* Add find_private_gpu and arbor.env.

- Add stacktraces to
   1. arbor_exception (and all derived) as `where`
   2. arbor_internal_error as `where`
   3. arb_assert
- Propagate stacktraces to Python exceptions derived from the above.
- Expand dev/doc on debugging

* Pyarb specific.
* `proc_allocation_shim()` throws error if user sets threads to zero.
* `arbor.context` constructor accepts `threads` set to `"avail_threads"`, which sets the number of threads to `arbenv::thread_concurrency()`
  * This introduces a dependency on arbenv for Pyarb.
* Docs and tests added.

Fixes #1692 

* Add platform abstraction for loading DLL/SOs.
* Throw more informative exceptions when handling DLL/SOs.
* More informative errors when dealing with dynamically loaded catalogues.
* Translate `arb::file_not_found_error` to `FileNotFoundError` in Python.

* Sort collected spikes in Python API lfirst by time, then gid, then lid.
* Remove redundant old spike handling code from Python lib.

* Implements parsers and writers in `arborio` for the s-expression based Arbor Cable-Cell Format defined in #1336.
* Moves `s_expr.hpp` to the public interface.
* Adds python wrappers to support the features in pyarb.  
* Adds unit tests.
* Adds docs.

Fixes #1336
Partially addresses #1233

Make the `cable_cell` interface read only by passing the decorations
to its constructor in a new `decor` type.

C++ library
* Remove the paint/place/set_default interface from `cable_cell`
* Create a `decor` type that:
  * stores lists of paintings and placings
  * stores a set of cable cell parameters
  * uses the `paint`, `place`, `set_default` interface that was deprecated
    from `cable_cell`.
* Create `paintable`, `placeable` and `defaultable` variants that are sum types
  over the respective types that can be painted, placed and defaulted.
* Remove the overloaded `cable_cell::paint`, `cable_cell::place`,
  `cable_cell::set_default` methods to single methods that consume the sum types.

Unit Tests
* Many small changes because many many tests use cable cell API.
* There were no `cable_cell` unit tests! Not such a big deal, since cable_cell
  is tested implicitly in so many other tests
  * but I added cable_cell tests: not much at the moment but will quickly fill
    up as we work on reading, writing, etc.                                                            

Python
* Wrap the new decor type.
* Update cable cell type to reflect read only API.
* Wrap the cv_policy types and implement the same operator overloading.

Major changes in Python library and documentation:

* Add global state (immutable after initialization) for the Python module that
  manages the mapping between probe metadata types and the method by which the
  corresponding [sample data can be collected and presented as Python objects.
  This is necessary for decoupling the implementation of the simulation wrapper
  from that of the various cable cell probe types.

* Wrap each of the C++ cable cell probe types with a Python function that
  returns a `probe_info` object.

* Add code for converting and accumulating C++ probe metadata and sample
  data, registered in the module global state against the metadata type info.

* Make the `arbor.simulator` object responsible for recording all spike and
  sample data, with corresponding new methods.

* Use NumPy arrays and structured datatypes for returning spike and
  sample data.

* Place Python schedule proxies under an abstract interface so that consumers
  of the proxies can be made generic over schedule types.

* Add unit tests for the `arbor.simulator` class and its new functionality,
  including distributed spike collection.

* Rework all Python API documentation concerning probes, sampling, and spike
  recording; add information on newly exposed cable cell probe addresses.

* Add new python example `single_cell_recipe.py` which is a generic recipe
  version of `single_cell_model.py`.

* Adjust other code in the wrapper and examples to accommodate these changes.

Minor changes in Python library:

* Add equality tests for `arbor.location` and `arbor.cable` Python classes.

* Use the `py::` namespace shorthand more often in the Python wrapping sources.

* Add an implicit conversion for a pair of numbers to `arbor.cell_member`, so
  that e.g. probe ids can be specified simply as `(gid, index)`.

* Add an implicit conversion from a tuple to `arbor.mpoint` so that a
  morphological point can be specified simply as `(x, y, z, radius)`.

* Modify the interface to `arbor.regular_schedule` so that the overloads
  correspond more closely to the C++ API. In particular,
  `arbor.regular_schedule(dt)` now describes a schedule with times 0, dt, 2*dt,
  etc.

Minor changes in C++ library:

* Change test in FVM lowered cell implementation and exception message for
  `bad_source_description`: assert number of detectors is exactly the number
  of sources promised by the recipe.

* Add comment describing `probe_metadata` object in `sampling.hpp` which
  asserts that the type and value of probe-specific metadata completely
  determines the correct interpretation of sampled data provided to a callback.

Update core library:
* support derivation of named mechanisms in catalogue from a string description of the parent.
* fix bug in radois_ge region expression that was finding region_lt.
* fix test for radius_ge region expression

Add support for mechanism, global properties and catalogue shenanigans to python wrapper

Improve the Python wrapper generation and installation:
  - install a proper module that can be extended with Python code;
  - give the user more control over where to install the module (e.g. as a user package or in a virtualenv).

During building, the following sub-directory is built in the build director (`CMAKE_BINARY_DIR`)
```
└── python
    └── arbor
            ├── __init__.py
            ├── arbor.so
            └── VERSION
```
This path can then be copied VERBATIM to the target installation path. By default this will be in `CMAKE_INSTALL_PREFIX/lib/python%d.%d/site-packages`.
An additional CMake parameter `ARB_PYTHON_PREFIX` can be used to specify an alternative destination for installing the Python module.

The Python part of the wrapper, implemented in `__init__.py` is currently very limited, only providing `__version__` and `__config__` variables.

The installation guide was updated to cover the Python installation.

A big update that wraps over 90% of the public C++ API, with enough functionality to let Python users to perform useful modelling.

Key features
- wrapping of cable cell functionality
  - user-defined explicit compartmentalisation not supported
- `single_cell_model` abstraction unique to the Python wrapper that simplifies developing and testing single cell models
- one-dimensional cell builder for Python wrapper that simplfies building cells that 
  - in and of itself limited in scope, but a very useful example of mapping a richer morphology builder onto `sample_tree`s.
- parsing of region and location expressions from strings
  - implements a generic s-expression parser that we can use for other purposes later

Adds

* to `recipe.cpp`: 
`num_probes` and `get_probe` with helper function `cable_probe(kind, id, location)`
* `sample.cpp`: 
`sample` type with attributes `time` and `value`; a `sampler` with `samples()` and `clear()` and helper functions `attach_sampler(sim, dt)` for adding all probes as well as `attach_sampler(sim, dt, probe_id)` for adding one probe
* `morphology.cpp`: 
`location` as `arb::mlocation` with `branch` and `position` 
* corresponding docs and example
* update to new cable cell semantics in c++ validation test

fixes #762

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

Wraps the `meter_manager` with
- the constructor
- `start(ctx)`
- `checkpoint(name, ctx)`
- `checkpoint_names`
- `times`

and the `meter_report` with
- `make_meter_report(meter_manager, ctx)`

Fixes #765

Support for recording spikes generated by a simulation in the Python wrapper
* Implement a `spike_recorder` that holds a shared pointer to a `std::vector` of spikes, and a callback for the `arb::simulation` spike recording API.
* Add `python/example/ring.py` that creates a ring network, then records and prints spikes.
* Some fixes to get the full `recipe` -> `domain_decomposition` -> `simulation` -> `spikes` workflow to work
  * always use default `global_parameters`: user customization of global parameters for cable cells can wait until the ion species interface is finished.
  * change the Python recipe interface for `recipe::connections_on` to use `pybind11::objects` because of shim.
* Some small improvements to error and help messages.

Fixes #764 

Add full wrappers for

- `lif_cell`
- `spike_source_cell`
- `benchmark_cell

And an opaque wrapper for cable_cell with a helper function that generates a random morphology identical to the ones in the nsuite benchmarks.

Fixes #767.

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

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
```

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.