Merge pull request #554 from remlapmot/v0-6-7

TwoSampleMR 0.6.7

Author: remlapmot

.github/workflows/check-full.yaml

@@ -54,8 +54,9 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: >
-            any::rcmdcheck
+            any::rcmdcheck, MendelianRandomization=?ignore-before-r=4.4.0
           needs: check
+          upgrade: 'TRUE'
 
       - name: Create and populate .Renviron file
         run: |

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MR Base Database
-Version: 0.6.6
+Version: 0.6.7
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,11 @@
+# TwoSampleMR v0.6.7
+
+(Release date 2024-08-21)
+
+* Update OpenGWAS API URLs
+* Minor tweak to `R CMD check` GitHub Actions due to the rjson hard dependency of the MendelianRandomization package now requiring R >= 4.4.0
+* Add dark mode to pkgdown site
+
 # TwoSampleMR v0.6.6
 
 (Release date 2024-07-06)

tests/testthat/test_otherformats.R

@@ -5,6 +5,7 @@ load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
 
 test_that("MRInput", {
+	skip_if(getRversion() < '4.4.0') # because MendelianRandomization will not be installed
 	w <- dat_to_MRInput(dat, get_correlations=FALSE)
 	expect_true(length(w) == 1)	
 	expect_true(class(w) == "list")
@@ -15,6 +16,7 @@ test_that("MRInput with cor", {
   skip_on_cran()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
+  skip_if(getRversion() < '4.4.0') # because MendelianRandomization will not be installed
 	w <- tryCatch(dat_to_MRInput(dat, get_correlations=TRUE)[[1]],
 	              error = skip("Server issues"),
 	              warning = expect_warning())

vignettes/gwas2020.Rmd

@@ -73,15 +73,15 @@ Automated download from the EBI repository, and an automated upload system and b
 
 ### Error messages are more informative
 
-Previously if a query to the database failed it didn't give a reason, hopefully there is more clarity regarding what is happening now. You can also check the status of the server here: https://gwas-api.mrcieu.ac.uk/
+Previously if a query to the database failed it didn't give a reason, hopefully there is more clarity regarding what is happening now. You can also check the status of the server here: https://api.opengwas.io/api/
 
 ### Easier programmatic access to the database
 
 We are trying to make it as flexible as possible to access the data. The TwoSampleMR R package was previously the only programmatic way to access the data, now we have the following options:
 
 - [ieugwasr R package](https://mrcieu.github.io/ieugwasr/): All the TwoSampleMR functions that access the data are done by calling this package now. It is a simple wrapper around the API that controls access to the database.
 - [ieugwaspy python package](https://github.com/MRCIEU/ieugwaspy/): Similar functionality to ieugwasr (Under construction).
-- [API](https://gwas-api.mrcieu.ac.uk/): You can use the API directly, e.g. for building your own services or applications.
+- [API](https://api.opengwas.io/api/): You can use the API directly, e.g. for building your own services or applications.
 
 ### Local LD operations
 
@@ -98,7 +98,7 @@ Either the data in the database, or the GWAS VCF files, can be queried and the r
 ## Key links
 
 - The IEU GWAS database: https://gwas.mrcieu.ac.uk
-- API to the IEU GWAS database: https://gwas-api.mrcieu.ac.uk
+- API to the IEU GWAS database: https://api.opengwas.io/api/
 - ieugwasr package, for R access to the API: https://mrcieu.github.io/ieugwasr/
 - ieugwaspy package, for python access to the API: https://github.com/MRCIEU/ieugwaspy/ (Under construction)
 - gwasvcf package, R interface to GWAS VCF files: https://mrcieu.github.io/gwasvcf/