update news, cran comments, and codemeta.json

NEWS.md

@@ -1,17 +1,22 @@
 taxize 0.9.99
 =============
 
+### DEFUNCT
+
+* `tnrs()` and `tnrs_sources()` functions are defunct. The service has been unreliable for years now, and AFAICT is down for good. Associated changes have been made throughout the package, eg. `resolve()` no longer has an option for tnrs, etc. (#841) (#842)
+
 ### MINOR IMPROVEMENTS
 
-* asdadf (#xxx)
-* asdadf (#xxx)
-* asdadf (#xxx)
+* new article/vignette added on issues with taxonomic ranks, e.g., "NCBI is weird", and how rank information is maintained and used within taxize (#852)
+* vignettes are no longer on cran - find them at the docs site linked in DESCRIPTION (#855)
+* re-instate a `tol_resolve()` test following new version of `rotl` package on cran (#816)
+* improve `class2tree()` function documentation regarding how the function works in more detail (#849) (#851)
+* improvements for WORMS, applies to functions `worms_downstream()`, `children(..., db="worms")` and `downstream(..., db="worms")`: now paginate automatically for the user to get all results, and allow parameter `marine_only` to be passed through the high level functions `children()`/`downstream()` down to `worrms::wm_children()` where it toggles whether marine only results are returned (#848) thanks @oharac !
 
 ### BUG FIXES
 
-* asdadf (#xxx)
-* asdadf (#xxx)
-* asdadf (#xxx)
+* fix to `ncbi_downstream()` (which cascades up to `downstream(..., db="ncbi")`): an unneeded line of code was removed that was also throwing an error in some cases (#850)
+* fixes for WORMS ranks, applies to functions `worms_downstream()`, `children(..., db="worms")` and `downstream(..., db="worms")`: added ranks `epifamily` and `infraphylum`. In addition, when a rank is missing in data returned from WORMS, we'll change the missing rank to "no rank" (#847)
 
 
 taxize 0.9.98

codemeta.json

@@ -10,13 +10,13 @@
   "codeRepository": "https://github.com/ropensci/taxize",
   "issueTracker": "https://github.com/ropensci/taxize/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.9.98",
+  "version": "0.9.99",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.0.2 Patched (2020-09-01 r79114)",
+  "runtimePlatform": "R version 4.0.3 (2020-10-10)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -131,30 +131,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=testthat"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "knitr",
-      "name": "knitr",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=knitr"
-    },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "rmarkdown",
-      "name": "rmarkdown",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "vegan",
@@ -323,7 +299,6 @@
       "@type": "SoftwareApplication",
       "identifier": "rredlist",
       "name": "rredlist",
-      "version": ">= 0.5.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -477,7 +452,7 @@
         }
       ],
       "name": "taxize - taxonomic search and retrieval in R",
-      "url": "https://f1000research.com/articles/2-191/v2/",
+      "url": "https://f1000research.com/articles/2-191/v2",
       "isPartOf": {
         "@type": "PublicationIssue",
         "datePublished": "2013",

cran-comments.md

@@ -14,7 +14,7 @@
 
 ------
 
-This version xxx.
+This version makes a few functions defunct for a web service that is no longer up, improves some docs, and fixes a few bugs. In addition, this fixes a failing test due to the latest rredlist on CRAN (an import here).
 
 Thanks!
 Scott Chamberlain