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Merge to main for 1.10.5 release #1318

Merged
merged 68 commits into from
Apr 2, 2024
Merged

Merge to main for 1.10.5 release #1318

merged 68 commits into from
Apr 2, 2024

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pgunn
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@pgunn pgunn commented Apr 2, 2024

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pgunn and others added 30 commits November 21, 2023 16:23
@pgunn
cnmf/params.py: Toards json serialisation
84d96a3
@pgunn
CNMFParams:to_dict() - key names should match attributes so saves/loa…
8ce73e1 
…ds are symmetric
@pgunn
CNMFParams.change_params() - dict follows struct of object, avoids re…
855b45a 
…setting unintended fields. No longer returns another reference to CNMFParams
@pgunn
CNMFParams: Properly scope dict load/save functions, add json functio…
516b8d8 
…ns, adjust tests
@pgunn
CNMFParams.change_params() - Add allow_legacy and warn_unused flags, …
be0cd87 
…internally implement set()
@pgunn
Fix documentation on CNMFParams, document some formerly-undocumented …
124487f 
…parameters
@pgunn
params.py: import optional
e3018c9
@pgunn
CNMFParams.change_params() - Don't use set(), and track unused params…
92505b1 
… everywhere
@pgunn
Fix a goof in the warning infrastructure
9258508
@pgunn
CNMFParams: more typing, some docs/message tweaks, mark set_if_not_ex…
6e92120 
…ists in set method as deprecated
@pgunn
num_splits_to_process_els: note that it does nothing, remove some plu…
6894829 
…mbing around it
@pgunn
Fix typo
0d0ed6c
@pgunn
cnmf/params.py: Improve zero check for decay time
cb0f53f
@pgunn
VERSION: 1.10.4 postrelease
cb6ed96
@pgunn
CNMFParams: nb parameter isn't actually used outside of the version i…
d618202 
…n init
@pgunn
CNMFParams: Update docs to note nb removed from temporal/spatial
bfc69dc
@pgunn
Merge pull request #1239 from flatironinstitute/dev-cnmfparams_json
70d14d3 
CNMFParams overhaul
@pgunn
Revert "CNMFParams: nb parameter isn't actually used outside of the v…
906d9ee 
…ersion in init"

This reverts commit d618202.
@pgunn
Revert "CNMFParams: Update docs to note nb removed from temporal/spat…
4232266 
…ial"

This reverts commit bfc69dc.
@pgunn
Hotfix: cnmfparams json load
f64a6f8
@pgunn
Fix issue with dev release and last refactor of pathing
9a40444
@pgunn
VERSION: Post release to 1.10.5
5985b28
@ethanbb
Update scanbox functions for new file format & features
7f77af9
@ethanbb
Return dxy in metadata and fix subindices case
20e6a0f
@pgunn
Backporting bugfix for recent CNMF refactor
c12fa7a
@EricThomson
updated discussion of memory optimizations
da257a0
@EricThomson
Merge pull request #1300 from flatironinstitute/optimization_update
c3b7342 
Updated discussion of optimizations in cnmf demo
@EricThomson
updated contributors doc
d43033a
@EricThomson
fixed words and formatting
083fb67
@pgunn
Merge pull request #1301 from flatironinstitute/contrib_doc_update
54915d3 
updated contributors doc
EricThomson and others added 29 commits March 21, 2024 15:10
@EricThomson
pylab removed from visualization.py
788a636
@EricThomson
changed pylab to pyplot back end
08eec02
@EricThomson
correct problem changing loaded params
8eb8d05
@EricThomson
handle grey_dilation import update
0629765
@EricThomson
get_colormap api updated before deprecation
fa38f06
@ethanbb
Add utils for converting SBX files to numpy format (and put updated s…
bc06acf 
…bxread in that file as well)
@ethanbb
Switch sbx destination format from npy to tif
1e04e69
@ethanbb
Support multidimensional subindices and add tests
2fc7676
@ethanbb
Merge branch 'dev' of https://github.com/flatironinstitute/CaImAn int…
300fd3d 
…o sbxload-update
@ethanbb
Alphebatize imports and use splitext
ec9ca6e
@pgunn
Merge pull request #1311 from proektlab/sbxload-update
16cb274 
Scanbox format updates
@pgunn
Github/CI: Add sudo install of Ubuntu packages to hopefully meet open…
0dbf510 
…cv build requirements
@pgunn
Merge pull request #1313 from flatironinstitute/dev-test_ci_fixes
ae20ae2 
Test ci fixes
@ethanbb
Fix invalid indexing for python <3.11
6aedb79
@ethanbb
Remove pipe syntax for type unions
d67ebed
@pgunn
Merge pull request #1314 from proektlab/sbxload-update
a93098d 
Fix incompatibilities in test_sbx for python <3.11
@pgunn
README: Fix minor spacing issue with Johannes's institution in credits
f74ff1b
@pgunn
CNMFParams: init.nb is now the authoritative nb, until a major future…
ff7fcce 
… refactor lets us clean it up more
@pgunn
CNMFParams: Add note discouraging use of the set() method
6963cbc
@pgunn
CNMFParams: only nag people once for deprecation
a422f0c
@pgunn
Merge pull request #1315 from flatironinstitute/dev-cnmfparams_nag_less
f9fa592 
CNMFParams: only nag people once for deprecation
@ethanbb
Prevent interpretation as RGB; add option to make 2D by extracting a …
ace51be 
…plane
@EricThomson
Merge pull request #1302 from flatironinstitute/remove_pylab
f29731e 
Remove pylab imports
@EricThomson
added explicit check for byte encoding
b6e28c6
@EricThomson
Merge pull request #1306 from flatironinstitute/handle_upcoming_depre…
97107ed 
…cations

Handle upcoming minor deprecations
@EricThomson
Merge pull request #1305 from flatironinstitute/fix_reload_typing
0452184 
Fix problem with using reloaded cnmf object
@ethanbb
Change keep3d argument to plane, and add tests for this and photometric
6a9d3d3
@pgunn
Merge pull request #1316 from proektlab/sbxload-update
f8a8102 
SBX utils: ensure correct photometric setting for TIFs and allow extracting single plane
@pgunn
Followup to SBX work: fix setup.py
66e2bcf
@pgunn pgunn merged commit 6470495 into main Apr 2, 2024
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3 participants
@pgunn @ethanbb @EricThomson