DRAFT Feature/minknow6 compatibility#369
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Add in the correct strand classifications for minknow 6
Explicitly exit if running on MInKNOW 5.X.X
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Do we need to add dorado tests as well? |
Contributor
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I've had a stab at addressing some of these issues in #feature/deprecate-guppy |
Fix tests for the _statistics too not use `read_number`
* This commit addresses the removal of guppy.py, partial removal of guppy tests, edits to documentation to largely replace guppy with dorado, removes the ont-pyguppy-client-lib and adds a warning to the readme. It also adds some extra classes to the read_until init in targets. * Remove builtin module for guppy * Update FAQ questions to focus dorado as well as Guppy * Change validate caller warning to mention dorado not guppy * Change readme warnings to Focus dorado and minknow braking changes more Add link/requiremtn for dorado_basecall_server not guppy_basecall_server * Rename tests to dorado validation tests * Add dorado to mappy-test install target --------- Co-authored-by: mattloose <matt.loose@nottingham.ac.uk>
alexomics
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alexomics
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Adoni5
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* Attempt at using pass_reads * Add message about generating the aligner description * FIX bug where parameter reads was being overwritten by empty list reads * DRAFT Feature/minknow6 compatibility (#369) * Made a proper SVG thought i'd just include it here * Remove setting the read_number on the result Add in the correct strand classifications for minknow 6 * Remove Read number from Result and all references to read number * Update target versions for MinKNOW to 6.0.0 - 6.0.0 Explicitly exit if running on MInKNOW 5.X.X * Update vendored read until API to v3.5.2 * Update test for conencted base caller version to work * Pin ont-pybasecall-client-lib at 7.4.12 * Add downgrade to 2024.2.0 to error message * Fix bug where unblocked_read_ids wasn't being written out * Chunk tracker uses read_id not read_number, update trackers internal variable names * bump version to 2024.3.0 * Fix tests for the new MinKNOW version compatibility Fix tests for the _statistics too not use `read_number` * Bump summarise version to 0.2.7 * Drop incorrect gotcha * Feature/deprecate guppy (#374) * This commit addresses the removal of guppy.py, partial removal of guppy tests, edits to documentation to largely replace guppy with dorado, removes the ont-pyguppy-client-lib and adds a warning to the readme. It also adds some extra classes to the read_until init in targets. * Remove builtin module for guppy * Update FAQ questions to focus dorado as well as Guppy * Change validate caller warning to mention dorado not guppy * Change readme warnings to Focus dorado and minknow breaking changes more Add link/requirement for dorado_basecall_server not guppy_basecall_server * Rename tests to dorado validation tests * Add dorado to mappy-test install target * Fix black formatting of accepted chunks list * rename read_id to read_number on _generate_action because I may as well * return action from override as for some pythons it doesn't mutate in place * add mappy-rs because I keep typing it and not mappy_rs * Don't clip RF from front, used cached read_id for the result
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* Attempt at using pass_reads * Add message about generating the aligner description * FIX bug where parameter reads was being overwritten by empty list reads * DRAFT Feature/minknow6 compatibility (LooseLab#369) * Made a proper SVG thought i'd just include it here * Remove setting the read_number on the result Add in the correct strand classifications for minknow 6 * Remove Read number from Result and all references to read number * Update target versions for MinKNOW to 6.0.0 - 6.0.0 Explicitly exit if running on MInKNOW 5.X.X * Update vendored read until API to v3.5.2 * Update test for conencted base caller version to work * Pin ont-pybasecall-client-lib at 7.4.12 * Add downgrade to 2024.2.0 to error message * Fix bug where unblocked_read_ids wasn't being written out * Chunk tracker uses read_id not read_number, update trackers internal variable names * bump version to 2024.3.0 * Fix tests for the new MinKNOW version compatibility Fix tests for the _statistics too not use `read_number` * Bump summarise version to 0.2.7 * Drop incorrect gotcha * Feature/deprecate guppy (LooseLab#374) * This commit addresses the removal of guppy.py, partial removal of guppy tests, edits to documentation to largely replace guppy with dorado, removes the ont-pyguppy-client-lib and adds a warning to the readme. It also adds some extra classes to the read_until init in targets. * Remove builtin module for guppy * Update FAQ questions to focus dorado as well as Guppy * Change validate caller warning to mention dorado not guppy * Change readme warnings to Focus dorado and minknow breaking changes more Add link/requirement for dorado_basecall_server not guppy_basecall_server * Rename tests to dorado validation tests * Add dorado to mappy-test install target * Fix black formatting of accepted chunks list * rename read_id to read_number on _generate_action because I may as well * return action from override as for some pythons it doesn't mutate in place * add mappy-rs because I keep typing it and not mappy_rs * Don't clip RF from front, used cached read_id for the result
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Highlights
Adds in compatibility for MinKNOW 6.
Warning
Breaking for any version of
MinKNOW <= 6.0.0It will not run against
MinKNOW <= 6.0.0, instead logging a critical message, suggesting a downgrade and raisingSystemExit.Key Changes
ont-readuntil-apitov3.5.2, which removes any use of read number in the API.read_numberin readfish code, including the logging ofread_numberin the debug log.connected_basecaller_versionfor compatibility checking.ont-pybasecall-clientto 7.4.12Todo before merging
**I suggest that we take this opportunity to drop
Guppysupport entirely. **Note
We are still using read_number in some trackers, these will definitely stop working properly until they are updated to use
read_idont-pyguppy-client-libfrompyproject.tomlread_idnotread_number