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ChangeLog
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ChangeLog
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2009-02-20 Naohisa Goto <ng@bioruby.org>
* BioRuby 1.3.0 is released.
2009-02-19 Naohisa Goto <ng@bioruby.org>
* lib/bio/version.rb
Preparation for bioruby-1.3.0 release.
(commit fd7fc9f78bc5f4d9a10b3c0d457d9781c9ec2e49)
* bioruby.gemspec.erb
Fixed a logic to determine whether in git repository, and file
lists are changed to be sorted.
(commit ede0c0d7aeab078b6183c4e0e7c74faec32739f7)
2009-02-18 Naohisa Goto <ng@bioruby.org>
* README.rdoc
Added list of document files bundled in the BioRuby distribution.
(commit 92748f848e4708766e44c22b2f02ac662491971f)
2009-02-10 Naohisa Goto <ng@bioruby.org>
* KNOWN_ISSUES.rdoc
Added details about the text mode issue on mswin32/mingw32/bccwin32
and about non-UNIX/Windows systems.
(commit 342a167a23d3b078bd77b3f16f0ceb1aa071df66)
2009-02-09 Naohisa Goto <ng@bioruby.org>
* test/unit/bio/db/test_gff.rb
Test bug fix: test_gff.rb failed in some environment (e.g. Windows)
because the default formatting rule of Float#to_s depends on the
libc implementation.
(commit f39bf88ed6a41bd328372ee7de7a23902235f833)
2009-02-06 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
* Bug fix: Bio::GFF::GFF3::Record#id and #id= should be changed
to follow the previous incompatible change of @attributes.
Thanks to Tomoaki NISHIYAMA who reports the bug ([BioRuby]
GFF3 status (possible bug?)).
* Unit tests are added.
(commit 5258d88ef98a12fd7829eb86aa8664a18a672a43)
(commit c0c7708b3e91b0d2f2d0d50a4a0ba36928057cc8)
2009-02-05 Naohisa Goto <ng@bioruby.org>
* Rakefile
New task "tutorial2html" to generate html from doc/Tutorial.rd
and doc/Tutorial.rd.ja.
(commit 8d66fae59477f01f12b2fa3509ea34c371102725)
* doc/Tutorial.rd.html, doc/Tutorial.rd.ja.html
Automatically generated tutorial html from RD formatted documents.
(commit 90c4a23eea08b06dd758aaa0a53bea789602d252)
* doc/bioruby.css
Newly added stylesheet for the tutorial html files. The bioruby.css
have been used in http://bioruby.org/ and have been maintained by
Toshiaki Katayama.
(commit b69dc243787525de065bdf2e6b7da68d6079ab91)
* test/runner.rb
Added workaroud for test-unit-2.0.x.
(commit 475ac6a6b38e8df30de3d9bf4c7e810759ab023d)
2009-02-04 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/blast/format0.rb
Bug fix: a null line can be inserted after query name lines.
(commit bea9ce35b4177f407575ed0752c36bba8a50f502)
2009-02-03 Naohisa Goto <ng@bioruby.org>
* Tutorial.rd.ja
* Document bug: BioRuby shell commands seq, ent, obj were renamed to
getseq, getent, getobj, respectively. Thanks to Hiroyuki Mishima
who reports the issue ([BioRuby-ja]).
* Changes of returned value of getseq are also reflected to the
document.
* Recommended Ruby version and installation procedure are also
changed.
(commit 916e96ca549db71a550e7a5d3bd49a3149614313)
* doc/Changes-0.7.rd
Documentation forgotten in 1.1.0: rename of BioRuby shell commands.
(commit 64113314caac3453b4cc3b80ece9b5fb5841e069)
2009-01-30 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/blast/format0.rb
Bug fix: incorrect parsing of hit sequence's whole length.
(commit 98e6f57630b2c3394a9403f58e76b102346c56ef)
Bug fix: Whole length of a hit sequence is mistakenly parsed when
it contains ",". WU-BLAST parser is also affected in addition to
NCBI BLAST parser.
* lib/bio/db/lasergene.rb, lib/bio/db/soft.rb,
lib/bio/util/color_scheme.rb, lib/bio/util/contingency_table.rb,
lib/bio/util/restriction_enzyme.rb
Removed ":nodoc:" in in "module Bio" which prevents RDoc of the
Bio module.
(commit 458db79b467d40ed02db0d085218f611e7dd5e04)
2009-01-29 Naohisa Goto <ng@bioruby.org>
* doc/Changes-1.3.rdoc
Added documents about Bio::TogoWS and Bio::BIORUBY_VERSION.
* lib/bio/shell/plugin/entry.rb
getent (BioRuby shell command) is changed to use EBI Dbfetch or
TogoWS in addition to NCBI or KEGG API.
(commit 0e172590f60dd5a5f27a24ecd230037a7909224c)
* lib/bio/shell/plugin/togows.rb, lib/bio/shell.rb
Added new shell plugin providing accesses to TogoWS REST services.
(commit 03f6720b90e90703c23536a11b3f12c8155550ff)
* lib/bio.rb
Added autoload of Bio::TogoWS.
(commit f8605e1234164a7aa7f236b4e96a4299229753d7)
* test/functional/bio/io/test_togows.rb,
test/unit/bio/io/test_togows.rb
Newly added functional and unit tests for Bio::TogoWS::REST.
(commit f04152b80d07f44f146fa3fa0729facede865aac)
* lib/bio/io/togows.rb
New class Bio::TogoWS::REST, a REST client for the TogoWS web
service (http://togows.dbcls.jp/site/en/rest.html).
(commit 652d2534163675182b9ce30cbb1dd5efff45cd60)
* bin/br_pmfetch.rb
Changed to use Bio::BIORUBY_VERSION_ID instead of CVS version ID.
(commit f69d538ffa9ded00eb68dd306e65505d03b6c656)
* lib/bio/shell/core.rb
Changed to use BIORUBY_VERSION_ID.
(commit 4ce11656a205e85cae64eca27cef7cd94eb80930)
* bioruby.gemspec.erb
Gem version is now determined from lib/bio/version.rb or
BIORUBY_GEM_VERSION environment variable.
(commit 1811e845e60bc2847ea5717ef936bad93f9f2c87)
* Rakefile
* Changed to use lib/bio/version.rb.
* Environment variable BIORUBY_EXTRAVERSION is renamed to
BIORUBY_EXTRA_VERSION.
* Added dependency on lib/bio/version.rb to bioruby.gemspec.
(commit fb27eaa584cda1bb4cb75e10085996503361c98a)
* lib/bio.rb, lib/bio/version.rb
Bio::BIORUBY_VERSION is split into lib/bio/version.rb.
(commit 9779398c3fa0e9405a875b754a5243e0d6922c32)
* New file lib/bio/version.rb contains BioRuby version information.
* New constants: Bio::BIORUBY_EXTRA_VERSION stores extra version
string (e.g. "-pre1") and Bio::BIORUBY_VERSION_ID stores BioRuby
version string (e.g. "1.3.0-pre1").
* Bio::BIORUBY_VERSION is changed to be frozen. Above two constants
also store frozen values.
2009-01-26 Naohisa Goto <ng@bioruby.org>
* KNOWN_ISSUES.rdoc
Newly added KNOWN_ISSUES.rdoc that describes known issues and
bugs in current BioRuby.
(commit 06b10262be0bf797a3b133e4697e9b0955408944)
(commit a65ad8b42613e46b0b4bb0650d6301da0dcc88c9)
* lib/bio/shell/plugin/ncbirest.rb, lib/bio/shell.rb
New shell plugin lib/bio/shell/plugin/ncbirest.rb, providing
"efetch", "einfo", "esearch", and "esearch_count" methods.
They act the same as those defined in Bio::NCBI::REST, except
that "efetch" fetches entries with pre-defined databases
depending on arguments.
(commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
(commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
* lib/bio/shell/plugin/entry.rb
Shell commands "getent" and "getseq" are changed to use
"efetch" method when "gb" or some variant is specified as
the database.
(commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
(commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
* bioruby.gemspec.erb, bioruby.gemspec
* Changed version to 1.2.9.9501.
* Changed to use "git ls-files" instead of "git-ls-files", and
changed not to redirect to /dev/null.
* Special treatment of bioruby.gemspec is removed.
* ChangeLog is included to RDoc.
* Set RDoc title to "BioRuby API documentation".
* Set "--line-numbers" and "--inline-source" to rdoc_options.
(commit f014685090c38eeb64219603f2c7e90574849431)
* added KNOWN_ISSUES.rdoc to files for no-git environment.
(commit 06b10262be0bf797a3b133e4697e9b0955408944)
* Ruby 1.9 support: command execution with shell can raise
an error.
(commit 3179de32f1dc746c8de975917b1718a523800d69)
* bioruby.gemspec is generated from bioruby.gemspec.erb.
(commit 4e1cd3bfb8207b357d5b71cc0fc8366f06491130)
(commit 06b10262be0bf797a3b133e4697e9b0955408944)
2009-01-21 Naohisa Goto <ng@bioruby.org>
* ChangeLog
Added recent changes and fixed typo for recent changes.
2009-01-20 Naohisa Goto <ng@bioruby.org>
* ChangeLog, doc/Changes-1.3.rdoc
Added ChangeLog and doc/Changes-1.3.rdoc for recent changes.
(commit be2254ddea152fddf51a2476eeb20d804b1e3123)
* bioruby.gemspec
Added bioruby.gemspec created from bioruby.gemspec.erb.
(commit 4c54597eaf09107c34ad06bc5f5f9cead77a0198)
* lib/bio/appl/blast/wublast.rb
Bug fix: parsing of exit code failed when ignoring fatal errors
(commit 44ed958acebe4324a9a48e7292c4f0ad5c0fb685)
* Bug fix: could not get exit code in WU-BLAST results executed
with a command line option "-nonnegok", "-novalidctxok", or
"-shortqueryok".
* New methods Bio::Blast::WU::Report#exit_code_message and #notes.
* Rakefile
Added package tasks and changed to use ERB instead of eruby.
(commit 7b081c173d3b1cbc46034297ea802a4e06f85b2f)
* bioruby.gemspec.erb
Use git-ls-files command to obtain list of files when available.
(commit 5d5cb24fdd56601bc43ee78facc255ca484245c0)
2009-01-17 Naohisa Goto <ng@bioruby.org>
* Rakefile
Simple Rakefile for dynamic generation of bioruby.gemspec
(commit d5161d164f3520db25bed9aececb962428b9d6bc)
* bioruby.gemspec.erb
bioruby.gemspec is renamed to bioruby.gemspec.erb with modification.
(commit bef311668e4a3be30965ce94d41e7bde4a4e17f9)
To prevent the error "Insecure operation - glob" in GitHub,
bioruby.gemspec is renamed to bioruby.gemspec.erb, and modified
to generate the file list by using eruby.
2009-01-15 Naohisa Goto <ng@bioruby.org>
* doc/Changes-1.3.rdoc
Changes-1.3.rd is renamed to Changes-1.3.rdoc with format
conversion, and fixed typo.
(commit 1aef599650d14362ed233dcc9a7db8d3c1db1777)
Added details about newly added classes etc.
(commit eda9fd0abbb8e430810468d777d0b585e33c25d8)
2009-01-13 Naohisa Goto <ng@bioruby.org>
* bioruby.gemspec
Changed version to 1.2.9001, set has_rdoc = true and rdoc options.
(commit 1f63d3d5389dd3b0316e9f312b56e62371caa253)
* Gem version number changed to 1.2.9.9001 for testing gem.
* Changed to has_rdoc = true.
* README.rdoc and README_DEV.rdoc are now included to gem's rdoc,
and README.rdoc is set to the main page.
* *.yaml is now excluded from rdoc.
2009-01-13 Jan Aerts <jan.aerts@gmail.com>
* bioruby.gemspec
Renamed gemspec.rb to bioruby.gemspec because so github builds
the gem automatically
(commit 561ae16d20f73dcd6fc3d47c41c97c32f9aadb1a)
(committer: Naohisa Goto)
(original commit date: Wed Jun 25 11:01:03 2008 +0100)
Edited gemspec because github returned an error while building gem.
(commit f0d91e07550872c2f0d5835e496af1add7759d42)
(committer: Naohisa Goto)
(original commit date: Wed Jun 25 11:03:04 2008 +0100)
2009-01-13 Naohisa Goto <ng@bioruby.org>
* README.rdoc
Changed format from RD to RDoc with some additional URLs
(commit cb8781d701f22cbaf16575bb237a9e0cbf8cd407)
Clarified copyright of README.rdoc and BioRuby
(commit acd9e6d6e6046281c6c9c03cff1021449b8e780f)
Updated descriptions about RubyGems, and added Ruby 1.9 partial
support
(commit ff63658b255988bf0e7a9f5a2d1523d5104fe588)
2009-01-09 Naohisa Goto <ng@bioruby.org>
* test/runner,rb
Ruby 1.9.1 support: using alternatives if no Test::Unit::AutoRunner
(commit 5df2a9dc0642d4f1e9a4398d6af908780d622a6e)
2009-01-05 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/fantom.rb
Bug fix: incomplete cgi parameter escaping, and suppressing warnings.
(commit 754d8815255a0f0db20df9dd74f9f146605d430e)
* Bug fix: incomplete cgi parameter escaping for ID string in
Bio::FANTOM.get_by_id (and Bio::FANTOM.query which internally
calls the get_by_id method).
* Warning message "Net::HTTP v1.1 style assignment found" when
$VERBOSE=true is suppressed.
* Removed obsolete "rescue LoadError" when require 'rexml/document'.
* lib/bio/io/fetch.rb
Bug fix: possible incomplete form key/value escaping.
(commit ecaf2c66261e4ce19ab35f73e305468e1da412ed)
* Bug fix: possible incomplete form key/value escaping
* Refactoring: changed to use private methods _get and _get_single
to access remote site.
* lib/bio/io/pubmed.rb
Bug fix: possible incomplete escaping of parameters, and
suppressing warnings
(commit 93daccabb1a82bb20e92798c1810182dfb836ba7)
* Bug fix: possible incomplete string escaping of REST parameters
in Bio::PubMed#query and #pmfetch.
* Warning message "Net::HTTP v1.1 style assignment found" when
$VERBOSE=true is suppressed.
* Removed obsolete "unless defined?(CGI)".
* lib/bio/command.rb, test/unit/bio/test_command.rb
Bug fix: incomplete escaping in Bio::Command.make_cgi_params etc.
(commit 17c8f947e5d94012921f9252f71460e9d8f593e3)
* Buf fix: in Bio::Command.make_cgi_params and
make_cgi_params_key_value, string escaping of form keys and values
is incomplete.
* Warning message "useless use of :: in void context" is suppressed
when running test/unit/bio/test_command.rb with $VERBOSE=true.
* Unit tests are added.
* lib/bio/appl/, lib/bio/io/ (9 files)
Suppress warning message "Net::HTTP v1.1 style assignment found"
when $VERBOSE = true.
(commit a2985eb1f3aed383f1b1b391f2184317c7fd21c7)
2009-01-02 Naohisa Goto <ng@bioruby.org>
* README.rdoc
Changing optional requirements, recommended Ruby version, and
setup.rb credit.
(commit a5462ab4bd403d2d833e5d6db26ae98ca763513c)
2008-12-30 Naohisa Goto <ng@bioruby.org>
* README.rdoc
Fixed grammar and spelling in README.rdoc, indicated by
Andrew Grimm at git://github.com/agrimm/bioruby.git
in Sun Sep 21 19:59:03 2008 +1000.
(commit 446918037bff392b9c6bc6828720c585733a8f4b)
2008-12-30 Naohisa Goto <ng@bioruby.org>
* lib/bio.rb
Changed BIORUBY_VERSION to 1.3.0, which will be the next BioRuby
release version number.
(commit b000b1c4a5a136ab287b517b8b8c66e54f99a8a8).
* doc/Changes-1.3.rd
Added documents about changed points for 1.3.0 release.
(commit 028e323e784eb60b18f941cce1e3752abff1433c)
* lib/bio/appl/blast/format8.rb
Ruby 1.9 support: String#each_line instead of String#each
(commit 1bc59708137fd46911d5892e4712cc49c71fa031)
* lib/bio/io/flatfile/splitter.rb
Checks for undefined constants are added for running without
"require 'bio'" in unit tests.
(commit 311176d4d390e5948348f623ff3632454136a03f)
* lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb,
test/unit/bio/appl/test_blast.rb
Support for default (-m 0) and tabular (-m 8) formats in
Bio::Blast.reports.
* Added support for default (-m 0) and tabular (-m 8) formats in
Bio::Blast.reports method. For the purpose, Bio::Blast::Report_tab
is added to read tabular format by using Bio::FlatFile.
* Unit tests are added.
2008-12-26 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/paml/codeml/rates.rb
Ruby 1.9 support: String#each_line instead of String#each
(commit 1789a3975c4c82d3b45f545893be8f2a7bf47a01)
2008-12-26 Naohisa Goto <ng@bioruby.org>
* lib/bio/command.rb, lib/bio/appl/fasta.rb,
lib/bio/appl/blast/genomenet.rb
Refactoring and following the change of the remote site
fasta.genome.jp.
(commit 671092dff67890fc48dd7ff2f606c4cedc2eb02c)
* New method Bio::Command.http_post_form.
* Bio::Blast::Remote::GenomeNet#exec_genomenet and
Bio::Fasta#exec_genomenet are changed to use the new method.
* Changed a regexp. in Bio::Fasta#exec_genomenet is changed
following the change of the remote GenomeNet (fasta.genome.jp).
2008-12-24 Naohisa Goto <ng@bioruby.org>
* lib/bio/location.rb, test/unit/bio/test_location.rb
New method Bio::Locations#to_s with bug fix, etc.
(commit 115b09456881e1d03730d0b9e7a61a65abf6a1fe)
* New method Bio::Locations#to_s is added.
* New attributes Bio::Locations#operator and Bio::Location#carat.
* Changed not to substitute from "order(...)" or "group(...)" to
"join(...)".
* Bug fix: Bio::Locations.new(str) changes the argument string
when the string contains whitespaces.
* Unit tests for Bio::Locations#to_s are added.
2008-12-20 Naohisa Goto <ng@bioruby.org>
* test/functional/bio/appl/test_pts1.rb,
test/unit/bio/appl/test_pts1.rb
Moved part of test_pts1.rb using network from test/unit to
test/functional.
(commit 933ff3e7d615fe6521934f137519ea84b3b517f2)
2008-12-18 Naohisa Goto <ng@bioruby.org>
* test/unit/bio/io/test_soapwsdl.rb
Ruby 1.9 support: following the change of Object#instance_methods
(commit 008cf5f43786f6143f74889e0ec53d1c8a452aa2)
Note that SOAP/WSDL library is no longer bundled with Ruby 1.9,
and tests in test_soapwsdl.rb may fail.
* test/unit/bio/io/test_ddbjxml.rb
Ruby 1.9 support: following the change of Module::constants
(commit ed1ad96e7ed9d6c7d67e5413a22ba935a3b36efa)
* lib/bio/util/restriction_enzyme/single_strand.rb
Ruby 1.9 support: changed Array#to_s to join, Symbol#to_i to __id__,
etc.
(commit a29debb8c03244c1ce61317d6df0a2c5d066de3d)
* Ruby 1.9 support: in pattern method, changed to use Array#join
instead of Array#to_s.
* Ruby 1.9 support: in self.once method, changed to use
Object#__id__ instead of Symbol#to_i.
* self.once is changed to be a private class method.
2008-12-18 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/rebase.rb
Ruby 1.9 support: changed not to use String#each, etc.
(commit 47ba6e9fcf864f5881211e766f2e47b60dde178a)
* Ruby 1.9 support: In parse_enzymes, parse_references, and
parse_suppliers methods, String#each is changed to each_line.
* Changed to use require instead of autoload, to reduce support cost.
2008-12-16 Moses Hohman <moses@moseshohman.com>
* lib/bio/db/medline.rb, test/unit/bio/db/test_medline.rb
fix medline parsing of author last names that are all caps
(commit 5f37d566fc2efa4878efbd19e83f909a58c4cb00)
2008-12-15 Mitsuteru Nakao <n@bioruby.org>
* lib/bio/db/kegg/glycan.rb
Bug fix in Bio::KEGG::GLYCAN#mass.
Thanks to a reporter.
(commit cb8f1acc4caebf1f04d4a6c141dd4477fcb5394b)
(committer: Naohisa Goto)
2008-12-15 Naohisa Goto <ng@bioruby.org>
* lib/bio/pathway.rb, test/unit/bio/test_pathway.rb
Fixed pending bugs described in unit test, and Ruby 1.9 support
(commit 97b3cd4cf78eff8aede16369298aaacf1c319b68)
* Pending bugs described in test/unit/bio/test_pathway.rb are fixed.
Fixed a bug in subgraph: does not include nodes w/o edges.
A bug in cliquishness depending on the subgraph bug is also fixed.
* Bio::Pathway#cliquishness is changed to calculate cliquishness
(clustering coefficient) for not only undirected graphs but also
directed graphs. Note that pending proposed specification changes
previously written in test_pathway.rb (raises error for directed
graphs, and return 1 for a node that has only one neighbor node)
are rejected.
* Ruby 1.9 support: To avoid dependency to the order of objects
in Hash#each (and each_keys, etc.), Bio::Pathway#index is used
to specify preferences of nodes in a graph. Affected methods
are: to_matrix, dump_matrix, dump_list, depth_first_search.
* Bug fix in the libpath magic in test/unit/bio/test_pathway.rb.
2008-12-09 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/newick.rb, lib/bio/tree.rb
Ruby 1.9 support: suppressing "warning: shadowing outer local
variable".
(commit 6fe31f0a42a87631bdee3796cff65afb053b2add)
2008-12-05 Naohisa Goto <ng@bioruby.org>
* test/unit/bio/io/test_fastacmd.rb
Ruby 1.9 support: changed to use respond_to?, etc.
(commit 5d6c92c752c00f07ed856fd209c8078ef9fdf57a)
* Following the change of Module#methods in Ruby 1.9, changed
to use respond_to?().
* The test path '/tmp/test' is replaced with '/dev/null'
* lib/bio/db/gff.rb
Ruby 1.9 support: changes following the change of String#[]
(commit c25cc506bffcf1f2397ac2210153cfbfbbcb4942)
* lib/bio/reference.rb
Ruby 1.9 support: using enumerator instead of String#collect
(commit ea99242570fc8b2e2a869db84b7daaa7737f23e0)
* test/unit/bio/test_location.rb
Test bug fix: wrong number in libpath magic
(commit aa45101246bc42f78a21ee110bc58e59f532e24a)
* test/unit/bio/db/test_nexus.rb
Test bug fix: missing libpath magic
(commit d54eed426461f3a3148953fda1f7b428e74051c6)
Thanks to Anthony Underwood who reports the bug in his Github
repository.
* test/unit/bio/db/pdb/test_pdb.rb
Test bug fix: wrong number in libpath magic
(commit b53d703a8dd72608ab5ea03457c2828470069f2f)
2008-12-04 Naohisa Goto <ng@bioruby.org>
* test/unit/bio/db/embl/test_embl_to_bioseq.rb
Test bug fix: typing error (found by using Ruby 1.9)
(commit fa52f99406ddd42221be354346f67245b3572510)
* test/unit/bio/db/embl/test_common.rb
Ruby 1.9 support: following the change of Module#instance_methods
(commit d18fa7c1c3660cf04ec2a8a42d543a20a77cee2c)
In Ruby 1.9, Module#instance_methods returns Array containing
Symbol objects instead of String. To support both 1.8 and 1.9,
"to_s" is added to every affected test method.
* lib/bio/appl/tmhmm/report.rb
Ruby 1.9 support: using enumerator if the entry is a string
(commit 36968122b64b722e230e3e1b52d78221c0b60884)
* lib/bio/appl/pts1.rb
Ruby 1.9 support: String#each to each_line and Array#to_s to join('')
(commit c4c251d5e94167512a0b8a38073a09b72994c08f)
* test/unit/bio/appl/test_fasta.rb
Ruby 1.9 support: changed to use Array#join instead of Array#to_s
(commit bf8823014488166c6e1227dd26bdca344c9f07b7)
* lib/bio/appl/blast.rb
Ruby 1.9 support: String#each is changed to String#each_line
(commit 3e177b9aecf6b54a5112fd81fc02386d18fc14b9)
* lib/bio/appl/hmmer/report.rb
Ruby 1.9 support: String#each is changed to String#each_line
(commit 63bdb3a098bc447e7bd272b3be8f809b4b56d451)
* lib/bio/appl/genscan/report.rb
Ruby 1.9 support: String#each is changed to String#each_line
(commit 082250786756de2b4171b3a00e0c4faaa816fc8f)
* test/functional/bio/io/test_ensembl.rb
Using jul2008.archive.ensembl.org for workaround of test failure.
(commit 1d286f222cdc51cf1323d57c1c79e6943d574829)
Due to the renewal of Ensembl web site, lib/bio/io/ensembl.rb
does not work for the latest Ensembl. For a workaround of
the failure of tests in test/functional/bio/io/test_ensembl.rb,
tests for Ensembl#exportview are changed using Ensembl archive
(http://jul2008.archive.ensembl.org/).
2008-12-03 Naohisa Goto <ng@bioruby.org>
* sample/demo_sequence.rb
sample/demo_sequence.rb, example of sequence manipulation.
(commit b7f52b47dbcc7d32f4eb7377d2b1510eb1991fd5)
The content of this file is moved from previous version of
lib/bio/sequence.rb (inside the "if __FILE__ == $0").
2008-12-02 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/paml/baseml.rb, etc. (17 files)
Support for baseml and yn00 (still under construction), and
incompatible changes to Bio::PAML::Codeml.
(commit d2571013409661b4d7be8c5c9db14dbe9a9daaaf)
* Security fix: To prevent possible shell command injection,
changed to use Bio::Command.query_command instead of %x.
* Bug fix with incompatible changes: Using Tempfile.new.path
as default values are removed because this can cause
unexpected file loss during garbage collection.
* Change of method/file names: The term "config file" is changed
to "control file" because the term "config file" is never used
in PAML documents. The term "options" is changed to "parameters"
because the "options" have been used for command-line arguments
in other wrappers (e.g. Bio::Blast, Bio::ClustalW). The term
"parameters" is also used in BioPerl's
Bio::Tools::Run::Phylo::PAML.
* Bio::PAML::Codeml.create_config_file, create_control_file,
Bio::PAML::Codeml#options, and #options= are now deprecated.
They will be removed in the future.
* New class Bio::PAML::Common, basic wrapper common to PAML programs.
Bio::PAML::Codeml is changed to inherit the Common class.
* New classes Bio::PAML::Baseml and Bio::PAML::Yn00, wrappers for
baseml and yn00.
* New classes Bio::PAML::Common::Report, Bio::PAML::Baseml::Report
and Bio::PAML::Yn00::Report, but still under construction.
* New methods Bio::PAML::Codeml#query(alignment, tree), etc.
* test/data/paml/codeml/dummy_binary is removed because
the default of Bio::PAML::Codeml.new is changed to use
"codeml" command in PATH.
* test/data/paml/codeml/config.missing_tree.txt is removed
because treefile can be optional parameter depending on runmode.
test/data/paml/codeml/config.missing_align.txt is also removed
because test is changed to use normal control file parameters.
* lib/bio/command.rb, test/functional/bio/test_command.rb
Improvement of Bio::Command.query_command, call_command, etc.
(commit e68ee45589f8063e5a648ab235d6c8bbc2c6e5ff)
* Improvement of Bio::Command.query_command, call_command,
query_command_popen, query_command_fork, call_command_popen,
and call_command_fork: they can get an option :chdir => "path",
specifying working directory of the child process.
* New method Bio::Command.mktmpdir backported from Ruby 1.9.0.
* New method Bio::Command.remove_entry_secure that simply calls
FileUtils.remove_entry_secure or prints warning messages.
* Tests are added in test/functional/bio/test_command.rb.
* Ruby 1.9 followup: FuncTestCommandQuery#test_query_command_open3
failed in ruby 1.9 due to the change of Array#to_s.
2008-11-19 Naohisa Goto <ng@bioruby.org>
* test/data/paml/codeml/
Removed some files in test/data/paml/codeml/ because of potential
copyright problem, because they are completely identical with
those distributed in PAML 4.1.
(commit 086b83d3e54f69d2b9e71af3f9647518768353b0)
2008-10-21 Naohisa Goto <ng@bioruby.org>
* lib/bio/sequence/compat.rb
Bug fix: TypeError is raised in Bio::Sequence#to_s before
Sequence#seq is called.
(commit ea8e068a5b7f670ce62bc0d3d4b21639e3ca2714)
Thanks to Anthony Underwood who reported the bug and sent the patch.
2008-10-19 Naohisa Goto <ng@bioruby.org>
* setup.rb, README.rdoc
install.rb is replaced by new setup.rb.
(commit 9def7df5b81340c49534ff0bb932de62402a1c8d)
* install.rb is replaced by the latest version of setup.rb taken
from the original author's svn repository (svn r2637, newer than
version 3.4.1, latest release version.
$ svn co http://i.loveruby.net/svn/public/setup/trunk setup).
* README.rdoc is modified to follow the rename of install.rb to
setup.rb.
2008-10-18 Toshiaki Katayama <k@bioruby.org>
* lib/bio/io/ncbirest.rb
* New methods: Bio::NCBI::REST#einfo, #esearch_count, etc.
* New classes: Bio::NCBI::REST::ESearch, Bio::NCBI::REST::EFetch.
(commit 637f97deefd6cc113ef18fe18ab628eb619f3dc1)
(committer: Naohisa Goto)
2008-10-14 Naohisa Goto <ng@bioruby.org>
* lib/bio/sequence/common.rb, test/unit/bio/sequence/test_common.rb,
test/unit/bio/sequence/test_compat.rb,
test/unit/bio/sequence/test_na.rb
Bug fix: Bio::Sequence::Common#randomize severely biased.
(commit 02de70cbf036b41a50d770954f3b16ba2beca880)
* Bug fix: Bio::Sequence::Common#randomize was severely biased.
To fix the bug, it is changed to used Fisher-Yates shuffle,
as suggested by Anders Jacobsen.
([BioRuby] Biased Bio::Sequence randomize())
* The module method Bio::Sequence::Common.randomize is removed
because it is not used anymore.
* Unit tests for Bio::Sequence::Common#randomize are added.
* To avoid possible test class name conflicts, class/module
names are changed in test_na.rb, test_compat.rb, and
test_common.rb.
2008-10-14 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
* lib/bio/io/sql.rb
Changed the demonstration code in the "if __FILE__ == $0".
(commit 9942105920182c809564554bb0d1dba33fe4caab)
* lib/bio/db/biosql/sequence.rb
Fix: typing error
(commit 67fbbb93adaa8b4b91de3703a235bc75eaef842a)
2008-10-14 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/biosql/sequence.rb, lib/bio/io/sql.rb
Merging patches by Raoul in commit
496561a70784d3a1a82bf3117b2d267c7625afac which are ignored
when rebasing, probably because of manually editing during merge.
(commit c699253d53510c0e76188a72004651a4635088b3)
2008-10-10 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
* lib/bio/db/biosql/sequence.rb
Fix: check on nil objects (to_biosql)
(commit f701e9a71f524ee4373c94ee1bd345e87f16f6ce)
BugFix: ex. /focus="true" in output was /focus="t",
qualifier.value.to_s fix the bug
(commit f6e1530f3372c87031b551e5c76e24f264891e64)
* lib/bio/io/biosql/seqfeature.rb
BugFix: seqfeature_qualifier_value returned ordered only by rank
(commit fb74009393eeca6743f78b7b45cb66858c41d733)
* lib/bio/io/biosql/bioentry.rb
BugFix: seqfeatures returned ordered by rank
(commit 25a249d87d23bd9cb4e671053019675836fcd38c)
* lib/bio/db/biosql/sequence.rb
Fixed to suppress warnings: Bio::Features is obsoleted.
(commit 198a1e893dd4515d61276c9cce8905f02130e721)
* lib/bio/db/biosql/biosql_to_biosequence.rb
Removed alias comment.
(commit c037ec565987634b354ff6d77dbbe7c9d83a9e7c)
* lib/bio/db/biosql/sequence.rb
Implemented Entry's comments and reference's comments.
Fixed species common name.
(commit bd3b24ea53ebd9b0ec9dd9f15c27091fe6143e28)
* lib/bio/io/biosql/bioentry.rb
Cleaned, deleted pk and seq reference
(commit 14bcf90334ec3c3f1c1784977b329ae641e9e106)
* lib/bio/io/biosql/comment.rb
cleaned codes
(commit 54976693350ab0512cecf946999c2868b9e88007)
* lib/bio/db/biosql/biosql_to_biosequence.rb
Added comments, comment adapter.
(commit 5394ecea34778c9f571eb35cfc16e3b1a6cb6d1b)
2008-10-09 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
* lib/bio/io/sql.rb
Changed the demonstration code in the "if __FILE__ == $0".
(commit efb61d7c21d229e882c6706838c284404343fa9c)
* lib/bio/db/biosql/sequence.rb
Added support for reference. ToDo: handling comments.
(commit 29211059ee04214d7879f900ec563c0708d8c9d6)
* lib/bio/io/biosql/bioentry_reference.rb
Fix: compisite primary keys :bioentry_id, :reference_id, :rank
(commit eba61ba670c591f58866b37ababc4acac0cc7883)
* lib/bio/io/biosql/dbxref.rb
removed explicit pk and seq
(commit e149f94484469fb3dfd881b45b14be7093b67e0d)
2008-10-09 Naohisa Goto <ng@bioruby.org>
* test/functional/bio/test_command.rb,
test/data/command/echoarg2.bat
Bug fix: tests in FuncTestCommandCall are failed on mswin32,
and URL changed.
(commit 921292f1188d85994742ce4aa156b39d6e720aad)
* Bug fix: tests in FuncTestCommandCall were failed on mswin32.
To fix the test bug, a batch file test/data/command/echoarg2.bat
is newly added. This file is only used on mswin32 or bccwin32.
* URL for test to fetch a web page is changed to
http://bioruby.open-bio.org/.
2008-10-07 Naohisa Goto <ng@bioruby.org>
* test/unit/bio/appl/paml/test_codeml.rb
Bug fix: error on mswin32 in
test_expected_options_set_in_config_file.
(commit 16b8f321c653502ef801d801383a019bc45f67de)
Bug fix: On mswin32, test_expected_options_set_in_config_file
in Bio::TestCodemlConfigGeneration failed with the error
"Errno::EACCESS: Permission denied" because it attempts to remove
the temporary file that is previously opened but not explicitly
closed, and, in Windows, the opend file is automatically locked
and protected from being removed.
* lib/bio/command.rb, test/functional/bio/test_command.rb,
test/unit/bio/test_command.rb
Bio::Command improved, and added functional tests.
(commit bb618cdfbfb56c40249aff81b6ef84742465851c)
* In Bio::Command.call_command_* and Bio::Command.query_command_*,
when giving command-line array with size 1, the command might
passed to shell. To prevent this, changed to call a new method
Bio::Command#safe_command_line_array internally.
* Added test/functional/bio/test_command.rb, contains unit tests
to call external commands and to access external web sites.
2008-10-06 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/biosql/sequence.rb
Bio::Sequence::SQL::Sequence#seq is changed to return a
Bio::Sequence::Generic object, because of avoiding to create
nested Bio::Sequence object in #to_biosequence and because
Bio::FastaFormat#seq also returns a Bio::Sequence::Generic object.
(commit 8fb944c964ab5e1ca8905e6c4ce8e68479952935)
2008-10-03 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
* lib/bio/io/biosql/taxon.rb
Added has_one :taxon_genbank_common_name,
:class_name => "TaxonName",
:conditions => "name_class = 'genbank common name'"
(commit dc7a18b17cad8e603e0d3c20a5a80bc2a6f0899c)
* lib/bio/db/biosql/sequence.rb
Fix taxon identification by splitting scientific name and genbank
common name. Fix organism/source's name composed by scientific
name and genbank common name.
(commit 5d6abcc0dcd05d7083622360489a5f4c361e0cc7)
* lib/bio/io/sql.rb
Working on tests about format import/export.
(commit d28a343e4bab3cc0c04ac65dce677cfee0f81a46)
* lib/bio/io/biosql/term.rb
Fix foreign keys
(commit c19c8766c7c0bec7561727abf2ef1bdf47d4e032)
* lib/bio/io/biosql/seqfeature_qualifier_value.rb
added composite primary keys :seqfeature_id, :term_id, :rank
(commit cdd6a3bfc1ab748acb0c0d9161ebeb3dc7a76544)
* lib/bio/io/biosql/ontology.rb
class cleaned.
(commit 81eb2c246d01790db72f0b08929bec5d862c959e)
* lib/bio/io/biosql/biodatabase.rb
class cleaned.
(commit 4aede5c5fee92c2f8cdf151a3e038025b6c7fd74)
* lib/bio/db/biosql/sequence.rb