merge

Makefile

 ADDITIONAL_MODULES=modules/sbml/sbml_utils.pl
-MODULES=$(shell sed -n -E 's/^- (.*\.pl)$$/\1/p' toc.org) $(ADDITIONAL_MODULES)
+MODULES=$(shell sed -n -E 's/^[+-] (.*\.pl)$$/\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))
 
@@ -60,6 +61,9 @@ biocham_tests: swipl-biocham $(MODULES) $(TEST_MODULES) Makefile
 		--goal="call_cleanup((run_tests, halt(0)), halt(1))" \
 		-c $(MODULES) $(TEST_MODULES)
 
+jupyter: biocham
+	jupyter kernelspec install --user --name=biocham biocham_kernel
+
 clean:
 	- make -C modules/graphviz clean
 	- make -C modules/sbml clean

biocham_kernel/__main__.py

+if __name__ == '__main__':
+    from ipykernel.kernelapp import IPKernelApp
+    from .kernel import BiochamKernel
+    IPKernelApp.launch_instance(kernel_class=BiochamKernel)

biocham_kernel/images.py

+import base64
+import os
+
+# TODO: add logo-64x64.png
+
+
+def display_data_for_image(filename):
+    with open(filename, 'rb') as f:
+        image = f.read()
+    os.unlink(filename)
+
+    image_type = filename.split('.')[-1]
+    if image_type == 'svg':
+        image_type = 'image/svg+xml'
+        image_data = image.decode('utf-8')
+    elif image_type == 'csv':
+        image_type = 'text/html'
+        image = image.decode('utf-8')
+        lines = [line.split(',') for line in image.splitlines()]
+        labels = ', '.join(['"' + label + '"' for label in lines.pop(0)[1:]])
+        series = '[' + ', '.join([
+            '[' +
+            ', '.join(['[' + lines[i][0] + ', ' + lines[i][j] + ']'
+                       for i in range(len(lines))]) +
+            ']' for j in range(1, len(lines[0]))]) + ']'
+        plotid = filename.split('.')[-2]
+        image_data = '''
+        <div id="{plotid}" style="height: 400px; width: 600px;"></div>
+        <script>
+            function waitForJQplot() {{
+                if (typeof $.jqplot !== 'undefined') {{
+                    $.jqplot.config.enablePlugins = true;
+                    $.jqplot('{plotid}', {data}, {{
+                        seriesDefaults: {{
+                            showMarker: false
+                        }},
+                        legend: {{
+                            show: true,
+                            placement: "outside",
+                            labels: [{labels}],
+                            renderer: $.jqplot.EnhancedLegendRenderer,
+                            rendererOptions: {{
+                                seriesToggle: true,
+                                showLineStyle: true
+                            }}
+                        }},
+                        cursor: {{
+                            show: true,
+                            zoom: true,
+                            tooltipFormatString: "%.2e, %.2e",
+                            cursorLegendFormatString: "%.2e, %.2e"
+                        }},
+                        highlighter: {{
+                            formatString: "%.2e"
+                        }}
+                    }});
+                    $('#{plotid}').contextmenu(function() {{
+                        $('#{plotid}').jqplotSaveImage();
+                        return false;
+                    }});
+                }} else {{ window.setTimeout(waitForJQplot, 250); }}
+            }}
+            $(document).ready(function(){{
+                waitForJQplot();
+            }});
+        </script>
+        '''.format(plotid=plotid, data=series, labels=labels)
+    else:
+        image_type = 'image/' + image_type
+        image_data = base64.b64encode(image).decode('ascii')
+
+    content = {
+        'data': {
+            image_type: image_data
+        },
+        'metadata': {}
+    }
+    return content
+
+
+def extract_image_filenames(output):
+    output_lines = []
+    image_filenames = []
+
+    for line in output.split("\n"):
+        if line.startswith('<img src="'):
+            filename = line.rstrip().split('"')[1]
+            image_filenames.append(filename)
+        else:
+            output_lines.append(line)
+
+    output = "\n".join(output_lines)
+    return image_filenames, output

biocham_kernel/jqplot.enhancedLegendRenderer.js

+/**
+ * jqPlot
+ * Pure JavaScript plotting plugin using jQuery
+ *
+ * Version: 1.0.9
+ * Revision: d96a669
+ *
+ * Copyright (c) 2009-2016 Chris Leonello
+ * jqPlot is currently available for use in all personal or commercial projects 
+ * under both the MIT (http://www.opensource.org/licenses/mit-license.php) and GPL 
+ * version 2.0 (http://www.gnu.org/licenses/gpl-2.0.html) licenses. This means that you can 
+ * choose the license that best suits your project and use it accordingly. 
+ *
+ * Although not required, the author would appreciate an email letting him 
+ * know of any substantial use of jqPlot.  You can reach the author at: 
+ * chris at jqplot dot com or see http://www.jqplot.com/info.php .
+ *
+ * If you are feeling kind and generous, consider supporting the project by
+ * making a donation at: http://www.jqplot.com/donate.php .
+ *
+ * sprintf functions contained in jqplot.sprintf.js by Ash Searle:
+ *
+ *     version 2007.04.27
+ *     author Ash Searle
+ *     http://hexmen.com/blog/2007/03/printf-sprintf/
+ *     http://hexmen.com/js/sprintf.js
+ *     The author (Ash Searle) has placed this code in the public domain:
+ *     "This code is unrestricted: you are free to use it however you like."
+ * 
+ */
+(function($) {
+    // class $.jqplot.EnhancedLegendRenderer
+    // Legend renderer which can specify the number of rows and/or columns in the legend.
+    $.jqplot.EnhancedLegendRenderer = function(){
+        $.jqplot.TableLegendRenderer.call(this);
+    };
+    
+    $.jqplot.EnhancedLegendRenderer.prototype = new $.jqplot.TableLegendRenderer();
+    $.jqplot.EnhancedLegendRenderer.prototype.constructor = $.jqplot.EnhancedLegendRenderer;
+    
+    // called with scope of legend.
+    $.jqplot.EnhancedLegendRenderer.prototype.init = function(options) {
+        // prop: numberRows
+        // Maximum number of rows in the legend.  0 or null for unlimited.
+        this.numberRows = null;
+        // prop: numberColumns
+        // Maximum number of columns in the legend.  0 or null for unlimited.
+        this.numberColumns = null;
+        // prop: seriesToggle
+        // false to not enable series on/off toggling on the legend.
+        // true or a fadein/fadeout speed (number of milliseconds or 'fast', 'normal', 'slow') 
+        // to enable show/hide of series on click of legend item.
+        this.seriesToggle = 'normal';
+        // prop: seriesToggleReplot
+        // True to replot the chart after toggling series on/off.
+        // This will set the series show property to false.
+        // This allows for rescaling or other maniplation of chart.
+        // Set to an options object (e.g. {resetAxes: true}) for replot options.
+        this.seriesToggleReplot = false;
+        // prop: disableIEFading
+        // true to toggle series with a show/hide method only and not allow fading in/out.  
+        // This is to overcome poor performance of fade in some versions of IE.
+        this.disableIEFading = true;
+        $.extend(true, this, options);
+        
+        if (this.seriesToggle) {
+            $.jqplot.postDrawHooks.push(postDraw);
+        }
+    };
+    
+    // called with scope of legend
+    $.jqplot.EnhancedLegendRenderer.prototype.draw = function(offsets, plot) {
+        var legend = this;
+        if (this.show) {
+            var series = this._series;
+            var s;
+            var ss = 'position:absolute;';
+            ss += (this.background) ? 'background:'+this.background+';' : '';
+            ss += (this.border) ? 'border:'+this.border+';' : '';
+            ss += (this.fontSize) ? 'font-size:'+this.fontSize+';' : '';
+            ss += (this.fontFamily) ? 'font-family:'+this.fontFamily+';' : '';
+            ss += (this.textColor) ? 'color:'+this.textColor+';' : '';
+            ss += (this.marginTop != null) ? 'margin-top:'+this.marginTop+';' : '';
+            ss += (this.marginBottom != null) ? 'margin-bottom:'+this.marginBottom+';' : '';
+            ss += (this.marginLeft != null) ? 'margin-left:'+this.marginLeft+';' : '';
+            ss += (this.marginRight != null) ? 'margin-right:'+this.marginRight+';' : '';
+            this._elem = $('<table class="jqplot-table-legend" style="'+ss+'"></table>');
+            if (this.seriesToggle) {
+                this._elem.css('z-index', '3');
+            }
+        
+            var pad = false, 
+                reverse = false,
+                nr, nc;
+            if (this.numberRows) {
+                nr = this.numberRows;
+                if (!this.numberColumns){
+                    nc = Math.ceil(series.length/nr);
+                }
+                else{
+                    nc = this.numberColumns;
+                }
+            }
+            else if (this.numberColumns) {
+                nc = this.numberColumns;
+                nr = Math.ceil(series.length/this.numberColumns);
+            }
+            else {
+                nr = series.length;
+                nc = 1;
+            }
+                
+            var i, j, tr, td1, td2, lt, rs, div, div0, div1;
+            var idx = 0;
+            // check to see if we need to reverse
+            for (i=series.length-1; i>=0; i--) {
+                if (nc == 1 && series[i]._stack || series[i].renderer.constructor == $.jqplot.BezierCurveRenderer){
+                    reverse = true;
+                }
+            }    
+                
+            for (i=0; i<nr; i++) {
+                tr = $(document.createElement('tr'));
+                tr.addClass('jqplot-table-legend');
+                if (reverse){
+                    tr.prependTo(this._elem);
+                }
+                else{
+                    tr.appendTo(this._elem);
+                }
+                for (j=0; j<nc; j++) {
+                    if (idx < series.length && (series[idx].show || series[idx].showLabel)){
+                        s = series[idx];
+                        lt = this.labels[idx] || s.label.toString();
+                        if (lt) {
+                            var color = s.color;
+                            if (!reverse){
+                                if (i>0){
+                                    pad = true;
+                                }
+                                else{
+                                    pad = false;
+                                }
+                            }
+                            else{
+                                if (i == nr -1){
+                                    pad = false;
+                                }
+                                else{
+                                    pad = true;
+                                }
+                            }
+                            rs = (pad) ? this.rowSpacing : '0';
+
+                            td1 = $(document.createElement('td'));
+                            td1.addClass('jqplot-table-legend jqplot-table-legend-swatch');
+                            td1.css({textAlign: 'center', paddingTop: rs});
+
+                            div0 = $(document.createElement('div'));
+                            div0.addClass('jqplot-table-legend-swatch-outline');
+                            div1 = $(document.createElement('div'));
+                            div1.addClass('jqplot-table-legend-swatch');
+                            div1.css({backgroundColor: color, borderColor: color});
+
+                            td1.append(div0.append(div1));
+
+                            td2 = $(document.createElement('td'));
+                            td2.addClass('jqplot-table-legend jqplot-table-legend-label');
+                            td2.css('paddingTop', rs);
+                    
+                            // td1 = $('<td class="jqplot-table-legend" style="text-align:center;padding-top:'+rs+';">'+
+                            //     '<div><div class="jqplot-table-legend-swatch" style="background-color:'+color+';border-color:'+color+';"></div>'+
+                            //     '</div></td>');
+                            // td2 = $('<td class="jqplot-table-legend" style="padding-top:'+rs+';"></td>');
+                            if (this.escapeHtml){
+                                td2.text(lt);
+                            }
+                            else {
+                                td2.html(lt);
+                            }
+                            if (reverse) {
+                                if (this.showLabels) {td2.prependTo(tr);}
+                                if (this.showSwatches) {td1.prependTo(tr);}
+                            }
+                            else {
+                                if (this.showSwatches) {td1.appendTo(tr);}
+                                if (this.showLabels) {td2.appendTo(tr);}
+                            }
+                            
+                            if (this.seriesToggle) {
+
+                                // add an overlay for clicking series on/off
+                                // div0 = $(document.createElement('div'));
+                                // div0.addClass('jqplot-table-legend-overlay');
+                                // div0.css({position:'relative', left:0, top:0, height:'100%', width:'100%'});
+                                // tr.append(div0);
+
+                                var speed;
+                                if (typeof(this.seriesToggle) === 'string' || typeof(this.seriesToggle) === 'number') {
+                                    if (!$.jqplot.use_excanvas || !this.disableIEFading) {
+                                        speed = this.seriesToggle;
+                                    }
+                                } 
+                                if (this.showSwatches) {
+                                    td1.bind('click', {series:s, speed:speed, plot: plot, replot:this.seriesToggleReplot}, handleToggle);
+                                    td1.addClass('jqplot-seriesToggle');
+                                }
+                                if (this.showLabels)  {
+                                    td2.bind('click', {series:s, speed:speed, plot: plot, replot:this.seriesToggleReplot}, handleToggle);
+                                    td2.addClass('jqplot-seriesToggle');
+                                }
+
+                                // for series that are already hidden, add the hidden class
+                                if (!s.show && s.showLabel) {
+                                    td1.addClass('jqplot-series-hidden');
+                                    td2.addClass('jqplot-series-hidden');
+                                }
+                            }
+                            
+                            pad = true;
+                        }
+                    }
+                    idx++;
+                }
+                
+                td1 = td2 = div0 = div1 = null;   
+            }
+        }
+        return this._elem;
+    };
+
+    var handleToggle = function (ev) {
+        var d = ev.data,
+            s = d.series,
+            replot = d.replot,
+            plot = d.plot,
+            speed = d.speed,
+            sidx = s.index,
+            showing = false;
+
+        if (s.canvas._elem.is(':hidden') || !s.show) {
+            showing = true;
+        }
+
+        var doLegendToggle = function() {
+
+            if (replot) {
+                var opts = {};
+
+                if ($.isPlainObject(replot)) {
+                    $.extend(true, opts, replot);
+                }
+
+                plot.replot(opts);
+                // if showing, there was no canvas element to fade in, so hide here
+                // and then do a fade in.
+                if (showing && speed) {
+                    var s = plot.series[sidx];
+
+                    if (s.shadowCanvas._elem) {
+                        s.shadowCanvas._elem.hide().fadeIn(speed);
+                    }
+                    s.canvas._elem.hide().fadeIn(speed);
+                    s.canvas._elem.nextAll('.jqplot-point-label.jqplot-series-'+s.index).hide().fadeIn(speed);
+                }
+
+            }
+
+            else {
+                var s = plot.series[sidx];
+
+                if (s.canvas._elem.is(':hidden') || !s.show) {
+                    // Not sure if there is a better way to check for showSwatches and showLabels === true.
+                    // Test for "undefined" since default values for both showSwatches and showLables is true.
+                    if (typeof plot.options.legend.showSwatches === 'undefined' || plot.options.legend.showSwatches === true) {
+                        plot.legend._elem.find('td').eq(sidx * 2).addClass('jqplot-series-hidden');
+                    }
+                    if (typeof plot.options.legend.showLabels === 'undefined' || plot.options.legend.showLabels === true) {
+                        plot.legend._elem.find('td').eq((sidx * 2) + 1).addClass('jqplot-series-hidden');
+                    }
+                }
+                else {
+                    if (typeof plot.options.legend.showSwatches === 'undefined' || plot.options.legend.showSwatches === true) {
+                        plot.legend._elem.find('td').eq(sidx * 2).removeClass('jqplot-series-hidden');
+                    }
+                    if (typeof plot.options.legend.showLabels === 'undefined' || plot.options.legend.showLabels === true) {
+                        plot.legend._elem.find('td').eq((sidx * 2) + 1).removeClass('jqplot-series-hidden');
+                    }
+                }
+
+            }
+
+        };
+
+        s.toggleDisplay(ev, doLegendToggle);
+    };
+    
+    // called with scope of plot.
+    var postDraw = function () {
+        if (this.legend.renderer.constructor == $.jqplot.EnhancedLegendRenderer && this.legend.seriesToggle){
+            var e = this.legend._elem.detach();
+            this.eventCanvas._elem.after(e);
+        }
+    };
+})(jQuery);

biocham_kernel/jquery.jqplot.min.css

+.jqplot-xaxis,.jqplot-xaxis-label{margin-top:10px}.jqplot-x2axis,.jqplot-x2axis-label{margin-bottom:10px}.jqplot-target{position:relative;color:#666;font-family:"Trebuchet MS",Arial,Helvetica,sans-serif;font-size:1em}.jqplot-axis{font-size:.75em}.jqplot-yaxis{margin-right:10px}.jqplot-y2axis,.jqplot-y3axis,.jqplot-y4axis,.jqplot-y5axis,.jqplot-y6axis,.jqplot-y7axis,.jqplot-y8axis,.jqplot-y9axis,.jqplot-yMidAxis{margin-left:10px;margin-right:10px}.jqplot-axis-tick,.jqplot-x2axis-tick,.jqplot-xaxis-tick,.jqplot-y2axis-tick,.jqplot-y3axis-tick,.jqplot-y4axis-tick,.jqplot-y5axis-tick,.jqplot-y6axis-tick,.jqplot-y7axis-tick,.jqplot-y8axis-tick,.jqplot-y9axis-tick,.jqplot-yMidAxis-tick,.jqplot-yaxis-tick{position:absolute;white-space:pre}.jqplot-xaxis-tick{top:0;left:15px;vertical-align:top}.jqplot-x2axis-tick{bottom:0;left:15px;vertical-align:bottom}.jqplot-yaxis-tick{right:0;top:15px;text-align:right}.jqplot-yaxis-tick.jqplot-breakTick{right:-20px;margin-right:0;padding:1px 5px;z-index:2;font-size:1.5em}.jqplot-x2axis-label,.jqplot-xaxis-label,.jqplot-yMidAxis-label,.jqplot-yaxis-label{font-size:11pt;position:absolute}.jqplot-y2axis-tick,.jqplot-y3axis-tick,.jqplot-y4axis-tick,.jqplot-y5axis-tick,.jqplot-y6axis-tick,.jqplot-y7axis-tick,.jqplot-y8axis-tick,.jqplot-y9axis-tick{left:0;top:15px;text-align:left}.jqplot-yMidAxis-tick{text-align:center;white-space:nowrap}.jqplot-yaxis-label{margin-right:10px}.jqplot-y2axis-label,.jqplot-y3axis-label,.jqplot-y4axis-label,.jqplot-y5axis-label,.jqplot-y6axis-label,.jqplot-y7axis-label,.jqplot-y8axis-label,.jqplot-y9axis-label{font-size:11pt;margin-left:10px;position:absolute}.jqplot-meterGauge-tick{font-size:.75em;color:#999}.jqplot-meterGauge-label{font-size:1em;color:#999}table.jqplot-table-legend{margin:12px}table.jqplot-cursor-legend,table.jqplot-table-legend{background-color:rgba(255,255,255,.6);border:1px solid #ccc;position:absolute;font-size:.75em}td.jqplot-table-legend{vertical-align:middle}td.jqplot-seriesToggle:active,td.jqplot-seriesToggle:hover{cursor:pointer}.jqplot-table-legend .jqplot-series-hidden{text-decoration:line-through}div.jqplot-table-legend-swatch-outline{border:1px solid #ccc;padding:1px}div.jqplot-table-legend-swatch{width:0;height:0;border-width:5px 6px;border-style:solid}.jqplot-title{top:0;left:0;padding-bottom:.5em;font-size:1.2em}table.jqplot-cursor-tooltip{border:1px solid #ccc;font-size:.75em}.jqplot-canvasOverlay-tooltip,.jqplot-cursor-tooltip,.jqplot-highlighter-tooltip{border:1px solid #ccc;font-size:.75em;white-space:nowrap;background:rgba(208,208,208,.5);padding:1px}.jqplot-point-label{font-size:.75em;z-index:2}td.jqplot-cursor-legend-swatch{vertical-align:middle;text-align:center}div.jqplot-cursor-legend-swatch{width:1.2em;height:.7em}.jqplot-error{text-align:center}.jqplot-error-message{position:relative;top:46%;display:inline-block}div.jqplot-bubble-label{font-size:.8em;padding-left:2px;padding-right:2px;color:rgb(20%,20%,20%)}div.jqplot-bubble-label.jqplot-bubble-label-highlight{background:rgba(90%,90%,90%,.7)}div.jqplot-noData-container{text-align:center;background-color:rgba(96%,96%,96%,.3)}
\ No newline at end of file

biocham_kernel/kernel.js

+define(function() {
+   var onload = function() {
+      $.ajaxSetup({ cache: true });
+      $.getScript("/kernelspecs/biocham/jquery.jqplot.js").done(function() {
+         $.getScript("/kernelspecs/biocham/jqplot.cursor.js");
+         $.getScript("/kernelspecs/biocham/jqplot.highlighter.js");
+         $.getScript("/kernelspecs/biocham/jqplot.enhancedLegendRenderer.js");
+      });
+      var cssNode = document.createElement('link');
+      cssNode.type = 'text/css';
+      cssNode.rel = 'stylesheet';
+      cssNode.href = '/kernelspecs/biocham/jquery.jqplot.min.css';
+      document.head.appendChild(cssNode);
+   }
+
+   return {onload: onload}
+
+})

biocham_kernel/kernel.json

+{
+   "argv": ["python3", "-m", "biocham_kernel", "-f", "{connection_file}"],
+   "display_name": "Biocham"
+}

biocham_kernel/kernel.py

+from subprocess import check_output
+
+from ipykernel.kernelbase import Kernel
+from pexpect import replwrap
+
+from .images import extract_image_filenames, display_data_for_image
+
+
+class BiochamKernel(Kernel):
+    implementation = 'Biocham'
+    implementation_version = '0.1.0'
+    language = 'biocham'
+    language_info = {
+        'name': 'biocham',
+        'mimetype': 'text/plain',
+        'file_extension': '.bc',
+    }
+    banner = check_output(['biocham4', '--version']).decode('utf-8')
+    language_version = banner.split()[1]
+
+    def __init__(self, **kwargs):
+        Kernel.__init__(self, **kwargs)
+        self._start_biocham()
+
+    def _start_biocham(self):
+        self.biocham = replwrap.REPLWrapper(
+            'biocham4 --jupyter',
+            'biocham: ',
+            None
+        )
+
+    def do_execute(self, code, silent, store_history=True,
+                   user_expressions=None, allow_stdin=False):
+        output = self.biocham.run_command(code)
+
+        image_filenames, output = extract_image_filenames(output)
+
+        if not silent:
+            stream_content = {'name': 'stdout', 'text': output}
+            self.send_response(self.iopub_socket, 'stream', stream_content)
+
+        for filename in image_filenames:
+            try:
+                data = display_data_for_image(filename)
+            except ValueError as e:
+                message = {'name': 'stdout', 'text': str(e)}
+                self.send_response(self.iopub_socket, 'stream', message)
+            else:
+                self.send_response(self.iopub_socket, 'display_data', data)
+
+        return {'status': 'ok',
+                # The base class increments the execution count
+                'execution_count': self.execution_count,
+                'payload': [],
+                'user_expressions': {},
+                }
+
+    # TODO: do_complete

commandline.pl

@@ -60,6 +60,17 @@ option('', '--generate-doc', Arg, Arg) :-
   generate_doc,
   quit.
 
+option('', '--version', Arg, Arg) :-
+   quit.
+
+option('', '--jupyter', Arg, Arg) :-
+  set_counter(graph_svg, 0),
+  set_counter(plot_csv, 0),
+  set_plot_driver(gnu_plot_csv),
+  set_image_viewer_driver(img_tag),
+  set_draw_graph_driver(graph_svg).
+
+
 add_files(Files) :-
   \+ (
     member(File, Files),

conservation_laws.pl

@@ -62,7 +62,7 @@ check_conservations :-
     'checks all conservation laws against reactions, and if necessary kinetics
     (see also \\command{add_conservation/1}).'
   ),
-  compute_ode,
+  ode_system,
   forall(
     (
       % model: current_model? compute_ode already supposes a single model

doc.pl

@@ -245,6 +245,10 @@ read_toc(Stream, Type) :-
     ;
       atom_codes(Atom, Line),
       (
+        atom_concat('%', _, Atom)
+      ->
+        true
+      ;
         atom_concat('* ', Section, Atom)
       ->
         add_section(1, Section)
@@ -257,7 +261,7 @@ read_toc(Stream, Type) :-
       ->
         add_section(3, Section)
       ;
-        Atom = '+ index'
+        Atom = '- index'
       ->
         assertz(toc(index))
       ;

graph_editor.pl

@@ -10,6 +10,7 @@
     delete_vertex/1,
     edge/1,
     add_edge/1,
+    edgeref/1,
     delete_edge/1,
     list_edges/0,
     list_isolated_vertices/0,
@@ -116,15 +117,22 @@ add_edge(EdgeList) :-
   ).
 
 
-delete_edge(EdgeList) :-
+:- grammar(edgeref).
+
+