Merge pull request #49 from sparsh-989/pandoc_support

Added pandoc export

brian2tools/mdexport/expander.py

@@ -8,6 +8,8 @@
 from sympy.printing import latex
 from sympy.abc import *
 from markdown_strings import *
+from jinja2 import Template
+from .template import templates
 import numpy as np
 import re
 import inspect
@@ -284,7 +286,7 @@ def render_expression(self, expression, differential=False):
         # to remove `$` (in most md compiler single $ is used)
         return rend_exp[1:][:-1]
 
-    def create_md_string(self, net_dict):
+    def create_md_string(self, net_dict, template_name):
         """
         Create markdown text by checking the standard dictionary and call
         required expand functions and arrange the descriptions
@@ -373,6 +375,8 @@ def create_md_string(self, net_dict):
                                                              for connector in initializers_connectors
                                                              if connector['type'] == 'connect' and
                                                                 connector['synapses'] == obj_mem['name']]
+                                if obj_key == 'neurongroup' and current_order == 1:
+                                    obj_mem['template_name'] = template_name    
                             run_string += ('- ' +
                                            func_map[obj_key]['f'](obj_mem))
 
@@ -478,6 +482,7 @@ def expand_NeuronGroup(self, neurongrp):
         neurongrp : dict
             Standard dictionary of NeuronGroup
         """
+        template_name = neurongrp['template_name']
         # start expanding
         md_str = ''
         # name and size
@@ -508,8 +513,18 @@ def expand_NeuronGroup(self, neurongrp):
             self.check_plural(neurongrp['run_regularly']) + ': ' + endll)
             for run_reg in neurongrp['run_regularly']:
                 md_str += self.expand_runregularly(run_reg)
-
+
+        # Create Jinja2 Template object
+        if template_name not in templates :
+            print(md_str)
+            return md_str
+        # Create Jinja2 Template object
+        template = Template(templates[template_name])
+        # # Render the template with the provided NeuronGroup dictionary
+        md_str = template.render(neurongrp=neurongrp)
+        print (md_str)
         return md_str
+
 
     def expand_SpikeSource(self, source):
         """
@@ -862,6 +877,7 @@ def expand_StateMonitor(self, statemon):
                 md_str += (', for member' +
                            self.check_plural(statemon['record']) +
                            ': ' +
+
                            ','.join([str(ind) for ind in statemon['record']]))
         return md_str + endll
 
@@ -907,6 +923,7 @@ def expand_EventMonitor(self, eventmon):
                     ','.join([str(ind) for ind in eventmon['record']]))
         md_str += (' when event ' + bold(eventmon['event']) +
                     ' is triggered')
+
         return md_str + endll
 
     def expand_PopulationRateMonitor(self, popratemon):

brian2tools/mdexport/mdexporter.py

@@ -2,6 +2,7 @@
 from brian2tools.baseexport.device import BaseExporter
 import os
 import inspect
+import subprocess
 from .expander import *
 
 
@@ -13,7 +14,7 @@ class MdExporter(BaseExporter):
     """
 
     def build(self, direct_call=True, debug=False, expander=None,
-              filename=None):
+              filename=None, additional_formats=None, template_type=None):
         """
         Build the exporter
 
@@ -34,6 +35,15 @@ def build(self, direct_call=True, debug=False, expander=None,
             If mentioned, the markdown text would be written in that
             particular filename. When empty string '' is passed the user file
             name would be taken
+
+        additional_formats : str or list of str or all
+                If user wants to have the output file in additional_formats they
+                can specify them under this variable and the options are pdf, 
+                latex, html and all.  
+
+        template_type : str   
+            Based on your selected template, it will rendered otherwise
+            a default template will be used for rendering              
         """
         # buil_on_run = True but called build() directly
         if self.build_on_run and direct_call:
@@ -70,7 +80,7 @@ def build(self, direct_call=True, debug=False, expander=None,
             self.expander = MdExpander()
 
         # start creating markdown descriptions using expander
-        self.md_text = self.expander.create_md_string(self.runs)
+        self.md_text = self.expander.create_md_string(self.runs, template_type)
 
         # check output filename
         if filename:
@@ -90,9 +100,33 @@ def build(self, direct_call=True, debug=False, expander=None,
             print(self.md_text)
         elif self.filename:
             # start writing markdown text in file
-            md_file = open(self.filename + '.md', "w")
+            source_file = self.filename + ".md"
+            md_file = open(source_file, "w")
             md_file.write(self.md_text)
             md_file.close()
+
+            # Check if Pandoc is installed
+            try:
+                subprocess.check_call(["pandoc", "--version"], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            except FileNotFoundError:
+                raise Exception("Pandoc is not installed. Please install Pandoc and try again.")
+
+            formats_extensions = {'latex':'.tex', 'html':'.html', 'pdf':'.pdf'}
+            if isinstance(additional_formats, str):
+                if additional_formats == "all":
+                    formats = ['latex', 'html', 'pdf']
+                else:
+                    formats = [additional_formats]
+            else:
+                formats = additional_formats if additional_formats is not None else []
+            for format_name in formats:
+                filename = self.filename + formats_extensions[format_name]
+                try:
+                    subprocess.run(["pandoc", "--from", "markdown", "--to", format_name, "-o", filename, source_file],
+                                   check=True)
+                    print("Conversion complete! Files generated:", filename) 
+                except subprocess.CalledProcessError as ex:
+                    print(f"Could not generate format '{format_name}': {str(ex)}")
         else:
             pass  # do nothing
 

brian2tools/mdexport/template.py

@@ -0,0 +1,54 @@
+# Define the Jinja2 template string
+templates = {
+    'template_str' : """
+        ## Network details
+
+        **Neuron population:**
+        - Group {{ neurongrp.name }}, consisting of {{ neurongrp.N }} neurons.
+
+        # Model dynamics
+        {% for key, eqn in neurongrp.equations.items() %}
+        - $\frac{d}{d t} {{ key }}$ = {{ eqn.expr }}{% if eqn.unit %} [{{ eqn.unit }}]{% endif %}
+        {% endfor %}
+
+        {% if neurongrp.user_method %}
+        The equations are integrated with the '{{ neurongrp.user_method }}' method.
+        {% endif %}
+
+        # Events (if present)
+        {% if 'events' in neurongrp %}
+        **Events:**
+
+        {% for event, details in neurongrp.events.items() %}
+        - If {{ details.threshold.code }}, a {{ event }} event is triggered and {{ details.reset.code }}.
+        {% endfor %}
+        {% endif %}
+
+        # Constants (if present)
+        {% if 'identifiers' in neurongrp %}
+        **Constants:**
+
+        {% for identifier, value in neurongrp.identifiers.items() %}
+        - {{ identifier }}: {{ value }}
+        {% endfor %}
+        {% endif %}
+
+        # Initial values (if present)
+        {% if 'initializer' in neurongrp and neurongrp['initializer'] %}
+        **Initial values:**
+
+        {% for initializer in neurongrp['initializer'] %}
+        - {{ initializer.variable }}: {{ initializer.value }}{% if initializer.unit %} [{{ initializer.unit }}]{% endif %}
+        {% endfor %}
+        {% endif %}
+
+        # Run regularly (if present)
+        {% if 'run_regularly' in neurongrp %}
+        **Run regularly:**
+
+        {% for run_reg in neurongrp['run_regularly'] %}
+        - {{ run_reg }}
+        {% endfor %}
+        {% endif %}
+"""
+}