From 334830ae9cf25e74c9d51018900a2d9840315dac Mon Sep 17 00:00:00 2001
From: Brent Huisman <brenthuisman@users.noreply.github.com>
Date: Tue, 6 Apr 2021 10:55:22 +0200
Subject: [PATCH] Assorted docs fixes (#1471)
* Correct the installation page.
* Custom css is not supported by theme, so a css snippet improving table formatting was moved to the theme css.
* Non cable-cell concept docs were wrong, improved formatting
* Some typos
Co-authored-by: @clinssen
---
doc/concepts/benchmark_cell.rst | 16 +------
doc/concepts/lif_cell.rst | 14 +++----
doc/concepts/spike_source_cell.rst | 17 +++++++-
doc/conf.py | 1 -
doc/install/index.rst | 10 +----
doc/python/simulation.rst | 6 +--
.../divio_docs_theme/static/css/divio.css | 12 ++++++
doc/static/custom.css | 42 -------------------
8 files changed, 41 insertions(+), 77 deletions(-)
delete mode 100644 doc/static/custom.css
diff --git a/doc/concepts/benchmark_cell.rst b/doc/concepts/benchmark_cell.rst
index 7fd13efb..b3f30750 100644
--- a/doc/concepts/benchmark_cell.rst
+++ b/doc/concepts/benchmark_cell.rst
@@ -3,20 +3,8 @@
Benchmark cells
===============
-The description of a LIF cell is used to control the leaky integrate-and-fire dynamics:
-
- * Resting potential.
- * Reset potential.
- * Initial value of membrane potential.
- * Membrane potential decaying constant.
- * Membrane capacitance.
- * Firing threshold.
- * Refractory period.
-
-The morphology of a LIF cell is automatically modelled as a single :term:`compartment <control volume>`; each cell has one built-in
-**source** and one built-in **target** which do not need to be explicitly added in the cell description.
-LIF cells do not support adding additional **sources** or **targets** to the description. They do not support
-**gap junctions**. They do not support adding density or point mechanisms.
+The description of a benchmark cell is used to determine the spiking schedule of the cell and manipulate its
+performance efficiency. This cell is mainly used by developers.
API
---
diff --git a/doc/concepts/lif_cell.rst b/doc/concepts/lif_cell.rst
index f6447cd2..e611f0ca 100644
--- a/doc/concepts/lif_cell.rst
+++ b/doc/concepts/lif_cell.rst
@@ -5,13 +5,13 @@ LIF cells
The description of a LIF cell is used to control the leaky integrate-and-fire dynamics:
- * Resting potential.
- * Reset potential.
- * Initial value of membrane potential.
- * Membrane potential decaying constant.
- * Membrane capacitance.
- * Firing threshold.
- * Refractory period.
+* Resting potential.
+* Reset potential.
+* Initial value of membrane potential.
+* Membrane potential decaying constant.
+* Membrane capacitance.
+* Firing threshold.
+* Refractory period.
The morphology of a LIF cell is automatically modelled as a single :term:`compartment <control volume>`; each cell has one built-in
**source** and one built-in **target** which do not need to be explicitly added in the cell description.
diff --git a/doc/concepts/spike_source_cell.rst b/doc/concepts/spike_source_cell.rst
index c7eca607..0cf3955b 100644
--- a/doc/concepts/spike_source_cell.rst
+++ b/doc/concepts/spike_source_cell.rst
@@ -3,8 +3,21 @@
Spike source cells
==================
-The description of a benchmark cell is used to determine the spiking schedule of the cell and manipulate its
-performance efficiency. This cell is mainly used by developers.
+Spiking cells act as spike sources from user-specified values inserted via a `schedule description`.
+They are typically used as stimuli in a network of more complex cells.
+
+A spike source cell:
+
+* has its morphology is automatically modelled as a single :term:`compartment <control volume>`;
+* has one built-in **source**, which does not need to
+ be explicitly added in the cell description;
+* has no **targets**;
+* does not support adding additional **sources** or **targets**;
+* does not support **gap junctions**;
+* does not support adding density or point mechanisms;
+* can only interact with other cells via spike exchange over a :ref:`connection <modelconnections>`
+ where they be a *source* of spikes to cells that have target sites
+ (i.e. *cable* and *lif* cells), but they can not *receive* spikes.
API
---
diff --git a/doc/conf.py b/doc/conf.py
index 41bedfaf..2a88e542 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -12,7 +12,6 @@ sys.path.append(script_path)
html_static_path = ['static']
def setup(app):
- app.add_css_file('custom.css')
app.add_object_type('generic', 'gen', 'pair: %s; generic')
app.add_object_type('label', 'lab', 'pair: %s; label')
diff --git a/doc/install/index.rst b/doc/install/index.rst
index 892fb004..6b91076c 100644
--- a/doc/install/index.rst
+++ b/doc/install/index.rst
@@ -3,16 +3,10 @@
Get Arbor
=========
-Currently we offer two ways to get Arbor.
-
-1. **Python Package**. To get started quickly with Arbor using its Python API on your personal machine, see the :ref:`Python installation guide <in_python>`.
-2. **Build and install from source**. To build and install Arbor, on your own machine or HPC environment, see :ref:`in_build_install`.
-
-If you wish to use the C++ API, you'll need to build Arbor from source. Note that you can also build the Python bindings using this method.
+To get started quickly with Arbor using its Python API on your personal machine, we advise that you install Arbor's Python package. If you wish to use the C++ API, you can use the Spack package, or build Arbor from source. Note that you can also build the Python bindings using these methods.
.. toctree::
- :maxdepth: 2
- :caption: Install Arbor:
+ :maxdepth: 1
python
spack
diff --git a/doc/python/simulation.rst b/doc/python/simulation.rst
index a5e2573f..f00b22b4 100644
--- a/doc/python/simulation.rst
+++ b/doc/python/simulation.rst
@@ -31,7 +31,7 @@ over the local and distributed hardware resources (see :ref:`pydomdec`). Then, t
# Get a description of the partition of the model over the cores.
decomp = arbor.partition_load_balance(recipe, context)
- # Instatitate the simulation.
+ # Instantiate the simulation.
sim = arbor.simulation(recipe, decomp, context)
# Run the simulation for 2000 ms with time stepping of 0.025 ms
@@ -185,7 +185,7 @@ over the local and distributed hardware resources (see :ref:`pydomdec`). Then, t
.. class:: sampling_policy
- Enumeration for deteriming sampling policy.
+ Enumeration for determining sampling policy.
.. attribute:: lax
@@ -216,7 +216,7 @@ Spikes recorded during a simulation are returned as a NumPy structured datatype
import arbor
- # Instatitate the simulation.
+ # Instantiate the simulation.
sim = arbor.simulation(recipe, decomp, context)
# Direct the simulation to record all spikes.
diff --git a/doc/scripts/divio_docs_theme/static/css/divio.css b/doc/scripts/divio_docs_theme/static/css/divio.css
index 2729786f..2548d517 100644
--- a/doc/scripts/divio_docs_theme/static/css/divio.css
+++ b/doc/scripts/divio_docs_theme/static/css/divio.css
@@ -3580,6 +3580,18 @@ input[type="radio"][disabled], input[type="checkbox"][disabled] {
.wy-table-responsive table td, .wy-table-responsive table th {
white-space: nowrap; }
+@media screen and (min-width: 767px) {
+ .wy-table-responsive table td {
+ /* !important prevents the common CSS stylesheets from overriding
+ this as on RTD they are loaded after this stylesheet */
+ white-space: normal !important;
+ }
+
+ .wy-table-responsive {
+ overflow: visible !important;
+ }
+}
+
a {
color: #0099ee;
text-decoration: none;
diff --git a/doc/static/custom.css b/doc/static/custom.css
deleted file mode 100644
index 2430843e..00000000
--- a/doc/static/custom.css
+++ /dev/null
@@ -1,42 +0,0 @@
-.example-code>div[class^='highlight']:before {
- font-weight: bold;
- display: block;
- padding-bottom: 2pt;
- padding-left: 3pt;
- content: "Example";
- background: #6ab0de;
- color: #ffffff;
-}
-
-.api-code>div[class^='highlight']:before {
- font-weight: bold;
- display: block;
- padding-bottom: 2pt;
- padding-left: 3pt;
- content: "API";
- background: #e0e0e0;
-}
-
-.api-code>div[class^='highlight'] {
- background: #f4f4f4;
-}
-
-li>p:last-child {
- padding-bottom: 2ex;
-}
-
-table.docutils td {
- vertical-align: top !important;
-}
-
-em {
- font-style: bold;
- color: #000099;
-}
-
-@media screen and (min-width: 40em) {
- .wy-table-responsive table td,
- .wy-table-responsive table th {
- white-space: normal;
- }
-}
--
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