bio 2.0.3 → 2.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.github/workflows/ruby.yml +38 -0
- data/.gitignore +32 -0
- data/ChangeLog +366 -0
- data/Gemfile +3 -0
- data/LEGAL +11 -0
- data/README.rdoc +1 -1
- data/RELEASE_NOTES.rdoc +50 -0
- data/appveyor.yml +14 -13
- data/bioruby.gemspec +9 -10
- data/lib/bio/appl/blast/genomenet.rb +2 -1
- data/lib/bio/appl/pts1.rb +1 -1
- data/lib/bio/db/embl/uniprotkb.rb +184 -26
- data/lib/bio/version.rb +1 -1
- data/test/data/uniprot/P03589.uniprot +127 -0
- data/test/data/uniprot/P28907.uniprot +551 -0
- data/test/data/uniprot/P49144.uniprot +232 -0
- data/test/functional/bio/test_command.rb +2 -0
- data/test/network/bio/db/kegg/test_genes_hsa7422.rb +26 -12
- data/test/unit/bio/db/embl/test_uniprotkb_P03589.rb +378 -0
- data/test/unit/bio/db/embl/test_uniprotkb_P28907.rb +325 -0
- data/test/unit/bio/db/embl/test_uniprotkb_P49144.rb +359 -0
- metadata +14 -15
- data/.travis.yml +0 -71
- data/gemfiles/Gemfile.travis-jruby1.8 +0 -6
- data/gemfiles/Gemfile.travis-jruby1.9 +0 -5
- data/gemfiles/Gemfile.travis-rbx +0 -10
- data/gemfiles/Gemfile.travis-ruby1.8 +0 -6
- data/gemfiles/Gemfile.travis-ruby1.9 +0 -5
- data/gemfiles/Gemfile.windows +0 -6
- data/gemfiles/modify-Gemfile.rb +0 -28
- data/gemfiles/prepare-gemspec.rb +0 -29
@@ -0,0 +1,359 @@
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# frozen_string_literal: true
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#
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# test/unit/bio/db/embl/test_uniprotkb_P49144.rb - Unit tests for Bio::UniProtKB
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#
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# Copyright::: Copyright (C) 2022 BioRuby Project <staff@bioruby.org>
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# License:: The Ruby License
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# Contributor:: 2005 Mitsuteru Nakao <n@bioruby.org>
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# 2022 Naohisa Goto <ng@bioruby.org>
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#
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# loading helper routine for testing bioruby
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require 'pathname'
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
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'bioruby_test_helper.rb')).cleanpath.to_s
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# libraries needed for the tests
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require 'test/unit'
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require 'bio/db/embl/uniprotkb'
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module Bio
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class TestUniProtKB_P49144 < Test::Unit::TestCase
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def setup
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data = File.read(File.join(BioRubyTestDataPath,
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'uniprot', 'P49144.uniprot'))
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@obj = Bio::UniProtKB.new(data)
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end
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def test_id_line
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assert(@obj.id_line)
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end
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def test_id_line_entry_name
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assert_equal('5HT1B_RABIT', @obj.id_line('ENTRY_NAME'))
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end
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def test_id_line_data_class
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assert_equal('Reviewed', @obj.id_line('DATA_CLASS'))
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end
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#def test_id_line_molecule_type
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# assert_equal('PRT', @obj.id_line('MOLECULE_TYPE'))
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#end
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def test_id_line_sequence_length
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assert_equal(390, @obj.id_line('SEQUENCE_LENGTH'))
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end
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def test_entry
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entry = '5HT1B_RABIT'
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assert_equal(entry, @obj.entry)
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assert_equal(entry, @obj.entry_name)
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assert_equal(entry, @obj.entry_id)
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end
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#def test_molecule
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# assert_equal('PRT', @obj.molecule)
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# assert_equal('PRT', @obj.molecule_type)
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#end
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def test_sequence_length
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seqlen = 390
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assert_equal(seqlen, @obj.sequence_length)
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assert_equal(seqlen, @obj.aalen)
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end
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def test_ac
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acs = ["P49144"].freeze
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assert_equal(acs, @obj.ac)
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assert_equal(acs, @obj.accessions)
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end
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def test_accession
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assert_equal('P49144', @obj.accession)
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end
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def test_dr
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assert_equal(28, @obj.dr.size)
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assert_equal(12, @obj.dr['GO'].size)
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assert_equal([["IPR002147", "5HT1B_rcpt"],
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["IPR002231", "5HT_rcpt"],
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["IPR000276", "GPCR_Rhodpsn"],
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["IPR017452", "GPCR_Rhodpsn_7TM"]],
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@obj.dr['InterPro'])
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end
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def test_dr_with_key
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pfam = [{"Accession" => "PF00001",
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"Version" => "7tm_1",
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" " => "1",
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"Molecular Type" => nil}
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].freeze
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assert_equal(pfam, @obj.dr('Pfam'))
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embl = [{"Accession" => "Z50163",
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"Version" => "CAA90531.1",
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" " => "-",
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"Molecular Type" => "Genomic_DNA"},
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{"Accession" => "X89731",
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"Version" => "CAA61883.1",
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" " => "-",
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"Molecular Type" => "mRNA"},
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{"Accession" => "U60826",
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"Version" => "AAB58467.1",
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" " => "-",
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"Molecular Type" => "Genomic_DNA"}
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].freeze
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assert_equal(embl, @obj.dr('EMBL'))
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end
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def test_dr_with_key_empty
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assert_equal([], @obj.dr('NOT_A_DATABASE'))
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end
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def test_dt
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assert(@obj.dt)
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end
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def test_dt_created
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assert_equal('01-FEB-1996, integrated into UniProtKB/Swiss-Prot.',
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@obj.dt('created'))
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end
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def test_dt_sequence
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assert_equal('01-FEB-1996, sequence version 1.',
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@obj.dt('sequence'))
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end
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def test_dt_annotation
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assert_equal('22-FEB-2023, entry version 127.',
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@obj.dt('annotation'))
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end
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def test_de
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assert(@obj.de)
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end
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def test_protein_name
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assert_equal("5-hydroxytryptamine receptor 1B",
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@obj.protein_name)
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end
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def test_synonyms
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ary = [
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"5-HT-1B",
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"5-HT1B",
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"Serotonin 1D beta receptor",
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"5-HT-1D-beta",
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"Serotonin receptor 1B"
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].freeze
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assert_equal(ary, @obj.synonyms)
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end
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def test_protein_name_after_calling_de
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assert(@obj.de)
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assert_equal("5-hydroxytryptamine receptor 1B",
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@obj.protein_name)
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end
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def test_synonyms_after_calling_de
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assert(@obj.de)
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assert_equal(5, @obj.synonyms.size)
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end
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def test_gn
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assert_equal([{:orfs=>[], :synonyms=>[], :name=>"HTR1B", :loci=>[]}],
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@obj.gn)
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end
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def test_gn_uniprot_parser
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assert_equal([{:orfs=>[], :loci=>[], :name=>"HTR1B", :synonyms=>[]}],
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@obj.instance_eval("gn_uniprot_parser"))
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end
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def test_gn_old_parser
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assert_equal([["Name=HTR1B;"]],
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@obj.instance_eval("gn_old_parser"))
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end
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def test_gene_names
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assert_equal(["HTR1B"], @obj.gene_names)
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end
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def test_gene_name
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assert_equal('HTR1B', @obj.gene_name)
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end
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def test_os
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assert(@obj.os)
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end
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def test_os_access
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assert_equal("Oryctolagus cuniculus (Rabbit)", @obj.os(0))
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end
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def test_os_access2
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assert_equal({"name"=>"(Rabbit)", "os"=>"Oryctolagus cuniculus"},
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@obj.os[0])
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end
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def test_oc
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assert_equal(["Eukaryota", "Metazoa", "Chordata", "Craniata",
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"Vertebrata", "Euteleostomi", "Mammalia", "Eutheria",
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"Euarchontoglires", "Glires", "Lagomorpha",
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"Leporidae", "Oryctolagus"],
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@obj.oc)
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end
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def test_ox
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assert_equal({"NCBI_TaxID"=>["9986"]}, @obj.ox)
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end
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def test_ref # Bio::UniProtKB#ref
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assert_equal(Array, @obj.ref.class)
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end
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def test_cc
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assert_equal(Hash, @obj.cc.class)
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end
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def test_cc_database
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assert_equal(nil, @obj.cc('DATABASE'))
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end
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def test_cc_alternative_products
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assert_equal(nil, @obj.cc('ALTERNATIVE PRODUCTS'))
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end
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def test_cc_mass_spectrometry
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assert_equal(nil, @obj.cc('MASS SPECTROMETRY'))
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end
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def test_kw
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keywords = [ "Behavior", "Cell membrane", "Disulfide bond",
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"G-protein coupled receptor", "Glycoprotein",
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"Lipoprotein", "Membrane", "Palmitate",
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"Phosphoprotein", "Receptor", "Reference proteome",
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"Transducer", "Transmembrane", "Transmembrane helix" ]
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assert_equal(keywords, @obj.kw)
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end
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def test_ft
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assert(@obj.ft)
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name = 'TOPO_DOM'
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data = [{"From"=>1,
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"To"=>49,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"1",
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"49",
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[["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
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"note"=>"Extracellular",
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"evidence"=>"ECO:0000250"},
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{"From"=>76,
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"To"=>84,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"76",
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"84",
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[["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
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"note"=>"Cytoplasmic",
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"evidence"=>"ECO:0000250"},
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{"From"=>111,
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"To"=>123,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"111",
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"123",
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[["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
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"note"=>"Extracellular",
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"evidence"=>"ECO:0000250"},
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{"From"=>146,
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"To"=>165,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"146",
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"165",
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[["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
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"note"=>"Cytoplasmic",
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"evidence"=>"ECO:0000250"},
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{"From"=>188,
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"To"=>205,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"188",
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"205",
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[["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
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"note"=>"Extracellular",
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"evidence"=>"ECO:0000250"},
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{"From"=>229,
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"To"=>315,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"229",
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"315",
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[["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
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"note"=>"Cytoplasmic",
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"evidence"=>"ECO:0000250"},
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{"From"=>337,
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"To"=>349,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"337",
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"349",
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[["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
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"note"=>"Extracellular",
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"evidence"=>"ECO:0000250"},
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{"From"=>372,
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"To"=>390,
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"diff"=>[],
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"original"=>
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["TOPO_DOM",
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"372",
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"390",
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[["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
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"note"=>"Cytoplasmic",
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"evidence"=>"ECO:0000250"}].freeze
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assert_equal(data, @obj.ft[name])
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end
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def test_sq
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assert_equal({"CRC64"=>"C22EBC077C6C897D", "aalen"=>390, "MW"=>43496},
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@obj.sq)
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end
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def test_sq_crc64
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assert_equal("C22EBC077C6C897D", @obj.sq('CRC64'))
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end
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def test_sq_mw
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mw = 43496
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assert_equal(mw, @obj.sq('mw'))
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assert_equal(mw, @obj.sq('molecular'))
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assert_equal(mw, @obj.sq('weight'))
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end
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def test_sq_len
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length = 390
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assert_equal(length, @obj.sq('len'))
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assert_equal(length, @obj.sq('length'))
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assert_equal(length, @obj.sq('AA'))
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end
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def test_seq
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|
+
seq = "MEEPGAQCAPPLAAGSQIAVPQANLSAAHSHNCSAEGYIYQDSIALPWKVLLVLLLALFTLATTLSNAFVVATVYRTRKLHTPANYLIASLAVTDLLVSILVMPISTMYTVTGRWTLGQVVCDLWLSSDITCCTASIMHLCVIALDRYWAITDAVEYSAKRTPKRAAIMIRLVWVFSICISLPPFFWRQAKAEEEVSECLVNTDHVLYTVYSTVGAFYLPTLLLIALYGRIYVEARSRILKQTPNRTGKRLTRAQLITDSPGSTTSVTSINSRAPDVPSESGSPVYVNQVKVRVSDALLEKKKLMAARERKATKTLGIILGVFIVCWLPFFIISLVMPICKDACWFHQAIFDFFTWLGYVNSLINPIIYTMSNEDFKQAFHKLIRFKCTS"
|
353
|
+
assert_equal(seq, @obj.seq)
|
354
|
+
assert_equal(seq, @obj.aaseq)
|
355
|
+
end
|
356
|
+
|
357
|
+
end # class TestUniProtKB_P49144
|
358
|
+
end # module Bio
|
359
|
+
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 2.0.
|
4
|
+
version: 2.0.5
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- BioRuby project
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2023-09-27 00:00:00.000000000 Z
|
12
12
|
dependencies: []
|
13
13
|
description: BioRuby is a library for bioinformatics (biology + information science).
|
14
14
|
email: staff@bioruby.org
|
@@ -26,7 +26,8 @@ extra_rdoc_files:
|
|
26
26
|
- doc/RELEASE_NOTES-1.4.3.rdoc
|
27
27
|
- doc/RELEASE_NOTES-1.5.0.rdoc
|
28
28
|
files:
|
29
|
-
- ".
|
29
|
+
- ".github/workflows/ruby.yml"
|
30
|
+
- ".gitignore"
|
30
31
|
- BSDL
|
31
32
|
- COPYING
|
32
33
|
- COPYING.ja
|
@@ -60,14 +61,6 @@ files:
|
|
60
61
|
- doc/Tutorial.rd.ja.html
|
61
62
|
- doc/bioruby.css
|
62
63
|
- etc/bioinformatics/seqdatabase.ini
|
63
|
-
- gemfiles/Gemfile.travis-jruby1.8
|
64
|
-
- gemfiles/Gemfile.travis-jruby1.9
|
65
|
-
- gemfiles/Gemfile.travis-rbx
|
66
|
-
- gemfiles/Gemfile.travis-ruby1.8
|
67
|
-
- gemfiles/Gemfile.travis-ruby1.9
|
68
|
-
- gemfiles/Gemfile.windows
|
69
|
-
- gemfiles/modify-Gemfile.rb
|
70
|
-
- gemfiles/prepare-gemspec.rb
|
71
64
|
- lib/bio.rb
|
72
65
|
- lib/bio/alignment.rb
|
73
66
|
- lib/bio/appl/bl2seq/report.rb
|
@@ -465,6 +458,9 @@ files:
|
|
465
458
|
- test/data/sim4/simple2-A4.sim4
|
466
459
|
- test/data/soft/GDS100_partial.soft
|
467
460
|
- test/data/soft/GSE3457_family_partial.soft
|
461
|
+
- test/data/uniprot/P03589.uniprot
|
462
|
+
- test/data/uniprot/P28907.uniprot
|
463
|
+
- test/data/uniprot/P49144.uniprot
|
468
464
|
- test/data/uniprot/p53_human.uniprot
|
469
465
|
- test/functional/bio/sequence/test_output_embl.rb
|
470
466
|
- test/functional/bio/test_command.rb
|
@@ -509,6 +505,9 @@ files:
|
|
509
505
|
- test/unit/bio/db/embl/test_embl_to_bioseq.rb
|
510
506
|
- test/unit/bio/db/embl/test_uniprot.rb
|
511
507
|
- test/unit/bio/db/embl/test_uniprotkb.rb
|
508
|
+
- test/unit/bio/db/embl/test_uniprotkb_P03589.rb
|
509
|
+
- test/unit/bio/db/embl/test_uniprotkb_P28907.rb
|
510
|
+
- test/unit/bio/db/embl/test_uniprotkb_P49144.rb
|
512
511
|
- test/unit/bio/db/embl/test_uniprotkb_new_part.rb
|
513
512
|
- test/unit/bio/db/fasta/test_defline.rb
|
514
513
|
- test/unit/bio/db/fasta/test_defline_misc.rb
|
@@ -594,7 +593,7 @@ homepage: http://bioruby.org/
|
|
594
593
|
licenses:
|
595
594
|
- Ruby
|
596
595
|
metadata: {}
|
597
|
-
post_install_message:
|
596
|
+
post_install_message:
|
598
597
|
rdoc_options:
|
599
598
|
- "--main"
|
600
599
|
- README.rdoc
|
@@ -617,8 +616,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
617
616
|
- !ruby/object:Gem::Version
|
618
617
|
version: '0'
|
619
618
|
requirements: []
|
620
|
-
rubygems_version: 3.
|
621
|
-
signing_key:
|
619
|
+
rubygems_version: 3.4.10
|
620
|
+
signing_key:
|
622
621
|
specification_version: 4
|
623
622
|
summary: Bioinformatics library
|
624
623
|
test_files: []
|
data/.travis.yml
DELETED
@@ -1,71 +0,0 @@
|
|
1
|
-
language: ruby
|
2
|
-
rvm:
|
3
|
-
- 2.6
|
4
|
-
- 2.5
|
5
|
-
- 2.4
|
6
|
-
- 2.3.8
|
7
|
-
- 2.2.10
|
8
|
-
env:
|
9
|
-
- TESTOPTS=-v
|
10
|
-
gemfile:
|
11
|
-
- Gemfile
|
12
|
-
before_install:
|
13
|
-
- mkdir /tmp/bioruby
|
14
|
-
- ruby gemfiles/modify-Gemfile.rb
|
15
|
-
- ruby gemfiles/prepare-gemspec.rb
|
16
|
-
matrix:
|
17
|
-
include:
|
18
|
-
- rvm: 2.0.0
|
19
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
20
|
-
env: TESTOPTS=-v
|
21
|
-
- rvm: 2.1.10
|
22
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
23
|
-
env: TESTOPTS=-v
|
24
|
-
- rvm: truffleruby
|
25
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
26
|
-
env: TESTOPTS=-v
|
27
|
-
- rvm: rbx-3.29
|
28
|
-
gemfile: gemfiles/Gemfile.travis-rbx
|
29
|
-
env: TESTOPTS=-v
|
30
|
-
- rvm: jruby
|
31
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
32
|
-
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
|
33
|
-
- rvm: 2.5
|
34
|
-
gemfile: Gemfile
|
35
|
-
env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
|
36
|
-
- rvm: jruby
|
37
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
38
|
-
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
|
39
|
-
allow_failures:
|
40
|
-
- rvm: 1.8.7
|
41
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.8
|
42
|
-
env: TESTOPTS=-v
|
43
|
-
- rvm: 1.9.3
|
44
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
45
|
-
env: TESTOPTS=-v
|
46
|
-
- rvm: truffleruby
|
47
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
48
|
-
env: TESTOPTS=-v
|
49
|
-
- rvm: rbx-3.29
|
50
|
-
gemfile: gemfiles/Gemfile.travis-rbx
|
51
|
-
env: TESTOPTS=-v
|
52
|
-
- rvm: jruby
|
53
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
54
|
-
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
|
55
|
-
- rvm: jruby
|
56
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
57
|
-
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
|
58
|
-
|
59
|
-
# uncomment this line if your project needs to run something other than `rake`:
|
60
|
-
# script: bundle exec rspec spec
|
61
|
-
|
62
|
-
#before_install:
|
63
|
-
# - sudo apt-get update
|
64
|
-
# - sudo apt-get install libxml2-dev libexpat1-dev
|
65
|
-
|
66
|
-
# block build for the branches
|
67
|
-
branches:
|
68
|
-
except:
|
69
|
-
- biohackathon2008
|
70
|
-
- bioruby-1.4.3
|
71
|
-
|
data/gemfiles/Gemfile.travis-rbx
DELETED
data/gemfiles/Gemfile.windows
DELETED
data/gemfiles/modify-Gemfile.rb
DELETED
@@ -1,28 +0,0 @@
|
|
1
|
-
#
|
2
|
-
|
3
|
-
require 'pathname'
|
4
|
-
|
5
|
-
envname_default_task = 'BIORUBY_RAKE_DEFAULT_TASK'
|
6
|
-
|
7
|
-
gem_dir = Pathname.new(File.join(File.dirname(__FILE__), '..')).realpath
|
8
|
-
|
9
|
-
case t = ENV[envname_default_task]
|
10
|
-
when 'gem-test'
|
11
|
-
# do nothing
|
12
|
-
else
|
13
|
-
$stderr.print "#{$0}: skipped: ENV[#{envname_default_task}]=#{t.inspect}\n"
|
14
|
-
exit(0)
|
15
|
-
end
|
16
|
-
|
17
|
-
target = ENV['BUNDLE_GEMFILE']
|
18
|
-
unless target then
|
19
|
-
$stderr.puts("Error: env BUNDLE_GEMFILE is not set.")
|
20
|
-
end
|
21
|
-
|
22
|
-
File.open(target, 'a') do |w|
|
23
|
-
$stderr.puts "Add a line to #{target}"
|
24
|
-
$stderr.puts "gem 'bio', :path => '#{gem_dir}'"
|
25
|
-
w.puts ""
|
26
|
-
w.puts "gem 'bio', :path => '#{gem_dir}'"
|
27
|
-
end
|
28
|
-
|
data/gemfiles/prepare-gemspec.rb
DELETED
@@ -1,29 +0,0 @@
|
|
1
|
-
#
|
2
|
-
|
3
|
-
require 'pathname'
|
4
|
-
require 'fileutils'
|
5
|
-
|
6
|
-
envname_default_task = 'BIORUBY_RAKE_DEFAULT_TASK'
|
7
|
-
|
8
|
-
gem_dir = Pathname.new(File.join(File.dirname(__FILE__), '..')).realpath
|
9
|
-
|
10
|
-
case t = ENV[envname_default_task]
|
11
|
-
when 'gem-test'
|
12
|
-
# do nothing
|
13
|
-
else
|
14
|
-
$stderr.print "#{$0}: skipped: ENV[#{envname_default_task}]=#{t.inspect}\n"
|
15
|
-
exit(0)
|
16
|
-
end
|
17
|
-
|
18
|
-
# update bundler to avoid Bundler's bug fixed in the latest version
|
19
|
-
$stderr.puts "gem update bundler"
|
20
|
-
system("gem update bundler")
|
21
|
-
|
22
|
-
$stderr.puts "cd #{gem_dir}"
|
23
|
-
Dir.chdir(gem_dir)
|
24
|
-
|
25
|
-
args = [ 'bioruby.gemspec', '.gemspec' ]
|
26
|
-
|
27
|
-
$stderr.puts(['cp', *args].join(" "))
|
28
|
-
FileUtils.cp(*args)
|
29
|
-
|