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Merged
Jhsmit merged 108 commits into from
Dec 9, 2025
Merged

hdxms-datasets version 0.3.0 #15

Jhsmit merged 108 commits into from
Dec 9, 2025

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@Jhsmit Jhsmit commented Oct 28, 2025

Updates to the open hdxms datasets format to version 0.3.0:

Jhsmit added 30 commits October 17, 2025 12:48
@Jhsmit
remove residue offset
7650d47
@Jhsmit
use cif structure in example
264adeb
@Jhsmit
assign filter result to variable
89f946f
@Jhsmit
add peterle et al test data
f2891ea
@Jhsmit
delete test data
e5ec367
@Jhsmit
store current known ids
54ad70a
@Jhsmit
add hdx_id to spec
854b14a
@Jhsmit
add hdx_id to spec
5646853
@Jhsmit
remove unused import of re from models.py
ab2fe1a
@Jhsmit
only check for unique if state column is present
48da87b
@Jhsmit
update fields information
0994634
@Jhsmit
pull out extra column conversion to function
e122c1d
@Jhsmit
add converter for hxms format
53bf6b0
@Jhsmit
cleanup double check of dataset id
0259aec
@Jhsmit
add hxms format
5035f8d
@Jhsmit
add loading of hxms format
d476258
@Jhsmit
make license explict requirement
e5cbfd6
@Jhsmit
add hxms peptide format
a12d2ec
@Jhsmit
add mock intensity column if missing
512d273
@Jhsmit
add frameslicer util
3cc6183
@Jhsmit
generate residue dataframe from sequence
d63863e
@Jhsmit
bump narwhals requirement
cbb881f
@Jhsmit
fix typo
78eeaf6
@Jhsmit
rename conversion example scripts
16c3a05
@Jhsmit
add hxms file format example
b196415
@Jhsmit
StructureView takes a mapping to relate peptides to structure
0509f3e
@Jhsmit
custom serializers for filters
0a6f780
@Jhsmit
add new StructureMapping model
c30aa38
@Jhsmit
move to StructureMapping
8a6b290
@Jhsmit
update to use StructureMapping model
89732a8
Jhsmit added 29 commits December 5, 2025 14:26
@Jhsmit
update secb dataset to 030 format
ff93098
@Jhsmit
remove intensity column from reference data
9be650c
@Jhsmit
rename vault to db
e7620ad
@Jhsmit
allow dictionary mapping of residue numbers
83dd5dd
@Jhsmit
use mapping.map to map residue numbers from hdxms to structure
dd63bf7
@Jhsmit
return df and dont write it
9628e4b
@Jhsmit
output to the same directory as input data dir
a446db1
@Jhsmit
add DHFR test data
f661a80
@Jhsmit
add n_replicates and n_clusters fields
b8095d2
@Jhsmit
script for regenerating processed test data
f355322
@Jhsmit
parameterize processing test
ba6a53b
@Jhsmit
we dont expect sequence after reading hdxs files
6295f7a
@Jhsmit
move clear function to remote database
3e1c4b6
@Jhsmit
add ecDHFR HXMS format data to readme
1d12cad
@Jhsmit
try/except loading peptides
5f12971
@Jhsmit
import submit dataset from init
7906888
@Jhsmit
feat: strict checking, including version number
c8ae736
@Jhsmit
feat: update Python version matrix to include 3.14
e5e1339
@Jhsmit
remove unused imports
ee590c6
@Jhsmit
drop py3.10, add py3.14
e006c9d
@Jhsmit
fix: odnt use color in CLI test invocations
62f42c4
@Jhsmit
update python versions, add uv lockfile
0fbd16f
@Jhsmit
update python versions
c36a190
@Jhsmit
merge lockfiles
79913e9
@Jhsmit
need only one lockfile per matrix
dae6968
@Jhsmit
update pinned requirements
f7bbd83
@Jhsmit
add uv lockfile to requirements
5ac8c99
@Jhsmit
fix: no color via env var
2fc7b97
@Jhsmit
strip ansi codes
adf67fa
@Jhsmit Jhsmit merged commit c2696ae into master Dec 9, 2025
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@Jhsmit