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Pydantic2 migration & multidimensional matrices for nexus #1

Merged
merged 27 commits into from
Aug 20, 2024
Merged

Pydantic2 migration & multidimensional matrices for nexus #1

merged 27 commits into from
Aug 20, 2024

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vedina
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@vedina vedina commented Aug 20, 2024

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vedina and others added 27 commits August 15, 2024 10:57
@vedina
pydantic2 migration using bump-pydantic
03a0a91
@vedina
test pass
fa5053a 
(almost)
@vedina
pydantic meets numpy arrays
c5d7c90
@vedina
roundtrip tests
72ab1ea
@vedina
roundtrip for loaded json
9513056
@vedina
format
faff8f9
@vedina
fixture
7c6d0aa
@vedina
convert EffectRecords to EffectArray
584435c 
write to NeXuS EffectArrays
@vedina
optional hierarchy in nexus
7cf5825
@vedina
split effectarrays by unique values in string axis (e.g. sample/contr…
078634a 
…ols)

(nexus has trouble with string axes)
@vedina
account for nans in string columns
d978a6a
@vedina
axes_indices
082509c 
 data dimensions have alternative axis coordinates (e.g. concentration in mass and surface)
https://manual.nexusformat.org/classes/base_classes/NXdata.html
@vedina
changed axis_groups in EffetArray to dict
6bec5fc
@vedina
multidimensional matrix with primary and alternative axes
82b24f4 
nexus using axes_indices
@vedina
now working with concentrations (and other cols) with string values
612675b 
valid nexus, though h5view doesn't display string / mixed axes
@vedina
errorvalues written properly
0cdabcd 
aux signal initial support
interpretation field
@vedina
small reordering
22a6a8b
@vedina
long_name for the signal
f40bdec
@vedina
auxiliary signals can hold textvalues, but primary signals can't
55ba092
@vedina
remove old nexus code
3b4d148 
we convert everything to EffectArrays and write them in nexus
@vedina
test file with issues
624723d 
/ char in paths is an issue
some, but not all fixes
@vedina
demo notebook
dd938ab
@vedina
test with more complex valuearray
d6760c8
@vedina
now this doesn't work within poetry
a882d66
@kerberizer
ops: restore pre-commit
b4baa24
@kerberizer
fix all problems that pre-commit hooks found (except linting)
3663167
@kerberizer
Merge pull request #2 from ideaconsult/restore-precommit
0c54f54 
ops: restore pre-commit
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Coverage report

Click to see where and how coverage changed

FileStatementsMissingCoverageCoverage
(new stmts)		Lines missing
  src/pyambit
  datamodel.py 52, 90, 118, 131, 175, 186, 188, 192, 240-244, 318, 331, 356, 359, 380, 390, 396, 403, 415, 424-427, 455, 465, 496, 507, 528, 548, 560, 592, 671-687, 711, 808-812, 867-868, 903-906, 1018-1021, 1063-1068, 1094-1095, 1104, 1110, 1125, 1139-1146, 1156, 1170-1175, 1195-1203, 1221-1224, 1256-1265, 1302, 1318, 1346-1348, 1364, 1445, 1469-1478
  nexus_spectra.py
  nexus_writer.py 52, 299, 422
  tests/pyambit/datamodel
  datamodel_test.py
  nexus_writer_test.py 55-57
  spectra_writer_test.py
Project Total  

This report was generated by python-coverage-comment-action

@kerberizer kerberizer merged commit 655ba11 into main Aug 20, 2024
5 checks passed
@kerberizer kerberizer deleted the pydantic2 branch August 20, 2024 19:23
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2 participants
@vedina @kerberizer