15ad241303
Makes use of autoBIGS 0.14.* and fixes CSV export issue caused by missing target.
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2025-03-14 15:24:43 +00:00
b56c75849c
All branches pushes to git.reslate.systems now
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2025-03-07 16:10:11 +00:00
09cc9787fd
Fixed --csv output being blank when listing dbs
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2025-03-07 16:08:25 +00:00
8e1b30ae7d
Fixed typo in usage example
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2025-03-03 14:47:21 +00:00
a3189c6f3d
Updated usage instructions
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2025-03-03 14:44:20 +00:00
70e99f3639
Now splitting multiple fasta paths by comma
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2025-02-27 18:31:37 +00:00
48905f968f
Fixed scheme name argument not converting to ID
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Added additional error messages to help user with usage.
2025-02-27 04:55:43 +00:00
d9a16de97e
Merge branch 'main' into develop
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2025-02-26 15:25:23 +00:00
19b23539b3
Added bioconda and personal conda repos to channels
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2025-02-26 15:22:32 +00:00
41c05cc521
Increased user friendliness
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Added default MLST scheme
Added multiple ways of defining a MLST scheme
CSV output now shows database name for each scheme ID
Now uses native argparse library for ensuring mutual exclusivity of arguments and whether or not one is required.
Updated to use 0.13.* of engine
2025-02-26 07:37:34 +00:00
dbd8238cef
Added recipe patching script
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2025-02-21 14:14:02 +00:00
4b0fac0801
Added grayskull and curl to environment.yml
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2025-02-21 06:51:20 +00:00
d78ae19c4f
Re-added pytest-cov to conda environment.yml
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2025-02-21 06:40:20 +00:00
6b8376c470
Added publishing to personal git repo
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2025-02-21 06:33:07 +00:00
a4d8de7cc6
Changing CSV argument to --csv or -o
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2025-02-19 19:57:15 +00:00
5ef5b6ac08
Updated pyproject.toml to use license text and updated repo
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2025-02-19 16:26:59 +00:00
3aa2916324
Updated pipeline to not publish to system repo if it's a tagged version
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2025-02-19 16:02:31 +00:00
af9c8c70b8
Stop on fail argument now works
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2025-02-19 15:50:18 +00:00
319edf36af
Added option to output database and schemas lists to CSV
2025-02-19 15:01:57 +00:00
43a17d698b
Updated readme to reflect recent changes and discuss versioning
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2025-02-18 19:16:39 +00:00
e2f19acd5a
Updated CLI to follow APIs specified by the 0.12.0 engine
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2025-02-18 16:33:08 +00:00
1f6023b06b
Bumped engine version requirement to version 0.11.0
2025-02-18 14:53:21 +00:00
9100f83390
Removed unused file from repository
2025-02-13 21:56:38 +00:00
419aa36e9d
Removed unused parameter for typing
2025-02-13 21:56:20 +00:00
ca28068477
Made database name list predictable (sorted)
2025-02-13 21:56:06 +00:00
32dcfd99f8
Updated to reflect changes in Engine 0.10.*
2025-02-12 21:54:34 +00:00
4eca35a556
Fixed --version not showing
2025-02-11 16:56:04 +00:00
81d63bc54d
Updated private git credentials and now fails CI publishing steps
2025-01-24 21:01:14 +00:00
f263d380ca
Base command now requires parameter.
2025-01-24 19:09:28 +00:00
c73a89b8fa
Added license data to pyproject.toml
2025-01-24 18:44:25 +00:00
2dfac7c17f
Added default GPL license
2025-01-24 18:24:01 +00:00
e6d127369b
Updated python version requirement to 3.12 due to use of f-strings
2025-01-24 16:48:46 +00:00
2f189c8741
Added a planned features section on the README.md
2025-01-23 16:07:52 +00:00
53cd2e1260
Fixed typo in pyproject.toml
2025-01-22 21:51:07 +00:00
ffee4ee2e1
Fixed typo in pyproject.toml
2025-01-22 21:43:27 +00:00
9498fe7a45
Updated module imports
2025-01-22 21:36:45 +00:00
6305f5dbc9
Updated requirement to use pypi project name
2025-01-22 20:37:26 +00:00
706f127195
Continuation of refactoring package name
2025-01-22 18:44:58 +00:00
47c8951916
Refactoring package name
2025-01-22 18:43:21 +00:00
ba72199efc
Updated CLI to output more useful information.
2025-01-17 16:40:39 +00:00
ca59751c35
Now publishing to pypi.org on release
2025-01-17 15:31:14 +00:00
3b2cf916fd
Initial commit transfering files over from original automlst.engine project
2025-01-10 21:15:59 +00:00
