Changes in version 0.5.2                        

Minor improvements and fixes

  - Fix rules for FUT3, FUT4, FUT5, FUT6, and FUT9. (5e7d657)

                        Changes in version 0.5.1                        

Minor improvements and fixes

  - Fix rules for FUT1, FUT2, and B3GALT5. (50f3d5d)

                        Changes in version 0.5.0                        

Breaking changes

  - Rename APIs to use shorter, consistent names (#2):
      - all_enzymes() to db_enzymes()
      - create_enzyme() to make_enzyme()
      - get_involved_enzymes() to find_enzyme()
      - is_synthesized_by() to have_enzyme()
      - count_enzyme_steps() to count_enzyme()
      - find_synthesis_path() to path_biosynthesis()
      - rebuild_biosynthesis() to trace_biosynthesis()
      - spawn_glycans() to grow_glycans()
      - spawn_glycans_step() to grow_glycans_step()

New features

  - Add support for initiating enzymes including DPAGT1, FUT10, FUT11,
    POFUT1, POFUT2, POGLUT1, POGLUT2, POGLUT3, POMT1, POMT2, TMTC1,
    TMTC2, TMTC3, TMTC4, and GALNT1 through GALNT19. (#5)
  - Add support for N-glycan precursor synthesis enzymes (ALGs). (#6)
  - Add match_enzyme() to identify the residues added by a
    glycosyltransferase. (#3)
  - Add view_enzyme() to visualize residues added by an enzyme on a
    glycan cartoon. (#4)

Minor improvements and fixes

  - Fix the bug that find_enzyme didn't support paucimannose glycans.
    (1c79a04)

                        Changes in version 0.4.3                        

Minor improvements and fixes

  - Update dependency strategy to use the r-universe repo.

                        Changes in version 0.4.2                        

Minor improvements and fixes

  - Update internal data to adapt to glyrepr 0.10.0.

                        Changes in version 0.4.1                        

Minor improvements and fixes

  - glyenzy now depends on the CRAN version of glyparse.

                        Changes in version 0.4.0                        

Breaking changes

  - Strengthen validation of the rejects field in enzyme rules: each
    reject must contain the acceptor motif.
  - Rework rejects handling in apply_enzyme() (and callers) to evaluate
    rejects per match rather than per glycan, improving accuracy for
    glycans with multiple acceptor matches.
  - Update built-in rules for MAN2A1, MAN2A2, MGAT3, MGAT4A, and MGAT4B
    to align with the new reject semantics.
  - Remove the now-redundant rejects_alignment field from enzyme_rule
    objects; acceptor_alignment is reused for reject checks.

New features

  - Add make_enzyme(), enabling programmatic construction of custom
    enzymes.

Minor improvements and fixes

  - grow_glycans() now shows live glycan counts in the progress bar.

                        Changes in version 0.3.2                        

Minor improvements and fixes

  - Fix errors in the rules of some enzymes, including B3GALT1, B3GALT2,
    and FUT8.
  - Fix a bug in progress bar of grow_glycans().

                        Changes in version 0.3.1                        

Minor improvements and fixes

  - glyenzy now depends on the CRAN version of glyrepr.

                        Changes in version 0.3.0                        

Breaking changes

  - Remove FUT10, as it belongs to the starting point of some O-Fuc
    glycans.

New features

  - Add many new enzymes, including FUT5, FUT6, ST3GAL5, ST6GALNAC5,
    ST6GALNAC6, ST8SIA1, ST8SIA5, ST8SIA6, B3GAT3, CHPF, CHPF2, CHSY1,
    CHSY3, EXT1, EXT2, HAS1, HAS2, HAS3, LARGE1, LARGE2, B3GLCT, A4GALT,
    ABO, B3GALT6, B4GALT6, GXYLT1, GXYLT2, LARGE1, LARGE2, XXYLT1,
    B3GALNT1, B4GALNT1, B4GALNT3, B4GALNT4, CSGALNACT1, CSGALNACT2,
    B3GNT5, B3GNT7, POMGNT1, POMGNT2, LFNG, MFNG, RFNG, EXLT1, EXLT2,
    EXLT3
  - Update the rules of some existing enzymes, including FUT1, FUT2,
    FUT3, FUT4, FUT7, FUT8, FUT9, ST3GAL2, ST3GAL3, ST3GAL4, ST6GALNAC1,
    ST6GALNAC3, ST8SIA2, ST8SIA3, ST8SIA4, B3GALT4, B3GALT5, B4GALT1,
    B4GALT4, B4GALT5, B4GALNT2, MGAT5B, B3GNT8, GCNT2, GCNT3, A4GNT,
    ST3GAL1
  - trace_biosynthesis() now supports many new glycan types, including
    O-Man, O-GlcNAc, O-Fuc, and O-Glc.

Minor improvements and fixes

  - path_biosynthesis() and trace_biosynthesis() has been optimized for
    large glycans.
  - All functions explicitly check if the input glycans are concrete
    (e.g. "Glc", "GalNAc") and raise errors with helpful messages if
    not.

                        Changes in version 0.2.3                        

Minor improvements and bug fixes

  - Updated dependency on glymotif (>= 0.10.0) to ensure compatibility
    with recent changes in package igraph v2.2.0.

                        Changes in version 0.2.2                        

Minor improvements and bug fixes

  - Fix bugs introduced by the breaking changes in glymotif v0.7.0 and
    glyrepr v0.7.0.

                        Changes in version 0.2.1                        

Minor improvements and bug fixes

  - Update dependencies to depend on release versions of glycoverse
    packages.

                        Changes in version 0.2.0                        

Breaking changes

  - Remove return parameter from path_biosynthesis() and
    trace_biosynthesis(). Now they always return all possible paths.

New features

  - trace_biosynthesis() now supports multiple target glycans. The
    resulting graph contains all given target glycans and intermediate
    glycans.

Minor improvements and fixes

  - Update documentations of path_biosynthesis() and
    trace_biosynthesis() to include some important notes.
  - Fix bugs in path_biosynthesis() and trace_biosynthesis() that glycan
    structure strings other than IUPAC-condensed format cannot be
    parsed.
  - Add checks in all functions to ensure that the input glycans have
    intact linkages and no substituents, and raise errors with helpful
    messages if not.
  - Refactor apply_enzyme() to stop using internal glymotif functions to
    avoid fragile dependency.

                        Changes in version 0.1.1                        

Minor improvements and fixes

  - Fix bugs introduced by the breaking changes in glyrepr v0.7.0.

                        Changes in version 0.1.0                        

First release of glyenzy!