From ad6e0fbf54b6bc5ba0d8c9af726f9802537710c0 Mon Sep 17 00:00:00 2001 From: Gavin Rhys Lloyd Date: Fri, 13 Oct 2023 21:00:43 +0100 Subject: [PATCH] update webpages --- .Rbuildignore | 1 + .github/workflows/pkgdown.yaml | 48 ++++++++++++++++++++++++++++++++ .gitignore | 1 + DESCRIPTION | 2 +- README.md | 44 ++++++++++++++++++++++++++++++ README.rst | 50 ---------------------------------- _pkgdown.yml | 6 ++++ 7 files changed, 101 insertions(+), 51 deletions(-) create mode 100644 .github/workflows/pkgdown.yaml create mode 100644 README.md delete mode 100644 README.rst create mode 100644 _pkgdown.yml diff --git a/.Rbuildignore b/.Rbuildignore index 634bd55..d42b9e1 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -16,3 +16,4 @@ README.rst ^notebooks/ man-roxygen ^\.github$ +^pkgdown$ diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..174e23d --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,48 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [devel] + pull_request: + branches: [devel] + release: + types: [published] + workflow_dispatch: + +name: pkgdown + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} + + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.4.1 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.gitignore b/.gitignore index 6111e2b..d7306ae 100644 --- a/.gitignore +++ b/.gitignore @@ -16,3 +16,4 @@ vignettes/.build.timestamp doc vignettes/Bioconductor.sty vignettes/unsrturl.bst +docs diff --git a/DESCRIPTION b/DESCRIPTION index d179d03..9ee01c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -147,5 +147,5 @@ Suggests: agricolae, rappdirs VignetteBuilder: knitr biocViews: WorkflowStep, Metabolomics -URL: https://github.com/computational-metabolomics/structToolbox +URL: https://github.com/computational-metabolomics/structToolbox, https://computational-metabolomics.github.io/structToolbox/ Roxygen: list(markdown = TRUE) diff --git a/README.md b/README.md new file mode 100644 index 0000000..6921b52 --- /dev/null +++ b/README.md @@ -0,0 +1,44 @@ +# structToolbox + +An extensive set of data (pre-)processing and analysis methods and +tools for metabolomics and other omics, with a strong emphasis on statistics and +machine learning. + +This toolbox allows the user to build extensive and +standardised workflows for data analysis. The methods and tools have been +implemented using class-based templates provided by the `struct` (Statistics +in R Using Class-based Templates) package. +The toolbox includes pre-processing +methods (e.g. signal drift and batch correction, normalisation, missing value +imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, +Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and +PLS, including cross-validation and permutation testing) as well as machine +learning methods (e.g. Support Vector Machines). The +STATistics Ontology (STATO) has been integrated and implemented to provide +standardised definitions for the different methods, inputs and outputs. + +## Installation + +To install this package: + +``` +if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("structToolbox") +``` + +To install the development version: + +``` +if (!require("remotes", quietly = TRUE)) + install.packages("remotes") + +remotes::install_github("computational-metabolomics/structToolbox") +``` + + +[![BioC version](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fbioconductor.org%2Fconfig.yaml&query=%24.release_version&label=Bioconductor)](http://www.bioconductor.org) +[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/structToolbox.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/structToolbox) + + \ No newline at end of file diff --git a/README.rst b/README.rst deleted file mode 100644 index 3de4941..0000000 --- a/README.rst +++ /dev/null @@ -1,50 +0,0 @@ -============================================== -structToolbox -============================================== - -|Git| |Bioconda| |Build Status| |License| |Coverage| |mybinder| - - ------------- -Install ------------- - - -Github ------------- - -.. code-block:: r - - library(devtools) - library(testthat) - install_github('computational-metabolomics/structToolbox') - -Conda ------------- - -.. code-block:: command - - conda create -n structtoolbox bioconductor-structtoolbox -c conda-forge -c bioconda - conda activate structtoolbox - ------------- -References ------------- - -.. |Build Status| image:: https://github.com/computational-metabolomics/structToolbox/workflows/structToolbox/badge.svg - :target: https://github.com/computational-metabolomics/structToolbox/actions - -.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600 - :target: https://github.com/computational-metabolomics/structToolbox - -.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600 - :target: https://bioconda.github.io/recipes/bioconductor-structtoolbox/README.html - -.. |License| image:: https://img.shields.io/badge/licence-GNU_v3-teal.svg?style=flat&maxAge=3600 - :target: https://www.gnu.org/licenses/gpl-3.0.html - -.. |Coverage| image:: https://codecov.io/gh/computational-metabolomics/structToolbox/branch/master/graph/badge.svg - :target: https://codecov.io/gh/computational-metabolomics/structToolbox - -.. |mybinder| image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/computational-metabolomics/structToolbox/master?filepath=notebooks diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..eccc417 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,6 @@ +url: https://computational-metabolomics.github.io/structToolbox/ +template: + bootstrap: 5 + bootswatch: flatly + +