Update versions for release

SPAAM-community · Sep 30, 2023 · 5c7d9b6 · 5c7d9b6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project follows to [Calendar Versioning](https://calver.org/).
 
-## v23.09: Historic Centre of Cienfuegos [Unreleased]
+## v23.09: Historic Centre of Cienfuegos
 
 ### Added
 
@@ -20,7 +20,7 @@ and this project follows to [Calendar Versioning](https://calver.org/).
 - Long 2023 10.1371/journal.ppat.1011538 (added by @DianaSpurite)
 - Campos 2023 10.1038/s41467-023-39950-z (added by @DianaSpurite)
 - Parker2023 10.1371/journal.ppat.1011404 (added by @DianaSpurite)
-- Clavel 2023 10.1016/j.isci.2023.106787 (added by @DianaSpurite/ @theHatIsBack)
+- Clavel 2023 10.1016/j.isci.2023.106787 (added by @DianaSpurite/@theHatIsBack)
 
 #### Ancient Metagenome: Environmental
 

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3980833.svg)](https://doi.org/10.5281/zenodo.3980833)
 ![check_dataset](https://github.com/spaam-community/AncientMetagenomeDir/workflows/check_dataset/badge.svg)
 [![Joins us on Slack](https://img.shields.io/badge/slack-ancientmetagenomedir-blueviolet)](https://spaam-community.slack.com/channels/ancientmetagenomedir)
-[![latest_release](https://img.shields.io/badge/Latest%20Release-v23.06.0-yellow)](https://github.com/spaam-community/AncientMetagenomeDir/releases)
+[![latest_release](https://img.shields.io/badge/Latest%20Release-v23.09.0-yellow)](https://github.com/spaam-community/AncientMetagenomeDir/releases)
 
 AncientMetagenomeDir is a community curated resource of lists of all published
 **shotgun**-sequenced ancient metagenome or microbial genome-level enriched samples and libraries.

diff --git a/assets/analysis/release-stats-statement-generator.R b/assets/analysis/release-stats-statement-generator.R
@@ -1,25 +1,29 @@
 suppressPackageStartupMessages(library(tidyverse))
 
-previous_tag <- "v23.03.0"
+previous_tag <- "v23.06.0"
 release_tag <- "master"
-new_release <- "v23.06.0"
+new_release <- "v23.09.0"
 
 ## SAMPLES
 
 previous_env_samples <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", previous_tag, "/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv"), show_col_types = FALSE)
 previous_microb_samples <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", previous_tag, "/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv"), show_col_types = FALSE)
 previous_single_samples <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", previous_tag, "/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv"), show_col_types = FALSE)
-previous_pubs_samples <- c(previous_env_samples$publication_doi, previous_microb_samples$publication_doi, previous_single_samples$publication_doi) %>% unique() %>% length
+previous_pubs_samples <- c(previous_env_samples$publication_doi, previous_microb_samples$publication_doi, previous_single_samples$publication_doi) %>%
+       unique() %>%
+       length()
 
 new_env_samples <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", release_tag, "/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv"), show_col_types = FALSE)
 new_microb_samples <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", release_tag, "/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv"), show_col_types = FALSE)
 new_single_samples <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", release_tag, "/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv"), show_col_types = FALSE)
-new_pubs_samples <- c(new_env_samples$publication_doi, new_microb_samples$publication_doi, new_single_samples$publication_doi) %>% unique() %>% length
+new_pubs_samples <- c(new_env_samples$publication_doi, new_microb_samples$publication_doi, new_single_samples$publication_doi) %>%
+       unique() %>%
+       length()
 
 adds_pubs_samples <- new_pubs_samples - previous_pubs_samples
 adds_env_samples <- nrow(new_env_samples) - nrow(previous_env_samples)
 adds_microb_samples <- nrow(new_microb_samples) - nrow(previous_microb_samples)
-adds_single_samples <-  nrow(new_single_samples) - nrow(previous_single_samples)
+adds_single_samples <- nrow(new_single_samples) - nrow(previous_single_samples)
 
 tot_pubs_samples <- new_pubs_samples
 tot_env_samples <- nrow(new_env_samples)
@@ -31,17 +35,21 @@ tot_single_samples <- nrow(new_single_samples)
 previous_env_libraries <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", previous_tag, "/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv"), show_col_types = FALSE)
 previous_microb_libraries <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", previous_tag, "/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv"), show_col_types = FALSE)
 previous_single_libraries <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", previous_tag, "/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv"), show_col_types = FALSE)
-previous_pubs_libraries <- c(previous_env_libraries$data_publication_doi, previous_microb_libraries$data_publication_doi, previous_single_libraries$data_publication_doi) %>% unique() %>% length
+previous_pubs_libraries <- c(previous_env_libraries$data_publication_doi, previous_microb_libraries$data_publication_doi, previous_single_libraries$data_publication_doi) %>%
+       unique() %>%
+       length()
 
 new_env_libraries <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", release_tag, "/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv"), show_col_types = FALSE)
 new_microb_libraries <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", release_tag, "/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv"), show_col_types = FALSE)
 new_single_libraries <- read_tsv(paste0("https://github.com/SPAAM-community/AncientMetagenomeDir/raw/", release_tag, "/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv"), show_col_types = FALSE)
-new_pubs_libraries <- c(new_env_libraries$data_publication_doi, new_microb_libraries$data_publication_doi, new_single_libraries$data_publication_doi) %>% unique() %>% length
+new_pubs_libraries <- c(new_env_libraries$data_publication_doi, new_microb_libraries$data_publication_doi, new_single_libraries$data_publication_doi) %>%
+       unique() %>%
+       length()
 
 adds_pubs_libraries <- new_pubs_libraries - previous_pubs_libraries
 adds_env_libraries <- nrow(new_env_libraries) - nrow(previous_env_libraries)
 adds_microb_libraries <- nrow(new_microb_libraries) - nrow(previous_microb_libraries)
-adds_single_libraries <-  nrow(new_single_libraries) - nrow(previous_single_libraries)
+adds_single_libraries <- nrow(new_single_libraries) - nrow(previous_single_libraries)
 
 tot_pubs_libraries <- new_pubs_libraries
 tot_env_libraries <- nrow(new_env_libraries)
@@ -50,22 +58,22 @@ tot_single_libraries <- nrow(new_single_libraries)
 
 ## STATEMENTS
 
-cat("\nRelease", new_release, 
-       "includes", adds_pubs_samples, "new publications, representing", 
-       adds_microb_samples, "new ancient host-associated metagenome samples,", 
-       adds_single_samples, "new ancient microbial genomes, and", 
+cat(
+       "\nRelease", new_release,
+       "includes", adds_pubs_samples, "new publications, representing",
+       adds_microb_samples, "new ancient host-associated metagenome samples,",
+       adds_single_samples, "new ancient microbial genomes, and",
        adds_env_samples, "new ancient environmental samples.",
-       "This brings the repository to a total of", 
+       "This brings the repository to a total of",
        tot_pubs_samples, "publications,",
-       tot_microb_samples,  "ancient host-associated metagenome samples,", 
-       tot_single_samples,  "ancient microbial genomes, and", 
-       tot_env_samples,  "ancient environmental samples\n\nFurthermore, this release adds",
-       adds_microb_libraries, "new ancient host-associated metagenome libraries,", 
-       adds_single_libraries, "new ancient microbial genome libraries, and", 
+       tot_microb_samples, "ancient host-associated metagenome samples,",
+       tot_single_samples, "ancient microbial genomes, and",
+       tot_env_samples, "ancient environmental samples\n\nFurthermore, this release adds",
+       adds_microb_libraries, "new ancient host-associated metagenome libraries,",
+       adds_single_libraries, "new ancient microbial genome libraries, and",
        adds_env_libraries, "new ancient environmental libraries.",
-       "This brings the repository to a total of", 
-       tot_microb_libraries,  "ancient host-associated metagenome libraries,", 
-       tot_single_libraries,  "ancient microbial genomes libraries, and", 
-       tot_env_libraries,  "ancient environmental libraries.\n\n"
+       "This brings the repository to a total of",
+       tot_microb_libraries, "ancient host-associated metagenome libraries,",
+       tot_single_libraries, "ancient microbial genomes libraries, and",
+       tot_env_libraries, "ancient environmental libraries.\n\n"
 )
-