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RELEASE_NOTES.rdoc

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BioRuby 1.4.3 RELEASE NOTES ↑

A lot of changes have been made to the BioRuby 1.4.3 after the version 1.4.2 is released. This document describes important and/or incompatible changes since the BioRuby 1.4.2 release.

For known problems, see KNOWN_ISSUES.rdoc.

New features ↑

Bio::KEGG::KGML ↑

  • New class Bio::KEGG::KGML::Graphics for storing a graphics element. In the instance of the class, “coords” attribute is now available.

  • New class Bio::KEGG::KGML::Substrate for storing a substrate element.

  • New class Bio::KEGG::KGML::Product for storing a product element.

  • New method Bio::KEGG::KGML::Reaction#id.

  • Improve RDoc documentation.

  • Unit tests are added.

  • There are incompatible changes. See Incompatible changes below.

Other new features ↑

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Bug fixes ↑

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Other bug fixes ↑

  • Fixed: (…)

  • Fixed: (…)

Incompatible changes and removed features ↑

Bio::FlatFile use binmode (binary mode) when opening a file ↑

In Bio::FlatFile.open and Bio::FlatFile.auto, binmode (binary mode) is used by default when opening a file, unless text mode is explicitly specified with open mode string or with options. Due to the change, files using CR+LF line separator might not be read correctly.

Bio::KEGG::KGML ↑

  • Bio::KEGG::KGML::Reaction#substrates and Bio::KEGG::KGML::Reaction#products are changed to return an array containing Bio::KEGG::KGML::Substrate and Bio::KEGG::KGML::Product objects, respectively. The changes enables us to get ID of substrates and products that were thrown away in the previous versions.

  • Most attribute methods that were different from the KGML attribute names are renamed to the names compatible with the KGML attribute names. Old method names are changed to aliases of them and marked as deprecated. The old names will be removed in the future.

    • Bio::KEGG::KGML::Entry#id (old name: entry_id)

    • Bio::KEGG::KGML::Entry#type (old name: category)

    • Bio::KEGG::KGML::Entry#entry1 (old name: node1)

    • Bio::KEGG::KGML::Entry#entry2 (old name: node2)

    • Bio::KEGG::KGML::Entry#type (old name: rel)

    • Bio::KEGG::KGML::Reaction#name (old name: entry_id)

    • Bio::KEGG::KGML::Reaction#type (old name: direction)

  • Following attribute methods are deprecated because two or more graphics elements may exist in an entry element. They will be removed in the future. Instead, please use instance methods of Bio::KEGG::KGML::Graphics, which can be obtained from Bio::KEGG::KGML::Entry#graphics attribute.

    • Bio::KEGG::KGML::Entry#label

    • Bio::KEGG::KGML::Entry#shape

    • Bio::KEGG::KGML::Entry#x

    • Bio::KEGG::KGML::Entry#y

    • Bio::KEGG::KGML::Entry#width

    • Bio::KEGG::KGML::Entry#height

    • Bio::KEGG::KGML::Entry#fgcolor

    • Bio::KEGG::KGML::Entry#bgcolor

BioRuby development ↑

  • rdoc.zsh is removed because it have not been used for a long time.

(tbd) ↑

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Known issues ↑

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other already known issues.

  • (tbd)

Other important news ↑

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