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Dev -> Main for release of 1.11.0 #1342

Merged
merged 93 commits into from
May 3, 2024
Merged

Dev -> Main for release of 1.11.0 #1342

merged 93 commits into from
May 3, 2024

Commits on Apr 1, 2024

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

    …s after using)
    @ethanbb
    ethanbb committed Apr 1, 2024
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Commits on Apr 3, 2024

  1. VERSION: 1.10.10 post-release

    @pgunn
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Commits on Apr 8, 2024

  1. Extensions starts with a dot

    @marberi
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Commits on Apr 10, 2024

  1. Use memmap to load only indexed parts of files

    @ethanbb
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  2. Simplify by using the same loading code for all time index types

    @ethanbb
    ethanbb committed Apr 10, 2024
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  3. Merge branch 'dev' of https://github.com/flatironinstitute/CaImAn int… 

    …o sbxload-update
    @ethanbb
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Commits on Apr 11, 2024

  1. Revert tifffile write to what is in dev since it works

    @ethanbb
    ethanbb committed Apr 11, 2024
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  2. Merge pull request #1326 from marberi/dev 

    Extensions starts with a dot
    @pgunn
    pgunn committed Apr 11, 2024
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Commits on Apr 12, 2024

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

    @ethanbb
    ethanbb committed Apr 12, 2024
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  2. Add comment about not viewing memmap and rename Ns

    @ethanbb
    ethanbb committed Apr 12, 2024
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  3. Merge pull request #1329 from proektlab/sbxload-update 

    Simplify .sbx loading & improve space efficiency; explicitly close memmapped files
    @pgunn
    pgunn committed Apr 12, 2024
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Commits on Apr 16, 2024

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

    …pp-y
    @pgunn
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  2. note on single_thread

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

    …e .txt)
    @pgunn
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  4. Demos readme: format it a little more nicely

    @pgunn
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  5. Smaller cleanups, move logger setup into main(), preparing this to be… 

    … a model for other demo refactors
    @pgunn
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  6. bringing demo_pipeline and demo_caiman_basic closer together as I ref… 

    …actor demo_pipeline
    @pgunn
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  7. CLI Demos: Finish re-syncing demo_caiman_basic and demo_pipeline

    @pgunn
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  8. Rebasing

    @pgunn
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  9. Work on converting more CLI demos

    @pgunn
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  10. cli_demos work: convert more, regularise more

    @pgunn
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  11. cli_demos: Initial conversion of demo_pipeline_cnmfE to "app"

    @pgunn
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  12. cli demos: convert demo_pipeline_voltage_imaging to "app"

    @pgunn
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  13. rebasing

    @pgunn
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  14. cli demos: make amount of parallelism in the backend a CLI parameter

    @pgunn
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  15. demo_OnACID CLI: Use the new CNMFParams JSON API to let people specif… 

    …y configs as json
    @pgunn
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  16. CLI demo_caiman_basic.py: only set params once

    @pgunn
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  17. demo_caiman_basic CLI demo: move to json config files, only provide o… 

    …ne inbuilt config
    @pgunn
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  18. Demos/jsonconfigs: Fix misuse of params api

    @pgunn
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  19. Revise the three CLI demos that have been refactored to do argument/f… 

    …ile-input parsing in the right order
    @pgunn
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  20. Demo revisions: remove inline parameters

    @pgunn
    pgunn committed Apr 16, 2024
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  21. demos_refactor: demo_onacid file load fix

    @pgunn
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  22. demos_refactor: demo_pipeline rework to use json

    @pgunn
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  23. demo_pipeline_NWB conversion work

    @pgunn
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  24. cli demos json format fix whoops

    @pgunn
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  25. demos refactor: fixing demos as testing

    @pgunn
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  26. demos_refactor: params files should not try to set quality.decay_time… 

    … (nothing reads it, not a valid parameter)
    @pgunn
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  27. CLI demos rework: fix demo_onacid_mesoscope's visualisation defaults,… 

    … match old vals
    @pgunn
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  28. demo_behaviour:rebasing

    @pgunn
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  29. demo refactor: demo_pipeline_voltage_imaging: make method a commandli… 

    …ne argument
    @pgunn
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  30. demos_refactor: volpy demo import tweaks

    @pgunn
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  31. CNMF: Fix some issues from recent CNMFParams refactor

    @pgunn
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  32. demo_pipeline_cnmfE.py: ready for testing

    @pgunn
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  33. remove param temporal.memory_efficient which doesn't seem to do anything

    @pgunn
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  34. Params: Remove doc for temporal.memory_efficient which was documented… 

    … but not present in code
    @pgunn
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  35. CNMFParams: Remove documented but never-implemented data.mmap_C and d… 

    …ata.mmap_F (verified they never were filled in)
    @pgunn
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  36. Fix bug from 2019 with #030bc6d35

    @pgunn
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  37. CNMF: "is True" -> ""

    @pgunn
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  38. Remove spatial.block_size_spat 

    This tuned memory usage when it was added in #c55b95 but later refactors removed its use
    @pgunn
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  39. Remove merging.max_merge_area 

    This once was functional, with #52a0c4b1, but became vestigial with a later refactor of cnmf.merging.merge_components()
    @pgunn
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  40. demo_behavior: more rebase nonsense

    @pgunn
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  41. demo_behavior: rebase nonsense

    @pgunn
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  42. After rebase, add demo_behavior back in

    @pgunn
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Commits on Apr 18, 2024

  1. CLI demo refactor: forgot to import os

    @pgunn
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  2. CLI demos refactor: demo_pipeline_cnmfE: Fix a mistake in move to params

    @pgunn
    pgunn committed Apr 18, 2024
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  3. Fix paths for more temporary files over a run to land in caiman_data/… 

    …temp/
    @pgunn
    pgunn committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. Adjust gating, path handling to try harder not to drop temporary file… 

    …s anywhere but caiman_data/temp/
    @pgunn
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  2. Note in docs that caiman.movie.save() returns the filename. Fix a tes… 

    …t suite's sloppy path code
    @pgunn
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  3. Movie.save(): Always return filename (before it only did it for some … 

    …target file formats)
    @pgunn
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Commits on Apr 23, 2024

  1. environment.yml: be smarter about alternate builds of conda, set chan… 

    …nel-priority to handle if user/distro has set it to something else
    @pgunn
    pgunn committed Apr 23, 2024
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Commits on Apr 24, 2024

  1. environment.yml: can't actually set channel priority in environment.yml

    @pgunn
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  2. Try adjusting CI to use environment-minimal.yml

    @pgunn
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  3. minimal environment needs a few more things

    @pgunn
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  4. environment-minimal hasn't seen enough testing over the years.

    @pgunn
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  5. If we're to use environment-minimal for CI we need to include nose

    @pgunn
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  6. prevent old numpy breaking typing

    @pgunn
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  7. yaml: Prevent old versions of numpy and associated problems

    @pgunn
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  8. CI's way of managing updating the test environment means lots of mini… 

    …mal version pins
    @pgunn
    pgunn committed Apr 24, 2024
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  9. Merge pull request #1334 from flatironinstitute/dev-environment_rework 

    environment.yml: handle variant and newer condas better
    @pgunn
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  10. Hotfix: Fix issue in demo_caiman_cnmf_3D from a past refactor to visu… 

    …alization.py
    @pgunn
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  11. cherry-pick 73d572

    @pgunn
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Commits on Apr 26, 2024

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

    …isdesign of CNMFParams)
    @pgunn
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  2. params: better handle if user provides ring_CNN (compensating for a m… 

    …isdesign of CNMFParams)
    @pgunn
    pgunn committed Apr 26, 2024
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  3. Fix goof in last hotfix to CNMFParams

    @pgunn
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  4. Fix goof in last hotfix to CNMFParams

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

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

    @pgunn
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  7. mat file revamp: Use consistent phrasing

    @pgunn
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  8. Update docs on mat file support

    @pgunn
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  9. Merge pull request #1337 from flatironinstitute/dev-fix_mat_support 

    fix mat support
    @pgunn
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Commits on Apr 30, 2024

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

    …n, but still a good commit)
    @pgunn
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  2. CLI OnACID demos: correctly handle display of results

    @pgunn
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  3. CLI demo pipeline: get rid of qt errors

    @pgunn
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  4. Add note to demo_behaviour that it needs a qt6 build of opencv

    @pgunn
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  5. demo_behavior and caiman.behavior.behavior: fix ancient calls

    @pgunn
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  6. CLI demo: fix demo_behavior

    @pgunn
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Commits on May 1, 2024

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

    … spams library, now hard to package)
    @pgunn
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  2. caiman.behavior.extract_components(): remove method_factorization of … 

    …dict_learn (which needed spams)
    @pgunn
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  3. Add note about commandline demos to the main README

    @pgunn
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  4. Merge pull request #1211 from flatironinstitute/cli_demos_refactor 

    Refactor CLI demos to be applications
    @pgunn
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  5. caimanmanager: don't copy __pycache__ dirs out of the library bundle

    @pgunn
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  6. Merge pull request #1341 from flatironinstitute/dev-fix_pycache_creation 

    caimanmanager: don't copy __pycache__ dirs out of the library bundle
    @pgunn
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Commits on May 3, 2024

  1. VERSION: next release will be 1.11.0

    @pgunn
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