Work in progress (#176)

* Synchronise wip with master (#173)

* 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>

* Switched from `aws.s3` to `paws` dependecy see cloudyr/aws.signature#68

* Fix for failing 'noSuggests' check on CRAN

* Promoted 'experimental' functions to 'stable' after a period of testing

* Added 'family' tags to documentation

* added s3 example

* Updated glossary

* removed redundant 'TODO'

* updated _pkgdown.yml and @family tags

---------

Co-authored-by: Anna Krystalli <annakrystalli@googlemail.com>

Author: pepijn-devries

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CopernicusMarine
 Type: Package
 Title: Search Download and Handle Data from Copernicus Marine Service Information
-Version: 0.4.6.0005
+Version: 0.4.6.0006
 Authors@R: c(person("Pepijn", "de Vries", role = c("aut", "cre", "dtc"),
     email = "pepijn.devries@outlook.com",
     comment = c(ORCID = "0000-0002-7961-6646")))

NEWS.md

@@ -1,4 +1,4 @@
-CopernicusMarine v0.4.6.0005
+CopernicusMarine v0.4.6.0006
 -------------
 
  * Fixed tests

R/cms_cite_product.r

@@ -8,7 +8,7 @@
 #' listed at Copernicus. Note that the citing formatting does not appear to be standardised.
 #' @rdname cms_cite_product
 #' @name cms_cite_product
-#' @family product-functions
+#' @family product
 #' @examples
 #' cms_cite_product("SST_MED_PHY_SUBSKIN_L4_NRT_010_036")
 #' @author Pepijn de Vries

R/cms_product_details.r

@@ -8,7 +8,7 @@
 #' @returns Returns a named `list` with product details.
 #' @rdname cms_product_details
 #' @name cms_product_details
-#' @family product-functions
+#' @family product
 #' @examples
 #' if (interactive()) {
 #'   cms_product_details("GLOBAL_ANALYSISFORECAST_PHY_001_024")

R/cms_product_services.r

@@ -13,7 +13,7 @@
 #' if (interactive()) {
 #'   cms_product_services("GLOBAL_ANALYSISFORECAST_PHY_001_024")
 #' }
-#' @family product-functions
+#' @family product
 #' @author Pepijn de Vries
 #' @family product
 #' @export

R/cms_products_list.r

@@ -15,7 +15,7 @@
 #' unavailable.
 #' @rdname cms_products_list
 #' @name cms_products_list
-#' @family product-functions
+#' @family product
 #' @examples
 #' cms_products_list()
 #' 

_pkgdown.yml

@@ -1,4 +1,24 @@
 url: https://pepijn-devries.github.io/CopernicusMarine/
 template:
   bootstrap: 5
-
+reference:
+  - title: "Authentication Functions"
+    desc: "Functions related to Copernicus Marine authentication"
+    contents:
+      - has_concept("authentication")
+  - title: "Product Functions"
+    desc: "Functions retrieving information about Copernicus Marine products"
+    contents:
+      - has_concept("product")
+  - title: "Download Functions"
+    desc: "Functions for downloading data from Copernicus Marine services"
+    contents:
+      - has_concept("download")
+  - title: "Leaflet Functions"
+    desc: "Functions that can be used with interactive maps using leaflet"
+    contents:
+      - has_concept("supporting")
+  - title: "Support Functions"
+    desc: "Supporting functions for Copernicus Marine"
+    contents:
+      - has_concept("supporting")