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• 06dbb56c28 Revert "Recipe meta.yaml also archived as artifact" develop Harrison Deng 2025-02-21 06:34:59 +00:00
• 79fcce8b84 Recipe meta.yaml also archived as artifact Harrison Deng 2025-02-21 06:22:27 +00:00
• f4064f087e Fixed typos in pipeline script Harrison Deng 2025-02-21 06:12:35 +00:00
• 276665f5fd Added curl to environment requirements Harrison Deng 2025-02-21 06:01:39 +00:00
• fd536862e2 Twine version specified to 6.0.1 to avoid Twine issue 15611 Harrison Deng 2025-02-21 05:53:08 +00:00
• 576dc303f4 Changed requested kubernetes container to be miniforge Harrison Deng 2025-02-21 05:52:34 +00:00
• 2822a483e3 Initial attempt at switching to a conda based build environment Harrison Deng 2025-02-21 05:37:56 +00:00
• b8cebb8ba4 Infrastructure for concurrent processing implemented Harrison Deng 2025-02-19 15:49:46 +00:00
• 62ce1c9b2f Updated README.md to explain versioning main Harrison Deng 2025-02-18 16:32:02 +00:00
• 7384895578 Writing now uses named MLST profile 0.12.0 Harrison Deng 2025-02-18 16:03:17 +00:00
• 5a03c7e8d8 Multiple string profiling now respects grouped queries (for non-WGS) Harrison Deng 2025-02-18 15:34:18 +00:00
• ddf9cde175 Added a license text to pyproject.toml Harrison Deng 2025-02-14 20:47:06 +00:00
• 2e8cdd8da9 Updated URL links 0.11.1 Harrison Deng 2025-02-14 20:37:13 +00:00
• d0318536b2 Changed FASTA reading to group based on file for merging partial targets 0.11.0 Harrison Deng 2025-02-14 14:35:53 +00:00
• 765cf9d418 Merge branch 'features/improved-oop-architecture' into features/non-exact-notation 0.10.0 Harrison Deng 2025-02-12 17:53:25 +00:00
• 348c3d00b4 Updated README.md to be more clear Harrison Deng 2025-02-12 17:52:53 +00:00
• 1c3f7f9ed8 Removed test for instantiating local MLST profiler Harrison Deng 2025-02-12 17:46:55 +00:00
• e4ddaf2e8c Changed to a MLST typable sequence for pubMLST tests Harrison Deng 2025-02-12 17:43:26 +00:00
• 73aade2bde Merge branch 'features/improved-oop-architecture' into features/non-exact-notation Harrison Deng 2025-02-12 17:07:51 +00:00
• af8590baa7 Removed import of deleted feature Harrison Deng 2025-02-12 17:07:10 +00:00
• 36bca1b70d Merge branch 'features/improved-oop-architecture' into features/non-exact-notation Harrison Deng 2025-02-12 17:02:22 +00:00
• 09a693b696 Removed features being worked on in separate branch Harrison Deng 2025-02-12 17:02:00 +00:00
• f76bf86ef6 Fixed bad profile for H. influenzae non-exact test case Harrison Deng 2025-02-12 16:59:50 +00:00
• a60daf3ee2 Updated H. influenzae database API url Harrison Deng 2025-02-12 16:39:13 +00:00
• fbfd993269 Copied tests over from CSV tests and updated to reflect current code base Harrison Deng 2025-02-12 16:36:59 +00:00
• ba606c35a9 conversion of collection of alleles to map now produces results with tuples instead of lists Harrison Deng 2025-02-12 16:36:31 +00:00
• 4183840ba0 Added notation to indicate inexact matching in CSV Harrison Deng 2025-02-12 15:59:19 +00:00
• 7fb3eab5b6 Added pubMLST test case to bigsdb tests and updated to reflect codebase changes Harrison Deng 2025-02-12 15:53:14 +00:00
• 175a51f968 Replaced local profiler with a not implemented exception Harrison Deng 2025-02-12 15:52:48 +00:00
• 897f7ee922 Merge branch 'develop' into features/local-typing features/local-typing Harrison Deng 2025-02-12 15:01:12 +00:00
• bfc286e6b0 Updated test cases to reflect changes in codebase 0.9.0 Harrison Deng 2025-02-12 14:57:51 +00:00
• a88225fcff Added check to wrap string into list to prevent decomposing string for querying Harrison Deng 2025-02-12 14:46:29 +00:00
• c18d817cd9 Added test to verify that CSV target columns are ordered Harrison Deng 2025-02-12 14:38:12 +00:00
• f462e6d5e0 Moved "LazyPersistentCachedBIGSdbMLSTProfiler" to separate branch and deleted from current branch Harrison Deng 2025-02-11 19:24:23 +00:00
• e568e9fb2c Adapted latest merged reading codebase to current codebase Harrison Deng 2025-02-11 19:13:29 +00:00
• 4b9eb8674d Merge branch 'develop' into features/local-typing Harrison Deng 2025-02-11 17:55:34 +00:00
• f75707e4fe CSV output column order is now predictable (sorted) Harrison Deng 2025-02-11 17:54:48 +00:00
• b4845fab34 Added automatic handling of strings instead of arrays of sequences to typing Harrison Deng 2025-02-06 21:15:50 +00:00
• fe999f1cab Added a unit test for multithreaded alignments Harrison Deng 2025-02-06 18:01:50 +00:00
• 85946eb110 Fixed match metric difference between remote and local Harrison Deng 2025-02-06 17:12:31 +00:00
• a27e09da31 Added code to retrieve sequences and annotations from NCBI GenBank Harrison Deng 2025-02-06 17:11:20 +00:00
• ba2b688e89 Removed sorting as it seems unecessary Harrison Deng 2025-02-05 22:06:50 +00:00
• 49f31b7943 Async aligner work tracking issue fixed Harrison Deng 2025-02-05 21:47:51 +00:00
• 1c6e1cfb35 Fixed issue with hashing a ndarray by using tuple. Harrison Deng 2025-02-05 20:43:53 +00:00
• fb99526162 Updated iteration on asynchronous aligner Harrison Deng 2025-02-05 17:17:37 +00:00
• ff8a1aff08 Implemented annotated local typing method without testing Harrison Deng 2025-02-04 16:19:00 +00:00
• 341ca933a3 Fixed typo in CI script Harrison Deng 2025-01-29 17:00:25 +00:00
• 3e3898334f Began implementing LazyPersistentCachedBIGSdbMLSTProfiler Harrison Deng 2025-01-27 22:03:49 +00:00
• ba1f0aa318 Fixed potential memory leak Harrison Deng 2025-01-27 22:02:52 +00:00
• 6d0157581f Removed conda environment step for now Harrison Deng 2025-01-24 21:43:55 +00:00
• 4bcbfa0c6a Began adding conda steps for automatic PRs to Bioconda Harrison Deng 2025-01-24 19:33:27 +00:00
• ca0f9673b0 Upgraded Python version requirement due to use of f-strings 0.8.0 Harrison Deng 2025-01-24 17:00:57 +00:00
• 5048fa8057 Deleted uneeded file 0.7.2 Harrison Deng 2025-01-23 19:23:56 +00:00
• 39125c848e Added a wildcard patch specifier for aiohttp Harrison Deng 2025-01-23 19:23:42 +00:00
• 744a6c2009 Pinned key dependency versions 0.7.1 Harrison Deng 2025-01-23 17:57:07 +00:00
• 1773bb9dcb Updated naming (again). 0.7.0 Harrison Deng 2025-01-22 21:05:19 +00:00
• 1372141b57 Fixed typo in Jenkinsfile Harrison Deng 2025-01-22 20:30:55 +00:00
• 677c5e1aa8 Revert "Reapply "Began preparing for conda deployment"" 0.6.0 Harrison Deng 2025-01-22 18:29:37 +00:00
• 53e74af20a Refactoring project name to autoBIGSst.engine Harrison Deng 2025-01-22 18:24:04 +00:00
• ade2f3b845 Reapply "Began preparing for conda deployment" Harrison Deng 2025-01-20 19:56:51 +00:00
• c2c6d0b016 Changed package publishing on git.reslate.systems back to username and password authentication Harrison Deng 2025-01-20 19:04:44 +00:00
• fc8eede420 (Re-)added license file 0.5.2 Harrison Deng 2025-01-20 18:14:46 +00:00
• 3bbef9ac3e Revert "Began preparing for conda deployment" Harrison Deng 2025-01-20 17:52:29 +00:00
• 660d803c9e Updated to not regenerate build recipe each time during CI Harrison Deng 2025-01-20 17:28:42 +00:00
• cb3aec554e Added git author information as environment variables Harrison Deng 2025-01-20 17:04:45 +00:00
• 05e132c066 Updated pipeline to refer to python module correctly Harrison Deng 2025-01-20 16:54:00 +00:00
• de36956cc0 Updating kubernetes definitions to match CI server Harrison Deng 2025-01-20 16:26:11 +00:00
• fe797be34f Began preparing for conda deployment Harrison Deng 2025-01-17 21:31:38 +00:00
• b89f24a3fa Fixed issue where multiple allele identifiers were not returned in output. 0.5.1 Harrison Deng 2025-01-17 17:04:22 +00:00
• e7c8c5bcf9 Changed allele CSV output to non-lists 0.5 Harrison Deng 2025-01-17 16:56:52 +00:00
• ab44dfaa48 Publish to pypi if it has a release tag 0.4 Harrison Deng 2025-01-17 15:13:47 +00:00
• 611b956d88 Elaborated on the README.md and added references to it in pyproject.toml Harrison Deng 2025-01-17 15:08:47 +00:00
• cb22dfac9b Merge branch 'develop' 0.3 Harrison Deng 2025-01-17 14:34:16 +00:00
• 7ea7ead46a Moved ABIF code to separate project Harrison Deng 2025-01-17 14:27:25 +00:00
• a3c864b565 Refactored code layout Harrison Deng 2025-01-16 21:54:52 +00:00
• bad7dfc3a8 Changing all publishing steps to use API keys Harrison Deng 2025-01-16 21:29:20 +00:00
• 4fe0f0f287 Added stage for publishing to test.pypi.org when the tag a version number. Harrison Deng 2025-01-16 21:22:49 +00:00
• 3fd3ef9f20 Updated package description 0.2.0 Harrison Deng 2025-01-10 21:13:26 +00:00
• 206a105bf9 Rermoved publishing branch and tag conditions, publish errors are no longer considered failures Harrison Deng 2025-01-10 17:59:04 +00:00
• ad082b8af6 Revert "Always publish on build success" Harrison Deng 2025-01-10 17:43:14 +00:00
• 5118a25b6a publish step will now fail if twine upload fails Harrison Deng 2025-01-10 17:41:42 +00:00
• cc6a7563ca Always publish on build success Harrison Deng 2025-01-10 17:35:58 +00:00
• 484e31879e Removed test installation step from CI Harrison Deng 2025-01-10 17:28:25 +00:00
• 5449ae0c68 Moved CLI to automlst.cli repo Harrison Deng 2025-01-10 17:22:12 +00:00
• e634647774 Added untested partial matching Harrison Deng 2025-01-10 16:12:56 +00:00
• f20a656f45 Fixed multiple string typing failure handling Harrison Deng 2025-01-10 16:00:27 +00:00
• 0c0a2c9d4c Finished adding partial allele matching Harrison Deng 2025-01-10 15:25:31 +00:00
• 03fbbe542e allele profiling partial matching works Harrison Deng 2025-01-09 21:44:28 +00:00
• e60dba936c Added a tag name check for publishing Harrison Deng 2025-01-09 18:32:51 +00:00
• 9589761ddd Now tracks failed profilings Harrison Deng 2025-01-09 17:27:15 +00:00
• 2843d0d592 Added tests to test continuous MLST despite failure Harrison Deng 2025-01-09 17:04:53 +00:00
• 7bd28db6d4 Updated code coverage to only report on source code Harrison Deng 2025-01-09 16:51:08 +00:00
• 463e320386 Updated BIGSdb API to be more tolerant towards failures Harrison Deng 2025-01-09 16:49:12 +00:00
• d4f890a150 Added specific tests for BIGSdbIndex Harrison Deng 2025-01-09 16:23:42 +00:00
• 022200f197 Refactored class name Harrison Deng 2025-01-09 16:22:50 +00:00
• e66525d341 Updated README.md Harrison Deng 2025-01-09 16:08:44 +00:00
• 1d531aff42 Updated CI to only report on automlst and fixed report publishing Harrison Deng 2025-01-09 16:08:30 +00:00
• 8febfad282 Added publishing of coverage results Harrison Deng 2025-01-09 15:55:39 +00:00
• 42bcfcf61d Added coverage tracking Harrison Deng 2025-01-09 15:54:22 +00:00
• 2c412c5526 Renamed tests subdirectory to mirror source 0.1.0 Harrison Deng 2025-01-09 15:00:46 +00:00