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

- Add (again) a reset voltage E_R that for V_m = E_R in the refractory period.
- Make V_m decay towards resting potential E_L instead of 0.
- Adjust docs and tests accordingly.
- Double check this against literature.
- Explain weight, add C++ API.

* Added fixture dev docs. Made fixtures more robust.

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

* Functionality
  * Add probes to LIF cells.
* Docs
  * Remove errorneous statement(s) about LIF cells (there never was an E_reset...)
  * Move probing chapter one level up (concepts/cable_cells -> concepts)
* Tests
  * Add tests for LIF probes

Closes #1861 
Closes #1783 

- arbor-build-catalogue (a-b-c) does no longer need to be in a fixed location
- nor do we statically fix the configuration for a-b-c
- instead, we rely on `arbor.config` to read the relevant default values
- each value can be overriden, if desired
- added many more values to the configuration
  - gpu type and arch
  - paths and prefix 
  - CXX
- report default settings for better diagnosis
- implement a fallback for prefix if that does not exist; in particular for the amazing skbuild.

In essence you can now use a-b-c as a standalone tool, as long as you have a properly 
configured py-arbor.

Example output after removing `_skbuild`
```
Warning: prefix '/Users/hater/src/arbor/_skbuild/macosx-11.0-x86_64-3.10/cmake-install' does not exist, falling back to '/Users/hater/src/arbor/.direnv/python-3.10.6'.
usage: arbor-build-catalogue catalogue_name mod_source_dir

Generate dynamic catalogue and build it into a shared object.

positional arguments:
  name              Catalogue name.
  modpfx            Directory name where *.mod files live.

options:
  --raw raw [raw ...]
                    Advanced: Raw mechanisms as C++ files. Per <name> the files <name>.hpp, <name>_cpu.cpp (if CPU
                    is enabled) must be present in the target directory and with GPU support also <name>_gpu.cpp and
                    <name>_gpu.cu.
  -v, --verbose     Verbose.
  -q, --quiet       Less output.
  --cpu CPU         Enable CPU support.
  --debug [path]    Don't clean up the generated temp cpp code. Can be a target path for the generated code.
  --gpu gpu         Enable GPU support
  --gpu-arch gpu_arch
                    Enable GPU support; default=-
  --cxx cxx         Use this C++ compiler; default=/usr/local/opt/llvm/bin/clang++.
  --prefix prefix   Arbor's install prefix; default=/Users/hater/src/arbor/.direnv/python-3.10.6.
  --bin bin         Look here for Arbor utils like modcc; relative to prefix, default=bin.
  --lib lib         Look here for Arbor's CMake config; relative to prefix, default=lib.
  --data data       Look here for Arbor supplementals like generate_catalogue; relative to prefix, default=lib
  -h, --help        Display this help and exit.
```

* build for py311
* update dependencies.csv

- Use ninja instead of make.
- Use ccache with a per-config cache key.

* Support for exporting models with parameters optimized in BluePyOpt to a mixed JSON/ACC-format that can be loaded in Arbor (with faithful axon-replacement modelling)
* A tutorial and examples on how to run simulations with such models including a neocortical layer-5 pyramidal cell exported from BluePyOpt
* Support for using Arbor as a backend for single cell optimization in BluePyOpt

Co-authored-by: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>

- GCC: goes up to 9 from 8, needed by CUDA 11
- CUDA: goes up to 11 from 10
- Clang: 10 up from 8

Closes #1815 

Add missing virtual destructors to some classes. Removes warnings and ensures correct behaviour.

- bump OpenMPI version in hope of fixing the intermittent memory corruption
- bump Ubuntu and clang versions in `sanitize.yml` workflow.

* Use HTTPS access instead of ssh/git for gtest.

* Make decor mandatory and labels optional.
* Sort morphology, decor, labels
* No more optional decor.

Fix clash betwenn Ninja build and CMake external_project

- Bump CI actions to latest (cache, checkout, cmake)
- Bump mimimal compiler versions
- Bump minimal test OS to Ubuntu 20.04 LTS
- gtest as submodule (version 1.12.1)
- fixes heap corruptions
- update gtest macros, include paths

Co-authored-by: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>

* Discuss q10 pattern in NMODL docs.

Adds the Heaviside step function to Arbor's iexpr

Co-authored-by: boeschf <48126478+boeschf@users.noreply.github.com>

1. Fix Python bindings for `recipe::update`
   - *drop* the GIL before handing off to C++
   - tighten exception safety
2. Run plasticity examples with threads; both C++ and Python.
   - C++: Guard against I/O interleaving.
   - Py: Drop spikes from source, prettify reporting.
   - C++: use decor chaining.
3. Modernise PYBIND11_OVERLOAD -> *RIDE (advised since 2.6).
4. No longer do we initialise connectivity twice.
   - Simplify communicator construction.
   - Fix unit tests that needed to two-phase init communicator.

Inline NMODL `PROCEDURE`s into their callers.

Main changes
- uncorrelated and independently distributed white noise generation for point and density mechanisms
- enabled by extending nmodl dialect and adjusting modcc (WHITE_NOISE block, stochastic solver method)
- SDEs are solved by Euler-Maruyama method (synapse collapsing disabled in this case)
- CPU and GPU backends responsible for creating random numbers using random123
- simulation takes a seed value
- bumped ABI due to addition of random numbers in ppack
Incidental changes
- builder pattern for simulation
- pimpl idiom supported by util classes

* remove storage of RHS and face-conductance in solvers
* elide copy RHS->U and RHS->Xd respectively
  -> solve will now directly mangly U and Xd
* fix tests accordingly
* Introduce wrapper macro for __restrict__ to Isolate against compiler specifics.

use std variants of sqrt and move (removes warnings, and is safer)

Fix a typo preventing the generation of GPU mechs.

* Add pybind11 version to config.
* Add version check for PB11.
* Bump CMake a tiny bit.

This is prep for meson in addition to simplifying (ie reducing) the amount of scripting
we have. In the long run, I'd like to remove `BuildModules.cmake` too, but this might
be superseded by meson and this PR is self-contained.

# Changes
- `modcc` accepts now a list of NMODL files
- likewise, `modcc` is now able to spit out a catalogue.cpp file
- remove the `generate-catalogue` script, simplify a-b-c
- remove some options from `modcc` we never use
- No longer allow external modcc

- BREAKING: Rename spike detector -> threshold detector in Python
- `spike_detector` is still around, will throw a deprecation error; will be removed 0.9
- this brings Python closer to the C++ API and removes lots of ambiguities in the docs.

* Add segment tree editing: join and split
* Add equivalence and equality on trees
* Apply isometries to trees
* Add raw loaders to NeuroLucida ASC and SWC that return segment trees instead of morphologies

Spike source cells can now generate events based on the interleaving of arbitrarily many schedules.
This should simplify the required connectivity.