Switch XML parser to pugixml; one less runtime dependency and one less blocker to WASM via emscripten.

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.
```

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

- build-catalogue
  - now installed by pip
  - enable GPU-backends
  - isolate from being installed in a non-default dir
  - rename to arbor-build-catalogue
  - allow hand-written C++ mechanisms to be linked in the same catalogue.
- CMake
  - enable PIC on arbor always to allow linking to shared objects
  - use relative paths when configuring a-b-c, to make relocation less of a problem
- Python
    - ensure a-b-c is installed by pip, along with headers and libarbor.a
    - throw errors if tools (cmake scripts, arbor package, modcc) missing
    - transition setup.py setuptools -> skbuild.
- Wheels
    - Add NML2 support to wheels
    - scripts/build-wheels.sh builds wheels, in principle valid for submission to PyPI, on your own hardware. This should be kept in sync with .github/workflows/ciwheel.yml
    - scripts/patchwheel.py corrects the rpath in the libraries in the wheels, working around a bad interplay between auditwheel and skbuild, see pypa/auditwheel#363
    - Python Wheels are tested as part of the Github Action 
    - Add nml and bundled status to config().

Adds the `profiler_initialize(ctx)` and `profiler_summary()` functions to the Python module and the `profiling` key to `arbor.config()`. closes #1685.

* Add VECTORIZE configuration feature macro to config, record in python lib.
* Add  ARB_ARCH configuration string as preprocessor define and character string in config and version info respectively.

akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

- wraps `partition_hint` struct for python
- `partition_hint`struct in `load_balance.hpp` is adjusted in a way that in case of zero unsigned int `cpu_group_size`/`gpu_group_size` it is set to the default value (via setter/getter)
- adds documentation for `partition_hint`  
- adds testing for `domain_decomposition` including `partition_hint` (in unit and unit_distributed)
- adds `partition_hint` in example `ring.py`
- corrects `config.cpp` (and doc) to test for `ARB_GPU_ENABLED` instead of `ARB_WITH_GPU`

Fixes #776 
Addresses #799, #769

akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

Domain decomposition in python wrapper
* functions: `partition_load_balance`
*  types: `group_description` and `domain_decomposition`

Also includes
* remove comment that `gid` in a `group_description` must be sorted.
* a host of small clean ups of python wrapper

Fixes #761

akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

Wrapped the following C++ features in Python: 
- Identifiers (`cell_member`) + according tests
- `event_generator` and schedules (`regular_schedule`, `explicit_schedule`, `poisson_schedule`) + according tests

akuesters authored 6 years ago and Benjamin Cumming committed 6 years ago

Remove old code and comments from Python config code.

akuesters authored 6 years ago and Benjamin Cumming committed 6 years ago

Fixes #700

Usage in python as: 

```
>>>import arbor
>>>arbor.config()
{'mpi': True, 'mpi4py': True, 'gpu': False, 'version': '0.1.1-dev'}
>>>d = arbor.config()
>>>arbor.print_config(d)
Arbor's configuration:
     mpi    :       True
     mpi4py :       True
     gpu    :      False
     version:  0.1.1-dev
```