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Improve mat #1197

Merged
merged 52 commits into from
Apr 28, 2022
Merged

Improve mat #1197

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e853060
speedup mat reading
Mar 30, 2022
52e893d
using dictionary comprehension to be a bit faster
Mar 30, 2022
06e5039
vectorized metabolite processing and added annotations
Mar 31, 2022
e58f9cf
vectorize reaction processing
Mar 31, 2022
189b869
functionalize cell processing
Mar 31, 2022
3e811ec
functionalize cell processing for floats
Mar 31, 2022
bc52649
added docstring
Mar 31, 2022
f9c1b8a
added rxn annotations, including pubmed and EC
Mar 31, 2022
12a0c56
added rxn annotations, including pubmed and EC
Mar 31, 2022
9020a70
tidying
Apr 1, 2022
c3d6faa
functionalize annotations
Apr 1, 2022
ebc58d6
fixed minor mistake with REV
Apr 1, 2022
c331d80
started annotations_to_mat
Apr 1, 2022
7385d78
fast version of mat_annotations, need to split to list
Apr 1, 2022
c859a1e
black and some tidying, including an else
Apr 1, 2022
a664914
annotations will be lists
Apr 2, 2022
f3f1d14
fixed outputting of annotations. Added parsing of Rxn Notes from mat …
Apr 4, 2022
8209d83
some minor name changes
Apr 4, 2022
9b11ee7
mat writing and reading work on all fields
Apr 6, 2022
5041835
removed pymatbridge
Apr 6, 2022
5df0391
fixed some errors
Apr 6, 2022
ad7b01d
black
Apr 6, 2022
b324453
minor correction since number of arrays is inconsistent. Harvey and H…
Apr 7, 2022
a8e86eb
removed unnecessary function and kludgy modification of MET_PROVIDERS
Apr 7, 2022
82f0673
modified regular expression. Added check for empty compartments which…
Apr 7, 2022
0c2eede
ran black becase I had forgotten it
Apr 7, 2022
4307f8c
added logger warning about compartments via regular expressions
Apr 8, 2022
e457ca9
log compartments found
Apr 8, 2022
8824f7b
some typing correction and test modification
Apr 11, 2022
d4827c7
some more typing correction
Apr 11, 2022
86df12d
some corrections according to comments
Apr 11, 2022
4d8a123
some corrections according to discussion on PR
Apr 11, 2022
2b2cb71
fix bug in GPR.from_string()
Apr 18, 2022
911df9e
updated tests. Was treating logger.warning like warn.warning but the …
Apr 18, 2022
115f943
corrected according to comments.
Apr 19, 2022
a1ae556
removed deprecated function remove_from_model in gene.py
Apr 19, 2022
0b7c011
some corrections according to discussion on PR and cobratoolbox test …
Apr 15, 2022
a7331e6
some corrections according to cobratoolbox test models
Apr 18, 2022
e95b47d
added subsystem to groups. some tidying
Apr 19, 2022
a397c98
removed unnecessary functions now need to update tests for coverage
Apr 19, 2022
02e70ac
not using enumerate
Apr 19, 2022
510bc23
added some tests
Apr 20, 2022
e684f6f
raven style model should be written properly
Apr 21, 2022
8c75456
cobratoolbox created models seem to be inconsistent about capitalizat…
Apr 22, 2022
cd9a0c3
CHEBI: shouldn't be removed from metCHEBIID since that how it is acce…
Apr 23, 2022
548c17e
mat models seem to be read and rewritten correctly
Apr 24, 2022
3b8d92f
read gene names and make sure to add genes to model (otherwise gene n…
Apr 25, 2022
ffc57d8
fix for old cobratoolbox fields
Apr 25, 2022
d2a9d4e
save model name only if it exists
Apr 25, 2022
a15fb54
Merge branch 'devel' into improve_mat
akaviaLab Apr 25, 2022
ef20327
variable name fixes
Apr 26, 2022
49cc180
revert changes in test_sbml.py
Apr 26, 2022
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236 changes: 0 additions & 236 deletions documentation_builder/pymatbridge.ipynb
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6 changes: 6 additions & 0 deletions release-notes/next-release.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@

## New features

Improve reading of matlab models, which will include metaboilte
and reaction annotations.

## Fixes

`model.copy()` will now correctly copy GPRs.
Expand All @@ -22,3 +25,6 @@ test_gpr_that_needs_two_replacements()
## Deprecated features

## Backwards incompatible changes

Removed pymatlib direct transfer of models to matlab process.
Please use save_matlab_model() and then read the model in matlab.
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