path(LibraryPath),
@@ -68,6 +85,6 @@ compile_program(Compiler, SourceFiles, Options, ExecutableFilename) :-
   ;
     AllOptions0 = AllOptions
   ),
-  call_subprocess(
-    path(Compiler), ['-o', ExecutableFilename, '-I.' | AllOptions0], []
+  callp(
+    Compiler, ['-o', ExecutableFilename, '-I.' | AllOptions0], []
   ).

conda/README.txt

+conda install conda-build
+
+Currently, swi-prolog is not available in conda. To get around this:
+- clone the brown data science recipes.
+- perform a build of swi-prolog (`conda build .`)
+- install it locally (`conda install --use-local swi-prolog`)
+
+libSBML is unavailable in conda too.
+- use the local recipe
+- perform a build (`conda build .`)
+- install it locally (`conda install --use-local libsbml`)
+
+NuSMV is packaged in colomoto.
+
+To build the biocham prototype package:
+
+conda-build -c colomoto -c conda-forge .
+
+ls /opt/conda/conda-bld/linux-64/
+
+conda install --use-local biocham -c conda-forge -c colomoto
+
+rpath + install target in Makefile...
+
+There seem to be relocation issues... -> solved by instructing conda to not attempt automatic relocation
+
+There seem to be dependency downgrading issues -> solution ?
+
+Right now, an environment variable must be set : 
+BIOCHAMLIB=/opt/conda/bin/biochamlib biocham
+
+Running unit tests :
+echo "run_tests_and_halt." | BIOCHAMLIB=/opt/conda/bin/biochamlib biocham_debug
+
+We could have the 'make install' target set that up... ?
+
+## Misc. notes
+
+When building swi-prolog, pass --merge-build-host

conda/build.sh

+#!/bin/bash
+
+make install

conda/meta.yaml

+package:
+  name: biocham
+  version: "4.1.5"
+
+source:
+  path: ..
+
+build:
+  skip: true # [win]
+  ignore_prefix_files:
+    - share/biocham/biocham
+    - share/biocham/biocham_debug
+
+# swi-prolog is currently not packaged
+# see https://github.com/conda-forge/staged-recipes/pull/4114
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - gsl
+    - graphviz
+    - swi-prolog
+    - gmp
+    - libsbml
+    - nusmv
+    - pkg-config
+  run:
+# A c and c++ compiler, and the associated support (pkg-config)
+# are required at runtime
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - pkg-config 
+    - gsl
+    - graphviz
+    - swi-prolog
+    - gmp
+    - libsbml
+    - nusmv
+  test:
+    commands:
+      - make quick
+
+about:
+  home: https://lifeware.inria.fr/biocham4/
+  license: GPL
+  license_file: LICENSE

conservation_laws.plt

@@ -107,7 +107,7 @@ test(
     true(InvarNumber = 9)
   ]
 ) :-
-  load('library/examples/mapk/BIOMD0000000009.xml'),
+  load('library:examples/mapk/BIOMD0000000009.xml'),
   with_output_to(string(Invariants), command(search_conservations)),
   split_string(Invariants, "\n", "", InvarList),
   length(InvarList, InvarNumber).

gpac.pl

-/** <module> Tools to generate set of chemical reactions
+/** <gpac> Tools to generate set of chemical reactions
 
 The two main functions to be exported are compile_from_expression and
 compile_from_pivp that generates set of equations starting from a
@@ -41,8 +41,6 @@ Rq: The distinction between pivp_string and pivp_list is not always obvious.
     format_pivp/2
   ]).
 
-:- load_test_files([]). % Placed here, load only gpac.plt
-
 :- use_module(doc).
 :- use_module(objects).
 :- use_module(reaction_rules).
@@ -60,8 +58,13 @@ Rq: The distinction between pivp_string and pivp_list is not always obvious.
 %! compile_from_expression(+Expr, +Input, +Output)
 %
 % biocham command
-% creates a biochemical reaction network such that Output = Expr(Input)
-% the basic value for Input is time
+%
+% Creates a biochemical reaction network such that Output = Expr(Input)
+% 
+% Typical usage will be:
+% ==
+% :- compile_from_expression(4 + id*id, time, output).
+% ==
 
 compile_from_expression(Expr, Input, Output) :-
   biocham_command,
@@ -130,6 +133,11 @@ compile_from_expression(Expr, Input, Output) :-
 % pivp, pode, polynomial and monomial
 % the tagging ':- grammar(_)' is here for the documentation
 
+
+%! pivp(+Expression)
+%
+% Test if the expression correspond to a valid PIVP_string
+
 :- grammar(pivp).
 
 pivp((X;Y)):-
@@ -140,12 +148,22 @@ pivp((X,Y)):-
   number(X),
   pode(Y).
 
+
+%! pode(+Expression)
+%
+% Test if the expression correspond to a valid pODE
+
 :- grammar(pode).
 
 pode((d(X)/dt = Y)):-
   name(X),
   polynomial(Y).
 
+
+%! polynomial(+Expression)
+%
+% Test if the expression correspond to a valid polynomial
+
 :- grammar(polynomial).
 
 polynomial(+ X):-
@@ -165,6 +183,11 @@ polynomial(X - Y):-
 polynomial(X):-
   monomial(X).
 
+
+%! monomial(+Expression)
+%
+% Test if the expression correspond to a valid monomial
+
 :- grammar(monomial).
 
 monomial(X ^ Y):-
@@ -185,9 +208,14 @@ monomial(X) :-
 %! compile_from_pivp(+PIVP_string, +Input , +Output)
 %
 % biocham command
-% creates a biochemical reaction network such that Output = f(Input)
+%
+% Creates a biochemical reaction network such that Output = f(Input)
 % where f is the solution of the PIVP.
-% the basic value for Input is time
+%
+% Typical usage will be:
+% ==
+% :- compile_from_pivp( ((1,(d(y)/dt=z)); (0,(d(z)/dt= (-1*y)))),time,output).
+% ==
 
 compile_from_pivp(PIVP, Input, Output) :-
   biocham_command,
@@ -211,6 +239,10 @@ compile_from_pivp(PIVP, Input, Output) :-
    \\end{todo}
    ').
 
+%! test_2908
+%
+% Test runs at the compilation of biocham
+