[DATALAD RUNCMD] Do interactive fixing of some ambigous typos

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w -i 3 -C 2",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

scripts/lems/sourceannotations.xml

@@ -213,7 +213,7 @@ An optional description of the ComponentReference        </Property>
         <Property name="name" type="String"/>
     </ElementType>
     <ElementType name="Collection" section="componenttypes">
-        <Info>Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree.</Info>
+        <Info>Specifies that instances of components based on this class can contain a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree.</Info>
         <Property name="name" type="String"/>
     </ElementType>
     <ElementType name="PairCollection" section="componenttypes">
@@ -319,7 +319,7 @@ The dimension, or 'none'. This should be the name of an already defined dimensio
         <Property name="description" type="String">
 An optional description of the derived variable        </Property>
         <Property name="reduce" type="String">
-Either 'add' or 'multiply'. This applies if ther are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error.        </Property>
+Either 'add' or 'multiply'. This applies if there are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error.        </Property>
         <Property name="exposure" type="String"/>
         <Property name="required" type="boolean">
 Set to true if it OK for this variable to be absent. See 'reduce' for what happens in this case        </Property>
@@ -358,7 +358,7 @@ Name of state variable in state elements        </Property>
         <Property name="edgeSource" type="String">
 The name of the attribute in the rate element that defines the source of the transition        </Property>
         <Property name="edgeTarget" type="String">
-Attribute tha defines the target        </Property>
+Attribute that defines the target        </Property>
         <Property name="forwardRate" type="String">
 Name of forward rate exposure        </Property>
         <Property name="reverseRate" type="String">

scripts/schemas/asttemplates.py

@@ -387,12 +387,12 @@ def format_math(expr):
 dynamics = env.from_string(textwrap.dedent(
     """
     ````{tab-item} {{ title }}
-    {% if comp_type.structure  and (comp_type.structure.withs|length +
+    {% if comp_type.structure  and (comp_type.structure.widths|length +
     comp_type.structure.child_instances|length +
     comp_type.structure.multi_instantiates|length +
     comp_type.structure.event_connections|length) > 0 %}
     <i>**Structure**</i>
-    {%- for w in comp_type.structure.withs %}
+    {%- for w in comp_type.structure.widths %}
     : WITH **{{ w.instance }}** AS **{{ w.as_ }}**
     {%- endfor -%}
     {% for ci in comp_type.structure.child_instances %}

source/Events/2012-Edinburgh.md

@@ -207,7 +207,7 @@ Chair: Michael Hines
 * - 11:00
   - **The OpenWorm project: Using NeuroML in a highly detailed model of C. elegans ([PPT](https://docs.neuroml.org/_static/NeuroML2012/Open_Worm_03-13-12.ppt))**
 
-    Stephen presented the OpenWorm project. This ambitious project aims to build an in silico model of C. elegans. This well studied system with ~1000 cells and 302 identified neurons is an ideal system with which to attempt a full simulation of a living organism down to cellular scale. Many different approaches are being take in the project at the moment, including investigatin Smoothed Particle Hydrodynamics (SHP) to allow simulation of the interaction of the worm with its environment, and creating a new parallel (GPU based) simulator in Java which will support physical and electrical simulations. Full reconstructions of all of the cells are available in 3D and those of the neurons have been converted to NeuroML, which will form the basis of a simulation of the worm's nervous system.
+    Stephen presented the OpenWorm project. This ambitious project aims to build an in silico model of C. elegans. This well studied system with ~1000 cells and 302 identified neurons is an ideal system with which to attempt a full simulation of a living organism down to cellular scale. Many different approaches are being take in the project at the moment, including investigating Smoothed Particle Hydrodynamics (SHP) to allow simulation of the interaction of the worm with its environment, and creating a new parallel (GPU based) simulator in Java which will support physical and electrical simulations. Full reconstructions of all of the cells are available in 3D and those of the neurons have been converted to NeuroML, which will form the basis of a simulation of the worm's nervous system.
 
     One of the concrete outcomes of code sprinting work on the fringes of the NeuroML/CodeJam meeting was the updated OpenWorm Browser, where the full cellular structure of the worm can be browsed in 3D.
 

source/Userdocs/ConvertingModels.md

@@ -138,7 +138,7 @@ export_to_neuroml2("test.hoc", "test.morphonly.cell.nml", includeBiophysicalProp
 
 Alternatively manually add the `<channelDensity>` elements to the cell file (as [here](https://github.com/OpenSourceBrain/SmithEtAl2013-L23DendriticSpikes/blob/master/NeuroML2/L23_NoHotSpot.cell.nml#L16711)).
 
-You can use the tools for {ref}`visualising NeuroML Models <userdocs:visualising_models>` to compare how these versions look agains the originals.
+You can use the tools for {ref}`visualising NeuroML Models <userdocs:visualising_models>` to compare how these versions look against the originals.
 
 As with the single compartment example, it's best to **start off with the passive case**, i.e no active channels on the soma or dendrites, and compare that to the original code (for membrane potential at multiple locations!), and gradually add channels.
 

source/Userdocs/LEMSExample1.md

@@ -294,7 +294,7 @@ Although the channel models have now been defined, they still need to be used in
 For this we'll just define a basic channel population type.
 There is one new construct here: the ComponentRef element which in this case says that a channel population needs a reference to a component of type HHChannel. This is much like a Child element, but instead of the component being defined then and there inside the channel population, there is just a reference to it.
 
-The Dynamics block for a cannel population just computes the total conductance and then the current, in this case using Ohm's law.
+The Dynamics block for a channel population just computes the total conductance and then the current, in this case using Ohm's law.
 
 ```{code-block} xml
 <ComponentType name="ChannelPopulation">     

source/Userdocs/LEMS_elements/Definingcomponenttypes.md

@@ -697,7 +697,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c
 (lemsschema:collection_)=
 ## Collection
 
-<i>Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree.</i>
+<i>Specifies that instances of components based on this class can contain a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree.</i>
 
 `````{tab-set}
 ````{tab-item} Properties

source/Userdocs/LEMS_elements/Dynamics.md

@@ -267,7 +267,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c
 **select**$ String$ A path to the variable that supplies the value. Note that to select a variable from another component, the variable must be marked as an Exposure. Exactly one of 'select' and 'value' is required
 **dimension**$ String$ The dimension, or 'none'. This should be the name of an already defined dimension element
 **description**$ String$ An optional description of the derived variable
-**reduce**$ String$ Either 'add' or 'multiply'. This applies if ther are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error.
+**reduce**$ String$ Either 'add' or 'multiply'. This applies if there are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error.
 **exposure**$ String$ 
 **required**$ boolean$ Set to true if it OK for this variable to be absent. See 'reduce' for what happens in this case
 **value**$ String$ A string defining the value of the element
@@ -553,7 +553,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c
 **edges**$ String$ The element that provides the transitions for the scheme
 **stateVariable**$ String$ Name of state variable in state elements
 **edgeSource**$ String$ The name of the attribute in the rate element that defines the source of the transition
-**edgeTarget**$ String$ Attribute tha defines the target
+**edgeTarget**$ String$ Attribute that defines the target
 **forwardRate**$ String$ Name of forward rate exposure
 **reverseRate**$ String$ Name of reverse rate exposure