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b8cebb8ba4
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Infrastructure for concurrent processing implemented
autoBIGS.engine/pipeline/head This commit looks good
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2025-02-19 15:49:46 +00:00 |
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7384895578
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Writing now uses named MLST profile
automlst.engine/pipeline/head This commit looks good
automlst.engine/pipeline/tag This commit looks good
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2025-02-18 16:03:17 +00:00 |
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5a03c7e8d8
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Multiple string profiling now respects grouped queries (for non-WGS)
automlst.engine/pipeline/head This commit looks good
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2025-02-18 15:34:18 +00:00 |
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d0318536b2
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Changed FASTA reading to group based on file for merging partial targets
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2025-02-14 14:35:53 +00:00 |
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73aade2bde
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Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
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2025-02-12 17:07:51 +00:00 |
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af8590baa7
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Removed import of deleted feature
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2025-02-12 17:07:10 +00:00 |
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36bca1b70d
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Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
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2025-02-12 17:02:22 +00:00 |
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09a693b696
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Removed features being worked on in separate branch
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2025-02-12 17:02:00 +00:00 |
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ba606c35a9
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conversion of collection of alleles to map now produces results with tuples instead of lists
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2025-02-12 16:36:31 +00:00 |
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4183840ba0
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Added notation to indicate inexact matching in CSV
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2025-02-12 15:59:19 +00:00 |
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175a51f968
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Replaced local profiler with a not implemented exception
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2025-02-12 15:52:48 +00:00 |
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e568e9fb2c
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Adapted latest merged reading codebase to current codebase
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2025-02-11 19:13:29 +00:00 |
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4b9eb8674d
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Merge branch 'develop' into features/local-typing
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2025-02-11 17:55:34 +00:00 |
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f75707e4fe
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CSV output column order is now predictable (sorted)
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2025-02-11 17:54:48 +00:00 |
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b4845fab34
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Added automatic handling of strings instead of arrays of sequences to typing
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2025-02-06 21:15:50 +00:00 |
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fe999f1cab
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Added a unit test for multithreaded alignments
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2025-02-06 18:01:50 +00:00 |
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85946eb110
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Fixed match metric difference between remote and local
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2025-02-06 17:12:31 +00:00 |
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a27e09da31
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Added code to retrieve sequences and annotations from NCBI GenBank
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2025-02-06 17:11:20 +00:00 |
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ba2b688e89
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Removed sorting as it seems unecessary
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2025-02-05 22:06:50 +00:00 |
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49f31b7943
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Async aligner work tracking issue fixed
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2025-02-05 21:47:51 +00:00 |
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1c6e1cfb35
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Fixed issue with hashing a ndarray by using tuple.
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2025-02-05 20:43:53 +00:00 |
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fb99526162
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Updated iteration on asynchronous aligner
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2025-02-05 17:17:37 +00:00 |
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ff8a1aff08
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Implemented annotated local typing method without testing
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2025-02-04 16:19:00 +00:00 |
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3e3898334f
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Began implementing LazyPersistentCachedBIGSdbMLSTProfiler
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2025-01-27 22:03:49 +00:00 |
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ba1f0aa318
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Fixed potential memory leak
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2025-01-27 22:02:52 +00:00 |
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1773bb9dcb
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Updated naming (again).
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2025-01-22 21:05:19 +00:00 |
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53e74af20a
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Refactoring project name to autoBIGSst.engine
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2025-01-22 18:24:04 +00:00 |
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b89f24a3fa
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Fixed issue where multiple allele identifiers were not returned in output.
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2025-01-17 17:04:22 +00:00 |
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e7c8c5bcf9
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Changed allele CSV output to non-lists
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2025-01-17 16:56:52 +00:00 |
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7ea7ead46a
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Moved ABIF code to separate project
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2025-01-17 14:27:25 +00:00 |
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a3c864b565
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Refactored code layout
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2025-01-16 21:54:52 +00:00 |
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4fe0f0f287
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Added stage for publishing to test.pypi.org when the tag a version number.
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2025-01-16 21:22:49 +00:00 |
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5449ae0c68
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Moved CLI to automlst.cli repo
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2025-01-10 17:22:12 +00:00 |
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e634647774
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Added untested partial matching
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2025-01-10 16:12:56 +00:00 |
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f20a656f45
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Fixed multiple string typing failure handling
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2025-01-10 16:00:27 +00:00 |
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0c0a2c9d4c
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Finished adding partial allele matching
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2025-01-10 15:25:31 +00:00 |
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03fbbe542e
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allele profiling partial matching works
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2025-01-09 21:44:28 +00:00 |
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9589761ddd
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Now tracks failed profilings
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2025-01-09 17:27:15 +00:00 |
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2843d0d592
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Added tests to test continuous MLST despite failure
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2025-01-09 17:04:53 +00:00 |
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463e320386
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Updated BIGSdb API to be more tolerant towards failures
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2025-01-09 16:49:12 +00:00 |
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022200f197
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Refactored class name
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2025-01-09 16:22:50 +00:00 |
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9b8e448512
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Completed updating CLI to be more organized with bettert error messages
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2025-01-09 07:39:18 +00:00 |
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42d0f56b18
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Moved to a general BIGSdb implementation
Updated tests
Removed ABIF UI for the time being
Began updating CLI
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2025-01-08 21:32:10 +00:00 |
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645357ac58
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Added unit tests for pubMLST MLST profiling
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2025-01-08 17:34:30 +00:00 |
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424beeb559
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Refactored CLI naming
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2025-01-08 16:55:55 +00:00 |
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d580402523
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began adding PubMLST support
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2025-01-08 16:54:57 +00:00 |
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ad28d9bf20
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Added additional test for fully automatic typing based on sequence
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2025-01-08 16:31:06 +00:00 |
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c3a492fa8f
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restructured MLST profiling classes
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2025-01-08 16:24:42 +00:00 |
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e9ffab5526
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Removed unused code
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2025-01-08 15:15:21 +00:00 |
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02985d5e37
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Copied over most code from another of my projects
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2025-01-08 15:14:06 +00:00 |
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