~tfardet: 1 Doc+Plot: move to Furo + directed chord diagram 25 files changed, 95 insertions(+), 437 deletions(-)
Copy & paste the following snippet into your terminal to import this patchset into git:
curl -s https://lists.sr.ht/~tfardet/nngt-developers/patches/35652/mbox | git am -3Learn more about email & git
From: Tanguy Fardet <tanguyfardet@protonmail.com> --- README.md | 7 +- doc/_static/custom.css | 24 ++ doc/_templates/base.html | 5 + doc/_templates/customtoc.html | 6 - doc/_templates/layout.html | 6 - doc/_templates/nngt_logo.png | Bin 13400 -> 0 bytes doc/conf.py | 81 ++--- doc/developer/contributing.rst | 4 - .../graph_structure/plot_chord_diagram.py | 9 +- doc/index.rst | 3 + doc/modules/database.rst | 4 - doc/modules/nngt.rst.in | 3 - doc/modules/nngt/graph-classes.rst.in | 3 - doc/modules/nngt/side-classes.rst.in | 3 - doc/nngt_theme/static/nngt_theme.css | 302 ------------------ doc/nngt_theme/theme.conf | 4 - doc/user/activity-analysis.rst | 3 - doc/user/component-properties.rst | 5 - doc/user/graph-generation.rst | 6 - doc/user/nest-interaction.rst | 6 - doc/user/neural-groups.rst | 5 - doc/user/parallelism.rst | 3 - doc/user/tutorial.rst | 6 - nngt/generation/func_connect.h | 14 +- nngt/plot/plt_networks.py | 20 +- 25 files changed, 95 insertions(+), 437 deletions(-) create mode 100644 doc/_static/custom.css create mode 100644 doc/_templates/base.html delete mode 100755 doc/_templates/customtoc.html delete mode 100644 doc/_templates/layout.html delete mode 100755 doc/_templates/nngt_logo.png delete mode 100755 doc/nngt_theme/static/nngt_theme.css delete mode 100755 doc/nngt_theme/theme.conf diff --git a/README.md b/README.md index 8ea1457..71b6133 100755 --- a/README.md +++ b/README.md @@ -18,9 +18,14 @@ activity simulators to make the study of neuronal activity as easy and efficient as possible. Source code is available and contributions are accepted on -[SourceHut](https://sr.ht/~tfardet/NNGT) and +[SourceHut](https://sr.ht/~tfardet/NNGT) (preferred), +[Codeberg](https://codeberg.org/tfardet/NNGT), and [GitHub](https://github.com/tfardet/NNGT). +For questions or issues, please check the +[mailing list](https://lists.sr.ht/~tfardet/nngt-users) and the +[issue tracker](https://codeberg.org/tfardet/NNGT/issues). + ## Principle diff --git a/doc/_static/custom.css b/doc/_static/custom.css new file mode 100644 index 0000000..ef90ae8 --- /dev/null +++ b/doc/_static/custom.css @@ -0,0 +1,24 @@ +footer { + font-size: 95%; +} + +.toc-drawer { + font-size: 110%; +} + +.sidebar-logo { + max-width: 90% !important; +} + +.sphx-glr-thumbnails{ + grid-template-columns: repeat(auto-fill, minmax(320px, 1fr)) !important; +} + +.sphx-glr-thumbcontainer img { + max-height: 320px !important; + max-width: 320px !important; +} + +.admonition { + font-size: 90%; +} diff --git a/doc/_templates/base.html b/doc/_templates/base.html new file mode 100644 index 0000000..59dc79b --- /dev/null +++ b/doc/_templates/base.html @@ -0,0 +1,5 @@ +{% extends "!base.html" %} +{% block site_meta %} + <meta name="keywords" content="nngt, network, graph, topology, complex networks, networkx, igraph, graph-tool, neuron, neuronal, python, nest" /> + <meta name="description" content="Documentation for the python module NNGT, aimed at generating and analyzing complex graphs, with specific additions for GIS and to describe neuronal networks plus interface them with simulators." /> +{% endblock %} diff --git a/doc/_templates/customtoc.html b/doc/_templates/customtoc.html deleted file mode 100755 index 899200a..0000000 --- a/doc/_templates/customtoc.html @@ -1,6 +0,0 @@ -<a href={{ pathto(master_doc) }}><img class="logo" src={{ pathto("_static/nngt_logo.svg",1) }}></a> -<p class="toctitle">Table of content</p> -<ul class="globaltoc"> - {{ toctree(maxdepth=-1, collapse=True,includehidden=True) }} -</ul> -<br /> diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html deleted file mode 100644 index 0e7863b..0000000 --- a/doc/_templates/layout.html @@ -1,6 +0,0 @@ -{% extends "!layout.html" %} -{% block extrahead %} - {{ super() }} - <meta name="keywords" content="nngt, neuron, network, graph, topology, neuronal, python, nest" /> - <meta name="description" content="Documentation for the python module NNGT, aimed at describing neuronal networks and interfacing them with simulators." /> -{% endblock %} diff --git a/doc/_templates/nngt_logo.png b/doc/_templates/nngt_logo.png deleted file mode 100755 index 2cd83f6cdcad7a7c98608d336bee902bc0eb6458..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 13400 zcmWk#19Tl-5RR<|ZEQPfY@1En*tYGYu^L-1w(Z7AUu@fE<A4A2&b~cw-{Rhxx!=ru zGaI3zB#nxMj|2e$fhsE_@eSCg0Gl}i9Pqs}*`WvQ;Ed#@B_KZj|KxR*Bmzee9b`0} 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See the documentation for # a list of builtin themes. -#~ html_theme = 'sphinx_rtd_theme' -html_theme = 'nngt_theme' -html_theme_path = ["."] + sphinx_bootstrap_theme.get_html_theme_path() -html_use_smartypants = False +html_theme = 'furo' + +html_sidebars = { + "**": [ + "sidebar/scroll-start.html", + "sidebar/brand.html", + "sidebar/search.html", + "sidebar/navigation.html", + "sidebar/scroll-end.html", + ] +} html_theme_options = { - # A list of tuples containing pages or urls to link to. - # Valid tuples should be in the following forms: - # (name, page) # a link to a page - # (name, "/aa/bb", 1) # a link to an arbitrary relative url - # (name, "http://example.com", True) # arbitrary absolute url - # Note the "1" or "True" value above as the third argument to indicate - # an arbitrary url. - 'navbar_links': [ - ("Modules", "py-modindex"), - ("Index", "genindex"), - ("SourceHut", "https://git.sr.ht/~tfardet/NNGT", True), - ("GitHub", "https://github.com/tfardet/NNGT", True), - ], - - # Render the next and previous page links in navbar. (Default: true) - 'navbar_sidebarrel': False, - - # Render the current pages TOC in the navbar. (Default: true) - 'navbar_pagenav': True, - - # Tab name for the current pages TOC. (Default: "Page") - 'navbar_pagenav_name': "Current", - - # Global TOC depth for "site" navbar tab. (Default: 1) - # Switching to -1 shows all levels. - 'globaltoc_depth': 2, - - # Include hidden TOCs in Site navbar? - # - # Note: If this is "false", you cannot have mixed ``:hidden:`` and - # non-hidden ``toctree`` directives in the same page, or else the build - # will break. - # - # Values: "true" (default) or "false" - 'globaltoc_includehidden': "true", - - # Fix navigation bar to top of page? - # Values: "true" (default) or "false" - 'navbar_fixed_top': "false", - - # Location of link to source. - # Options are "nav" (default), "footer" or anything else to exclude. - 'source_link_position': "", - - # Bootswatch (http://bootswatch.com/) theme. - 'bootswatch_theme': "yeti" + "light_css_variables": { + "color-brand-primary": "#527fbf", + "color-brand-content": "#527fbf", + }, + "dark_css_variables": { + "color-brand-primary": "#82afdf", + "color-brand-content": "#82afdf", + }, } -html_sidebars = {'**': ['customtoc.html', 'searchbox.html']} +html_css_files = [ + 'custom.css', +] # The name for this set of Sphinx documents. If None, it defaults to # "<project> v<release> documentation". -#html_title = None +html_title = f'NNGT {nngt.__version__}' # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. -#~ html_logo = 'images/nngt_logo.png' -#~ html_logo = 'images/nngt_ico.png' +html_logo = '_static/nngt_logo.svg' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 diff --git a/doc/developer/contributing.rst b/doc/developer/contributing.rst index 9a9095f..e6faa0c 100644 --- a/doc/developer/contributing.rst +++ b/doc/developer/contributing.rst @@ -3,10 +3,6 @@ Contributing to NNGT ==================== -.. contents:: - :local: - - Signaling issues and bugs ========================= diff --git a/doc/examples/graph_structure/plot_chord_diagram.py b/doc/examples/graph_structure/plot_chord_diagram.py index d3fe9eb..e99481f 100644 --- a/doc/examples/graph_structure/plot_chord_diagram.py +++ b/doc/examples/graph_structure/plot_chord_diagram.py @@ -42,7 +42,7 @@ names = ["R1", "R2", "R3", "R4"] struct = nngt.Structure.from_groups((room1, room2, room3, room4), names) -g = nngt.Graph(structure=struct) +g = nngt.Graph(structure=struct, directed=True) for room in struct: nngt.generation.connect_groups(g, room, room, "all_to_all") @@ -59,5 +59,10 @@ nngt.generation.connect_groups(g, room4, room3, "erdos_renyi", avg_deg=10) sg = g.get_structure_graph() +# undirected version of the chord diagram nngt.plot.chord_diagram(sg, names="name", sort="distance", fontcolor="grey", - use_gradient=True, show=True) + use_gradient=True, directed=False, show=False) + +# directed chord diagram +nngt.plot.chord_diagram(sg, names="name", sort="distance", fontcolor="grey", + use_gradient=True, directed=True, show=True) diff --git a/doc/index.rst b/doc/index.rst index ed1edd9..a25cd5c 100755 --- a/doc/index.rst +++ b/doc/index.rst @@ -92,6 +92,9 @@ The docs :caption: Contributing developer/contributing + SourceHut <https://git.sr.ht/~tfardet/NNGT> + Codeberg <https://codeberg.org/tfardet/NNGT> + GitHub <https://github.com/tfardet/NNGT> .. toctree:: :glob: diff --git a/doc/modules/database.rst b/doc/modules/database.rst index 5e6cd51..292491c 100755 --- a/doc/modules/database.rst +++ b/doc/modules/database.rst @@ -11,10 +11,6 @@ The commands are then used by calling ``nngt.database`` to access the database tools. -.. contents:: - :local: - - Functions --------- diff --git a/doc/modules/nngt.rst.in b/doc/modules/nngt.rst.in index a33c71b..09f6d45 100644 --- a/doc/modules/nngt.rst.in +++ b/doc/modules/nngt.rst.in @@ -4,9 +4,6 @@ Main module (API) ================= -.. contents:: Overview - :local: - For more details regarding the main classes, see: .. toctree:: diff --git a/doc/modules/nngt/graph-classes.rst.in b/doc/modules/nngt/graph-classes.rst.in index c2f1705..6fb8d86 100644 --- a/doc/modules/nngt/graph-classes.rst.in +++ b/doc/modules/nngt/graph-classes.rst.in @@ -19,9 +19,6 @@ Unless specified, child classes can use all methods from the parent class (the only exception is :meth:`~nngt.Graph.set_types` which is not available to the :class:`~nngt.Network` subclasses). -.. contents:: - :local: - Summary of the class members and methods ---------------------------------------- diff --git a/doc/modules/nngt/side-classes.rst.in b/doc/modules/nngt/side-classes.rst.in index 9036617..2c2486b 100755 --- a/doc/modules/nngt/side-classes.rst.in +++ b/doc/modules/nngt/side-classes.rst.in @@ -21,9 +21,6 @@ Unless specified, child classes can use all methods from the parent class :class:`~nngt.MetaNeuralGroup` inherit from :class:`~nngt.Group` while :class:`~nngt.NeuralPop` inherits from :class:`~nngt.Structure`). -.. contents:: - :local: - Group +++++ diff --git a/doc/nngt_theme/static/nngt_theme.css b/doc/nngt_theme/static/nngt_theme.css deleted file mode 100755 index 60ce9f4..0000000 --- a/doc/nngt_theme/static/nngt_theme.css @@ -1,302 +0,0 @@ -@import url("bootstrap-sphinx.css"); 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-} - - -/* -Sphinx gallery image size -*/ - -.sphx-glr-thumbcontainer { - min-height: 330px !important; - margin-bottom: 10px !important; - background: var(--bg-color) !important; - border-color: var(--admonition-a) !important; -} - -.sphx-glr-thumbcontainer .figure { - width: 320px !important; -} - -.sphx-glr-thumbcontainer img { - max-height: 300px !important; - width: 300px !important; - max-width: 300px !important; -} - -.sphx-glr-thumbcontainer a.internal { - padding: 310px 10px 0 !important; -} - -div.sphx-glr-download a { - background-color: var(--bg-color) !important; - border-color: #aaaaaa !important; - background-image: linear-gradient(to bottom, var(--bg-color), var(--sb-color)) !important; -} - -div.sphx-glr-download a:hover { - background-image: linear-gradient(to top, var(--sb-color), var(--sb-color)) !important; -} diff --git a/doc/nngt_theme/theme.conf b/doc/nngt_theme/theme.conf deleted file mode 100755 index 2056a7a..0000000 --- a/doc/nngt_theme/theme.conf @@ -1,4 +0,0 @@ -[theme] -inherit = bootstrap -stylesheet = nngt_theme.css -pygments_style = sphinx diff --git a/doc/user/activity-analysis.rst b/doc/user/activity-analysis.rst index 5ba84fd..71c1a9d 100755 --- a/doc/user/activity-analysis.rst +++ b/doc/user/activity-analysis.rst @@ -4,9 +4,6 @@ Activity analysis ================= -.. contents:: - :local: - Principle ========= diff --git a/doc/user/component-properties.rst b/doc/user/component-properties.rst index c353bbb..fd20fdd 100755 --- a/doc/user/component-properties.rst +++ b/doc/user/component-properties.rst @@ -7,11 +7,6 @@ Properties of graph components This section details the different attributes and properties which can be associated to nodes/neurons and connections in graphs and networks. -**Content:** - -.. contents:: - :local: - Components of a graph ===================== diff --git a/doc/user/graph-generation.rst b/doc/user/graph-generation.rst index 41ce8bb..b683afe 100755 --- a/doc/user/graph-generation.rst +++ b/doc/user/graph-generation.rst @@ -12,12 +12,6 @@ The example files can be found at: :source:`docs/examples/simple_graphs.py`, :source:`docs/examples/nest_receptor_ports.py`. -**Content:** - -.. contents:: - :local: - - Principle ========= diff --git a/doc/user/nest-interaction.rst b/doc/user/nest-interaction.rst index a66cf8c..e3c81e8 100644 --- a/doc/user/nest-interaction.rst +++ b/doc/user/nest-interaction.rst @@ -37,12 +37,6 @@ found here: :source:`docs/examples/nest_network.py` / :source:`docs/examples/nest_receptor_ports.py`. -**Content:** - -.. contents:: - :local: - - Creating detailed neuronal networks =================================== diff --git a/doc/user/neural-groups.rst b/doc/user/neural-groups.rst index 4d2a2d4..a96fba4 100644 --- a/doc/user/neural-groups.rst +++ b/doc/user/neural-groups.rst @@ -13,11 +13,6 @@ additional information on how to access :class:`~nngt.NeuralGroup` and :class:`~nngt.NeuralPop` properties can be found there: :source:`docs/examples/introduction_to_groups.py`. -**Contents** - -.. contents:: - :local: - Neuronal groups =============== diff --git a/doc/user/parallelism.rst b/doc/user/parallelism.rst index a17df12..3aeb489 100755 --- a/doc/user/parallelism.rst +++ b/doc/user/parallelism.rst @@ -8,9 +8,6 @@ Parallelism When using ``graph-tool``, read carefully the `Graph-tool caveat`_ section before playing with multiple threads! -.. contents:: - :local: - Principle ========= diff --git a/doc/user/tutorial.rst b/doc/user/tutorial.rst index 8556d9d..cd36131 100644 --- a/doc/user/tutorial.rst +++ b/doc/user/tutorial.rst @@ -35,12 +35,6 @@ The source file for the tutorial can be found here: * :ref:`graph-prop` -**Content:** - -.. contents:: - :local: - - NNGT properties and configuration ================================= diff --git a/nngt/generation/func_connect.h b/nngt/generation/func_connect.h index 35337be..e7731de 100644 --- a/nngt/generation/func_connect.h +++ b/nngt/generation/func_connect.h @@ -5,14 +5,14 @@ #ifndef FUNC_CONNECT_H #define FUNC_CONNECT_H +#include <algorithm> +#include <cmath> +#include <functional> #include <string> #include <vector> #include <tuple> #include <unordered_set> -#include <cmath> -#include <algorithm> - namespace generation { @@ -46,7 +46,7 @@ typedef std::unordered_set<edge_t, key_hash, key_equal> set_t; * Sort a vector to move the N unique numbers in the N first entries. * * \param a - Source array. - * + * * .. note:: * The array is modified inplace. * @@ -60,7 +60,7 @@ size_t _unique_1d(std::vector<size_t>& a, * Sort a 2-D vector to move the N unique pairs in the N first columns. * * \param a - Source array. - * + * * .. note:: * The array is modified inplace. * @@ -119,7 +119,7 @@ void _gen_edges( /* * Parallel distance-rule generator. - * + * * \param ia_edges - array that will contain the edges * \param source_nodes - array containing the ids of the source nodes * \param target_nodes - array containing the ids of the target nodes @@ -151,7 +151,7 @@ static inline float _proba( { float p = 0.; // probability value - switch (rule) + switch (rule) { case 0: // linear p = norm*std::max(0., 1. - distance * inv_scale); diff --git a/nngt/plot/plt_networks.py b/nngt/plot/plt_networks.py index 7b4dd47..a7bb391 100755 --- a/nngt/plot/plt_networks.py +++ b/nngt/plot/plt_networks.py @@ -1531,7 +1531,7 @@ def library_draw(network, nsize="total-degree", ncolor=None, nshape="o", def chord_diagram(network, weights=True, names=None, order=None, width=0.1, pad=2., gap=0.03, chordwidth=0.7, axis=None, colors=None, cmap=None, alpha=0.7, use_gradient=False, chord_colors=None, - show=False, **kwargs): + start_at=0, extent=360, directed=None, show=False, **kwargs): """ Plot a chord diagram. @@ -1579,6 +1579,17 @@ def chord_diagram(network, weights=True, names=None, order=None, width=0.1, (in this case, RGB tuples are accepted as entries to the list). Each chord will get its color from its associated source node, or from both nodes if `use_gradient` is True. + start_at : float, optional (default : 0) + Location, in degrees, where the diagram should start on the unit circle. + Default is to start at 0 degrees, i.e. (x, y) = (1, 0) or 3 o'clock), + and move counter-clockwise + extent : float, optional (default : 360) + The angular aperture, in degrees, of the diagram. + Default is to use the whole circle, i.e. 360 degrees, but in some cases + it can be useful to use only a part of it. + directed : bool, optional (default: same as network) + Whether the chords should be directed with one part of each arc + dedicated to outgoing chords and the other to incoming ones. show : bool, optional (default: False) Whether the plot should be displayed immediately via an automatic call to `plt.show()`. @@ -1600,11 +1611,14 @@ def chord_diagram(network, weights=True, names=None, order=None, width=0.1, mat = network.adjacency_matrix(weights=ww) + if directed is None: + directed = network.is_directed() + return _chord_diag( mat, nn, order=order, width=width, pad=pad, gap=gap, chordwidth=chordwidth, ax=axis, colors=colors, cmap=cmap, alpha=alpha, - use_gradient=use_gradient, chord_colors=chord_colors, show=show, - **kwargs) + use_gradient=use_gradient, chord_colors=chord_colors, start_at=start_at, + extent=extent, directed=directed, show=show, **kwargs) # ----- # -- 2.34.4
builds.sr.ht <builds@sr.ht>NNGT/patches/.build.yml: SUCCESS in 25m17s [Doc+Plot: move to Furo + directed chord diagram][0] from [~tfardet][1] [0]: https://lists.sr.ht/~tfardet/nngt-developers/patches/35652 [1]: mailto:tanguyfardet@protonmail.com ✓ #852097 SUCCESS NNGT/patches/.build.yml https://builds.sr.ht/~tfardet/job/852097
