* Python examples: Updated to use region expressions (quotes)
* Python examples: Uniform plotting
* Python examples: Removed tutorial directory (example roughly matches python/example/single_cell_model.py)
* Python examples: Rewrote flat_cell_builder() to segment_tree()

* Update `dryrun` to generate some spikes again, add a voltage printer.
* Fix `ring.py` recipe.
* Fix labels in `single_cell_builder.py` and `single_cell_swc.py`.

* Move label and s-expr parsing code and unit tests from Python to arbor C++ library.
* Update `locset` and `region` constructors that take string arguments to parse strings as s-expressions or "quoted" labels.
* Modify the input stream modifier used to parse asc files to use a lookup table for substitutions, renamed it transmogrifier.                                                             
* Replace `hopefully` type implemented in python headers with an `arb::util::expected`.
* Add `ARBDEV_COLOR` CMake option that forces gcc and clang to always output color output.
* Allow arbitrary strings in labels in region and locset expressions.
* Add `parse_region_expression` and `parse_locset_expression` functions alongside the existing `parse_label_expression` function for use when a region or locset is expected. These calls will promote a quoted string `"label"` to `(region "label")` or 
 `(locset "label")` respectively.
* Add user-defined string literals for labels so that the C++ interface can use `"soma"_lab` instead of awkward escaping `"\"soma\""`.
* Simplify Python wrapper code.

Fix a Python example that was out of date.

* Remove spherical root/soma from morphology representations and logic.
* Replace `sample_tree` with `segment_tree`, which represents sample points in pairs and allows the representation of detached branches and cable segments.
* Remove sample point properties and predicates.
* Remove `cv_policy_flag::single_root_cv` as somata with a single attached dendrite will have a representation in the morphology of a single branch.
* Remove `arb::math::{volume/area}_sphere`, which are no longer being used.
* Remove spherical root special cases from `embed_pwlin` and `place_pwlin` objects.
* Add textual representation of `mnpos` in morphology exception text.
* Rename `sample_tree_from_swc` to `segement_tree_from_swc` and remove any special casing for one point somata.
* Remove `msample` and `mbranch` types.
* Update unit tests and python wrapper to reflect the changes.

Add `cable_cell::concrete_region(region)` method that returns a the cable segments in a region.

This is required by the Arbor GUI #953 so that it can illustrate regions (and locsets) defined by users on a concrete cell morphology.

Note that the `concrete_region` and `concrete_locset` interfaces will need to be extended with random number seed information when we add full support for that, but shouldn't need to be replaced or changed otherwise.

Fixes #960.

Use locset names to set probe sites in single cell model.

1. Extend C++ cable_cell interface to provide a concrete list of locations associated with a locset on the cell.
2. Extend Python single_cell_model to allow placement of probes on locsets.
3. Remove "debug" output in Python ring example.

The single cell model maintains a trace callback for each probe location, and needs to know the explicit locations before starting the simulation. The first step is required to enumerate and record the locations associated with a locset when attaching probes.

Open issues: 

1. The extension to `cable_cell` won't sufficiently support locsets that rely on random number generators with global seeds (it would require passing additional meta data required to fully instantiate the locset)
2. Enhancing the probe recipe interface to be able to associate one `probe_id` with all locations in a locset (the number of which is not specified at the time the `probe_id` is created) would support the interface implemented for the `single_cell_model`.

Note: The richer interface on the C++ side will be implemented in time (see #957).

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 `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

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

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