# Introduction

Plasticity processes are mediated by signalling ions, eg Ca++, which are generated by 
synapses upon reception of a spike. This adds a quantity `Xd` for any ion `X`
- initialised as `Xi`
- read from and written to by NMODL density and point mechanisms.
- propagates according to a diffusion law `∂_t Xd = ∂_z c X ∂_z Xd + iX/qi`.
- in contrast to `Xi` and `Xo` there's no buffering and the update in mechanisms
  occurs atomically (and at a different time)

More details can be found in the documentation.

For the future there are some low hanging optimisations
- per-ion conductivity for the matrix solver could be disabled if no diffusion is computed
- cable and diffusion solvers store duplicates of the solver state, could be merged

Closes #1651 

Introduces the new policy `round_robin_halt`. This enables to halt at the current item until the policy `round_robin` is called again.

Related to issue #1749.

Fix a number of small issues regarding performance and correctness found by PVS Studio in the quest for a better code base.

# Changes
- Bump ABI to v0.1.1
- Add `arb_mechanism` to bundle `type` and `interface`s
- Adjust `generate_catalogue` and `build_catalogue`
- Return `nullptr` for GPU interfaces if not enabled

# Open Questions
- How to tell CMake not to link against `libarbor.a` and only use headers?
- ~~How to get around `#ifdef ARB_GPU_ENABLED`~~ Update: just embrace it.

# Linked Issues
Fixes #1834 

Add tutorial on how to integrate a specific Allen Institute cell DB into Arbor. 
Use the example shown at Bernstein'20.

Add tutorial on using all logical cores on a machine, facilitated by the new flag to context creation.

Extend the probe demo example with point probes sampling the conductance of two synapses.

Co-authored-by: Brent Huisman <brenthuisman@users.noreply.github.com>

As per #1731, this PR adds a dependencies version policy to the docs. It also includes a file containing a list of all configure-time deps.

Obsoletes wiki page.

Add a first round of developer documentation, evolving from the older `internal` part of the docs.

Remove checks for move ctor when it could be elided

Add accessors for the following items in `global_properties`
- ion_species (name -> valence) RO
- ion_data (name -> initial values) RO
- ion_rev_pot (name -> rev pot mech) RO
- Vm, rL, TK, Cm: RW

Fixes: #1802 

Upstream bug: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006615



Currently affects Ubuntu 22.04 users.

Co-authored-by: Simon Frasch <simon.frasch@cscs.ch>

EOM

Ensure all indices into ABI variables are generated in dependency order, eg
```
idx = indices[iy]
foo = foos[ix]
```

Fix a crash in GPU code when threshold detector is used for the first time and its internal state is allocated with a wrong size.

- Add a callback to be executed between epochs.
- Add example: print progress indicator

TL;DR: Simple change for ~2% gain on GPU in a typical workload.

* add support for parsing markers defined in asc files
* add hitherto unknown "High" leaf branch type

Since we have support for ACC loading, the errors thrown by `paint` are no longer
sufficiently informative. Even before that it was already hard to correlate source 
and locus of painting errors.

Example
```
$> python3 main.C51A.py
Traceback (most recent call last):
  File "main.C51A.py", line 33, in <module>
    cell = A.cable_cell(morph, labels, decor)
RuntimeError: cable_cell: cable (cable 6 0 1) overpaints
```
This adds more details to the error message
```
$> python3 main.C51A.py
Traceback (most recent call last):
  File "main.C51A.py", line 33, in <module>
    cell = A.cable_cell(morph, labels, decor)
RuntimeError: cable_cell: Setting property 'ion-reversal-potential' on region '(region "soma_group")' overpaints at '(cable 6 0 1)'
```

* Make brunel.py setup faster.
* Use one generator for both populations.

filter out death test on daint single_node_release

Exports all symbols so arbor can be compiled as set of shared libraries. 

In order to export all symbols correctly, one macro per library and one global macro are added. The content of the macros is determined at configure time depending on build variant (static/shared), compiler, and platforms (linux, mac os) and goes into the library's include directory as `export.hpp` when installed (at build time it resides at cmake's temporary build directory). The per-library macro is named `ARB_LIBNAME_API` and goes in front of to-be-exported symbols. The global macro is `ARB_SYMBOL_VISIBLE`. 

This PR adds the annotation in all of the places where it is required. Most of them are in the public headers (and corresponding sources) but some are also added in internal headers, which were required for the unit tests to link properly.

Fixes #1752

Half-half dev and user docs on NMODL optimisation. Actually apply that advice in hh.mod