automated simulation and visualization

interview_kernel/exaoutput.py

 
 import os
 from pathlib import Path
+import subprocess
 from collections import OrderedDict
 from pylatexenc.latexencode import utf8tolatex, utf82latex
 
@@ -241,14 +242,23 @@ class ExaOutput:
                 "configList=\"\" \n"\
                 "configList+=\"{}/{} \" \n".format(self.probname, self.probname))
 
-class ExaRunner():
+class ExaRunner:
+    """A class to run exastencils using the files generated by an Exaoutput class, and to get the results"""
+
     from functools import lru_cache
 
     def __init__(self, exaout):
         self.exaout = exaout
 
+    def run_exastencils(self):
+        p = subprocess.run(["./generate_compile_and_run_list.sh"], cwd=str(self.exaout.exastencils_path),
+                           stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+        out = p.stdout
+        if p.returncode != 0:
+            print(out)
+
     @lru_cache()
-    def load_data(self, data_name="u"):
+    def load_data(self, data_name="u"): #TODO name of unknowns
         import pandas as pd
         data_path = self.exaout.exastencils_path.joinpath("generated").joinpath(self.exaout.probname).joinpath(data_name).with_suffix(".dat")
         df = pd.read_csv(data_path, sep=' ', index_col=0)

interview_kernel/interview_kernel.py

 from sys import executable
 from os.path import join
 #from pathlib import Path
+
 from metakernel import MetaKernel
 from IPython.display import HTML, Javascript
 from metakernel import IPythonKernel
@@ -20,6 +21,8 @@ from bokeh.models import ColumnDataSource
 #from tempfile import NamedTemporaryFile
 
 from pde_state_machine import *
+from string_handling import build_url, get_recursively
+
 
 # This "main class" is two things: a REPL loop, by subclassing the cmd2 Cmd class
 # and a state machine as given by the pytransitions package
@@ -50,7 +53,7 @@ class Interview(MetaKernel):
 
     def __init__(self, **kwargs):
 
-        self.state_machine = PDE_States(self.poutput, self.update_prompt, self.please_prompt)
+        self.state_machine = PDE_States(self.poutput, self.update_prompt, self.please_prompt, self.display_html)
 
         # call superclass constructor
         super(Interview, self).__init__(**kwargs)
@@ -143,14 +146,11 @@ class Interview(MetaKernel):
         if arg.startswith("recap"):
             self.state_machine.recap(arg)
             return True
-        if arg.startswith("html"):
-            self.display_html()
+        if arg.startswith("tgview"):
+            self.display_tgview(arg)
             return True
-        if arg.startswith("plt"):
-            self.display_plt()
-            return True
-        if arg.startswith("bokeh"):
-            self.display_bokeh()
+        if arg.startswith("undo"):
+            self.do_undo(arg)
             return True
         return False
 
@@ -207,7 +207,9 @@ class Interview(MetaKernel):
             super(Interview, self).do_complete(code, cursor_pos)
             return
 
-    def display_html(self):
+    def display_html(self, code=None):
+
+        # highlight some of the code entered and show line numbers (just to play around)
         self.Display(HTML("""
         <style type="text/css">
               .styled-background { background-color: #ff7; }
@@ -226,85 +228,43 @@ class Interview(MetaKernel):
         </script>
                             """ % (1, 0, 3, 0)))
 
-        tgview_url = join(self.state_machine.mmtinterface.serverInstance, "graphs/tgview.html?type=thgraph&graphdata=", self.state_machine.mmtinterface.URIprefix, self.state_machine.mmtinterface.namespace + "?u")
+        if code:
+            self.Display(HTML(code))
+
+    def display_tgview(self, args=''):
+        """displays the theory graph viewer as html, cf. https://github.com/UniFormal/TGView/wiki/"""
+        server_url = str(self.state_machine.mmtinterface.serverInstance)
+
+        args_dict = {
+            "type": "thgraph",
+        }
+
+        args = args.replace("tgview ", '', 1).strip()
+
+        if args == '':
+            args_dict["graphdata"] = self.state_machine.mmtinterface.URIprefix + \
+                                     self.state_machine.mmtinterface.namespace + "?u"
+        else:
+            args_dict["graphdata"] = self.state_machine.mmtinterface.URIprefix + \
+                                     self.state_machine.mmtinterface.namespace + "?" + args
+
+        # if applicable, highlight the ephemeral parts https://github.com/UniFormal/TGView/issues/25
+        thynames = get_recursively(self.state_machine.simdata, "theoryname")
+        if thynames:
+            args_dict["highlight"] = ",".join(thynames)
 
-        othercode = """
+        tgview_url = build_url(server_url, "graphs/tgview.html", args_dict=args_dict)
+
+        code = """
             <iframe 
-                src="https://mmt.mathhub.info/graphs/tgview.html" 
+                src="{}" 
                 style="width: 100%; height: 510px; border: none"
             >
             </iframe>
-        """
-        # a futile attempt to set the size
-        metadata = {
-                        #'text/html': {
-                            'width': 1600,
-                            'height': 1400
-                        #}
-                    }
-        self.Display(HTML(othercode, metadata=metadata))
-
-    # cf. nbviewer.jupyter.org/github/bokeh/bokeh-notebooks/blob/master/tutorial/01 - Basic Plotting.ipynb
-    def display_bokeh(self):
-        from exaoutput import ExaOutput, ExaRunner
-
-        # create a new plot with default tools, using figure
-        p = figure(plot_width=1000, plot_height=400)
-
-        runner = ExaRunner(ExaOutput())
-        data = runner.load_data("u")
-        #source = ColumnDataSource(data=data)
-        source = ColumnDataSource(data=dict(x=[], u=[]))
-        source.data = source.from_df(data )#[['x', 'u']])
-        source.add(data.index, 'index')
-
-        # add a circle renderer with a size, color, and alpha
-        p.circle(x='index', y='u', size=2, line_color="navy", fill_color="orange", fill_alpha=0.5, source=source)
-        #show(p)
+        """.format(tgview_url)
+
+        self.display_html(code)
 
-        output_notebook()
-        # cf. http://bokeh.pydata.org/en/0.10.0/docs/user_guide/embed.html
-        self.Display(HTML(file_html(p, CDN, "my plot")))  # show the results
-
-        # using JS requires jupyter widgets extension
-        #script, div = components(p)
-        #div = notebook_div(p)
-        #self.Display(Javascript(script + div))  # show the results
-
-
-    def display_plt(self):
-        # plt.ion()
-
-        # plot = plt.plot([3, 8, 2, 5, 1])
-        #self.Display(plot)
-        # plt.show() #TODO find out why there is no comm and interactive shell - and if it should be there
-
-        # cf. http://ipython-books.github.io/16-creating-a-simple-kernel-for-jupyter/
-        fig = plt.figure()
-        ax = fig.add_subplot(111)
-        ax.plot([3, 8, 2, 5, 1])
-
-        # We create a PNG out of this plot.
-        png = _to_png(fig)
-
-        # and send it along as rich content
-        self.richcontent = dict()
-
-        # We prepare the response with our rich data (the plot).
-        self.richcontent['source'] = 'kernel'
-
-        # This dictionary may contain different MIME representations of the output.
-        self.richcontent['data'] = {
-                                        'image/png': png  #TODO error: Notebook JSON is invalid: [{'image/png': ...
-                                    },
-        # We can specify the image size in the metadata field.
-        self.richcontent['metadata'] = {
-                                            'image/png': {
-                                                'width': 600,
-                                                'height': 400
-                                            }
-                                        }
-        self.poutput("image!")
 
 if __name__ == '__main__':
     # from ipykernel.kernelapp import IPKernelApp

interview_kernel/mmtinterface.py

@@ -28,12 +28,8 @@ def start_mmt_server(port_number, mmtjar):
                           stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
     out = p.stdout
     if p.returncode != 0 and p.returncode != 130:
-        raise MMTServerError("Could not start the MMT server, return code " + str(p.returncode) + ", " + str(out))
-    #outs, errs = p.communicate()
-    #if outs is not None:
-        #print("MMT server terminated before rest of program, ")  # this just wont stay alive!!!
-        #p.terminate()
-        #raise MMTServerError("MMT server terminated before rest of program, ")  # + p.stdout)
+        raise MMTServerError("Server aborted, return code " + str(p.returncode) + ", " + str(out))
+
 
 def exit_mmt_server(port_number, mmtjar, timeout=3.0):
     completed = subprocess.run(["/usr/bin/java", "-jar", mmtjar, ":send", str(port_number),
@@ -41,9 +37,10 @@ def exit_mmt_server(port_number, mmtjar, timeout=3.0):
                                stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
     if completed.stdout != None and "(Connection refused)" in str(completed.stdout):
         if timeout > 0.0:
-            start_mmt_extension(port_number, mmtjar, timeout - 0.1)
+            exit_mmt_server(port_number, mmtjar, timeout - 0.1)
         else:
-            raise MMTServerError("unable to start interview extension")
+            raise MMTServerError("unable to exit mmt server")
+
 
 def start_mmt_extension(port_number, mmtjar, timeout=3.0):
     time.sleep(0.1)  # hope for server to have started communication already

interview_kernel/pde_state_machine.py

@@ -7,9 +7,14 @@ from collections import OrderedDict
 import getpass
 
 from string_handling import *
-from exaoutput import ExaOutput
+from exaoutput import ExaOutput, ExaRunner
 from mmtinterface import *
 
+from bokeh.io import output_notebook, show, export_svgs
+from bokeh.plotting import figure
+from bokeh.resources import CDN
+from bokeh.embed import file_html, components#, notebook_div
+from bokeh.models import ColumnDataSource
 
 class InterviewError(Exception):
     """Errors that occur during the course of the interview and are not due to mmt server errors"""
@@ -61,12 +66,14 @@ class CriticalSubdict():
 class PDE_States:
     """Just a state machine using pytranisitions that walks our theory graph and creates ephemeral theories and views"""
 
-    def __init__(self, output_function, after_state_change_function, prompt_function):
+    def __init__(self, output_function, after_state_change_function, prompt_function, display_html_function=None):
         # just act like we were getting the right replies from MMT
         self.cheating = True
 
+        # callback handles
         self.poutput = output_function
         self.please_prompt = prompt_function
+        self.display_html = display_html_function
 
         # Initialize a state machine
         self.states = [
@@ -297,8 +304,10 @@ class PDE_States:
         self.poutput("")
         self.poutput("To get explanations, enter \"explain <optional keyword>\". ")
         self.poutput("To see a recap of what we know so far, enter \"recap <optional keyword>\". ")
+        self.poutput("To interact with the current theory graph, enter \"tgwiev <optional theory name>\". ")
         self.poutput("Otherwise, you can always try and use LaTeX-type input.")
-        self.poutput("Have a look at the currently loaded MMT theories under " + self.mmtinterface.serverInstance)
+        self.poutput("")
+        self.poutput("You can inspect the currently loaded MMT theories under " + self.mmtinterface.serverInstance)
         self.poutput("")
         self.poutput("")
         self.poutput("")
@@ -791,7 +800,8 @@ class PDE_States:
 
     ##### for state sim
     def sim_begin(self):
-        self.please_prompt("Would you like to try and solve the PDE using the Finite Difference Method in ExaStencils?",
+        self.please_prompt("Would you like to try and solve the PDE using the Finite Difference Method in ExaStencils?"
+                           "If yes, you can provide a configuration name, or we'll just use your name.",
                            self.sim_ok_fd)
 
     def sim_handle_input(self, userstring):
@@ -801,9 +811,42 @@ class PDE_States:
 
     def sim_exit(self):
         # generate output
-        ExaOutput(self.simdata)
-        self.poutput("Generated ExaStencils input.")
-        # TODO generate and run simulation
+        exaout = ExaOutput(self.simdata)
+        print("Generated ExaStencils input; running ExaStencils")
+        # generate and run simulation
+        runner = ExaRunner(exaout)
+        runner.run_exastencils()
+        print("Ran ExaStencils; preparing visualization")
+        # output
+        self.display_result_as_bokeh()
+
+
+    # cf. nbviewer.jupyter.org/github/bokeh/bokeh-notebooks/blob/master/tutorial/01 - Basic Plotting.ipynb
+    def display_result_as_bokeh(self):
+
+        # create a new plot with default tools, using figure
+        p = figure(plot_width=1000, plot_height=400)
+
+        runner = ExaRunner(ExaOutput())
+        data = runner.load_data("u")
+        #source = ColumnDataSource(data=data)
+        source = ColumnDataSource(data=dict(x=[], u=[]))
+        source.data = source.from_df(data)
+        source.add(data.index, 'index')
+
+        # add a circle renderer with a size, color, and alpha
+        p.circle(x='index', y='u', size=2, line_color="navy", fill_color="orange", fill_alpha=0.5, source=source)
+        #show(p)
+
+        output_notebook()
+        # cf. http://bokeh.pydata.org/en/0.10.0/docs/user_guide/embed.html
+        self.display_html(file_html(p, CDN, "my plot"))  # show the results
+
+        # using JS requires jupyter widgets extension
+        #script, div = components(p)
+        #div = notebook_div(p)
+        #self.Display(Javascript(script + div))  # show the results
+
 
 
     def sim_ok_fd(self):

interview_kernel/string_handling.py

@@ -2,6 +2,7 @@
 
 from distutils.util import strtobool
 import re
+from urllib.parse import urlparse, urlencode, ParseResult
 
 def means_no(answer):
     try:
@@ -12,6 +13,14 @@ def means_no(answer):
         return False
     return False
 
+def build_url(baseurl, path, args_dict={}, query_dict={}):
+    # Returns a list in the structure of urlparse.ParseResult
+    url = urlparse(baseurl)
+    # construct new parseresult
+    new_url = ParseResult(url.scheme, url.netloc, path, urlencode(args_dict),
+                          urlencode(query_dict, doseq=True), url.fragment)
+    return new_url.geturl()
+
 # cf. https://stackoverflow.com/questions/14962485/finding-a-key-recursively-in-a-dictionary
 def get_recursively(search_dict, field):
     """