* Functionality
  * Add probes to LIF cells.
* Docs
  * Remove errorneous statement(s) about LIF cells (there never was an E_reset...)
  * Move probing chapter one level up (concepts/cable_cells -> concepts)
* Tests
  * Add tests for LIF probes

- Generate timestamped VERSION once, to properly group on Test.PyPI. Example:
  - https://github.com/arbor-sim/arbor/actions/runs/2696804929
  - https://test.pypi.org/project/arbor/0.7rc20220719101015/
- Update/simplify release documentation.
- Update to v0.7

As per #1731, this PR adds a dependencies version policy to the docs. It also includes a file containing a list of all configure-time deps.

Obsoletes wiki page.

Add a first round of developer documentation, evolving from the older `internal` part of the docs.

* Some badges corrected (build) and added (Gitter)
* Minor Spack backports
* Small updates to `release.rst`

* Update VERSION to `v0.6.1-dev`
* Updates to `doc/release.rst`
* Update Zenodo citation info for v0.6
* Update copyright info and maintainers in `spack/package.py` from upstream
* Fix error in build-badge docs

Emphasize pip as the preferred method of installation.

- zenodo entry for v0.5.2
- minor formatting update to spack file

* Update URLs to arbor-sim.org
* update badge links

* Adapt CSS for the HTML5 transition in docutils 0.17
* Fix some reST markup errors
* Add meta-tag to enable indexation control at Google (current indexation appears at least a year old).

* Add Zenodo citation snippet.
* Correct Nora's last name, which is Abi Akar.
* Small css fix for change in docutils, see: https://github.com/readthedocs/sphinx_rtd_theme/issues/1115

Fixes #1297.

* Implements parsers and writers in `arborio` for the s-expression based Arbor Cable-Cell Format defined in #1336.
* Moves `s_expr.hpp` to the public interface.
* Adds python wrappers to support the features in pyarb.  
* Adds unit tests.
* Adds docs.

Fixes #1336
Partially addresses #1233

Basic support for reading morphologies from Neurolucida ASCII (.asc) files.

Added to the arborio C++ library, and wrapped similarly to the other arborio features in Python.

Fixes #1429

* Remove parts of the C++ API which leaked into `doc/fileformat/neuroml.rst`
* Add links to the relevant C++ and Python API

* Refactor Documentation layout. 
* Display Spack page.
* Display Extending catalogues page.

Fixes #1353.

* Update `README.md`: moved citation to `doc/index.rst`.
* Advertise Py3.9 compat PyPI in setup.py
* Fix typos.

Reomove Travis CI integration.

* remove Travis yaml and build scripts
* remove Travis badges from README and RTD docs
* replace Travis badge with GitHub Actions badge
* add a RTD badge to the README

Fixes #1338.

* Add 2 new examples to `python/examples` and their corresponding tutorials in the docs. 
    1. `single_cell_detailed.py` : a slightly more complex example using `single_cell_model`
    2. `single_cell_detailed_recipe.py`: equivalent to `single_cell_detailed.py` but using a recipe. 
* Change `load_swc`-> `load_swc_arbor` for consistency.
* Run Sphinx with specified PYTHON_EXECUTABLE.
* Set PYTHONPATH env var in doc/CMakeLists.txt, such that it propagates correctly, including locally.
* Build pyarb BEFORE html such that docs build can import arbor in Github Actions script.

Set up contribution guides.

Add a contribution guide, as well as 
* Added contribution section.
* Moved content here from the wiki regarding (contribution) processes.

Also added some incomplete / placeholder sections that can be improved later.
* How to write an example
* How to add a test
* Coding style guidelines

* An explanation of documentation structure.
* Added HBP/Ebrains to acknowledgements.

* Fix some broken links and typos.
* Fix out-of-date documentation.
* Reword some of the existing sections.

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

* Add CMake infrastructure for new `arbornml` library comprising Arbor's NeuroML2 (C++) support.
* Implement NeuroML2 parsing and interpretation, using libxml2 for XML parsing.
* Add associated documentation, unit tests.
* Replace `arb::util::optional` with `std::optional` in stitch morphology interface.
* Add optional prefix to `arb::label_dict` import.
* Update CI to test arbornml, with associated workarounds for OS X targets.
* Remove glob functionality from `sup`, as it is no longer needed (it was used for lmorpho) and it triggers yet another OS X issue.

Fixes #1088.

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

Guide Python users to the Python installation steps early in the installation guide.

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

* 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.

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

Add citation information to the readme.

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.

Update Hardware API documentation

* split the domain decomposition and hardware API docs into separate pages
* update hardware API to reflect new *libarbor* and *libarborenv*
* add basic documentation for `optional`, `any` and `unique_any` types.