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merge for version 1.0 update #29

Merged
merged 86 commits into from
Dec 4, 2023
Merged

merge for version 1.0 update #29

merged 86 commits into from
Dec 4, 2023

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Bribak
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@Bribak Bribak commented Dec 4, 2023

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Bribak and others added 30 commits August 28, 2023 23:30
@Bribak
extend canonicalize_iupac to more cases
6390187
@Bribak
further expand & robustify canonicalize_iupac
9fbabdf
@lundstrm
get_heatmap, auto-detect if normalization is needed
c3e8dfb
@Bribak
change MissForest to max_iter and update enforce_class with GalNAc4S
c81cb29
@Bribak
allow get_k_saccharides to construct motifs with tokens outside of lib
38f2a2e
@Bribak
minor style improvements
b423909
@Bribak
patch min_process_glycans for glycans ending in linkages
d8a2143
@Bribak
support narrow wildcards in subgraph_isomorphism and compare_glycans
db434cd
@Bribak
enforce order of monosaccharides in position-encoding mode of subgrap…
faa0494 
…h_isomorphism
@Bribak
termini_list now only requires encoded monosaccharide positions
4d582fb
@Bribak
Added Internal_LewisX and Internal_LewisA to motif_list
656c478
@Bribak
start some of the network.biosynthesis optimizations (fingers-crossed)
f76b49a
@Bribak
further network.biosynthesis optimizations
961dc6e
@Bribak
optimize network.evolution
ccfbd30
@Bribak
dev version bump and optimize ml
3ba81a3
@Bribak
optimize motif.tokenization
fbfa1f2
@Bribak
minor optimizations in motif.processing
42992e0
@Bribak
optimize motif.analysis
ef9c3a6
@Bribak
start motif.draw optimization
3f07111
@Bribak
continue with motif.draw
c199211
@Bribak
finish .draw pass
3a2fa85
@Bribak
subgraph_isomorphism now supports wildcards and positional encoding a…
76bcb07 
…t the same time
@Bribak
indentation hotfix .draw
04cadf0
@Bribak
fix branched motif formatting in count_unique_subgraphs_of_size_k
c04df95
@Bribak
make df_species static again to speed up package import
de96428
@Bribak
add Zenodo badge and refactor generate_graph_features
06b8ab6
@lundstrm
add simple motif highlighting
377d84a
@lundstrm
hotfix motif highlighing
85af4dd
@lundstrm
highlight multiple occurrences of motif
7b715d4
@lundstrm
positional encoding and wildcards for motif highlighting
012d2b0
Bribak and others added 29 commits November 7, 2023 06:34
@Bribak
allow using filepaths as additional df input in .analysis
4d86a53
@Bribak
start supporting WURCS as input format
4c75e9e
@Bribak
extend WURCS support
941855e
@Bribak
support extended branching in WURCS and add find_nth_reverse
e396e99
@Bribak
WURCS: more extensive branching and more monosaccharides
df2e5f7
@Bribak
extend branching updates to GlycoCT
a072594
@Bribak
robustify GlycoCT parsing and start supporting floaty bits
558e824
@Bribak
double branch swap fix in find_isomorphs and further improvement of G…
b656b57 
…lycoCT
@Bribak
support extended floaty bits in GlycoCT and accommodate weird modific…
ebdda58 
…ation placement
@Bribak
start supporting floaty bits for WURCS
16badce
@Bribak
fix handling of Pen in canonicalize_iupac
fb6c0d8
@Bribak
small WURCS adjustments
c0da593
@Bribak
WURCS: handle multiple sources of uncertainty + better branching
37f1b91
@Bribak
improve WURCS parsing
7bfa4d6
@Bribak
handling extended floating bits in WURCS
83bf91b
@Bribak
minor bracket fixing in WURCS
74f7a07
@Bribak
add helper function for stripping out unmatched brackets
fa3db89
@Bribak
expand input namespace
58021e3
@Bribak
minor improvements for WURCS and GlycoCT parsing
4136762
@Bribak
further generalize GlycoCT branching and namespace for WURCS
e0c380a
@Bribak
update sugarbase and downstream changes
6606d4d 
- changed target column name to glycan
- got rid of literal evaluation
- fixed docs & added examples for the new functions
- wrapped the decorators to maintain show_doc behavior
- regenerated glycan representations
@Bribak
start supporting Oxford nomenclature for universal input
4e7a868
@Bribak
extend support for Oxford
e8c39f8
@Bribak
WURCS and GlycoCT bug fixes
172cb82
@lundstrm
add glycodraw support for repeating units
d332951
@Bribak
potentially final WURCS, GlycoCT, and Oxford refinement, for now
aa81da3
@Bribak
improve robustness of graph_to_string_int
401cc91
@Bribak
robustify graph_to_string against weirdly induced subgraphs + add new…
81a2f89 
… GlycoDraw docs examples
@Bribak
harmonize output format of subgraph_isomorphism
19bf1bd
@Bribak Bribak merged commit 044e18d into master Dec 4, 2023
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2 participants
@Bribak @lundstrm