From 5c7d9b696ffac049b1ba4547fa042a889bb7f578 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 30 Sep 2023 11:38:24 +0200 Subject: [PATCH] Update versions for release --- CHANGELOG.md | 4 +- README.md | 2 +- .../release-stats-statement-generator.R | 54 +++++++++++-------- 3 files changed, 34 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fd830dbd5..3365585fe 100644 --- 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 index 9b75dd561..a5e4b2c14 100644 --- 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 index aff26b4c8..63cab79f2 100644 --- 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" ) -