miga-base 1.0.2.0 → 1.0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 42180f18b6cf955c87a7bd4e5d798bba23f529e5a0571409186e6be566067907
-  data.tar.gz: 85d1f429054d5b773938018bd91523dbf0d5f040e266e8bb3bf263eea48b08d7
+  metadata.gz: 3fdcceb4a8c5751e23241e0db5390e8d10f4aa2d62077b3bc73508d9da15bd75
+  data.tar.gz: 9c221524ad7f8e7240a9f7b02c9fe2275a3728a7290d22cfedce26972c7d7db8
 SHA512:
-  metadata.gz: 0d238933adb3c6799b66c5d5e36854c49dd24cc86a330a45c10531fe341a70b5e684a9f6a35e899f582ed64d33494e4300fa4c37236696187b0e2df7da195ad2
-  data.tar.gz: 31ab6d81294dee95801cdc3c38c515493e65d9b727659f856af474212e5ef5dd44d0c733f92d432e1b5d946bbf45580b70a6a815d4163c894ba967bfef343a0c
+  metadata.gz: 8f05075e290329eb9a4b9a889c0fae6c379dca8e949a0beefb84de2e7d37f3bdfe04e7ccad63c2dd6258cacf2e3ce47e4b2a39bdd1abbb796eea6338e54d0fb6
+  data.tar.gz: d6358abaa5041631b3b3bd9e6a74656aae7739d14b031b2218382084f3d7384fb679bff7423ac0c31c673339fe80ab02a173df7042814fedd8dfb325ec6c0005

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

@@ -0,0 +1,26 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require 'miga/cli/action'
+
+class MiGA::Cli::Action::Env < MiGA::Cli::Action
+  def parse_cli
+    cli.parse { |_| }
+  end
+
+  def perform
+    puts <<~BASH
+      MIGA="#{MiGA::MiGA.root_path}"
+      MIGA_HOME=${MIGA_HOME:-"$HOME"}
+      . "$MIGA_HOME/.miga_rc"
+      # Ensure MiGA & submodules are first in PATH
+      export PATH="$MIGA/bin:$PATH"
+      for util in enveomics/Scripts FastAAI/FastAAI multitrim ; do
+        export PATH="$MIGA/utils/$util:$PATH"
+      done
+    BASH
+  end
+
+  def empty_action
+  end
+end

data/lib/miga/cli/base.rb

@@ -41,6 +41,7 @@ module MiGA::Cli::Base
     lair: 'Control groups of daemons for several MiGA projects',
     date: 'Return the current date in standard MiGA format',
     console: 'Open an IRB console with MiGA',
+    env: 'Shell code to load MiGA environment',
     # Taxonomy
     tax_set: 'Register taxonomic information for datasets',
     tax_test: 'Return test of taxonomic distributions for query datasets',

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 = [1.0, 2, 0].freeze
+  VERSION = [1.0, 3, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 4, 13)
+  VERSION_DATE = Date.new(2021, 6, 4)
 
   ##
   # References of MiGA

data/scripts/miga.bash

@@ -1,21 +1,21 @@
 #!/bin/bash
 
+###
 # Setup environment
 set -e
-MIGA_HOME=${MIGA_HOME:-"$HOME"}
+eval "$("$MIGA/bin/miga" env)"
 SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
-# shellcheck source=/dev/null
-. "$MIGA_HOME/.miga_rc"
-
-# Ensure MiGA & submodules are first in PATH
-export PATH="$MIGA/bin:$PATH"
-for util in enveomics/Scripts FastAAI/FastAAI multitrim ; do
-  export PATH="$MIGA/utils/$util:$PATH"
-done
 
+###
 # Ancillary functions
+
+# Evaluates if the first passed argument is an existing file
 function exists { [[ -e "$1" ]] ; }
+
+# Evaluates if the first passed argument is a function
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
+
+# Initiate a project-wide run
 function miga_start_project_step {
   local dir="$1"
   local dir_r="${dir}.running"
@@ -24,6 +24,8 @@ function miga_start_project_step {
   cd "$dir_r"
   miga date > "miga-project.start"
 }
+
+# Finalize a project-wide run
 function miga_end_project_step {
   local dir="$1"
   local dir_r="${dir}.running"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.0.2.0
+  version: 1.0.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-13 00:00:00.000000000 Z
+date: 2021-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -141,6 +141,7 @@ files:
 - lib/miga/cli/action/doctor.rb
 - lib/miga/cli/action/doctor/base.rb
 - lib/miga/cli/action/edit.rb
+- lib/miga/cli/action/env.rb
 - lib/miga/cli/action/files.rb
 - lib/miga/cli/action/find.rb
 - lib/miga/cli/action/generic.rb