Merge pull request #12 from kbroman/main

Fix URL for GN API + other small things

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

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GNapi
-Version: 0.3-7
-Date: 2022-10-25
+Version: 0.3-8
+Date: 2023-07-26
 Title: Connection to the GeneNetwork API
 Description: Tools for connecting to the GeneNetwork API.
 Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
@@ -26,5 +26,5 @@ LazyData: true
 Encoding: UTF-8
 ByteCompile: true
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown=TRUE)

NEWS.md

@@ -1,3 +1,13 @@
+## GNapi 0.3-8 (2023-07-26)
+
+### Minor changes
+
+- Updated URL for GeneNetwork API
+
+- Remove an example from the vignette that no longer works:
+  "get the information for a specific group," `list_groups("rat", "HSNIH-Palmer")`
+
+
 ## GNapi 0.3-7 (2022-10-25)
 
 ### Bug fixes

R/gnapi_url.R

@@ -10,5 +10,5 @@
 #' @export
 gnapi_url <- function()
 {
-    "http://gn2.genenetwork.org/api/v_pre1"
+    "https://genenetwork.org/api/v_pre1"
 }

README.md

@@ -1,6 +1,6 @@
-## R/GNapi - R package to connect to the [GeneNetwork](http://gn2.genenetwork.org/) API
+## R/GNapi - R package to connect to the [GeneNetwork](https://genenetwork.org/) API
 
-[![R build status](https://github.com/rqtl/GNapi/workflows/R-CMD-check/badge.svg)](https://github.com/rqtl/GNapi/actions)
+[![R-CMD-check](https://github.com/rqtl/GNapi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rqtl/GNapi/actions/workflows/R-CMD-check.yaml)
 
 ---
 
@@ -24,7 +24,7 @@ Then use `remotes::install_github()` to install R/GNapi.
 ### Usage
 
 For an understanding of the
-[GeneNetwork](http://gn2.genenetwork.org) API, see
+[GeneNetwork](https://genenetwork.org) API, see
 [its
 documentation](https://github.com/genenetwork/genenetwork2/blob/testing/api_readme.md),
 as well as [Zachary Sloan](https://github.com/zsloan?tab=repositories)'s

vignettes/GNapi.Rmd

@@ -15,7 +15,7 @@ opts_chunk$set(fig.width=7, fig.height=4.5,
 ```
 
 The [R/GNapi](https://github.com/rqtl/GNapi) package provides
-access to the [GeneNetwork2](http://gn2.genenetwork.org) API; for
+access to the [GeneNetwork2](https://genenetwork.org) API; for
 details on the API, see [its
 documentation](https://github.com/genenetwork/genenetwork2/blob/testing/api_readme.md)
 The present vignette simply follows that documenation and shows the
@@ -49,12 +49,6 @@ You can also get the list of groups for a single species:
 list_groups("rat")
 ```
 
-You can also get the information for a specific group:
-
-```r
-list_groups("rat", "HSNIH-Palmer")
-```
-
 ## Fetch genotypes for Group/RIset
 
 ```r