Merge pull request #50 from sparsh-989/Template_Support

Template support

brian2tools/mdexport/mdexporter.py

@@ -14,7 +14,7 @@ class MdExporter(BaseExporter):
     """
 
     def build(self, direct_call=True, debug=False, expander=None,
-              filename=None, additional_formats=None, template_type=None):
+              filename=None, additional_formats=None, template_name='default', template_dir=None):
         """
         Build the exporter
 
@@ -41,7 +41,7 @@ def build(self, direct_call=True, debug=False, expander=None,
                 can specify them under this variable and the options are pdf, 
                 latex, html and all.  
 
-        template_type : str   
+        template_name : str   
             Based on your selected template, it will rendered otherwise
             a default template will be used for rendering              
         """
@@ -79,8 +79,12 @@ def build(self, direct_call=True, debug=False, expander=None,
             # default standard md expander
             self.expander = MdExpander()
 
+        if template_dir is not None:
+            self.expander.set_temp_dir_path(template_dir)
+
+
         # start creating markdown descriptions using expander
-        self.md_text = self.expander.create_md_string(self.runs, template_type)
+        self.md_text = self.expander.create_md_string(self.runs, template_name)
 
         # check output filename
         if filename:

brian2tools/templates/EventMonitor-default.md

@@ -0,0 +1,7 @@
+Monitors variable{{ expander.check_plural(group['variables']) }}: {%- for var in group['variables'] -%}
+    {{ expander.render_expression(var) }}{%- if not loop.last -%}, {%- endif -%}
+{%- endfor %} of {{ expander.expand_SpikeSource(group['source']) }} {%- if group['record'] is boolean -%}
+    {%- if group['record'] -%} for all members {%- else -%} for no member {%- endif -%}
+{%- else -%}
+    {%- if group['record']|length == 0 -%} for no member {%- else -%} for member{{ expander.check_plural(group['record']) }}: {{ group['record'] | join(', ') }} {%- endif -%}
+{%- endif -%} when event **{{ group['event'] }}** is triggered

brian2tools/templates/EventMonitor-table.md

@@ -0,0 +1,10 @@
+| **Monitors**    | **Variables**                                                                                               | **Source**                                           | **Record**                                                                                                 | **Event**                           |
+|-----------------|------------------------------------------------------------------------------------------------------------|-----------------------------------------------------|------------------------------------------------------------------------------------------------------------|-------------------------------------|
+| Monitors variable{{ expander.check_plural(group['variables']) }}: {%- for var in group['variables'] -%}
+    {{ expander.render_expression(var) }}{%- if not loop.last -%}, {%- endif -%}
+{%- endfor %} | of {{ expander.expand_SpikeSource(group['source']) }} | 
+    {%- if group['record'] is boolean -%}
+        {%- if group['record'] -%} for all members {%- else -%} for no member {%- endif -%}
+    {%- else -%}
+        {%- if group['record']|length == 0 -%} for no member {%- else -%} for member{{ expander.check_plural(group['record']) }}: {{ group['record'] | join(', ') }} {%- endif -%}
+    {%- endif -%} | when event **{{ group['event'] }}** is triggered |

brian2tools/templates/NeuronGroup-default.md

@@ -0,0 +1,30 @@
+## Network details
+ **Neuron population:**
+Group {{ (group['name']) }}, consisting of {{ (group['N']) }} neurons.
+{{ tab }}{{ ('Model dynamics:') }}
+{{ expander.expand_equations(group['equations']) }}
+{% if group['user_method'] %}
+    {{ tab }}The equations are integrated with the '{{ group['user_method'] }}' method.
+{% endif %}
+{% if 'events' in group %}
+    {{ tab }}{{ ('Events:') }}
+    {{ expander.expand_events(group['events']) }}
+{% endif %}
+{% if 'identifiers' in group %}
+    {{ tab }}{{ ('Constants:') }} {{ expander.expand_identifiers(group['identifiers']) }}
+{% endif %}
+{% if not expander.keep_initializer_order and 'initializer' in group and group['initializer']|length %}
+    {{ tab }}{{ ('Initial values:') }}
+    {% for initializer in group['initializer'] %}
+        {{ tab }}* {{ expander.expand_initializer(initializer) }}
+    {% endfor %}
+{% endif %}
+{% if 'run_regularly' in group %}
+    {{ tab }}{{ ('Run regularly') }}{{ expander.check_plural(group['run_regularly']) }}:
+    {% for run_reg in group['run_regularly'] %}
+        {{ expander.expand_runregularly(run_reg) }}
+    {% endfor %}
+{% endif %}
+
+
+

brian2tools/templates/NeuronGroup-table.md

@@ -0,0 +1,8 @@
+|-------------------------------|------------------------------------------------|
+| **Neuron population**         | Group {{ (group['name']) }}, consisting of {{ (group['N']) }} neurons. |
+| **Model dynamics**            | {{ expander.expand_equations(group['equations']) }} |
+| **Integration method**        | {% if group['user_method'] %} The equations are integrated with the '{{ group['user_method'] }}' method. {% endif %} |
+| **Events** (if present)       | {% if 'events' in group %} {{ expander.expand_events(group['events']) }} {% endif %} |
+| **Constants** (if present)    | {% if 'identifiers' in group %} {{ expander.expand_identifiers(group['identifiers']) }} {% endif %} |
+| **Initial values** (if present)| {% if not expander.keep_initializer_order and 'initializer' in group and group['initializer']|length %} {% for initializer in group['initializer'] %} {{ initializer.variable }}: {{ initializer.value }}{% if initializer.unit %} [{{ initializer.unit }}]{% endif %} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |
+| **Run regularly** (if present)| {% if 'run_regularly' in group %} {% for run_reg in group['run_regularly'] %} {{ expander.expand_runregularly(run_reg) }} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |

brian2tools/templates/PoissonGroup-default.md

@@ -0,0 +1,17 @@
+Name {{ group['name'] }} of population size {{ group['N'] }} and rate as {{ expander.render_expression(group['rates']) }}.
+
+        {% if group.get('identifiers', None) %}
+        Constants:
+        {{ expander.expand_identifiers(group['identifiers']) }}
+        {% endif %}
+
+        {% if group.get('run_regularly', None) %}
+     
+        Run regularly:
+        {% for run_reg in group['run_regularly'] %}
+        {{ expander.expand_runregularly(run_reg) }}
+        {% endfor %}
+        {% endif %}
+
+
+      

brian2tools/templates/PoissonGroup-table.md

@@ -0,0 +1,7 @@
+        | **Variable**                     | **Value**                                      |
+|---------------------------------|------------------------------------------------|
+| **Name**                        | {{ group['name'] }}                        |
+| **Population size**             | {{ group['N'] }}                           |
+| **Rate**                        | {{ expander.render_expression(group['rates']) }}     |
+| **Constants** (if present)      | {% if group.get('identifiers', None) %} {{ expander.expand_identifiers(group['identifiers']) }} {% endif %} |
+| **Run regularly** (if present)  | {% if group.get('run_regularly', None) %} {% for run_reg in group['run_regularly'] %} {{ expander.expand_runregularly(run_reg) }} {% endfor %} {% endif %} |

brian2tools/templates/PoissonInput-default.md

@@ -0,0 +1,10 @@
+{# Jinja2 template for PoissonInput in a simple text format #}
+
+PoissonInput with size {{ group['N'] }} gives input to variable {{ expander.render_expression(group['target_var']) }} with rate {{ expander.render_expression(group['rate']) }} and weight of {{ expander.render_expression(group['weight']) }}.
+
+{% if 'identifiers' in group %}
+**Constants:**
+{% for identifier, value in group['identifiers'].items() %}
+- {{ identifier }}: {{ value }}
+{% endfor %}
+{% endif %}

brian2tools/templates/PoissonInput-table.md

@@ -0,0 +1,8 @@
+{# Jinja2 template for PoissonInput in table format #}
+
+|-------------------------------|------------------------------------------------|
+| **PoissonInput Size**          | {{ group['N'] }}                              |
+| **Target Variable**            | {{ expander.render_expression(group['target_var']) }} |
+| **Rate**                       | {{ expander.render_expression(group['rate']) }}    |
+| **Weight**                     | {{ expander.render_expression(group['weight']) }}  |
+| **Constants** (if present)     | {% if 'identifiers' in group %} {% for identifier, value in group['identifiers'].items() %} {{ identifier }}: {{ value }} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |

brian2tools/templates/PopulationRateMonitor-default.md

@@ -0,0 +1,5 @@
+{# Jinja2 template for PopRateMonitor in simple text format #}
+
+Monitors the population of {{ expander.expand_SpikeSource(group['source']) }}.
+
+{{ endll }}

brian2tools/templates/PopulationRateMonitor-table.md

@@ -0,0 +1,4 @@
+{# Jinja2 template for PopRateMonitor in table format #}
+
+|-------------------------------|--------------------------------------------------|
+| **Monitored Population**      | {{ expander.expand_SpikeSource(group['source']) }} |

brian2tools/templates/SpikeGeneratorGroup-default.md

@@ -0,0 +1,18 @@
+{# Basic information about the SpikeGeneratorGroup #}
+{{ tab }}Name {{ (group['name']) }},
+with population size {{ (group['N']) }},
+has neuron{{ 's' if group['indices']|length > 1 else '' }}: 
+{{ expander.prepare_array(group['indices']) }}
+that spike at times 
+{{ expander.prepare_array(group['times']) }},
+with period {{ group['period'] }}.
+{{ endll }}
+
+{# Check for the 'run_regularly' key and expand if it exists #}
+{% if 'run_regularly' in group %}
+    {{ tab }}{{ ('Run regularly:') }}
+    {{ endll }}
+    {% for run_reg in group['run_regularly'] %}
+        {{ expander.expand_runregularly(run_reg) }}
+    {% endfor %}
+{% endif %}

brian2tools/templates/SpikeGeneratorGroup-table.md

@@ -0,0 +1,9 @@
+{# Jinja2 template for SpikeGeneratorGroup in table format #}
+
+|-------------------------------|------------------------------------------------|
+| **Name**                      | {{ group['name'] }}                           |
+| **Population Size**           | {{ group['N'] }}                              |
+| **Neurons**                   | {{ expander.prepare_array(group['indices']) }}    |
+| **Spike Times**               | {{ expander.prepare_array(group['times']) }}      |
+| **Period**                    | {{ group['period'] }}                         |
+| **Run Regularly** (if present) | {% if 'run_regularly' in group %} {% for run_reg in group['run_regularly'] %} {{ expander.expand_runregularly(run_reg) }}{% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |

brian2tools/templates/SpikeMonitor-default.md

@@ -0,0 +1 @@
+{%extends "EventMonitor-default.md" %}

brian2tools/templates/SpikeMonitor-table.md

@@ -0,0 +1 @@
+{%extends "EventMonitor-table.md" %}

brian2tools/templates/StateMonitor-default.md

@@ -0,0 +1,9 @@
+{# Jinja2 template for Statemon in simple text format #}
+Monitors variable{{ expander.check_plural(group['variables']) }}: {%- for var in group['variables'] -%}
+    {{ expander.render_expression(var) }}{%- if not loop.last -%}, {%- endif -%}
+{%- endfor %} of {{ expander.expand_SpikeSource(group['source']) }} {%- if group['record'] is boolean -%}
+    {%- if group['record'] -%} for all members {%- else -%} for no member {%- endif -%}
+{%- else -%}
+    {%- if group['record']|length == 0 -%} for no member {%- else -%} for member{{ expander.check_plural(group['record']) }}: {{ group['record'] | join(', ') }} {%- endif -%}
+{%- endif -%}
+

brian2tools/templates/StateMonitor-table.md

@@ -0,0 +1,10 @@
+| **Monitors**    | **Variables**                                                                                               | **Source**                                           | **Record**                                                                                                 |
+|-----------------|------------------------------------------------------------------------------------------------------------|-----------------------------------------------------|------------------------------------------------------------------------------------------------------------|
+| Monitors variable{{ expander.check_plural(group['variables']) }}: {%- for var in group['variables'] -%}
+    {{ expander.render_expression(var) }}{%- if not loop.last -%}, {%- endif -%}
+{%- endfor %} | of {{ expander.expand_SpikeSource(group['source']) }} | 
+    {%- if group['record'] is boolean -%}
+        {%- if group['record'] -%} for all members {%- else -%} for no member {%- endif -%}
+    {%- else -%}
+        {%- if group['record']|length == 0 -%} for no member {%- else -%} for member{{ expander.check_plural(group['record']) }}: {{ group['record'] | join(', ') }} {%- endif -%}
+    {%- endif -%} |

brian2tools/templates/Synapses-default.md

@@ -0,0 +1,31 @@
+Connections {{ group['name'] }}, connecting {{ expander.expand_SpikeSource(group['source']) }} to {{ expander.expand_SpikeSource(group['target']) }}
+{% if not expander.keep_initializer_order and 'connectors' in group and group['connectors']|length -%}
+    {{ tab }}{{ expander.expand_connector(group['connectors'][0]) }}
+{% endif %}
+{% if 'equations' in group -%}
+    {{ tab }}{{ bold('Model dynamics:') }}
+    {{ expander.expand_equations(group['equations']) }}
+    {% if 'user_method' in group -%}
+        {{ tab }}The equations are integrated with the '{{ group['user_method'] }}' method.{{ endll }}
+    {% endif %}
+{% endif %}
+{% if 'pathways' in group -%}
+    {{ expander.expand_pathways(group['pathways']) }}
+    {% if 'equations' not in group and 'identifiers' in group -%}
+        {{ tab }}, where {{ expander.expand_identifiers(group['identifiers']) }}.
+    {% endif %}
+{% endif %}
+{% if 'summed_variables' in group -%}
+    {{ tab }}{{ bold('Summed variables:') }}
+    {{ expander.expand_summed_variables(group['summed_variables']) }}
+{% endif %}
+{% if 'identifiers' in group and 'equations' in group -%}
+    {{ tab }}{{ bold('Constants:') }} {{ expander.expand_identifiers(group['identifiers']) }}
+{% endif %}
+{% if not expander.keep_initializer_order and 'initializer' in group and group['initializer']|length -%}
+    {{ tab }}{{ bold('Initial values:') }}
+    {% for initializer in group['initializer'] -%}
+        {{ tab }}* {{ expander.expand_initializer(initializer) }}
+    {% endfor %}
+{% endif %}
+

brian2tools/templates/Synapses-table.md

@@ -0,0 +1,9 @@
+|-------------------------------|------------------------------------------------|
+| **Connections**                | {{ group['name'] }}, connecting {{ expander.expand_SpikeSource(group['source']) }} to {{ expander.expand_SpikeSource(group['target']) }} |
+| **Connector** (if present)     | {% if not expander.keep_initializer_order and 'connectors' in group and group['connectors']|length %} {{ expander.expand_connector(group['connectors'][0]) }} {% endif %} |
+| **Model dynamics** (if present)| {% if 'equations' in group %} {% for key, eqn in group['equations'].items() %} $\frac{d}{d t} {{ key }}$ = {{ eqn.expr }}{% if eqn.unit %} [{{ eqn.unit }}]{% endif %} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |
+| **Integration method** (if present) | {% if 'user_method' in group %} The equations are integrated with the '{{ group['user_method'] }}' method. {% endif %} |
+| **Pathways** (if present)      | {% if 'pathways' in group %} {{ expander.expand_pathways(group['pathways']) }} {% if 'equations' not in group and 'identifiers' in group %} , where {{ expander.expand_identifiers(group['identifiers']) }}. {% endif %} {% endif %} |
+| **Summed variables** (if present) | {% if 'summed_variables' in group %} {{ expander.expand_summed_variables(group['summed_variables']) }} {% endif %} |
+| **Constants** (if present)     | {% if 'identifiers' in group and 'equations' in group %} {% for identifier, value in group['identifiers'].items() %} {{ identifier }}: {{ value }} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |
+| **Initial values** (if present) | {% if not expander.keep_initializer_order and 'initializer' in group and group['initializer']|length %} {% for initializer in group['initializer'] %} {{ initializer.variable }}: {{ initializer.value }}{% if initializer.unit %} [{{ initializer.unit }}]{% endif %} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |