- Apr 06, 2021
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Brent Huisman authored
* 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
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- Feb 17, 2021
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Brent Huisman authored
`/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.).
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- Feb 11, 2021
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Brent Huisman authored
* 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.
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- Jan 05, 2021
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Benjamin Cumming authored
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.
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- Dec 18, 2020
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thorstenhater authored
* 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.
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- Oct 08, 2020
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Brent Huisman authored
Remove Python API ref page, Spack Install, fix some links
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- Oct 05, 2020
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Brent Huisman authored
* 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
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- Aug 27, 2020
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Benjamin Cumming authored
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.
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- Aug 26, 2020
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Brent Huisman authored
Update the docs landing page and add pip install from git. Fixes #1118
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- Jan 20, 2020
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Benjamin Cumming authored
* Add logo to read the docs as HTML header. * Lighten nav bar background so as to not clash with logo.
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- Mar 04, 2019
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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.
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- Jun 25, 2018
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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.
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- Sep 01, 2017
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Sam Yates authored
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`.
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- Aug 24, 2017
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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.
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