bfc286e6b0
Updated test cases to reflect changes in codebase
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MLSTProfile will always return a value, even if there were no exact matches.
Removed a test case specifically testing for stopping on failure, which is a removed feature.
2025-02-12 14:57:51 +00:00
a88225fcff
Added check to wrap string into list to prevent decomposing string for querying
2025-02-12 14:46:29 +00:00
c18d817cd9
Added test to verify that CSV target columns are ordered
2025-02-12 14:38:12 +00:00
f462e6d5e0
Moved "LazyPersistentCachedBIGSdbMLSTProfiler" to separate branch and deleted from current branch
2025-02-11 19:24:23 +00:00
f75707e4fe
CSV output column order is now predictable (sorted)
2025-02-11 17:54:48 +00:00
341ca933a3
Fixed typo in CI script
2025-01-29 17:00:25 +00:00
3e3898334f
Began implementing LazyPersistentCachedBIGSdbMLSTProfiler
2025-01-27 22:03:49 +00:00
ba1f0aa318
Fixed potential memory leak
2025-01-27 22:02:52 +00:00
6d0157581f
Removed conda environment step for now
2025-01-24 21:43:55 +00:00
4bcbfa0c6a
Began adding conda steps for automatic PRs to Bioconda
2025-01-24 19:33:27 +00:00
ca0f9673b0
Upgraded Python version requirement due to use of f-strings
2025-01-24 17:00:57 +00:00
5048fa8057
Deleted uneeded file
2025-01-23 19:23:56 +00:00
39125c848e
Added a wildcard patch specifier for aiohttp
2025-01-23 19:23:42 +00:00
744a6c2009
Pinned key dependency versions
2025-01-23 17:57:07 +00:00
1773bb9dcb
Updated naming (again).
2025-01-22 21:05:19 +00:00
1372141b57
Fixed typo in Jenkinsfile
2025-01-22 20:30:55 +00:00
677c5e1aa8
Revert "Reapply "Began preparing for conda deployment""
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This reverts commit ade2f3b84572b4356d404da2dbcd1d7266f10205.
2025-01-22 18:29:37 +00:00
53e74af20a
Refactoring project name to autoBIGSst.engine
2025-01-22 18:24:04 +00:00
ade2f3b845
Reapply "Began preparing for conda deployment"
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This reverts commit 3bbef9ac3e0ca58f6f5f62a1e9bd1d8ae02fd75c.
2025-01-20 19:56:51 +00:00
c2c6d0b016
Changed package publishing on git.reslate.systems back to username and password authentication
2025-01-20 19:04:44 +00:00
fc8eede420
(Re-)added license file
2025-01-20 18:14:46 +00:00
3bbef9ac3e
Revert "Began preparing for conda deployment"
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This reverts commit fe797be34f5c2e77cdde00acfd32eeaaab259f2b.
2025-01-20 17:52:29 +00:00
660d803c9e
Updated to not regenerate build recipe each time during CI
2025-01-20 17:28:42 +00:00
cb3aec554e
Added git author information as environment variables
2025-01-20 17:04:45 +00:00
05e132c066
Updated pipeline to refer to python module correctly
2025-01-20 16:54:00 +00:00
de36956cc0
Updating kubernetes definitions to match CI server
2025-01-20 16:26:11 +00:00
fe797be34f
Began preparing for conda deployment
2025-01-17 21:31:38 +00:00
b89f24a3fa
Fixed issue where multiple allele identifiers were not returned in output.
2025-01-17 17:04:22 +00:00
e7c8c5bcf9
Changed allele CSV output to non-lists
2025-01-17 16:56:52 +00:00
ab44dfaa48
Publish to pypi if it has a release tag
2025-01-17 15:13:47 +00:00
611b956d88
Elaborated on the README.md and added references to it in pyproject.toml
2025-01-17 15:08:47 +00:00
cb22dfac9b
Merge branch 'develop'
2025-01-17 14:34:16 +00:00
7ea7ead46a
Moved ABIF code to separate project
2025-01-17 14:27:25 +00:00
a3c864b565
Refactored code layout
2025-01-16 21:54:52 +00:00
bad7dfc3a8
Changing all publishing steps to use API keys
2025-01-16 21:29:20 +00:00
4fe0f0f287
Added stage for publishing to test.pypi.org when the tag a version number.
2025-01-16 21:22:49 +00:00
3fd3ef9f20
Updated package description
2025-01-10 21:13:26 +00:00
206a105bf9
Rermoved publishing branch and tag conditions, publish errors are no longer considered failures
2025-01-10 17:59:04 +00:00
ad082b8af6
Revert "Always publish on build success"
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This reverts commit cc6a7563cafc15686e61810da6c412f27c82c1c8.
2025-01-10 17:43:14 +00:00
5118a25b6a
publish step will now fail if twine upload fails
2025-01-10 17:41:42 +00:00
cc6a7563ca
Always publish on build success
2025-01-10 17:35:58 +00:00
484e31879e
Removed test installation step from CI
2025-01-10 17:28:25 +00:00
5449ae0c68
Moved CLI to automlst.cli repo
2025-01-10 17:22:12 +00:00
e634647774
Added untested partial matching
2025-01-10 16:12:56 +00:00
f20a656f45
Fixed multiple string typing failure handling
2025-01-10 16:00:27 +00:00
0c0a2c9d4c
Finished adding partial allele matching
2025-01-10 15:25:31 +00:00
03fbbe542e
allele profiling partial matching works
2025-01-09 21:44:28 +00:00
e60dba936c
Added a tag name check for publishing
2025-01-09 18:32:51 +00:00
9589761ddd
Now tracks failed profilings
2025-01-09 17:27:15 +00:00
2843d0d592
Added tests to test continuous MLST despite failure
2025-01-09 17:04:53 +00:00
