From 22419b7fb44f5245eb3fec2f6b0327d6b0ef4fdd Mon Sep 17 00:00:00 2001 From: Heiko Strathmann Date: Fri, 5 Jul 2019 10:52:52 +0100 Subject: [PATCH 1/2] Bump version to 6.1.4 --- NEWS | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/NEWS b/NEWS index c86b4a66636..4d90f703072 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,10 @@ +2017-12-05 Heiko Strathmann + + * SHOGUN Release version 6.1.4 (libshogun 18.0, data 0.11, parameter 1) + + * Bugfixes: + - Fix cookbookx examples for website + 2017-12-05 Viktor Gal * SHOGUN Release version 6.1.3 (libshogun 18.0, data 0.11, parameter 1) From 7536fe99910c60a59c21017e8ef5319c60631492 Mon Sep 17 00:00:00 2001 From: Pattarawat Chormai Date: Sat, 16 Feb 2019 22:47:27 +0100 Subject: [PATCH 2/2] Cleanup broken links and fix some issues on Shogun's webpages. (#4516) * Remove the link to the old team page. Fix #4512. * Fix deadlinks in INTERFACES.md For #4512 * Use inline script tag for custom LaTeX commands. (#4512) Previoulsy, we load MathJax and mathconfig.js asynchronously. This is not good for mathconfig.js because it requires the main variable for MathJax.js. * Fix style of reference section. (#4512) Note: the problem seems to originally come from boostrap and how our biblatex plugin uses `label class` to generates reference entries. * Update links and some installation information. (#4512) The information includes Docker and MacOS brew installation. * Remove duplicated years in references.bib. (#4512) "Gaussian Processes for Machine Learning" has duplicate years and causes an error when generating the cookbook webpages. According to the book's webpage, the published year is 2006. * Remove duplicate import statements for shogun-style.css (#4512). * Revert "Use inline script tag for custom LaTeX commands. (#4512)" This reverts commit 4413403e2ad014f349c1f2de98ca615d828f0f7e. * set mathjax configuration using window.MathJax (#4512) * use relative urls for links to documents. (#4512) --- doc/cookbook/source/references.bib | 3 +-- doc/cookbook/source/static/mathconf.js | 4 ++-- doc/cookbook/source/static/shogun-style.css | 5 +++++ doc/cookbook/source/templates/layout.html | 5 ----- doc/readme/INSTALL.md | 8 ++++---- doc/readme/INTERFACES.md | 6 ++++-- doc/readme/MISSION.md | 2 +- 7 files changed, 17 insertions(+), 16 deletions(-) diff --git a/doc/cookbook/source/references.bib b/doc/cookbook/source/references.bib index 073d5a70290..b21584f1d1c 100644 --- a/doc/cookbook/source/references.bib +++ b/doc/cookbook/source/references.bib @@ -35,9 +35,8 @@ @article{fan2008liblinear @book{Rasmussen2005GPM, author = {Rasmussen, C. E. and Williams, C. K. I.}, title = {Gaussian Processes for Machine Learning}, - year = {2005}, publisher = {The MIT Press}, - year={2008}, + year={2006}, } @article{gretton2012kernel, diff --git a/doc/cookbook/source/static/mathconf.js b/doc/cookbook/source/static/mathconf.js index a1213328c11..788c1f5f1ac 100644 --- a/doc/cookbook/source/static/mathconf.js +++ b/doc/cookbook/source/static/mathconf.js @@ -1,8 +1,8 @@ -MathJax.Hub.Config({ +window.MathJax = { TeX: { Macros: { argmax: ["\\mathop{\\rm arg\\,max}\\limits"], argmin: ["\\mathop{\\rm arg\\,min}\\limits"] } } -}); +}; diff --git a/doc/cookbook/source/static/shogun-style.css b/doc/cookbook/source/static/shogun-style.css index 2329d699def..70d0c78ddc2 100644 --- a/doc/cookbook/source/static/shogun-style.css +++ b/doc/cookbook/source/static/shogun-style.css @@ -57,3 +57,8 @@ div.toctree-wrapper > p.caption { font-weight: 300; margin-bottom: 0.5em; } + +.citation td.label { + display: block; +} + diff --git a/doc/cookbook/source/templates/layout.html b/doc/cookbook/source/templates/layout.html index 1c16d0a1683..47cef79f6af 100644 --- a/doc/cookbook/source/templates/layout.html +++ b/doc/cookbook/source/templates/layout.html @@ -1,11 +1,6 @@ {% extends "!layout.html" %} {% set script_files = script_files + ["_static/mathconf.js"] %} -{% set bootswatch_css_custom = ['_static/shogun-style.css'] %} -{# - bootswatch_css_custom is removed in sphinx-bootstrap-theme v0.5.0 - css_files should be used instead -#} {% set css_files = (css_files or []) + ['_static/shogun-style.css'] %} {% block rootrellink %} diff --git a/doc/readme/INSTALL.md b/doc/readme/INSTALL.md index 9a8116d1dfd..72c4c58a207 100644 --- a/doc/readme/INSTALL.md +++ b/doc/readme/INSTALL.md @@ -82,17 +82,17 @@ Install as ### MacOS -Shogun is part of [homebrew-science](https://github.com/Homebrew/homebrew-science). +Shogun is part of [Homebrew](https://formulae.brew.sh/formula/shogun). Install the latest stable version as - brew install homebrew/science/shogun + brew install shogun ### Windows Shogun natively compiles under Windows using MSVC, see the [AppVeyor CI build](https://ci.appveyor.com/project/vigsterkr/shogun) and the [Windows section](#manual-windows). We currently only support binary packages via conda. If you are interested in packaging, documenting, or contributing otherwise, please contact us. ## Docker images -You can run Shogun in [our own cloud](cloud.shogun.ml) or set up your own using our +You can set up Shogun using our [Docker images](https://hub.docker.com/r/shogun/shogun/) as: sudo docker pull shogun/shogun:master @@ -142,7 +142,7 @@ You need at least 1GB free disk space. If you compile any interface, roughly 4 G ## Basics Shogun uses [CMake](https://cmake.org/) for its build. The general workflow is now explained. -For further details on testing etc, see [DEVELOPING.md](DEVELOPING.md). +For further details on testing etc, see [DEVELOPING.md](docs/DEVELOPING.md). Download the latest [stable release source code](https://github.com/shogun-toolbox/shogun/releases/latest), or (as demonstrated here) clone the latest develop code. Potentially update submodules diff --git a/doc/readme/INTERFACES.md b/doc/readme/INTERFACES.md index b5e2aef34ca..faf55e1d9e8 100644 --- a/doc/readme/INTERFACES.md +++ b/doc/readme/INTERFACES.md @@ -1,7 +1,7 @@ Running Shogun from the interfaces ================================== -We assume that installation (including the interfaces) was successful and all dependencies are installed. See [INSTALL.md](INSTALL.md) and our website. +We assume that installation (including the interfaces) was successful and all dependencies are installed. See [INSTALL.md][installation-page]. Note that setting some the enviromental variables should not be necessary in case you installed Shogun to the default folder or installed it from a binary package. @@ -110,7 +110,7 @@ Running it again requires the above class path and some more options java -Xmx1024m -cp /path/to/jblas.jar:/path/to/shogun.jar:path/to/java_example.java -Djava.library.path=/path/to/shogun.jar java_example ### Provided Examples -Stand-alone, executable code for all interface examples on our website (and more) can be generated locally, see [INSTALL.md](INSTALL.md). +Stand-alone, executable code for all interface examples on our website (and more) can be generated locally, [see INSTALL.md][installation-page]. As the examples load data files, they requires the `shogun-data` submodule to be checked out. All examples should be run in the respective folder they are located in, for example (assuming that all described variables are set) @@ -122,3 +122,5 @@ Or, for a compiled language with a manually compiled, not yet installed Shogun, cd /path/to/shogun-source/build/examples/meta/csharp/regression/ mono linear_ridge_regression.cs + +[installation-page]: docs/INSTALL.md \ No newline at end of file diff --git a/doc/readme/MISSION.md b/doc/readme/MISSION.md index 52ca11390e8..f9219be58da 100644 --- a/doc/readme/MISSION.md +++ b/doc/readme/MISSION.md @@ -72,6 +72,6 @@ The original focus was on large-scale kernel methods and bioinformatics. Since then, Shogun has continuously been used for scientific research (a list of papers citing Shogun can be found [here](http://scholar.google.com/scholar?hl=en&q=shogun+toolbox&btnG=&as_sdt=1%2C33&as_sdtp=)) and massively expanded. Shogun joined [NumFocus](https://www.numfocus.org/) in early 2017. -Currently, Shogun is developed by a diverse team of students, scientists and professionals, see the [website](http://shogun-toolbox.org/page/about/ourteam) and Shogun's [AUTHORS](https://github.com/shogun-toolbox/shogun/wiki/AUTHORS). +Currently, Shogun is developed by a diverse team of students, scientists and professionals, see Shogun's [AUTHORS](https://github.com/shogun-toolbox/shogun/wiki/AUTHORS). None of their work would have been possible without the patches and bug reports by various contributors.