Commit 5de4b1e6 authored by FAGES Francois's avatar FAGES Francois

update devcoms

parent 269196a7
......@@ -109,5 +109,5 @@ biocham_command(_) :-
unlimited number of arguments.
The additional arguments are given as a list in the last parameter.').
:-devcom('FF: big question ! should not we make biocham commands functional ? We need to know the result type for the gui... Furthermore, the show, list, enumerate,... commands are not so nice. The print result should be a textual form (or a widget) associated to the returned type.').
:-devcom('FF: big question ! should not we make biocham commands functional ? We need to know the result type for the gui... Furthermore, the show, list, enumerate,... commands are not so nice. The print result should be a text or a widget associated to the returned type.').
......@@ -114,10 +114,9 @@ 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.').
:- doc('\\texttt{biocham --trace --generate-doc --version --list-commands} are possible options (prefixed by two dashes).').
:- doc('\\texttt{biocham --notebook [notebook.ipynb]} (i.e. two dashes
followed by the word notebook) launches Jupyter (see
:- doc('\\texttt{biocham --notebook [notebook.ipynb]} launches Jupyter (see
\\url{http://jupyter-notebook.readthedocs.io/}) with a biocham kernel, and
loads the corresponding notebook (ipynb suffix). If no notebook is provided, a biocham notebook can be created with the new menu.
......@@ -140,7 +139,9 @@ and
\\texttt{%slider k1 k2 …}, which creates sliders to change the given
parameters'' value, and run \\command{numerical_simulation} followed by
\\command{plot} at each change.
').
:- doc('
The environment variable \\texttt{BIOCHAM_TIMEOUT} can be used to change the
default notebook-kernel communication timeout of 120 (seconds).
').
......
......@@ -16,7 +16,6 @@
).
doc(_) :- % this predicate must just succeed in prolog
!,
true.
......@@ -41,25 +40,19 @@ devcom(_) :-
grammar_doc(_) :-
doc('Writes documentation annotation for a grammar.').
:- devcom('FF: As a general rule I would like that the output of a biocham command be always accepted as input as a Biocham command, making possible to edit a model by copy and paste For instance for list-parameters etc.').
:- devcom('FF: As a general rule I would like that the output of a biocham command be always accepted as input as a Biocham command, making possible to edit a model by copy and paste. For instance for list-parameters etc.').
:- devcom('SS: for some commands, it seems like a good idea, but for others I
am not so sure. A well formatted table might be more readable than a list of
commands…').
:- devcom('FF: If so it may mean that the well formatted table should accepted as input of the command').
:- devcom('FF: If so it may mean that the well formatted table should be accepted as input of the command').
:- devcom('FF: I would like that also for creating the tests .plt but this is even more complicated with the distinction between prolog predicates, command(), biocham() and the differences for passing the options which seem to me artificially complicated and should be uniform. To discuss together to see how to improve that...').
:- devcom('FF: In fact I do not see the point of unitary tests on biocham predicates, we should rather test the biocham command itself including the parser which we never test ?').
:- devcom('SS: by "nature" a unit-test should test at the lowest possible
level, whereas testing a biocham command is rather an integration test.
Currently we have a bit of both…').
:- devcom('FF: we should distinguish .plt and .bct files with respectively Prolog and Biocham syntax').
:- devcom('FF: Unitary tests on biocham predicates should rather be integration tests in different files: .plt for unitary tests and .bct or perhaps .ipynb for integration tests.').
:- devcom('FF: is not it best practice to put the Prolog edition styles in the git to uniformize the edition the source code ?').
:- devcom('FF: I twould be nice to put the Prolog edition styles in the git to uniformize the edition the source code but we had problems for emacs on Mac').
devdoc_biocham(_) :-
doc('Writes the trace of a Biocham execution in the Developer Manual.').
......@@ -70,9 +63,8 @@ grammar(_) :-
biocham(_).
:- devdoc('Calls a biocham command in a test file .plt').
:- devdoc('Calls a biocham command in a test file .plt. The argument may be either an atom parsed by the Biocham parser or a Prolog term.').
:- devcom('FF: This is wrong ! The argument is not a biocham command but a Prolog term that works most of the time but not always. This should be abandonned, the argument should be an atom to parse with the biocham parser.').
biocham_silent(_).
:- devdoc('Silent biocham call in test file.').
......@@ -89,7 +81,7 @@ classes in the HTML.
\\end{remark}
').
:- devcom('\\texttt{format_doc_html} and \\texttt{format_doc_tex} are specific and executed twice: once for html, once for tex. \\texttt{write_command} is executed once').
:- devcom('\\texttt{format_doc_html} and \\texttt{format_doc_tex} are specific and executed once for html, once for tex. \\texttt{write_command} is executed once for both.').
format_doc(Format) :- % specific clauses executed
......@@ -2084,3 +2076,6 @@ index_use_id(Key, Id) :-
),
append(List, [Counters - Id], NewList),
assertz(index_contents(Key, NewList)).
:- devcom('FF En fait il faudrait lister dans le developper manual toutes les commandes exportees').
......@@ -16,8 +16,6 @@
:- devdoc('\\section{Commands}').
:- devcom('FF: positive and negative influences should be distinguished. It is not the case yet.').
influence_graph :-
biocham_command,
......
......@@ -16,7 +16,7 @@
:- doc('The following commands enumerate all the boolean attractors of the positive boolean semantics of influence (and reaction?) systems \\cite{FMSR16cmsb}.').
:- devcom('FF: to generalize to reaction systems. Check the positive semantics option rather than influence model ?').
:- devcom('FF: to generalize to reaction systems. Check the positive semantics option (rather than influence model) both for reaction and influence systems').
list_stable_states :-
biocham_command,
......
......@@ -78,7 +78,6 @@ check_ctl :-
check_ctl_impl(Spec, NusmvInitialState, NusmvCX, BoolSem, Result),
format('~w is ~w\n', [Query, Result]).
:- devcom('FF: there is definitively something wrong with the "biocham" command since it imposes us to write an example with unuseful quotes on EX, i.e. a very bad example for the user... And the same goes with the tests which never test the Biocham parser... The "biocham" command should probably take a string as argument not a prolog term (cf previous copy and paste remark).').
:- doc('\\begin{example}\n').
:- biocham_silent(clear_model).
......
......@@ -28,11 +28,6 @@
:- devdoc('\\section{Grammars}').
:- devcom('FF: A concentration should be an arithmetic expression, in particular including parameters for using parameter search for initial state. This change will impact ode.pl initial_state.pl odefunction.pl wgpac.pl').
:- devcom('SS: Well, just use an arithmetic expression where you need one
(parameters, initial state, whatever).').
:- doc('The syntax of elementary types in Biocham is the following:').
:- grammar(concentration).
......
......@@ -27,9 +27,7 @@
:- doc('In Biocham v4, a reaction system is a multiset of reactions. Reactions can thus be in multiple copies in which case their reaction rates are summed.').
:-devcom('FF: I am not sure we should exclude hybrid reaction-influence models. We have shown in our CMSB 2016 paper the encoding of influence systems into reaction systems. Arguments against it welcome !').
:- devcom('FF: For several reasons, I am wondering whether we should automatically introduce kinetic parameters k_1, k_2, etc. for the default mass action law kinetics of reactions given without kinetic expression. The same could go for initial_state concentrations which BTW should be definable by parameters or functions, introducing concentration parameters c_1, c_2, etc. for present molecules. The pros are an encouragement to use parameters, parameter search, sensitivity and robustness analyses. The cons are are an irrelevant encouragement for logical models until it becomes relevant. ').
:- devcom('FF: For several reasons, I am wondering whether we should automatically introduce kinetic parameters k_1, k_2, etc. for the default mass action law kinetics of reactions given without kinetic expression. The same could go for initial_state concentrations which BTW should be definable by parameters or functions, introducing concentration parameters c_1, c_2, etc. for present molecules. The pros are an encouragement to use parameters, parameter search, sensitivity and robustness analyses. The cons are an irrelevant encouragement for logical models (until it becomes relevant). ').
add_reaction(Reaction) :-
biocham_command,
......
......@@ -15,13 +15,14 @@
:- devdoc('\\section{Commands}').
:- devcom('FF: Strange behavior on influence models, draw_reactions opens a widget !').
:- devcom('FF: It would be nice to have a notion of input/output and draw graphs accordingly, with inputs on top and outputs bottom in all (reaction or influence) graphs.
The input species could be those present at initial_state. The output species could be those not reactant (nor catalyst) of any reaction, nor source of any nfluence.
Alternatively we could have input/output annotations on molecular species. It could be useful also for some analyses.').
Alternatively we could have input/output annotations on molecular species which could also be useful also for some analyses.
Also the linear invariants could be used to enforce theur drawing in row like in MAPK...').
reaction_graph :-
biocham_command,
......
......@@ -134,8 +134,6 @@ kinetics(ArithmeticExpression) :-
arithmetic_expression(ArithmeticExpression).
:- devcom('FF: the last grammar item does not print properly').
:- devdoc('\\section{Public API}').
......
......@@ -18,10 +18,10 @@
:- devcom('FF: These commands should be generalized,
first, to deletions and merge of molecules and reactions (easy SEPI linear for deletions quadratic for mergings) done!
second, to influence systems and hybrid reaction-influence systems (great SEPI unification),
and third, to hybrid attractors, CTL, FOLTL, trace specifications of the behavior.
Yes it can work! See CMSB 2017 paper ;-)').
second, to influence systems and hybrid reaction-influence systems (great SEPI unification), See CMSB 2017 paper ;-)
and third, to hybrid attractors, CTL, FOLTL, trace specifications of the behavior.').
:- devdoc('\\section{Commands}').
......
......@@ -11,7 +11,7 @@
- toplevel.pl
- about.pl
- namespace.pl
* Part I: Models of Biochemical Processes
* Part I: Rule-based Models of Biochemical Processes
* Biochemical Objects
** Syntax
- filename.pl
......@@ -74,7 +74,7 @@
- reduce.pl
** Model revision from CTL specification
- revision.pl
* Part III: Quantitative Analyses
* Part III: Quantitative Analyses and Model Synthesis
* Numerical Simulations
** ODE and stochastic simulations
- arithmetic_rules.pl
......@@ -95,9 +95,9 @@
- foltl.pl
** Robustness of FO-LTL(Rlin) properties
** Sensitivity to parameters
** Parameter search
** Synthesis of parameter values
- search.pl
* Reaction Model Synthesis from Mathematical Functions and Programs
* Reaction System Synthesis from Input/Output Functions and Programs
** Synthesis from mathematical expressions
- odefunction.pl
** Synthesis from GPAC circuits
......
......@@ -15,7 +15,6 @@
]
).
:- devcom('FF En fait il faudrait lister dans le developper manual toutes les commandes exportees').
:- doc('This section describes commands for continuously varying the values of molecular species or parameters.
This can be used for drawing dose-response diagrams
......
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