Add 1.12.1-dj branch: pin CaImAn for worker images on upstream v1.12.1#15
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MilagrosMarin wants to merge 64 commits into
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Add 1.12.1-dj branch: pin CaImAn for worker images on upstream v1.12.1#15MilagrosMarin wants to merge 64 commits into
MilagrosMarin wants to merge 64 commits into
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…e-fix Fix incorrect framerate when loading bidirectional SBX files
Numpy 2.0 compatibility: change all np.Inf to np.inf
…cleanup_movie cleanup movie
…volpy_qt6 Addresses flatironinstitute#1454 using pyside6
…s that change self inline
…params in calls to sklearn's NMF
…_params_for_nmf CNMF.initialization.greedyROI() - Add a limited mechanism to specify params in calls to sklearn's NMF
…fix_calling_conventions Fix calling conventions
…demo_seeded_notebook Fix demo seeded notebook
…_bad_params_for_huge_files Handle cases where parameters end up with bad values for OnACID given long movies
…data, also slight path handling improvement
…redirect
Adds optional output_dir and return_mc keyword arguments to
CNMF.fit_file:
- When output_dir is set, CAIMAN_TEMP is redirected to that
directory for the duration of the call and restored afterwards,
so per-call outputs land in caller-specified locations without
leaking global state.
- When return_mc=True and motion_correct=True, fit_file returns
(cnm2, mc) so callers can inspect the motion-correction object.
Carried forward from datajoint/CaImAn fork (commits 2447620,
ecc6df6, 5a3ec02, ffcff31, 11417cc, 55969b1) onto upstream
v1.12.1.
Mirror the fn_relocated path-relocation pattern that is already used elsewhere in motion_correction.py (e.g. line 564) so that apply_shifts_movie writes its memmap into the relocated path when CAIMAN_TEMP is set. Carried forward from datajoint/CaImAn fork (commit fa9f0e7) onto upstream v1.12.1.
DataJoint patches applied on top of upstream v1.12.1. Uses PEP 440 local version identifier (+dj1) to mark this as a distro-patched build of upstream 1.12.1.
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Summary
Creates a
1.12.1-djbranch based on upstreamv1.12.1with the three DataJoint-specific patches that thefmi_luthiworker image depends on, so the worker Dockerfile can move off cloning unpinnedmain.Background
The worker image currently clones
datajoint/CaImAnwith no branch and no commit pin:RUN git clone https://github.com/datajoint/CaImAn.gitThat means two image builds on different days can ship two different CaImAn versions, which makes pipeline runs hard to reproduce. The fork has also drifted to 224 commits behind upstream
main. This branch gives us a versioned, pinnable target.Contents
Branched from upstream
v1.12.1, with the existing fork-specific patches replayed as two squashed commits + a VERSION bump:d31e6066feat(fit_file): addoutput_dirandreturn_mckwargs with CAIMAN_TEMP redirecte39cea7bfix: usecaiman.paths.fn_relocatedinapply_shifts_movie94d3bf22VERSION: bump to1.12.1+dj128 additions, 4 deletions across 3 files. The diff against upstream v1.12.1 is identical in behaviour to the fork-specific patches that landed on
mainbetween June 2024 and February 2025 (PRs #8, #9, #10, #13 on this repo) — only the upstream base has moved forward.Compatibility
The workflow code calls
fit_file(..., output_dir=...)atfmi_luthi/src/workflow/pipeline/field_processing.py:183. That call site keeps working unchanged against this branch.How to use
Pin in dependent projects with:
And in the worker Dockerfile:
RUN git clone -b 1.12.1-dj https://github.com/datajoint/CaImAn.gitTest plan