Merge to update links and fix pkgdown site (#28)

* Updated links to reflect the repo being under BrentLab

* Updated workflow versions

* Disabling the Mac r-cmd-check for now. Not a problem with the package but rather with the GitHub Action.

.github/workflows/R-CMD-check.yaml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'renv'} #'release'}
+          #- {os: macos-latest,   r: 'renv'} #'release'}
           - {os: ubuntu-latest,   r: 'renv'} #'release'}
           #- {os: windows-latest, r: 'renv'} #'release'}
 
@@ -28,7 +28,7 @@ jobs:
       RENV_PATHS_ROOT: ~/.local/share/renv
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,7 +47,7 @@ jobs:
         run: choco install glpk -y
 
       - name: Cache packages
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.RENV_PATHS_ROOT }}
           key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}

DESCRIPTION

@@ -20,7 +20,7 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
-URL: https://westbrooktm.github.io/GOeval/
+URL: https://BrentLab.github.io/GOeval/
 Imports: 
     data.table,
     gtools,

Dockerfile

@@ -6,11 +6,6 @@ ENV RENV_VERSION 0.16.0
 RUN R -e "install.packages(c('remotes'), repos = c(CRAN = 'https://cran.wustl.edu'))"
 RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
 
-# it would be a good idea to figure out what
-# each of these do. My method of dealing with this
-# is to reduce it, try installing, and then add
-# packages to deal with errors. I don't adjust this
-# as frequently as I should.
 RUN  apt-get update && \
      apt-get install -y --no-install-recommends \
       software-properties-common \

README.md

@@ -2,8 +2,8 @@
 # GOeval
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/westbrooktm/GOeval/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/westbrooktm/GOeval/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/westbrooktm/GOeval/branch/main/graph/badge.svg)](https://app.codecov.io/gh/westbrooktm/GOeval?branch=main)
+[![R-CMD-check](https://github.com/BrentLab/GOeval/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/BrentLab/GOeval/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/BrentLab/GOeval/branch/main/graph/badge.svg)](https://app.codecov.io/gh/BrentLab/GOeval?branch=main)
 <!-- badges: end -->
 
 Welcome to GOeval - a package for gene regulatory network evaluation using Gene Ontology and other gene set databases.
@@ -12,10 +12,10 @@ This package provides functions to systematically run over-representation analys
 
 ## Installation
 
-You can install the development version of GOeval like so:
+You can install GOeval with:
 
 ``` r
-devtools::install_github("westbrooktm/GOeval", ref = "dev")
+devtools::install_github("BrentLab/GOeval")
 ```
 
 You can then load the package with:
@@ -26,4 +26,4 @@ library("GOeval")
 
 ## Documentation
 
-https://westbrooktm.github.io/GOeval/
+https://BrentLab.github.io/GOeval/

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://westbrooktm.github.io/GOeval/
+url: https://BrentLab.github.io/GOeval/
 template:
   bootstrap: 5
 

index.md

@@ -1,12 +1,12 @@
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/westbrooktm/GOeval/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/westbrooktm/GOeval/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/westbrooktm/GOeval/branch/main/graph/badge.svg)](https://app.codecov.io/gh/westbrooktm/GOeval?branch=main)
+[![R-CMD-check](https://github.com/BrentLab/GOeval/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/BrentLab/GOeval/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/BrentLab/GOeval/branch/main/graph/badge.svg)](https://app.codecov.io/gh/BrentLab/GOeval?branch=main)
 <!-- badges: end -->
 
 Welcome to GOeval - a package for gene regulatory network evaluation using Gene Ontology and other gene set databases.
 
 This package provides functions to systematically run over-representation analysis (ORA) on multiple subsets of a gene regulatory network and its permutations using the 'WebGestaltR' package. It also provides functions to assess the quality of biological information captured by the network via metrics calculated from the ORA results.
 
-Here, you will find [Reference](https://westbrooktm.github.io/GOeval/reference/index.html) documentation on the purposes of the package's functions and their arguments, as well as a [Get started](https://westbrooktm.github.io/GOeval/articles/GOeval.html) vignette showing example usage of the package's functions.
+Here, you will find [Reference](https://BrentLab.github.io/GOeval/reference/index.html) documentation on the purposes of the package's functions and their arguments, as well as a [Get started](https://BrentLab.github.io/GOeval/articles/GOeval.html) vignette showing example usage of the package's functions.
 
 Input format: You will need a network file in which each row represents a directed edge. The tab-separated entries in each row are the the source node (e.g. transcription factor), the target node (e.g. the regulated gene), and optionally an edge score. The subset_network function requires edge scores. The webgestalt_network function requires a “gene universe” file that has a single column containing all the genes that could possibly be present in the network.

vignettes/GOeval.Rmd

@@ -17,9 +17,9 @@ knitr::opts_chunk$set(
 First, install and load this package. It is easiest to use either the "devtools" or "remotes" package to do so. "remotes" is a smaller package, so it might be the better option if you do not want to install all of "devtools."
 
 ```{r, eval = FALSE}
-devtools::install_github("westbrooktm/GOeval")
+devtools::install_github("BrentLab/GOeval")
 # OR
-remotes::install_github("westbrooktm/GOeval")
+remotes::install_github("BrentLab/GOeval")
 ```
 
 ```{r setup}
@@ -76,7 +76,7 @@ net_1_data <- evaluate(network_path, reference_path, out_dir, network_name,
 
 It is possible to customize the behavior of the `evaluate` function by using arguments in addition to the four required ones. In the above example, the 'edges' argument modifies the sizes of subsets to analyze from the input network. "permutations = 1" allows a faster run time than the default "permutations = 3" at the cost of running the analyses on fewer permuted versions of the input network. "get_annotation_overlap = TRUE" indicates that the "annotation_overlap" metric should be calculated.
 
-The available arguments for all functions can be found at the [Reference](https://westbrooktm.github.io/GOeval/reference/index.html) tab at the top of this page.
+The available arguments for all functions can be found at the [Reference](https://BrentLab.github.io/GOeval/reference/index.html) tab at the top of this page.
 
 After `evaluate` runs for a couple minutes, the directory at out_dir should contain a folder of subsets of the original network, a folder that contains the ORA summaries and sets of target genes, and a .pdf file with plots of metrics calculated from those summaries. The evaluate function returns the data used to make the plots as a list of data.frames.