Black formatting #14
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Black formatting #14
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ziw-liu
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Note that for the blame ignoring to work after merging, the commits in this PR cannot be squashed. |
talonchandler
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Dec 3, 2022
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ziw-liu
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Mar 14, 2023
* Merge pull request #14 from mehta-lab/QLIPP_pipeline recOrder pipeline infrastructure + qlipp pipeline submodule * Merge pull request #22 from mehta-lab/zarr_converter Zarr converter * Merge pull request #52 from mehta-lab/fluor_deconv Fluorescence Deconvolution and PhaseFromBF pipelines * Merge pull request #31 from mehta-lab/calibration_plugin Calibration/Acquisition Plugin * Merge pull request #112 from mehta-lab/cleanup-tests-and-readme Improved testing, configs, and dev tools * Merge pull request #123 from mehta-lab/zarr-converter-position-bug Fix ome-tif to zarr converter for acquisitions with micromanager beta * Merge pull request #140 from mehta-lab/restructure_tests Restructure tests * Merge pull request #148 from mehta-lab/pycromanager_converter_v2 Pycromanager converter v2 * Merge pull request #167 from mehta-lab/bkg-correction-fixes2 Fix background correction for non-square images and online mode * Merge pull request #157 from mehta-lab/RAM-warning Print RAM warning message in online and offline modes * Merge pull request #169 from mehta-lab/warn-bkg-averaging Remove background averaging * Merge pull request #174 from mehta-lab/show-ram-warning Show RAM warning in GUI / log in CLI * Merge pull request #175 from mehta-lab/better-messages Improved warning message * Merge pull request #181 from mehta-lab/error-mismatched-bkg-and-img Always load background and warn if background and image sizes are mismatched * Merge pull request #182 from mehta-lab/error-mismatched-bkg-and-img Mismatched x/y size of background and acquisition should error instead of warn * Merge pull request #210 from mehta-lab/0.2.0-gui-hide Remove fluorescence, preprocessing, and postprocessing; simplify GUI * Merge pull request #219 from mehta-lab/0.2.0-integration 0.2.0 integration PR * Introduce Black formatting into the code base (#229) * black-format all `.py` files except recorder_ui.py * create .git-blame-ignore-revs * Document how to ignore formatting commits * Document `git` version Co-authored-by: Talon Chandler <[email protected]> * draft refactor for imread * expose primary entry points * fix type check and tests Signed-off-by: Ziwen Liu <[email protected]> * fix formatting * update `imread` docstring * define supported formats Signed-off-by: Ziwen Liu <[email protected]> * rename pycromanager reader to ndtiff Pycromanager is no longer a dependency, and MM can also write NDTIFF. Signed-off-by: Ziwen Liu <[email protected]> * remove 'doesnt work' code * improve error messages * rearrange files from patch * depend on tqdm for progress bar in conversion * move util function * delete other util functions * make util function private * remove redundant file * rename converter file * fix some of the references and docstrings * draft refactor * write with new ngff module * fix position grid * fix image check * close writer after conversion * test ome-tiff conversion * handle invalid stage position metadata * support labelling positions * fix typo * fix path type * convert single page tiff datasets This is rather broken: the reader does not handle metadata well * allow longer conversion time in tests Signed-off-by: Ziwen Liu <[email protected]> * draft cli command Signed-off-by: Ziwen Liu <[email protected]> * fix argument * detect flat ndtiff * sort imports Signed-off-by: Ziwen Liu <[email protected]> * limit bar length * add -h shortcut for help * test cli * fix get_image * test against a random choice of dataset --------- Signed-off-by: Ziwen Liu <[email protected]> Co-authored-by: Cameron Foltz <[email protected]> Co-authored-by: Shalin Mehta <[email protected]> Co-authored-by: Talon Chandler <[email protected]> Co-authored-by: Ivan Ivanov <[email protected]>
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Resolves #8 with black formatting. Pre-commit hooks suggested by @JoOkuma are yet to be implemented.
Blame view should not be affected on GitHub.
To ignore the formatting commit locally, follow this guide. TLDR: in repo root directory run: