Code

merge for version 1.0 update#29

Code

Merged

Bribak merged 86 commits intomasterBojarLab/glycowork:masterfrom devBojarLab/glycowork:devCopy head branch name to clipboardDec 4, 2023

+81,123-92,800

Commits

Commits on Aug 28, 2023

• extend canonicalize_iupac to more cases

  Bribak

  committed
  6390187

Commits on Aug 31, 2023

• further expand & robustify canonicalize_iupac

  Bribak

  committed
  9fbabdf

Commits on Sep 4, 2023

• get_heatmap, auto-detect if normalization is needed

  lundstrm

  committed
  c3e8dfb

Commits on Oct 1, 2023

• change MissForest to max_iter and update enforce_class with GalNAc4S

  Bribak

  committed
  c81cb29

• allow get_k_saccharides to construct motifs with tokens outside of lib

  Bribak

  committed
  38f2a2e

Commits on Oct 4, 2023

• minor style improvements

  Bribak

  committed
  b423909

Commits on Oct 9, 2023

• patch min_process_glycans for glycans ending in linkages

  Bribak

  committed
  d8a2143

• support narrow wildcards in subgraph_isomorphism and compare_glycans

  Bribak

  committed
  db434cd

• enforce order of monosaccharides in position-encoding mode of subgraph_isomorphism

  Bribak

  committed
  faa0494

Commits on Oct 10, 2023

• termini_list now only requires encoded monosaccharide positions

  Bribak

  committed
  4d582fb

• Added Internal_LewisX and Internal_LewisA to motif_list

  Bribak

  committed
  656c478

• start some of the network.biosynthesis optimizations (fingers-crossed)

  Bribak

  committed
  f76b49a

Commits on Oct 11, 2023

• further network.biosynthesis optimizations

  Bribak

  committed
  961dc6e

Commits on Oct 12, 2023

• optimize network.evolution

  Bribak

  committed
  ccfbd30

• dev version bump and optimize ml

  Bribak

  committed
  3ba81a3

Commits on Oct 15, 2023

• optimize motif.tokenization

  Bribak

  committed
  fbfa1f2

• minor optimizations in motif.processing

  Bribak

  committed
  42992e0

Commits on Oct 17, 2023

• optimize motif.analysis

  Bribak

  committed
  ef9c3a6

Commits on Oct 18, 2023

• start motif.draw optimization

  Bribak

  committed
  3f07111

• continue with motif.draw

  Bribak

  committed
  c199211

Commits on Oct 21, 2023

• finish .draw pass

  Bribak

  committed
  3a2fa85

• subgraph_isomorphism now supports wildcards and positional encoding at the same time

  Bribak

  committed
  76bcb07

Commits on Oct 22, 2023

• indentation hotfix .draw

  Bribak

  committed
  04cadf0

Commits on Oct 24, 2023

• fix branched motif formatting in count_unique_subgraphs_of_size_k

  Bribak

  committed
  c04df95

• make df_species static again to speed up package import

  Bribak

  committed
  de96428

Commits on Oct 25, 2023

• add Zenodo badge and refactor generate_graph_features

  Bribak

  committed
  06b8ab6

Commits on Oct 26, 2023

• add simple motif highlighting

  lundstrm

  committed
  377d84a

• hotfix motif highlighing

  lundstrm

  committed
  85af4dd

Commits on Oct 27, 2023

• highlight multiple occurrences of motif

  lundstrm

  committed
  7b715d4

• positional encoding and wildcards for motif highlighting

  lundstrm

  committed
  012d2b0

• expand find_isomorphs

  Bribak

  committed
  59d146b

• hotfix double expand_termini_list & revisit index page text

  Bribak

  committed
  87bf9d7

• auto-infer narrow_wildcard_list

  Bribak

  committed
  6ccbd8a

• hotfix narrow_wildcards in .draw

  Bribak

  committed
  55518d7

• fully support narrow_wildcards in .draw

  Bribak

  committed
  f50da10

Commits on Oct 28, 2023

• add more masses to mass_dict

  Bribak

  committed
  e961977

• catch another modification edge case with canonicalize_iupac

  Bribak

  committed
  3fd2010

Commits on Oct 30, 2023

• structure_to_basic hotfix and new output mode for get_k_saccharides

  Bribak

  committed
  083b505

• temporarily disable autoreload & fix edge case in get_k_saccharides

  Bribak

  committed
  c9bf7e3

• added canonicalize_composition

  Bribak

  committed
  c4bbc4d

Commits on Oct 31, 2023

• adjustment in canonicalize_composition

  Bribak

  committed
  0cb6b72

Commits on Nov 2, 2023

• allow for retrieval of matches in subgraph_isomorphism

  Bribak

  committed
  7584d81

Commits on Nov 3, 2023

• make sure that graph_to_string works with induced subgraphs

  Bribak

  committed
  9bfddfc

• expand narrow wildcards to monosaccharide types

  Bribak

  committed
  5f7fd75

• add decorators: rescue_glycans and rescue_compositions

  Bribak

  committed
  936f03e

Commits on Nov 4, 2023

• support LinearCode as input format

  Bribak

  committed
  83e2834

• support IUPAC-extended as input format

  Bribak

  committed
  1e8b1b2

Commits on Nov 5, 2023

• further canonicalization robustification and warning messages for unsupported nomenclatures

  Bribak

  committed
  01b2bb5

• minor adjustments for canonicalization

  Bribak

  committed
  3f4b8c0

Commits on Nov 6, 2023

• start very basic support for GlycoCT as input format

  Bribak

  committed
  7307e90

• decorate GlycoDraw and deliver narrow wildcarded monosaccharides

  Bribak

  committed
  cf16106

• slightly extend GlycoCT support

  Bribak

  committed
  b6ea479

• more modifications & more monos for GlycoCT

  Bribak

  committed
  4a54b6f

• support shorthand notation for position-encoding

  Bribak

  committed
  4aa3e83

• get_k_saccharide count fix & glycoct fix

  Bribak

  committed
  d81c037

• support extended branching in GlycoCT

  Bribak

  committed
  f0109a0

Commits on Nov 7, 2023

• support native full wildcards and deprecate wildcard_list

  Bribak

  committed
  dab95bd

• allow using filepaths as additional df input in .analysis

  Bribak

  committed
  4d86a53

• start supporting WURCS as input format

  Bribak

  committed
  4c75e9e

• extend WURCS support

  Bribak

  committed
  941855e

• support extended branching in WURCS and add find_nth_reverse

  Bribak

  committed
  e396e99

Commits on Nov 8, 2023

• WURCS: more extensive branching and more monosaccharides

  Bribak

  committed
  df2e5f7

• extend branching updates to GlycoCT

  Bribak

  committed
  a072594

• robustify GlycoCT parsing and start supporting floaty bits

  Bribak

  committed
  558e824

• double branch swap fix in find_isomorphs and further improvement of GlycoCT

  Bribak

  committed
  b656b57

Commits on Nov 9, 2023

• support extended floaty bits in GlycoCT and accommodate weird modification placement

  Bribak

  committed
  ebdda58

• start supporting floaty bits for WURCS

  Bribak

  committed
  16badce

Commits on Nov 10, 2023

• fix handling of Pen in canonicalize_iupac

  Bribak

  committed
  fb6c0d8

Commits on Nov 13, 2023

• small WURCS adjustments

  Bribak

  committed
  c0da593

• WURCS: handle multiple sources of uncertainty + better branching

  Bribak

  committed
  37f1b91

Commits on Nov 16, 2023

• improve WURCS parsing

  Bribak

  committed
  7bfa4d6

Commits on Nov 22, 2023

• handling extended floating bits in WURCS

  Bribak

  committed
  83bf91b

• minor bracket fixing in WURCS

  Bribak

  committed
  74f7a07

Commits on Nov 23, 2023

• add helper function for stripping out unmatched brackets

  Bribak

  committed
  fa3db89

Commits on Nov 24, 2023

• expand input namespace

  Bribak

  committed
  58021e3

Commits on Nov 25, 2023

• minor improvements for WURCS and GlycoCT parsing

  Bribak

  committed
  4136762

Commits on Nov 27, 2023

• further generalize GlycoCT branching and namespace for WURCS

  Bribak

  committed
  e0c380a

Commits on Nov 28, 2023

• update sugarbase and downstream changes

  Show description for 6606d4d
  Bribak

  committed
  6606d4d

Commits on Nov 30, 2023

• start supporting Oxford nomenclature for universal input

  Bribak

  committed
  4e7a868

• extend support for Oxford

  Bribak

  committed
  e8c39f8

Commits on Dec 1, 2023

• WURCS and GlycoCT bug fixes

  Bribak

  committed
  172cb82

• add glycodraw support for repeating units

  lundstrm

  committed
  d332951

Commits on Dec 2, 2023

• potentially final WURCS, GlycoCT, and Oxford refinement, for now

  Bribak

  committed
  aa81da3

Commits on Dec 3, 2023

• improve robustness of graph_to_string_int

  Bribak

  committed
  401cc91

Commits on Dec 4, 2023

• robustify graph_to_string against weirdly induced subgraphs + add new GlycoDraw docs examples

  Bribak

  committed
  81a2f89

• harmonize output format of subgraph_isomorphism

  Bribak

  committed
  19bf1bd