From 6577e66231f1e7191b55dad39190e0e0888cd2d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jonas=20F=C3=B6rster?= Date: Sun, 6 Oct 2019 18:50:59 +0200 Subject: [PATCH] - upgrade website --- README.md | 49 +- development/site_upgrade.R | 6 +- docs/404.html | 203 ++++++ docs/LICENSE-text.html | 35 +- docs/articles/CoRC.html | 180 ++--- .../figure-html/unnamed-chunk-9-1.png | Bin 211287 -> 212057 bytes docs/articles/entity_management.html | 277 +++---- docs/articles/examples.html | 679 +++++++++--------- .../htmlwidgets.js | 58 +- .../plotly.js | 178 ++--- .../plotly-htmlwidgets.css | 0 .../plotly-main-1.39.2/plotly-latest.min.js | 7 - .../plotly-main-1.46.1/plotly-latest.min.js | 7 + docs/articles/index.html | 35 +- docs/articles/issues.html | 83 ++- docs/articles/model_building.html | 383 +++++----- .../figure-html/unnamed-chunk-3-1.png | Bin 45742 -> 45044 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 44700 -> 44205 bytes docs/articles/task_management.html | 493 ++++++------- 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docs/articles/examples_files/{plotly-htmlwidgets-css-1.39.2 => plotly-htmlwidgets-css-1.46.1}/plotly-htmlwidgets.css (100%) delete mode 100644 docs/articles/examples_files/plotly-main-1.39.2/plotly-latest.min.js create mode 100644 docs/articles/examples_files/plotly-main-1.46.1/plotly-latest.min.js delete mode 100755 docs/man/figures/logo.svg create mode 100644 pkgdown/favicon/apple-touch-icon-120x120.png create mode 100644 pkgdown/favicon/apple-touch-icon-152x152.png create mode 100644 pkgdown/favicon/apple-touch-icon-180x180.png create mode 100644 pkgdown/favicon/apple-touch-icon-60x60.png create mode 100644 pkgdown/favicon/apple-touch-icon-76x76.png create mode 100644 pkgdown/favicon/apple-touch-icon.png create mode 100644 pkgdown/favicon/favicon-16x16.png create mode 100644 pkgdown/favicon/favicon-32x32.png create mode 100644 pkgdown/favicon/favicon.ico diff --git a/README.md b/README.md index f9114ad8..b4163753 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,41 @@ -CoRC logo --- the COPASI R Connector -============================================================================================================ +# CoRC logo — the COPASI R Connector -Overview --------- +## Overview Development Stage: **Beta** -CoRC, the COPASI R Connector, links the Complex Pathway Simulator COPASI ([copasi.org](http://copasi.org)) and the (statistical) programming environment R ([r-project.org](http://r-project.org)). It provides easy access to the powerful biochemical model editing, simulation and analysis backend of COPASI from the convenient R command line interface. This allows the user to develop elaborate scripts and workflows for analyses that would require a great deal of tedious manual work otherwise. These scripts can then be run interactively from the R command line interface or be sent to cluster or cloud facilities for more demanding calculations. +CoRC, the COPASI R Connector, links the Complex Pathway Simulator COPASI +([copasi.org](http://copasi.org)) and the (statistical) programming +environment R ([r-project.org](http://r-project.org)). It provides easy +access to the powerful biochemical model editing, simulation and +analysis backend of COPASI from the convenient R command line interface. +This allows the user to develop elaborate scripts and workflows for +analyses that would require a great deal of tedious manual work +otherwise. These scripts can then be run interactively from the R +command line interface or be sent to cluster or cloud facilities for +more demanding calculations. CoRC features: -- high-level API for COPASI in the R language. -- Immediate access to R's data analysis capabilities and publication-ready plotting. -- Reproducible workflows from data generation to analysis and plotting (R scripts and notebooks). -- Rule-based modification of model structure to test structural variations or create large models. -- Scaling up assays, e.g. from 3 models to 3000. -- Handling of multiple models at once. -- Parallelization on multi-core machines or computing clusters. + - high-level API for COPASI in the R language. + - Immediate access to R’s data analysis capabilities and + publication-ready plotting. + - Reproducible workflows from data generation to analysis and plotting + (R scripts and notebooks). + - Rule-based modification of model structure to test structural + variations or create large models. + - Scaling up assays, e.g. from 3 models to 3000. + - Handling of multiple models at once. + - Parallelization on multi-core machines or computing clusters. -It is currently based on COPASI version 4.25 Build (207) and aims to closely follow COPASI releases in the future. +It is currently based on COPASI version 4.27 Build (217) and aims to +closely follow COPASI releases in the future. -CoRC comes with the Artistic License 2.0. By using CoRC you agree to this license. +CoRC comes with the Artistic License 2.0. By using CoRC you agree to +this license. -Installation ------------- +## Installation Install the development version from GitHub: @@ -34,10 +45,10 @@ remotes::install_github("jpahle/CoRC") CoRC::getCopasi() ``` -CoRC runs it's own version of the COPASI backend which it will download via the `getCopasi` function. +CoRC runs it’s own version of the COPASI backend which it will download +via the `getCopasi` function. -Usage ------ +## Usage ``` r library(CoRC) diff --git a/development/site_upgrade.R b/development/site_upgrade.R index d6cadc99..49191d5f 100644 --- a/development/site_upgrade.R +++ b/development/site_upgrade.R @@ -1,10 +1,10 @@ # For upgrading the site I want to have specific versions of relevant packages # use specific pkgdown to keep page stable for now -remotes::install_version("pkgdown", "1.3.0", upgrade = "never") +remotes::install_version("pkgdown", "1.4.1", upgrade = "never") # use fixed plotly versions to be able to keep the 8mb or so of plots frozen when updating the rest of the website -remotes::install_version("ggplot2", "3.1.0", upgrade = "never") -remotes::install_version("plotly", "4.8.0", upgrade = "never") +remotes::install_version("ggplot2", "3.2.1", upgrade = "never") +remotes::install_version("plotly", "4.9.0", upgrade = "never") devtools::document() devtools::install() devtools::test() diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 00000000..fcf58cdb --- /dev/null +++ b/docs/404.html @@ -0,0 +1,203 @@ + + + + + + + + +Page not found (404) • CoRC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Developed by Jonas Förster, Jürgen Pahle.

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