* Correct the installation page.
* Custom css is not supported by theme, so a css snippet improving table formatting was moved to the theme css.
* Non cable-cell concept docs were wrong, improved formatting
* Some typos

Co-authored-by: @clinssen 

`/doc/scripts/divio_docs_theme` has the contents of the tarball from PyPI, slightly modified (custom fonts removed, font-awesome reduced to woff2, logo enabled, divio banner/analytics removed.).

* Sync Cable Cell page names and ordering between sections (concept, python, cpp). Except cpp cable cell page. Is still one big page.
* Move CV definition across categories to consistent location.
* Move decor to separate page (cpp currently missing decor documentation) because it's a top-level concept that should be in the TOC like the other ingredients of the cable cell.
* Slight rework of Concept intro and Cable Cell pages.
* The Cable Cell page is now basically an intro, and lay out how the other pages/concepts relate to each other.

Revert a change introduced in #1282 that required the python module for arbor to build the documentation.

This breaks the readthedocs build, where arbor is not available.

* Remove arbor dependence from `doc/conf.py`, reverting to the original "out of core" approach
* Fix other recently introduced issues that lead to CMake errors when configuring the documentation
  when the Python target is not configured.
  * The CMake variable `PYTHON_EXECUTABLE` wasn't set, but was required to make calls to the
     Python interpreter.
  * Instead of relying on pybind11 to find Python, explicitly detect it using `find_package(Python3 ...)`
  * Make Python3 a hard requirement when building the Python wrapper
  * And a soft requirement otherwise, that will fail only when the docs are built.

* Expose and document the (segment id) region expressions.
* gen-labels.py was not up to speed with decor #1235.
* The SWC example is read from disk and inserted into the docs verbatim.
* The same file is used to generate the image.
* The missing decor constructor has been added.
* Generating inputs.py on the fly when building docs. That should prevent this issue from coming up again.

Remove Python API ref page, Spack Install, fix some links

* Synced pages between Concepts, Python API and C++ API wherever possible
    * Recipe pages conform between the three section (concepts, python, c++)
    * Cell, Cable Cell and Cell * pages are rearranged and provided with some copy explaining the relationship between them.
* Moved Python API out of Concepts
* Renamed Concepts "How does Arbor work?"
* Added Python Module Index plus mock import of Arbor for RTD build (unfortunately won't show there)
* Broke out Interconnectivity (synapses) page.
* Reworked Single Cell Model page into a quick start, with lots of cross referencing.
* Tweaked logo.
* Added Spack to install options.
* Updated blurb.
* Documentation now follows EU capitalization rules.
* Assorted typofixes

This PR adds a bunch of high-level docs for concepts related to single cell models.
  * morphologies
  * labels (region and locset expressions)
  * mechanisms
  * cable cells

It adds some python scripts to the `doc` path, which are called during documentation building to generate images of cell morphologies, regions and locsets that are generated in a separate script that uses the Arbor Python API.

The docs are not complete: the cable cell and mechanism docs are unfinished, and the tutorial section needs to build on these concepts to give more detailed step by step examples.

Update the docs landing page and add pip install from git.

Fixes #1118

* Add logo to read the docs as HTML header.
* Lighten nav bar background so as to not clash with logo.

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

Add gap junctions and improve general model overview in docs.

* Replace Arbor Model::Common Types with Arbor Model::Concepts, that introduces the concept of cells, connections and gap junctions. 
* Add gap junction documentation to cpp:recipe
* Document the implicit rule forcing cells connected by gap junctions to be in the same cell group.
* Add documentation that discusses core concepts in Arbor models.

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.

Towards resolution of issue #283.

* Replace probe/sample infrastructure with new API as outlined in the `sampling_api.rst` documentation.
* Separate `cell` probe information from `cell` description object.
* Add `--list` option to `tsplot`, to summarize available time series for plotting together with their metadata.
* Add `--sample-dt` option to validation tests.
* Change validation time series comparison behaviour: linf distance metric now estimated by comparing reference data points against linearly interpreted simulation samples, rather than the other way around.
* Add utility class `any_ptr` which allows lightweight and type-checked access to a type-erased pointer.
* Replace `singleton_recipe` with two simple recipe base classes used for unit and validation tests, in `tests/simple_recipes.hpp`.
* Simplify RSS cell implementation.
* Add statistical functions for testing of probabilistic methods in `tests/unit/stats.hpp` (and .cpp):
   * simple summary stats class;
   * Kolmogorov–Smirnov one-sided statistic and CDF;
   * approximate Poisson CDF.
* Simplify and refactor miniapp `sample_trace` code.
* Add new utility class `handle_set` for managing a collection of integer handles. (Near-simplest implementation.)
* Relax const-ness constraints on `transform_iterator`.

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.