Synchronise wip with master (#173)

pepijn-devries · annakrystalli · web-flow · commit c05d31c43483 · 2026-05-06T16:47:55.000+02:00
* Work in progress (#170) * Updated NEWS * Some small fixes and improved test coverage * Rerendered README * Version bump for CRAN release * Fixed test * Added rhub workflow * Fix for #127 * Added proxy vignette * Try to fix failing test-coverage workflow * Some fixes to vignette and cross references * Added login for functions that download from s3 storage * Updated NEWS file * Improved test coverage * Version bump for CRAN release. And added html and R files in vignettes dir to .buildignore * Don't make 'translate' vignette self-contained. Otherwise, it will embed the >2Mb gif animation * Don't run proxy-vignette chunks if password is not set... * And only if the HDF5 driver is present * added namespace * forgot some eval args * Explicitly retrieve an pass variable names when reading proxy object when missing * Added lifecycle badge to `cms_zarr_proxy()` * Added lifecycle badge to `cms_native_proxy()` as well * More rigorous checking for required dependencies when accessing online resources * updated news * Some final tweaks on BLOSC checks * Added eval checks to translate.rmd * Added startup message * Fix for #143 * added fix to NEWS * More informative error message * Added warnings for mismatching dimensions while subsetting. See #142 and #141 * Added test for #142 and #143 * Improved test coverage * fix for #133 * Some minor fixes * use latest geospatial container for pkgdown * revert yaml * Revert proxy vignette * attempt to fix windows-devel build on R-universe * silly typo * Removed duplicated code block * Updated pkgdown workflow * Rever proxy vignette * debug message * Driver detection will fail on any warning * Added `vignette("product-info")` * Fix for #158 * Minor tweaks and version bump for CRAN release * Fix for win old-rel check on CRAN * Test time-range subsetting to reproduce #164 * Resolved conflict * Fix for #167 * Attempt to fix #164 * Try and fix pkgdown workflow * Fix for pkgdown workflow * Fix in proxy vignette * Attempt to avoid embedding large gif file * Added `vignette("glossary")` and `cms_glossary()`. Fixed WMTS functions. Updated README.md * spell checked. Version bump for CRAN submission * Improved test coverage * fixed tests * docs: update EMODnet R tutorials URL after repo transfer (#172) * docs: update EMODnet R tutorials URL after repo transfer The EMODnet Biology Geospatial R Tutorials referenced from the README and the glossary vignette were transferred from r-rse/ to the EMODnet/ GitHub org earlier today. The rendered site is now at https://emodnet.github.io/emodnet-bio-r-geo-tutorials/. Updates the three references: - README.Rmd L75 - README.md L75 (kept in sync with the .Rmd) - vignettes/glossary.Rmd L27 * Bump version to 0.4.6.0002 * Update version to v0.4.6.0002 and documentation --------- Co-authored-by: Pepijn de Vries <pepijn-devries@users.noreply.github.com> --------- Co-authored-by: Anna Krystalli <annakrystalli@googlemail.com>
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CopernicusMarine
 Type: Package
 Title: Search Download and Handle Data from Copernicus Marine Service Information
-Version: 0.4.6.0001
+Version: 0.4.6.0002
 Authors@R: c(person("Pepijn", "de Vries", role = c("aut", "cre", "dtc"),
     email = "pepijn.devries@outlook.com",
     comment = c(ORCID = "0000-0002-7961-6646")))
diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,8 @@
-CopernicusMarine v0.4.6.0001
+CopernicusMarine v0.4.6.0002
 -------------
 
  * Fixed tests
+ * Updated documentation
 
 CopernicusMarine v0.4.6
 -------------
diff --git a/README.Rmd b/README.Rmd
@@ -72,7 +72,7 @@ Please check the manual for complete documentation of the package.
 
 For an excellent tutorial showing how to combine multiple spatial datasets
 from different sources (amongst which is CopernicusMarine), check out:
-[EMODnet Biology Geospatial R Tutorials (Tutorial 4)](https://r-rse.github.io/emodnet-bio-r-geo-tutorials/tutorials/tutorial-04.html)
+[EMODnet Biology Geospatial R Tutorials (Tutorial 4)](https://emodnet.github.io/emodnet-bio-r-geo-tutorials/tutorials/tutorial-04.html)
 by [Anna Krystalli](https://github.com/annakrystalli)
 
 <h3 id="sec-subset">Downloading a subset</h3>
diff --git a/README.md b/README.md
@@ -72,7 +72,7 @@ complete documentation of the package.
 For an excellent tutorial showing how to combine multiple spatial
 datasets from different sources (amongst which is CopernicusMarine),
 check out: [EMODnet Biology Geospatial R Tutorials (Tutorial
-4)](https://r-rse.github.io/emodnet-bio-r-geo-tutorials/tutorials/tutorial-04.html)
+4)](https://emodnet.github.io/emodnet-bio-r-geo-tutorials/tutorials/tutorial-04.html)
 by [Anna Krystalli](https://github.com/annakrystalli)
 
 <h3 id="sec-subset">
diff --git a/vignettes/glossary.Rmd b/vignettes/glossary.Rmd
@@ -24,7 +24,7 @@ so you don't have to know all technical aspects.
 
 However, since jargon can vary among data portals, I've put together
 a glossary of terms used by Copernicus Marine. It is based on the
-excellent [tutorial](https://r-rse.github.io/emodnet-bio-r-geo-tutorials/tutorials/tutorial-04.html)
+excellent [tutorial](https://emodnet.github.io/emodnet-bio-r-geo-tutorials/tutorials/tutorial-04.html)
 by [Anna Krystalli](https://github.com/annakrystalli). This
 tutorial also highlights some contrasts with other data portals.
 The table below lists some important definitions and their background.
