481870db97
Updated tests to reflect new fasta read naming
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2025-03-13 14:25:44 +00:00
62fdada9c1
Added original filename to csv output
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2025-03-13 14:17:08 +00:00
3074997db6
Removed unused file
2025-03-13 14:01:00 +00:00
3d6f36a722
Added test for non-exact allele matches
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2025-02-28 15:05:26 +00:00
bbd9e67c8c
Added test to check CSV name is not repeated
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2025-02-26 07:10:44 +00:00
2ea2f63f29
Pipeline will now only publish to git.reslate.systems on main branch
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2025-02-26 06:31:53 +00:00
17932ecd71
Alleles IDs obtained from one sequence is named the ID of that sequence
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autoBIGS.engine/pipeline/head There was a failure building this commit
Instead of generating a tuple comprised of the one sequence ID repeated
2025-02-26 06:15:56 +00:00
6cdc4ff4ae
Merge branch 'develop'
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2025-02-26 05:26:12 +00:00
4b34036d17
Fixed concurrent profile_multiple_strings implementation
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2025-02-26 05:16:24 +00:00
27ae89fde7
Replaced schema with scheme
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2025-02-26 04:50:54 +00:00
06dbb56c28
Revert "Recipe meta.yaml also archived as artifact"
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This reverts commit 79fcce8b8401554f69376f79787a786e5a97f31c.
2025-02-21 06:34:59 +00:00
79fcce8b84
Recipe meta.yaml also archived as artifact
autoBIGS.engine/pipeline/head Something is wrong with the build of this commit
2025-02-21 06:22:27 +00:00
f4064f087e
Fixed typos in pipeline script
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2025-02-21 06:12:35 +00:00
276665f5fd
Added curl to environment requirements
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2025-02-21 06:01:39 +00:00
fd536862e2
Twine version specified to 6.0.1 to avoid Twine issue 15611
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2025-02-21 05:53:08 +00:00
576dc303f4
Changed requested kubernetes container to be miniforge
2025-02-21 05:52:34 +00:00
2822a483e3
Initial attempt at switching to a conda based build environment
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2025-02-21 05:37:56 +00:00
b8cebb8ba4
Infrastructure for concurrent processing implemented
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2025-02-19 15:49:46 +00:00
62ce1c9b2f
Updated README.md to explain versioning
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2025-02-18 16:32:02 +00:00
7384895578
Writing now uses named MLST profile
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2025-02-18 16:03:17 +00:00
5a03c7e8d8
Multiple string profiling now respects grouped queries (for non-WGS)
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2025-02-18 15:34:18 +00:00
ddf9cde175
Added a license text to pyproject.toml
2025-02-14 20:47:06 +00:00
2e8cdd8da9
Updated URL links
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2025-02-14 20:37:13 +00:00
d0318536b2
Changed FASTA reading to group based on file for merging partial targets
2025-02-14 14:35:53 +00:00
765cf9d418
Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
2025-02-12 17:53:25 +00:00
348c3d00b4
Updated README.md to be more clear
2025-02-12 17:52:53 +00:00
1c3f7f9ed8
Removed test for instantiating local MLST profiler
2025-02-12 17:46:55 +00:00
e4ddaf2e8c
Changed to a MLST typable sequence for pubMLST tests
2025-02-12 17:43:26 +00:00
73aade2bde
Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
2025-02-12 17:07:51 +00:00
af8590baa7
Removed import of deleted feature
2025-02-12 17:07:10 +00:00
36bca1b70d
Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
2025-02-12 17:02:22 +00:00
09a693b696
Removed features being worked on in separate branch
2025-02-12 17:02:00 +00:00
f76bf86ef6
Fixed bad profile for H. influenzae non-exact test case
2025-02-12 16:59:50 +00:00
a60daf3ee2
Updated H. influenzae database API url
2025-02-12 16:39:13 +00:00
fbfd993269
Copied tests over from CSV tests and updated to reflect current code base
2025-02-12 16:36:59 +00:00
ba606c35a9
conversion of collection of alleles to map now produces results with tuples instead of lists
2025-02-12 16:36:31 +00:00
4183840ba0
Added notation to indicate inexact matching in CSV
2025-02-12 15:59:19 +00:00
7fb3eab5b6
Added pubMLST test case to bigsdb tests and updated to reflect codebase changes
2025-02-12 15:53:14 +00:00
175a51f968
Replaced local profiler with a not implemented exception
2025-02-12 15:52:48 +00:00
897f7ee922
Merge branch 'develop' into features/local-typing
automlst.engine/pipeline/head Something is wrong with the build of this commit
2025-02-12 15:01:12 +00:00
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
e568e9fb2c
Adapted latest merged reading codebase to current codebase
2025-02-11 19:13:29 +00:00
4b9eb8674d
Merge branch 'develop' into features/local-typing
2025-02-11 17:55:34 +00:00
f75707e4fe
CSV output column order is now predictable (sorted)
2025-02-11 17:54:48 +00:00
b4845fab34
Added automatic handling of strings instead of arrays of sequences to typing
2025-02-06 21:15:50 +00:00
fe999f1cab
Added a unit test for multithreaded alignments
2025-02-06 18:01:50 +00:00
85946eb110
Fixed match metric difference between remote and local
2025-02-06 17:12:31 +00:00
