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Pull changes from flatironinstitute and resolve merge conflicts #7

Merged
merged 642 commits into from
Jun 5, 2024
Merged

Pull changes from flatironinstitute and resolve merge conflicts #7

merged 642 commits into from
Jun 5, 2024

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kushalbakshi
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pgunn and others added 30 commits February 9, 2024 14:16
@pgunn
Notebooks advice in readme: don't tell users to cd all the way into n…
1c056eb 
…otebooks dir before launching jupyter, to avoid breakage
@pgunn
notebooks: revise intent of diff to store images used by notebooks in…
80abf0e 
… an images/ directory right next to the notebooks
@pgunn
Move more images for notebooks
b64a786
@pgunn
Merge pull request flatironinstitute#1270 from flatironinstitute/dev-…
32250b2 
…notebooks_revert_gh_pointer

Notebooks:images live in images/ subdir next to notebooks
@pgunn
Redoing the diff. Also removing an unused spatial function that calle…
b1f0ff3 
…d code removed a long time ago in e7a4305
@pgunn
More reimplementing into new diff
bd4fe8c
@pgunn
oasis.cpp got mistakenly added again. Removing it again
d550961
@pgunn
merging.py
170dc21
@pgunn
initialization.py convert from old diff; note local_nmf method goes a…
f1a4673 
…way because it never worked
@pgunn
estimates: going less ambitious with this one, for now
f84062c
@pgunn
cnmf/cnmf port over the diffs
811593f
@pgunn
motion_correction: merge intents of diffs
9a9134d
@pgunn
components_evaluation
bc2b2f6
@pgunn
caiman/cluster.py
ccd9dd5
@pgunn
base/traces: going less ambitious on this one for now
ccb6a70
@pgunn
base/rois.py: less ambitious for now
5cef076
@pgunn
caiman.base.movies: imports
542ffeb
@pgunn
"import caiman as cm" -> "import caiman"
e1c3f92
@pgunn
Remove ipython breakpoints, modernise some string interpolation, othe…
acc394a 
…r janitorial work
@pgunn
Fix a brain-o in an imports fix
f2eed29
@pgunn
import cleanup: fix "profile" decorator I accidentally removed, also …
a2baf62 
…fix some weird imports for cv2
@pgunn
import cleanup: fix another typo
ed63aab
@pgunn
import cleanup: more bug squashing
c7925a9
@pgunn
imports cleanup: another bug
f7a559f
@pgunn
import cleanup: more fixes until it passes testing locally
887a054
@pgunn
import cleanup: for traces we'll go with absolute import to make it c…
afa972b 
…lear it's a caiman thing
@pgunn
import cleanup: cluster.py - removed some unneded imports, a bit more…
b2a2ce0 
… tidying
@pgunn
import cleanup: order of imports
961676b
@pgunn
import cleanup: caiman_datadir() is never going to be confusing
7741c9f
@pgunn
import cleanup: remove another relative import
60c73cb
pgunn and others added 14 commits May 3, 2024 11:45
@pgunn
Merge pull request flatironinstitute#1342 from flatironinstitute/dev
a30d1b1 
Dev -> Main for release of 1.11.0
@pgunn
VERSION to 1.11.1 after release
f070226
@pgunn
VERSION to 1.11.1 after release
7174b3b
@pgunn
See if updating to latest github actions for CI is easy (maybe will f…
084e44a 
…ix environment file selection?)
@pgunn
Fix code goof that a random bot found flatironinstitute#1345
dea8431
@ethanbb
Fix map_async call on DirectView causing error
aa65ab3
@pgunn
Merge pull request flatironinstitute#1350 from proektlab/ipp-async-fix
50fafa3 
Fix map_async call on DirectView causing error
@ethanbb
Clean up special cases for loading from HDF5 and fix None handling
dbd27db
@ethanbb
Fix invalid comparison for non-scalars
09a8a02
@pgunn
Merge pull request flatironinstitute#1353 from proektlab/none-load-fix
1624347 
Fix medw loading as b'NoneType' instead of None
@pgunn
Pin tensorflow below 2.16, address flatironinstitute#1355
ae1fe4e
@kushalbakshi
Merge branch 'master' of https://github.com/datajoint/CaImAn
7826015
@kushalbakshi
Merge branch 'main' of https://github.com/flatironinstitute/CaImAn
9f95676
@kushalbakshi
Update(motion_correction.py): Remove unused imports
97b1784
@kushalbakshi kushalbakshi requested a review from ttngu207 May 31, 2024 15:36
@kushalbakshi kushalbakshi marked this pull request as draft May 31, 2024 15:40
pgunn and others added 11 commits May 31, 2024 12:29
@pgunn
caimanmanager: Detect and adjust behaviour for editable installs
b506e02
@pgunn
Improve messaging around editable installs
be70e72
@kushalbakshi
Fix(mmapping.py): Tuple -> tuple case-match
1ca3152
@pgunn
chdir for the user if needed
d0a5eb3
@pgunn
caimanmanager: "is None" still can't be used on a variable if it was …
ddca982 
…created in a branch, so assign =None
@pgunn
Merge pull request flatironinstitute#1357 from flatironinstitute/dev-…
2c890ca 
…caimanmanager_detect_editable

caimanmanager detect editable
@pgunn
Merge pull request flatironinstitute#1358 from flatironinstitute/dev
e970637 
dev->main for release 1.11.1
@pgunn
VERSION to 1.11.2 after release
e7e8641
@kushalbakshi
Merge branch 'main' of https://github.com/flatironinstitute/CaImAn
fb87e6b
@kushalbakshi
Add output_dir argument to motion_correct_batch_rigid()
6ecc83a
@kushalbakshi
Fix(motion_correction.py): update old_div() to division operator
4e9394a
@kushalbakshi kushalbakshi marked this pull request as ready for review June 5, 2024 22:51
@ttngu207 ttngu207 merged commit ff2858b into datajoint:master Jun 5, 2024
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@ttngu207 ttngu207 ttngu207 approved these changes

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6 participants
@kushalbakshi @ttngu207 @pgunn @EricThomson @ethanbb @marberi