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fixed typo and code style #2344

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merged 6 commits into from
Aug 8, 2024
Merged

fixed typo and code style #2344

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04b25f5
fixed typo and code style
ErbB4 Jul 31, 2024
2f53650
Update decor.rst
ErbB4 Aug 1, 2024
282d406
fixed unit
ErbB4 Aug 1, 2024
4b20500
Update doc/python/decor.rst
ErbB4 Aug 8, 2024
e123122
updated unit as requested
ErbB4 Aug 8, 2024
eabab9e
Update decor.rst
ErbB4 Aug 8, 2024
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16 changes: 9 additions & 7 deletions doc/python/decor.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ Cable cell decoration

.. py:class:: decor

A decor object contains a description of the cell dynamics, to be applied
A decor object contains a description of the cell dynamics to be applied
to a morphology when used to instantiate a :py:class:`cable_cell`

.. method:: __init__()
Expand Down Expand Up @@ -35,9 +35,10 @@ Cable cell decoration

.. code-block:: Python

import arbor as A
# Set cell-wide values for properties for resistivity and capacitance
decor = arbor.decor()
decor.set_property(rL=100, cm=0.1)
decor = A.decor()
decor.set_property(rL=100 [unit], cm=0.1[unit])
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Hi,

the units are explained here

arbor/python/cells.cpp

Line 626 in 7d20a79

.def("set_property",

in the code. Note, however, that only the dimension needs to match, not the scale.
So, you could happily pass kOhm to any resistance-type argument and Arbor will
scale it properly.

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I did mean to say that you could find the units there, not that they aren't needed

             " * Vm:    initial membrane voltage [mV].\n"
             " * cm:    membrane capacitance [F/m²].\n"
             " * rL:    axial resistivity [Ω·cm].\n"
             " * tempK: temperature [Kelvin].\n"


.. method:: set_ion(ion, int_con=None, ext_con=None, rev_pot=None, method=None)

Expand All @@ -60,8 +61,9 @@ Cable cell decoration

.. code-block:: Python

import arbor as A
# Set nernst reversal potential method for calcium.
ca_mech = arbor.mechanism('nernst/x=ca')
ca_mech = A.mechanism('nernst/x=ca')
decor.set_ion('ca', method=ca_mech)

# Set reversal potential and concentration for sodium.
Expand All @@ -74,7 +76,7 @@ Cable cell decoration
.. method:: paint(region, Vm=None, cm=None, rL=None, tempK=None)

Set cable properties on a region. A property ``v`` is given as a float
or a string. In the latter ``v`` will be interpreted as an inhomogeneous
or a string. In the latter, ``v`` will be interpreted as an inhomogeneous
expression.

:param str region: description of the region.
Expand Down Expand Up @@ -103,7 +105,7 @@ Cable cell decoration
:noindex:

Set ion species properties initial conditions on a region. A property
``v`` is given as a float or a string. In the latter ``v`` will be
``v`` is given as a float or a string. In the latter, ``v`` will be
interpreted as an inhomogeneous expression.

:param str name: name of the ion species.
Expand Down Expand Up @@ -141,7 +143,7 @@ Cable cell decoration

Place one instance of the gap junction mechanism described by ``junction`` at each location in ``locations``
and label the group of gap junction sites with ``label``. The label can be used to form gap junction
connections to/from one of labeled sites in the :py:class:`arbor.recipe` by creating a
connections to/from one of the labeled sites in the :py:class:`arbor.recipe` by creating a
:py:class:`arbor.gap_junction_connection`.

:param str locations: description of the locset.
Expand Down