Dev -> Main for release of 1.11.0 #1342

pgunn · 2024-05-03T15:45:24Z

Prep for release

…s after using)

…o sbxload-update

Extensions starts with a dot

Simplify .sbx loading & improve space efficiency; explicitly close memmapped files

…pp-y

…e .txt)

… a model for other demo refactors

…actor demo_pipeline

…y configs as json

…ne inbuilt config

…ile-input parsing in the right order

…mal version pins

environment.yml: handle variant and newer condas better

…alization.py

…isdesign of CNMFParams)

fix mat support

…n, but still a good commit)

… spams library, now hard to package)

…dict_learn (which needed spams)

Refactor CLI demos to be applications

caimanmanager: don't copy __pycache__ dirs out of the library bundle

ethanbb and others added 30 commits April 1, 2024 03:11

Fix SBX functions for older tifffile versions and Windows (close mmap…

98ef067

…s after using)

VERSION: 1.10.10 post-release

a5de8bf

Extensions starts with a dot

0fec0b0

Use memmap to load only indexed parts of files

4a08717

Simplify by using the same loading code for all time index types

163022f

Merge branch 'dev' of https://github.com/flatironinstitute/CaImAn int…

20bb8ab

…o sbxload-update

Revert tifffile write to what is in dev since it works

2647b59

Merge pull request #1326 from marberi/dev

f5d5295

Extensions starts with a dot

Use del to close memmaps rather than _mmap; reduce code duplication

c75a4f8

Add comment about not viewing memmap and rename Ns

6c836c0

Merge pull request #1329 from proektlab/sbxload-update

69772e3

Simplify .sbx loading & improve space efficiency; explicitly close memmapped files

Trying out a refactor of the basic demo to be less notebook-y, more a…

149d624

…pp-y

note on single_thread

cd64806

demos get a readme (that caimanmanager will deliver, so it needs to b…

4592b43

…e .txt)

Demos readme: format it a little more nicely

e17931b

Smaller cleanups, move logger setup into main(), preparing this to be…

f30b975

… a model for other demo refactors

bringing demo_pipeline and demo_caiman_basic closer together as I ref…

fab66bc

…actor demo_pipeline

CLI Demos: Finish re-syncing demo_caiman_basic and demo_pipeline

4ff7854

Rebasing

46a15dd

Work on converting more CLI demos

9b56d85

cli_demos work: convert more, regularise more

1315b9a

cli_demos: Initial conversion of demo_pipeline_cnmfE to "app"

2859174

cli demos: convert demo_pipeline_voltage_imaging to "app"

38436e1

rebasing

b882ddd

cli demos: make amount of parallelism in the backend a CLI parameter

21eb57f

demo_OnACID CLI: Use the new CNMFParams JSON API to let people specif…

7ee20e1

…y configs as json

CLI demo_caiman_basic.py: only set params once

2ffe070

demo_caiman_basic CLI demo: move to json config files, only provide o…

860ea9f

…ne inbuilt config

Demos/jsonconfigs: Fix misuse of params api

5a98259

Revise the three CLI demos that have been refactored to do argument/f…

3862d71

…ile-input parsing in the right order

pgunn and others added 29 commits April 24, 2024 10:33

If we're to use environment-minimal for CI we need to include nose

5082983

prevent old numpy breaking typing

b6e67c5

yaml: Prevent old versions of numpy and associated problems

0b81678

CI's way of managing updating the test environment means lots of mini…

14af8d5

…mal version pins

Merge pull request #1334 from flatironinstitute/dev-environment_rework

aabb25d

environment.yml: handle variant and newer condas better

Hotfix: Fix issue in demo_caiman_cnmf_3D from a past refactor to visu…

73d5721

…alization.py

cherry-pick 73d572

fd24f25

params: better handle if user provides ring_CNN (compensating for a m…

41cd982

…isdesign of CNMFParams)

params: better handle if user provides ring_CNN (compensating for a m…

75c95b2

…isdesign of CNMFParams)

Fix goof in last hotfix to CNMFParams

c45b9aa

Fix goof in last hotfix to CNMFParams

9ea5587

Remove (broken) support for the old non-hdf5 format of .mat files

b8e97f8

.mat files: give users better messages if they try to open a v1 file

fafffce

mat file revamp: Use consistent phrasing

2581815

Update docs on mat file support

29a3a67

Merge pull request #1337 from flatironinstitute/dev-fix_mat_support

df5b487

fix mat support

CNMFParams: remove some dead code (really just a commit to make CI ru…

7943ede

…n, but still a good commit)

CLI OnACID demos: correctly handle display of results

ac1e2aa

CLI demo pipeline: get rid of qt errors

0fa78a3

Add note to demo_behaviour that it needs a qt6 build of opencv

a5886c4

demo_behavior and caiman.behavior.behavior: fix ancient calls

fe1ad0c

CLI demo: fix demo_behavior

0c80201

Remove caiman.base.movies.online_NMF() which is unused (and needs the…

862dba8

… spams library, now hard to package)

caiman.behavior.extract_components(): remove method_factorization of …

887e99e

…dict_learn (which needed spams)

Add note about commandline demos to the main README

b45633a

Merge pull request #1211 from flatironinstitute/cli_demos_refactor

6581329

Refactor CLI demos to be applications

caimanmanager: don't copy __pycache__ dirs out of the library bundle

8e9ad9f

Merge pull request #1341 from flatironinstitute/dev-fix_pycache_creation

29743f0

caimanmanager: don't copy __pycache__ dirs out of the library bundle

VERSION: next release will be 1.11.0

63c1932

pgunn merged commit a30d1b1 into main May 3, 2024
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Dev -> Main for release of 1.11.0 #1342

Dev -> Main for release of 1.11.0 #1342

pgunn commented May 3, 2024

Dev -> Main for release of 1.11.0 #1342

Dev -> Main for release of 1.11.0 #1342

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pgunn commented May 3, 2024