miga-base 1.4.1.1 → 1.4.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f62f3128a245915ab0a7fc73a71e2819e672c68f1003ea387b51ad227654b59f
-  data.tar.gz: cb374513b9b38a32934a88dae8849ec80aafafded609eae429c90d4072bc4afa
+  metadata.gz: e8a9efe7d6856ed97bd734817d4c244e90aa217eb951862447b3cbc37de4e53a
+  data.tar.gz: 7f235a9dc35a5782c35857ef6fda7cd2ba31aadbf348e54ceffa42312b79f68c
 SHA512:
-  metadata.gz: 237e9a0dcd2ac5ee740233fd6912ff393ebb333a14897b9b0a4422b8931cab8a0e0a6c9fea68ee2075d6be40261d4f245453f8b2db97aa3e0845d8ea92dc8516
-  data.tar.gz: 85df874e633b48bdb0c98073c5f0557b248ab0b65a36e11eb0e0c78996539a6946665884b43af9a73e81ce73c3c3b8806c0aee268317ded831fba315797b180e
+  metadata.gz: dbc4345086a35fcac1837f8f5d24c16f73354e80c70d6bb52998e1503f29f3070073edc08af22e1b6462a4099c7947081914591c724581459ae661a79d1b8113
+  data.tar.gz: 1705185d4668bd5922729879e64d949c0b41f59bdee7bef325a9ed5c6909305559f7e5dcd47b31fe4a21a0d3eba74ba8775463e0b334b51720b510c36560d512

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

@@ -20,7 +20,7 @@ class MiGA::Cli::Action::Env < MiGA::Cli::Action
       done
       # Override gzip with pigz (if available)
       if command -v pigz &>/dev/null ; then
-        function gzip { pigz -p ${CORES:-2} "$@" ; }
+        gzip() { pigz -p ${CORES:-2} "$@" ; }
       fi
     BASH
   end

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 = [1.4, 1, 1].freeze
+  VERSION = [1.4, 1, 2].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2025, 11, 19)
+  VERSION_DATE = Date.new(2026, 2, 3)
 
   ##
   # References of MiGA

data/scripts/aai_distances.bash

@@ -10,7 +10,7 @@ DIR="$PROJECT/data/09.distances/02.aai"
 miga_start_project_step "$DIR"
 
 # Extract values
-function foreach_database_aai {
+foreach_database_aai() {
   local SQL="SELECT seq1, seq2, aai, sd, n, omega from aai;"
   local k=0
   while [[ -n ${DS[$k]} ]] ; do
@@ -19,7 +19,7 @@ function foreach_database_aai {
   done
 }
 
-function aai_tsv {
+aai_tsv() {
   DS=($(miga ls -P "$PROJECT" --ref --no-multi --active))
   echo "a b value sd n omega" | tr " " "\\t"
   if [[ ${#DS[@]} -gt 40000 ]] ; then

data/scripts/ani_distances.bash

@@ -10,7 +10,7 @@ DIR="$PROJECT/data/09.distances/03.ani"
 miga_start_project_step "$DIR"
 
 # Extract values
-function foreach_database_ani {
+foreach_database_ani() {
   local SQL="SELECT seq1, seq2, ani, sd, n, omega from ani;"
   local k=0
   while [[ -n ${DS[$k]} ]] ; do
@@ -19,7 +19,7 @@ function foreach_database_ani {
   done
 }
 
-function ani_tsv {
+ani_tsv() {
   DS=($(miga ls -P "$PROJECT" --ref --no-multi --active))
   echo "a b value sd n omega" | tr " " "\\t"
   foreach_database_ani

data/scripts/init.bash

@@ -2,7 +2,7 @@
 set -e
 
 #=======[ Functions ]
-function ask_user {
+ask_user() {
   local question=$1
   local default=$2
   echo "$question" >&2
@@ -12,7 +12,7 @@ function ask_user {
   echo -n "$user_answer"
 }
 
-function check_req {
+check_req() {
   local bin=$1
   local default
   default=$(dirname "$(which "$bin")")
@@ -26,14 +26,14 @@ function check_req {
   fi
 }
 
-function check_rlib {
+check_rlib() {
   local rlib=$1
   gotit=$(echo "if(require($rlib)) cat('GOT','IT')" | R --vanilla -q 2>&1 \
     | grep -c "GOT IT")
   [[ "$gotit" == "1" ]]
 }
 
-function check_gem {
+check_gem() {
   local gem=$1
   gotit=$(echo "require '$gem'" | ruby 2>/dev/null && echo 1)
   [[ "$gotit" == "1" ]]

data/scripts/miga.bash

@@ -10,13 +10,13 @@ SCRIPT=${SCRIPT:-"$(basename "$0" .bash)"}
 # Ancillary functions
 
 # Evaluates if the first passed argument is an existing file
-function exists { [[ -e "$1" ]] ; }
+exists() { [[ -e "$1" ]] ; }
 
 # Evaluates if the first passed argument is a function
-function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
+fx_exists() { [[ $(type -t "$1") == "function" ]] ; }
 
 # Initiate a project-wide run
-function miga_start_project_step {
+miga_start_project_step() {
   local dir="$1"
   local dir_r="${dir}.running"
   mkdir -p "$dir"
@@ -26,7 +26,7 @@ function miga_start_project_step {
 }
 
 # Finalize a project-wide run
-function miga_end_project_step {
+miga_end_project_step() {
   local dir="$1"
   local dir_r="${dir}.running"
   cd "$dir"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.4.1.1
+  version: 1.4.1.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-11-19 00:00:00.000000000 Z
+date: 2026-02-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons