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

Wrap `arb::simulation` type and interface for running `run()`, resetting `reset()`, and `set_binning_policy(policy, bin_interval)`. 

Wrap `enum binning_kind`, used to set event binning on `simulation` API.

Fixes #763 

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

Fixes #760

Wraps arbor recipe (without probes, i.e. num_probes, probe_info, get_probe) including 

- cell_connection, 
- gap_junction_connection, 
- recipe with
  - num_cells
  - cell_description
  - cell_kind
  - num_sources
  - num_targets
  - num_gap_junctions_sites
  - event_generators
  - connections_on
  - gap_junctions_on
  - global_properties
- enum cell_kind in `identifiers.cpp`

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

 + Included conversion from `pybind11::object()` to `arb::util::optional` for `arbor.proc_allocation().gpu_id` and exception handling for `arbor.context(mpi=comm)`.

+ cleaned-up `test_event_generator.py`

+ for discussion: How do we want to handle the strings? Include them in appropriate `.cpp` or collect them in `strings.c/hpp`?

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

Python 3.6 is tested (serial and mpi), in particular: 
- 3.6.3 on linux with a virtualenv, 
- 3.6.5 as downgrade from 3.7 on osx as in https://stackoverflow.com/questions/52584907/how-to-downgrade-python-from-3-7-to-3-6?rq=1 (other solutions did not work)

Fixes #715

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
```

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

First step towards the Python front end.

This commit sets up the structure of the python implementation
* directory structure
* git submodule for pybind11
* best practices for making bindings with pybind11
* unit testing for the python front end

It implements the following features in the Python front end
* execution contexts
* gpu detection
* thread count detection
* MPI initialization helpers.

Fixes #667.