Code

dev -> master for 1.10.3 release#1292

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pgunn merged 55 commits intomainflatironinstitute/CaImAn:mainfrom devflatironinstitute/CaImAn:devCopy head branch name to clipboardFeb 23, 2024

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Commits on Feb 2, 2024

• Update dev version 1.10.2 to 1.10.3

  EricThomson

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Commits on Feb 9, 2024

• Notebooks: revert 41828ff (based on mostly in-person discussion)

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• Notebooks advice in readme: don't tell users to cd all the way into notebooks dir before launching jupyter, to avoid breakage

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• notebooks: revise intent of diff to store images used by notebooks in an images/ directory right next to the notebooks

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• Move more images for notebooks

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Commits on Feb 14, 2024

• Merge pull request #1270 from flatironinstitute/dev-notebooks_revert_gh_pointer

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• Redoing the diff. Also removing an unused spatial function that called code removed a long time ago in e7a4305

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• More reimplementing into new diff

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• oasis.cpp got mistakenly added again. Removing it again

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• merging.py

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• initialization.py convert from old diff; note local_nmf method goes away because it never worked

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• estimates: going less ambitious with this one, for now

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• cnmf/cnmf port over the diffs

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• motion_correction: merge intents of diffs

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• components_evaluation

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• caiman/cluster.py

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• base/traces: going less ambitious on this one for now

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• base/rois.py: less ambitious for now

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Commits on Feb 15, 2024

• caiman.base.movies: imports

  pgunn

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• "import caiman as cm" -> "import caiman"

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• Remove ipython breakpoints, modernise some string interpolation, other janitorial work

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• Fix a brain-o in an imports fix

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• import cleanup: fix "profile" decorator I accidentally removed, also fix some weird imports for cv2

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• import cleanup: fix another typo

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• import cleanup: more bug squashing

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• imports cleanup: another bug

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• import cleanup: more fixes until it passes testing locally

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• import cleanup: for traces we'll go with absolute import to make it clear it's a caiman thing

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• import cleanup: cluster.py - removed some unneded imports, a bit more tidying

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• import cleanup: order of imports

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• import cleanup: caiman_datadir() is never going to be confusing

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• import cleanup: remove another relative import

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• Remove cnmf_optional_outputs.py, code that was broken 8 years ago with commit 07b82d3

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• Merge pull request #1277 from flatironinstitute/dev_no_relative_imports_2

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Commits on Feb 16, 2024

• Sphinx-doc-fixes: Fix everything sphinx calls an error

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• docs: Overview.rst: remove outdated info

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• Merge pull request #1279 from flatironinstitute/dev-fix_sphinx

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• docs_require needs ipywidgets

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• RTD: add zarr too

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Commits on Feb 19, 2024

• Switchover scipy.histogram() to numpy.histogram() to deal with scipy 1.12 changes

  pgunn

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• Adjust other scipy re-exports in stats

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• Merge pull request #1282 from flatironinstitute/dev-fix_scipy_histogram_import

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Commits on Feb 20, 2024

• Pull more docs into the sphinx doctree, fix some formatting issues and links

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• docs/sphinx - fix readme-gpu so its headers are appropriately summarised

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• Sphinx/docs: Change formatting of file formats doc to ensure it parses

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Commits on Feb 21, 2024

• sphinx/links-and-formatting fixup More touch-ups to docs, also remove most funky capitalisation there

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• handle problems that can come up with auto-percentile calculations for dff

  EricThomson

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Commits on Feb 22, 2024

• updated based on review

  EricThomson

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• Merge pull request #1286 from flatironinstitute/dev-sphinx_and_markdown_link_fixes

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• Merge pull request #1288 from flatironinstitute/dff_inception_debug

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• updated logo!

  EricThomson

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• Merge pull request #1289 from flatironinstitute/logo_update

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  pgunn

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• Move and rephrase info on caiman central

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• Readme: change section header

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• Merge pull request #1290 from flatironinstitute/dev-README_centralise_the_center

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