bump release to v1.0.0 w/ NEWS and w/o CHANGELOG

* this fixes #20 * add CRAN comments file * update the wordlist accordingly
ClavelLab · Sep 5, 2023 · 8ebfa04 · 8ebfa04
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^codecov\.yml$
 ^doc$
 ^Meta$
+^cran-comments\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: maldipickr
 Title: Dereplicate And Cherry-Pick Mass Spectrometry Spectra
-Version: 0.1.0
+Version: 1.0.0
 Authors@R: c(
     person("Charlie", "Pauvert", , "cpauvert@ukaachen.de", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-9832-2507")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,49 @@
+# maldipickr 1.0.0
+
+## Changed
+
+* (**BREAKING**) `read_biotyper_report()` first column is now `name` instead of `spot`, meaning `read_many_biotyper_reports()` renames all the `name` columns to `original_name`. This was to `pick_spectra()` easily usable with taxonomy identification reports (`38a614173fd21315a40e0823600a2082fa0935bb`)
+* (**BREAKING**) All functions now follow the `verb_concept` nomenclature, meaning clustering functions are now renamed accordingly (#24):
+    -  Change `similarity_to_clusters()` to `delineate_with_similarity()`
+    -  Change `identification_to_clusters()` to `delineate_with_identification()`
+* Refactor the `delineate_with_similarity()` clustering function (formerly: `similarity_to_clusters()`) without using the `{igraph}` nor `{tidygraph}` R packages, for fewer dependencies and simpler codebase (#18)
+* Update the `DESCRIPTION` to include the Strejcek reference (#22) and better highlight the package added-value
+* Refactor the `pkgdown` website with a more accessible font and color schema inline with the logo color palette
+* Change the vignettes titles and outline to better structure the documents
+* Refactor cosine similarity computation example by highlighting the dedicated `coop::tcosine()` instead of the `t() %>% coop::cosine()`
+
+## Added
+
+* Add long or wide output format for `read_biotyper_report()` (#12)
+* Document how to quickstart with the `{maldipickr}` package for those in a hurry (#15)
+* Document more precisely how to install tagged release of `{maldipickr}` package 
+* Add better tests for `merge_processed_spectra()` (`b39c1313fd38239b4b1821a243c9debf467fd092`)
+* Document authors list according to CRAN policy
+* Add CRAN comments file to track submission notes
+
+## Removed
+
+* Deprecate the `CHANGELOG.md` in favor of the R specific `NEWS.md` (#20)
+* Remove redundant check after symbolic links creation (#19)
+
+## Fixed
+
+* Fix `summarise()` usage in `pick_spectra()`, with code simplification (#11)
+* Remove symbolic links created for importing acqu spectra files (#21)
+* Fix CRAN warnings regarding `qpdf` (`3b19dd36a6ec0f5dc277418c98977c526981b6e3`)
+* Fix masked relevant `to_pick` column in the vignette (#17)
+
+# maldipickr 0.1.1
+
+## Added
+
+* Add citation file for R ([`CITATION`](inst/CITATION)) and for GitHub ([`CITATION.cff`](CITATION.cff))
+* Add a [`CHANGELOG.md`](CHANGELOG.md) ([Common Changelog](https://common-changelog.org))
+
+## Changed
+
+* Improve the package description according to CRAN recommendations
+
 # maldipickr 0.1.0
 
 * First stable version

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
diff --git a/dev/CHANGELOG.md b/dev/CHANGELOG.md
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -6,6 +6,7 @@ Bruker
 CMD
 Canck
 Carlier
+Changelog
 Cleenwerck
 Cnockaert
 Dawyndt
@@ -43,8 +44,10 @@ Uhlik
 Vandamme
 Verheyde
 Wieme
+acqu
 al
 bruker
+codebase
 codecov
 csv
 dereplicate
@@ -61,6 +64,7 @@ magrittr
 maldi
 modularity
 natively
+quickstart
 rRNA
 scalable
 spectrometry