* Collect cable cell parameter setting structures into `include/cable_cell_param.hpp`.
* Restructure electrical specifications (axial resistance, membrane capacitance) and ionic concentrations and reversal potentials on cable cells, so that these can be specified with a global default, per-cell defaults, and per-segment values.
* Allow reversal potentials to be set by a mechanism of a new kind 'revpot', which are prohibited from maintaining state or writing to any shared state other than ionic reversal potentials.
* Specify reversal potential mechanisms as global defaults or per-cell. Reversal potential mechanisms may not be specified at the level of a segment in order to avoid non-linearities arising from the discretization.
* Supply default cable cell parameter data that matches NEURON values (this is _not_ used by default).
* Replace the d_lambda calculation with one that approximates more faithfully the effect of tapered segments, and which will use the electrical values inherited by cell or global defaults.
* Supply a bundled mechanism 'nernst' that replaces the previous hard-coded Nernst potential calculation, for use (together with ion rebinding) in the new ion description scheme.
* All ions used in a cable_cell model must be present in the top level global parameter table, together with their charge.
* Extend semantics of external variables in modcc, to permit direct assignment (as opposed to just += or -=.)
* Extend `util::binary_search_index` to allow for a projection functional analagous to other range utilites.
* Add documentation on the cable cell API, sketching over many of the details, but describing in particular the interface changes for default parameters and reversal potential behaviour.
* Adjust pyarb for new API
* Hard code global cable cell properties in the python recipe shim to useneuron default parameters.

Addresses issues #814 and #815.
* Change the discretization so that a spherical soma comprises its own CV.
* Modify the `div_compartment_integrator` to accommodate the single CV soma, adjusting the discretization of the most proximal branches, adding a half-size CV attached to the soma, so as to leave the remainder of the discretization the same.
* Rename the confusing `ncomp` to `ncv` inside the discretization code.

Implement implicit derivation of mechanisms.

* When a mechanism of the form "foo/param=value,..." or "foo/newion" is
requested from a mechanism catalogue, attempt to perform a derive the
information or override set from the mechanism "foo" using the given
global parameter settings and/or ion remappings given in the name.
* Split mechanism catalogue implementation into a private catalogue
state with non-throwing behaviour and without any implicit mutation,
with mechanism_catalogue methods responsible for throwing any generated
errors, with the aim of avoiding throw/catch in expected program flow.

Implements #807.

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

* correct doc for meter_report and small word fixes
* shift make_report to next section

Remove the dead `cell_connection_shim` from the python wrapper.

Fix the connection printer to take an `arb::cell_connection` argument, to fix a runtime python crash caused by passing an `arb::cell_connection` where a `cell_connection_shim` was expected.

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

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

Add docs for Python wrapper to ReadTheDocs:

- Overview, Common Types, Hardware Management, Recipes, Domain Decomposition, Simulations, Metering
- Installing Arbor: Optional Requirements (Python), Buidling and Installing (Python Frontend), and Installation (Python Module)

Missing (, since not implemented yet): 

- probes
- arbor-sup 
- hint maps in domain_decomposition
- reset, events, empty schedule in event_generator
Also does not cover unit testing (since doc is user-centric).

Makes also defaults and units in wrapper consistent.

Fixes  #766

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Add missing check of whether to use direct or indirect indexing for simd procedure calls.

fixes #804

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

Address inconsistencies in unit conversions between current updates, initialization, ionic currents etc.

Fixes issues #793 and #798.

* Correct units in comments for ion state iX_ to a current density.
* Remove conversion factor for NMODL current densities [mA/cm²] to Arbor current densities [A/m²] from layout weight: from the point of view of Arbor, mechanisms now write in units that Arbor uses natively.
* Remove weight_ as a magic modcc variable; applying weight_ is now performed directly by code generated by printers.
* Change IndexedVariable interface: remove redundant index_name; remove 'op'. Whether external data is accumulated or assigned is now a property of the corresponding sourceKind.
* Conversion factors for NMODL <-> Arbor are collated in printerutils.cpp, determined by the external data sourceKind.
* Permit direct assignment of external data, as opposed to a weighted sum. This behaviour will be required for reversal potential handling...

* Add `::arb::` decoration to `fvm_value_type` and `fvm_index_type` in modcc simd cprinter output.
* Return stream from unwind stack trace printer.

Fixes #801 and also a long standing (but low impact) bug in unwind code.

* Correctly decorate required names from arb:: namespace.
* Put the unit test mechanisms in the 'testing::' namespace, to exercise this functionality.

Building validation data with python2 can raise an import error for `builtins`.

* Catch import error, and import from `__builtin__` instead.

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 

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Make global parameters and ion rebindings part of the instantiate interface, rather than insist that all concrete mechanisms implement these as methods.
* Mechanism catalogue instance() returns a pair, comprising the concrete mechanism for the requested backend, together with the override data.
* Extend catalgoue derive() method to take a list of old ion name -> new ion name remappings for a mechanism.
* Add exceptions for ion remapping errors, and check for these errors.
* Add convenience function for reparameterizing a mechanism with a single ion dependency over other ions. (This will be used for the future nernst pre-supplied mechanism.)
* Add unit tests for: chained renamings of ion names across multiple derivations; correct shared state ion assignment after renamings; ion remapping exceptions; parameterize_over_ion.

Eric Müller authored 5 years ago and Benjamin Cumming committed 5 years ago

* cmake/FindUnwind.cmake used the wrong variable (caused by commit ad1c78ab)
* CMakeLists.txt seems to use wrong syntax for providing a compiler define
  of `WITH_UNWIND` (used in `arbor/util/unwind.cpp`)

Fixes #782 
* consistent formatting of strings returned by `__repr__` and `__str__` for wrapped types
* rename enum wrappers to be less verbose, where it makes sense.

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 

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

Extended USEION VALENCE support.

* Augment modcc parser to accept identifier or signed integer after VALENCE.
* Treat identifer after VALENCE as global scalar, tied to ionic charge.
* Add ionic charge field to mechanism ion parameter pointers, replacing scalar in shared state with a length-1 array.
* Verify presence of ion name and check ion charge against numeric valence in mechanism info when discretizing in `fvm_build_mechanism_data`.
* Pass ion info, coalesce_synapse global state to `fvm_build_mechanism_data` just via cable cell global properties.
* Add more unit-test only mechanisms (test_ca_read_valence, test_cl_valence).
* Add unit tests for valence verification and reading into mechanism state (multicore only).
* Update existing unit tests for new interfaces.

Implements #780.

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Change occurances of 'ionKind' to corresponding string values in test_parser.cpp.
* Add unit-modcc to travis script.

Fixes #775.

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

clean up stringification in python wrappers

move python wrapper for schedules to their own files

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`

Addresses #757.

* Check if the multiplicity vector is empty before trying to use its contents. 
* Add unit test to catch the problem

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

Fix a memory error triggered on the GPU when assertions were enabled. An assertion was testing a value in shared memory, that should have been stored in host memory.

Python: mpi4py communicators as first class citizens

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Replace ionKind enumerations with corresponding string values.
* Rename `ion.hpp` as `ion_info.hpp`.
* Re-jig 'nonspecific' current handling in modcc: make explicit the external source of the corresponding current variable, and treat as non-indexed those locals with an external variable that has no data source, as opposed to special-casing the `ionKind::nonspecific` value.
* Add another field in ion dependency information that captures a write to an ionic reversal potential.

Fixes #748.

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`?

Fixes #746.

* Make `one_probe` an `inline` function rather than `static inline` in order to work around a linker issue (see issue #746).

* Fixes segmentation faults; output compiler errors instead.
* Consume units if provided in function/procedure prototypes or after function prototype.
* Consume UNITSON/UNITSOFF.
* Consume and store VALENCE as an ion property.

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

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

Changes implicit solve step from:
> solve (c/δt + L) v' = c/δt v - J

to
> solve (c/δt + g + L)v' = (c/δt +g) v - J

where _c_ is capacitance, _g_ is membrane conductance, _J_ is membrane current.

* Compute conductivity contribution for mechanisms from symbolic d/dv of current contribution (extracted from linearity test.)
* Add new modcc 'source kind' for conductivity; tie to `vec_g_`.
* Add conductivity field to fvm shared state.
* Include conductivity in matrix assemblies for solution.

Fixes #633.

Add citation information to the readme.