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Lifeware
biocham
Commits
9f66b109
Commit
9f66b109
authored
Oct 16, 2015
by
Thierry Martinez
Browse files
Examples in doc
parent
68c87a50
Changes
7
Hide whitespace changes
Inline
Side-by-side
biocham.pl
View file @
9f66b109
...
...
@@ -38,6 +38,7 @@ initialize :-
set_prolog_flag
(
allow_variable_name_as_functor
,
true
),
prolog_history
(
enable
),
set_counter
(
item_id
,
0
),
set_plot_driver
(
gnu_plot
),
new_model
.
...
...
doc.pl
View file @
9f66b109
...
...
@@ -4,6 +4,8 @@
doc
/
1
,
devdoc
/
1
,
grammar
/
1
,
biocham
/
1
,
biocham_silent
/
1
,
generate_doc
/
0
]
).
...
...
@@ -27,7 +29,15 @@ grammar(_) :-
doc
(
'Declares a grammar predicate to be written in the documentation.'
).
biocham
(
_
).
biocham_silent
(
_
).
generate_doc
:-
set_plot_driver
(
plot_png
),
set_counter
(
plot_png
,
0
),
generate_doc
(
doc
),
generate_doc
(
devdoc
).
...
...
@@ -38,12 +48,14 @@ generate_doc(Type) :-
error
(
existence_error
(
directory
,
_
),
_
),
true
),
format
(
atom
(
IndexFilename
),
'~a/index.html'
,
[
Type
]),
working_directory
(
OldDir
,
Type
),
format
(
atom
(
IndexFilename
),
'index.html'
,
[
Type
]),
setup_call_cleanup
(
open
(
IndexFilename
,
write
,
Stream
),
generate_doc
(
Stream
,
Type
),
close
(
Stream
)
).
),
working_directory
(
_OldDir
,
OldDir
).
generate_doc
(
Doc
,
Type
)
:-
...
...
@@ -222,7 +234,7 @@ filter_id([_ | Tail], Id) :-
read_toc
(
Type
)
:-
setup_call_cleanup
(
open
(
'toc.org'
,
read
,
Stream
),
open
(
'
../
toc.org'
,
read
,
Stream
),
read_toc
(
Stream
,
Type
),
close
(
Stream
)
).
...
...
@@ -315,8 +327,9 @@ generate_body_item(section(Level, Title), Doc, _Type) :-
generate_body_item
(
file
(
File
),
Doc
,
Type
)
:-
atom_concat
(
'../'
,
File
,
ParentFile
),
setup_call_cleanup
(
open
(
File
,
read
,
Stream
),
open
(
Parent
File
,
read
,
Stream
),
generate_body_item_stream
(
Stream
,
Doc
,
Type
),
close
(
Stream
)
).
...
...
@@ -487,11 +500,14 @@ generate_body_item_clause(Clause, Stream, Type) :-
format
(
Stream
,
'<h5 id="~a""><code>~a'
,
[
Id
,
Command
]),
write_arguments
(
Arguments
,
Stream
),
write
(
Stream
,
'.</code></h5>\n'
),
write
(
Stream
,
'<div>'
),
\
+
(
member
(
DocItem
,
Doc
),
write_doc_item
(
DocItem
,
Stream
,
Type
),
fail
)
\
+
(
write_doc_item
(
DocItem
,
Stream
,
Type
)
)
),
write
(
Stream
,
'</div>'
)
;
true
).
...
...
@@ -650,8 +666,32 @@ write_doc_item(doc(DocBody), Stream, _Type) :-
write_doc
(
Stream
,
DocBody
).
write_doc_item
(
devdoc
(
DocBody
),
Stream
,
devdoc
)
:-
write_doc
(
Stream
,
DocBody
).
write_doc_item
(
devdoc
(
DocBody
),
Stream
,
Type
)
:-
(
Type
=
devdoc
->
write_doc
(
Stream
,
DocBody
)
;
true
).
write_doc_item
(
biocham_silent
(
Command
),
_Stream
,
_Type
)
:-
command
(
Command
).
write_doc_item
(
biocham
(
Command
),
Stream
,
_Type
)
:-
with_output_to
(
atom
(
Output
),
command
(
Command
)
),
prompt
(
Prompt
),
format
(
Stream
,
'</div>
<div><code>~a</code><kbd>~w.</kbd></div>
<pre>~a</pre>
<div>'
,
[
Prompt
,
Command
,
Output
]
).
write_doc
(
Doc
,
DocBody
)
:-
...
...
@@ -812,6 +852,12 @@ write_command(end, enumerate, Doc) :-
close_opened_li
(
Doc
),
write
(
Doc
,
'</ol>'
).
write_command
(
example
,
Argument
,
Doc
)
:-
!,
write
(
Doc
,
'</div><div><strong>Example.</strong> '
),
atom_chars
(
Argument
,
ArgumentChars
),
write_doc_chars
(
ArgumentChars
,
Doc
).
write_command
(
Command
,
_Argument
,
_Doc
)
:-
throw
(
error
(
unknown_command
(
Command
))).
...
...
gsl.pl
View file @
9f66b109
...
...
@@ -296,5 +296,6 @@ compile_c_program(ExecutableFilename) :-
call_subprocess
(
ExecutableFilename
,
Arguments
)
:-
process_create
(
ExecutableFilename
,
Arguments
,
[
process
(
Pid
)]),
absolute_file_name
(
ExecutableFilename
,
Absolute
),
process_create
(
Absolute
,
Arguments
,
[
process
(
Pid
)]),
process_wait
(
Pid
,
exit
(
0
)).
numerical_simulation.pl
View file @
9f66b109
...
...
@@ -10,6 +10,13 @@
numerical_simulation
:-
biocham_command
,
doc
(
'performs a numerical simulation up to 20s.'
),
biocham_silent
(
clear_model
),
biocham
(
a
=>
b
),
biocham
(
present
(
a
)),
biocham
(
list_reactions
),
biocham
(
list_ODE
),
biocham
(
numerical_simulation
),
biocham
(
plot
),
numerical_simulation
(
20
).
...
...
plot.pl
View file @
9f66b109
...
...
@@ -2,6 +2,9 @@
plot
,
[
plot
/
0
,
set_plot_driver
/
1
,
gnu_plot
/
0
,
plot_png
/
0
,
export_plot
/
1
,
export_plot_to_png
/
1
]
...
...
@@ -10,10 +13,31 @@
plot
:-
biocham_command
,
doc
(
'plots the current trace.'
),
doc
(
'\\example'
),
get_plot_driver
(
Driver
),
Driver
.
get_plot_driver
(
Driver
)
:-
nb_getval
(
plot_driver
,
Driver
).
set_plot_driver
(
Driver
)
:-
nb_setval
(
plot_driver
,
Driver
).
gnu_plot
:-
export_plot
(
plot
),
execute_plot
([
'-persist'
,
'plot.plot'
]).
plot_png
:-
count
(
plot_png
,
Index
),
format
(
atom
(
Filename
),
'plot~d.png'
,
[
Index
]),
export_plot_to_png
(
Filename
),
format
(
'<img src="~a">'
,
[
Filename
]).
execute_plot
(
Options
)
:-
process_create
(
path
(
gnuplot
),
Options
,
[]).
...
...
toplevel.pl
View file @
9f66b109
...
...
@@ -4,7 +4,8 @@
execute_command
/
1
,
toplevel
/
0
,
quit
/
0
,
command
/
1
command
/
1
,
prompt
/
1
]).
...
...
types.pl
View file @
9f66b109
...
...
@@ -46,6 +46,10 @@ collect_info(DocItem, _Arguments, _ArgumentTypes, _BiochamCommand, Doc) :-
DocItem
=
doc
(
_
)
;
DocItem
=
devdoc
(
_
)
;
DocItem
=
biocham
(
_
)
;
DocItem
=
biocham_silent
(
_
)
),
!,
Doc
=
[
DocItem
].
...
...
@@ -126,6 +130,8 @@ check_type(Grammar, Item, NewItem) :-
clause
(
NewHead
,
NewBody
),
copy_term
((
NewHead
,
NewBody
),
(
Head
,
Body
)),
check_grammar_body
(
Body
,
NewBody
)
->
true
;
throw
(
error
(
expected
(
Grammar
)))
).
...
...
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