Update CMake configure to look for svgwrite when building docs.

Fixes #1128.

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.

In some places our CMake scripts were attempting to check out git submodules when required, if they have not already been checked out. The code that does this was cut and pasted, and was getting unwieldy.

To minimise the responsibilities of CMake, this PR

removes calls to git
introduces a function check_git_submodule that can be used to test if a git submodule is installed, and print a helpful message that informs the user how to check it out if needed.
introduces a function add_error_target that makes a target that prints a message then quits with an error. This can be used to generate a proxy target when a problem is detected during CMake setup. This means that an error is only generated when building a target with a missing dependency, instead of an error during CMake setup.
refactors the CMake setup for the docs and ubenches targets to use these new features.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

Adds support for building documentation with Sphinx from reStructuredText-formatted files in the `doc` subdirectory. Automatic building has been verified with ReadTheDocs.

* Add basic documentation to the `doc` path.
* Use a git submodule and associated CMake to pull in ReadTheDocs theme at configuration time.