apm em search sprint #70
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… purposes and testing the search interfaces, added dependencies in preparation for em_oim_ms parser h5web with support for RGB image stacks
…sets with signal from and elements across the periodic table, pylint, codestyle, mypy locally ok
… h5web, and ifes_apt_tc related changes
…s used by apm and em parsers and others if desired, pylint, pycode, and mypy on nexusutils showing no longer issues
…correct sequence for writing compressed template entries via h5py
…wn bug that upper-case attributes are not handled correctly
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The files in the deprecated folder here can be removed: nexusutils/dataconverter/readers/apm/utils/deprecated |
sherjeelshabih
requested changes
Feb 1, 2023
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There are many asserts, prints, and #comments that can be removed. I skipped some. Also, the shebangs at the top of the files are not needed.
Shebangs removed, license default text equalized, prints cleaned in many places, not immediately relevant ones commented out
asserts I will keep for now and experiment with in the em_oim_ms parser, ones working there successively changing in the older parsers
sanbrock
requested changes
Feb 1, 2023
nexusutils/dataconverter/readers/apm/utils/deprecated/aptfim_io_ods2metadata.py
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nexusutils/dataconverter/readers/em_spctrscpy/utils/em_utils.py
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LGTM |
sanbrock
approved these changes
Feb 2, 2023
RubelMozumder
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Jun 28, 2023
* Added functionalities for creating synthetic datasets for development purposes and testing the search interfaces, added dependencies in preparation for em_oim_ms parser h5web with support for RGB image stacks * styling, linting, mypy * Added support for creating simple synthetic em_spctrscpy example datasets with signal from and elements across the periodic table, pylint, codestyle, mypy locally ok * linting, styling, and mypy with 3.8 * Using double quotes consistently throughout, updated to mirror ipynb, h5web, and ifes_apt_tc related changes * Updated README.md to reflect py38 * Pulled code duplicates into shared to be used as a library for objects used by apm and em parsers and others if desired, pylint, pycode, and mypy on nexusutils showing no longer issues * Development stage fixing NXdata to use data_ and axis_ * Unclean state with annotated dataconverter print statement to hunt down bug that upper-case attributes are not handled correctly * fix the writing of undocumented items * feature dev complete, apm and em, search sprint * Changes from first revision round * Fix pylint CI issues * Handles NxdlAtrributeNotFound exception better in the writer * excluding definitions from CI * fixing assert --------- Co-authored-by: markus.kuehbach <markus.kuehbach@hu-berlin.de> Co-authored-by: sanbrock <sandor.brockhauser@gmail.com> Co-authored-by: Sherjeel Shabih <shabihsherjeel@gmail.com>
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