miga-base 1.3.7.2 → 1.3.7.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b57ca3778ff3605473ebae2ebf69aabdb231302a59605094721c6af9cbc7a798
-  data.tar.gz: fbe455bc223b23e5b906874fede98aa85ad443e83d3c0e87839f3bb9bf46ba29
+  metadata.gz: da6f90e73e7f3f740623ad77e09886b1c7618de2f484ba412e53d329fb771c12
+  data.tar.gz: 662eda2643f1695285e02ef18076aa3c3bed86bfbbd2d0fc9c91481fbe6fb384
 SHA512:
-  metadata.gz: 682cc9964783ebc692be1d8358708d800caa08713b818a9aae7a6ed4d25d0874ddc553ba7e17ce2712092c9e2874353c00b90c3d8f49a3d339a33f42a7cfed6e
-  data.tar.gz: 63e23a79b5af66e4f5816d6ece02b1f349f0477bcf46a2646328028654ffb9792a33c2ddb0e9237571112232c6e735e3a4df8433608495b43be7b6da038651c6
+  metadata.gz: 268833ab588449626fd9ee1c8374daea22482fe85d73570c6c9bec58dd1b00c8385e53f8c9d26f0903cf88451f715194c2ddd5bb330eff0a5695ffb9f0bcb51f
+  data.tar.gz: 1dabe6af4158fbb26c760aa2c4673d1cdba45b832a54eb01995418bf11a8cb7c02708e99c54a1862d9bf501101f0fc55afc6f9b44d487c37d7d35cd61a1ff688

data/lib/miga/cli/action/rm.rb

@@ -17,7 +17,7 @@ class MiGA::Cli::Action::Rm < MiGA::Cli::Action
   end
 
   def perform
-    if r = cli.load_result
+    if cli[:result] && r = cli.load_result
       cli[:remove] ? r.remove! : r.unlink
     elsif d = cli.load_dataset
       cli.load_project.unlink_dataset(d.name)

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 7, 2].freeze
+  VERSION = [1.3, 7, 3].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 6, 15)
+  VERSION_DATE = Date.new(2023, 6, 29)
 
   ##
   # References of MiGA

data/utils/subclades.R

@@ -311,7 +311,7 @@ ani_distance <- function (ani_file, sel) {
     sim <- read.table(gzfile(ani_file), sep = "\t", header = TRUE, as.is = TRUE)
   }
   
-  # If there is not data end process
+  # If there is no data, end process
   if (nrow(sim) == 0) return(NULL)
 
   # Apply filter (if requested)
@@ -319,7 +319,7 @@ ani_distance <- function (ani_file, sel) {
   if (!is.na(sel) && file.exists(sel)) {
     say("Filter selection")
     ids <- read.table(sel, sep = "\t", head = FALSE, as.is = TRUE)[,1]
-    sim <- sim[sim$a %in% ids & sim$b %in% ids, ]
+    sim <- sim[which(sim$a %in% ids & sim$b %in% ids), ]
   } else {
     ids <- with(sim, unique(c(a, b)))
   }
@@ -329,7 +329,7 @@ ani_distance <- function (ani_file, sel) {
   sim$d <- 1 - (sim$value / 100)
   return(as.dist(with(sim, {
     out <- matrix(
-      max(d) * 1.2, nrow = length(ids), ncol = length(ids),
+      min(max(d) * 1.2, 1.0), nrow = length(ids), ncol = length(ids),
       dimnames = list(ids, ids)
     )
     out[cbind(ids, ids)] <- 0

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.7.2
+  version: 1.3.7.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-15 00:00:00.000000000 Z
+date: 2023-06-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons