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Upgrade to Python >3.9, numpy >2.0, support SNIRF 1.2.0-development #51

Merged
merged 45 commits into from
Dec 31, 2024
Merged

Upgrade to Python >3.9, numpy >2.0, support SNIRF 1.2.0-development #51

merged 45 commits into from
Dec 31, 2024

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sstucker
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@sstucker sstucker commented Dec 26, 2024 •
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  • Upgrade to numpy 2.0, which requires Python >3.9
  • QoL improvements to gen: opt out of cached spec use, schema order verification
  • support measurementLists and dataOffset from SNIRF 1.2.0-development
  • measurementList_to_measurementLists and measurementLists_to_measurementLists conversion utility functions
  • moduleIndex removed from library and test data (it raises a warning if present)
  • On write, correct arrays with erroneous single dimensions (e.g. 1D arrays written as column vectors by MATLAB hdf5 functions)
  • No longer uses tempfile as backend for in-memory SNIRF objects, uses h5py backend instead
  • Enhancement: measurementList(s) are now validated against probe shape, >0
  • Fix: Groups are now deleted from files on disk with save-as
  • Enhancement: dataType and dataTypeLabel now validated against recognized values from specification appendix

sstucker and others added 30 commits December 26, 2024 13:12
@sstucker
Replaced numpy.str_ with numpy.bytes_ to support numpy 2
de9eeaf
@sstucker
path fiddling in test.py
7233502
@sstucker
Upgrade to Python >3.9
2e025c9
@sstucker
README
ced4c87
@sstucker
Removed < 3.9 python versions from test
85da3fc
@sstucker
Merge branch 'main' into main
4a1b35e
@sstucker
1.2-draft gen
6e40d60
@sstucker
added option to download spec even when local copy is present
76151eb
@sstucker
gen from 1.2-draft
228fdbc
@sstucker
Merge branch 'main' of https://github.com/BUNPC/pysnirf2
774ca8f
@sstucker
Added verbose test exceptions, began support for measurementLists
e00393a
@sstucker
Towards measurementLists, dataOffset support
2080abd
@sstucker
Added check for alignment of ingested schema table and descriptions
3588268
@sstucker
On write, pysnirf2 now attempts to correct arrays with erroneous sing…
5d9d8f5 
…ular dimensions (such as those produced by MATLAB) beyond the specified ndim. dataOffset and measurementList support added but not fully functional based on current official spec
@sstucker
measurementList/measurementLists are manually covalidated for presence
8c901f5
@sstucker
Merge branch 'main' of https://github.com/sstucker/pysnirf2
7ddcefd
@github-actions
CI: Automated docs update
12f1bd1
@sstucker
updated test files: removed moduleIndex
2e43ef6
@sstucker
Merge branch 'main' of https://github.com/sstucker/pysnirf2
e709a29
@sstucker
Support for dataOffset; switched memory only SNIRF representations fr…
6a36799 
…om tempfile to the h5py backend
@sstucker
Fix to tests; docstring
36829ab
@github-actions
CI: Automated docs update
53fc38c
@sstucker
"'
1d6a8a2
@sstucker
Template changes
69a9a4d
@sstucker
Merge branch 'main' of https://github.com/sstucker/pysnirf2
2dd8011
@sstucker
Fixed validation of probe vs. measurementList(s)
682fb1d
@github-actions
CI: Automated docs update
faa5053
@sstucker
Delete tests/data/v120dev-Simple_Probe_measLists.snirf
b44061f
@sstucker
Converting to numpy upon assignment of array; accidentally a logical
11060ed
@sstucker
Merge branch 'main' of https://github.com/sstucker/pysnirf2
9d0b525
github-actions bot and others added 15 commits December 30, 2024 19:02
@github-actions
CI: Automated docs update
3f23d10
@sstucker
Better input sanitization
97c12c7
@sstucker
Merge branch 'main' of https://github.com/sstucker/pysnirf2
d9f654b
@github-actions
CI: Automated docs update
98f4b96
@sstucker
Conversion interface
54b0842
@sstucker
Groups are now deleted from disk files with save; validation of measu…
295417b 
…rementList(s) fixes
@sstucker
Fix index > 0 validation
feef6ac
@sstucker
Accidentally a :
e0db231
@sstucker
tests of measurementList(s) validation and conversion utility functions
2dc3e0c
@github-actions
CI: Automated docs update
86b928e
@sstucker
Generator support for collecting recognized aux names, datatypes and …
751c489 
…datatype labels from spec
@sstucker
dataType and dataTypeLabel validation
09562f1
@sstucker
Fix to type/typeLabel validation for measurementLists
d5ac9a6
@sstucker
Merge branch 'main' of https://github.com/sstucker/pysnirf2
5ca9a7e
@github-actions
CI: Automated docs update
7dd14f8
@sstucker sstucker changed the title Upgrade to Python >3.9, numpy >2.0 Upgrade to Python >3.9, numpy >2.0, support SNIRF 1.2.0-development Dec 31, 2024
@sstucker sstucker merged commit 6369714 into BUNPC:main Dec 31, 2024
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Resolves #47, #48 and #49

This was linked to issues Dec 31, 2024
Crash when validating data entries with 0 length #49
Open
Ensure validator supports measurementLists #48
Open
Ensure validator supports St02 changes to spec #47
Closed
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