Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

CMake and build refactoring

*   Use CUDA as first-class language (leading to CMake 3.9 minimum version requirement).

*   Use 'modern CMake' interface libraries for compiler options, include file and library dependency tracking. Interface library targets:
    * `arbor-deps`: compiler options and library requirements for the `libarbor.a` static library, as governed by configure-time options and environment.
    * `arbor-private-headers`: include path for non-installed headers, as required by unit tests and arbor itself.
    * `arbor-aux`: helper classes and utilities used across tests and examples.
    * `ext-json`, `ext-tclap`, `ext-tbb`, `ext-benchmark`, `ext-sphinx_rtd_theme`: externally maintained software that we include (directly or via submodule) in the `ext/` subdirectory.
 
*   Single static library `libarbor.a` includes all built-in modules and CUDA objects.

*   Simply configuration options:
    *  `ARB_WITH_TRACE`, `ARB_AUTORUN_MODCC_ON_CHANGES` `ARB_SYSTEM_TYPE` removed.
    * External `modcc` is provided by `ARB_MODCC` configuration option; if provided `modcc` is still buildable, but is not included in the default target.
    * `ARB_PRIVATE_TBBLIB`, defaulting to `OFF`, instructs the build to make TBB from the included submodule.

*   Extend `ErrorTarget` functionality to provide a dummy target or an error target based on a condition.
*   Generate header version defines and library version variables based on git status and project version, via new script `include/git-source-id`.
*   All generated binaries now placed in `bin/` subdirectory at build.
*   Install targets installs: public headers (incomplete); static library; `modcc` tool; `lmorpho` executable; `html` documentation (examples, tests and validation data are currently not installed).
*   Executable targets have had the `.exe` suffix removed; unit tests are labelled `unit` (arbor unit tests), `unit-modcc` (modcc unit tests), `unit-local` (distributed tests with local context), `unit-mpi` (distributed tests with MPI context).
*   More graceful handling of configure-time detection of `nrniv`, Julia and required Julia modules for validation data generation.
*   Add `cmake/FindJulia.cmake`, `cmake/FindTBB.cmake`  package finders, and adjust `cmake/FindUnwind.cmake` to use link library-style properties.
*  Adjust travis script to test `unit-local` and `unit-mpi` if appropriate.
*  Simply documentation `conf.py`.

Source relocation and reorganization

* All external project sources and files moved to `ext/`.
* Source code refactoring to decouple library-using code from the configure-time definitions that govern arbor behaviour: removes conditional code in public headers that depends upon `ARB_WITH_X`-type definitions at compile time. Affected code is is in the public interfaces for MPI, the threading implementation, and the profiler.
* Remove `util/debug.hpp`; split out functionality for pretty-printing from assertion handling.
* Make FVM cell non-physical voltage check a run-time cell-group parameter.
* Move spike double buffer implementation to `simulation.cpp`.
* Make timer utility wrap POSIX `clock_gettime` independent of threading configuration.
* Make `mpi_error` derive from `system_error` and follow C++11 `system_error` semantics.
* `EXPECTS` macro replaced by `arb_assert` macro.
* JSON dependency removed from `libarbor.a` and header files: moved to auxiliary library.
* Publicly visible macros garner an `ARB_` prefix as required.
* Move SWC test file to `test/unit` directory.
* Work-in-progress splitting of public from private includes: as a convention not entirely adhered to as yet, private headers within arbor source are included with `""`, public headers with `<>`.

Modcc interface changes

* Expose via `--namespace` option the functionality that sets the namespace in generated code.
* Use `--profile` option to add profiler hooks to generated code; uses public function interface directly rather than `PE/PL` macros in order to avoid public `PE` and `PL` defines.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

fixes #90

The c and cuda printer were not printing else branches in if else statements.
* added logic for printing else branches
* added if-else expressions to data/test.mod

No unit tests were added because we don't currently have a unit testing framework for the output mechanisms.

* Move generation and data to top-level validation directory.
* Make BUILD_VALIDATION_DATA and VALIDATION_DATA_DIR cache vars.
* Add helper CMake functions for data generation.

Note `validation/ref/numeric/foo.sh` is just a placeholder.

Validation of simulation results by comparing L-infinity distance and maximum peak displacement in voltage traces taken at mid-points and end-points of sections.

Note that these tests will broadly _fail_ at this point.

Reference data generation and visualization:
* Use voltage traces as validation data from NEURON; refactor generation scripts.
* Generate validation data as a dependency of `validation.exe`.
* Store validation data in a `tsplot`-compatible format.
* Extend `tsplot` to handle multiple time series per file, a non-time 'time' axis (see `-A` option), filtering of time series by meta data queries (see `-s` option).
* Remove pre-generated spike-time validation data files.

Core extensions:
* Add a single-cell `singleton_recipe` recipe wrapper.
* Allow cell descriptions to be cloned (explicitly) for use with this wrapper.
* Add `simple_sampler` which maintains a trace of scalar observables as a vector of (time, value) pairs.
* Allow cell groups to be exposed from `mode...

The resulting trees are not equivalent to the initial ones. All
offending branches were split and their non-contiguous part was moved
directly below the root.

* Clean up validation CMake
* Use configure-time path to validation data by default
* Checks in validation data
* Bring validate_synapses up to date with current source API.
* Allow -p option in validation test to point to validation
  data directory.

Whitespace-only lines are now treated correctly in SWC file parser. This
automatically leads to a consistent and nice handling of old mac-style
eol; they are just another whitespace (not newline).

Refined the test cases a bit.

Added support for mapping swc record types to nest::mc::segmentKind.
This required the adjustment in some tests + the ball_and_stick file, since
the dendrite type of swc record is type '3'. Before, everything except
soma was added (hardcoded) as a dendrite. An swc_parse_error will be
thrown in case of an impossible mapping. Also, no check is performed for
inconsistencies of SWC record types along a branch; the type of the
branch is assumed to be the type of the first record (compartment) in
the branch.

Finally, adapted to the coding style.