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Jr dev #11

Merged
merged 55 commits into from
May 2, 2024
Merged

Jr dev #11

merged 55 commits into from
May 2, 2024

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mattheww95
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ChristyPeterson and others added 30 commits March 20, 2024 13:25
@ChristyPeterson
Merge pull request #3 from phac-nml/dev
a4cda91 
Merged dev into main for docs updates
@ChristyPeterson
Merge pull request #4 from phac-nml/dev
57dd015 
Update README.md
@jrober84
Word smithing introduction
0bd4c64
@jrober84
Word smithing introduction
5797705
@jrober84
corrected behaviour of extract for overlaping loci
7f01244
@jrober84
added new report mode
cc557c9
@mattheww95
Update version.py
096cc72 
version was behind, bumping again
@jrober84
corrected paralog handelling
47aae9a
@jrober84
paralog work
fab0272
@jrober84
removed testing code
4d08bed
@jrober84
updated paralog handelling
0977382
@jrober84
added int stop filter
5b8b71b
@jrober84
added int stop filter
2e2621a
@jrober84
updated report description
8e2040d
@jrober84
Merge branch 'tests' of https://github.com/phac-nml/locidex into tests
3227c61
@jrober84
updated report format to include db info and sequence data
c48fc95
@jrober84
updated report to use the same template as search module
7f85c69
@jrober84
updated report to use the same template as search module
2f346e7
@jrober84
added in seq_data
a9b0514
@jrober84
merge updated template and connection to new report format
38875fb
@jrober84
merge included mafft alignment and production of concatenated alignment
42dd4b3
@jrober84
added missing input file protection
0471762
@jrober84
added db_version validation
b4bf401
@jrober84
updated search to use manifest, created manifest module
1dae7cf
@jrober84
removed print
5a68dd6
@jrober84
removed blank space
12a3b01
@jrober84
added manifest module
367fbdd
@jrober84
removed print
814f1de
@jrober84
changed date format
4ebee55
@jrober84
updated db config to respect which db type is enabled
693d7dd
jrober84 and others added 25 commits April 23, 2024 10:34
@jrober84
corrected path issue with output seq_store
2ea2ba7
@jrober84
removed print
0b1aeed
@mattheww95
updated test_db.py tests to pass
5c5a371
@mattheww95
updated manifest tests
d7e76df
@mattheww95
updated db config to dataclass
a40b913
@mattheww95
Added refactor for database config class
b268bc4 
The Databaseconfig fields have been refactored into a dataclass allowing for continuity of the requried fields across the modules, a larger upgrade is still needed
@mattheww95
refactored merge module
156208f
@mattheww95
refactored manifest module
b1f6814
@mattheww95
refactored manifest module and tests
1bd9973
@mattheww95
refactored manifest module and tests
bef005a 
Updated the ManifestItem class to include the root directory passed to it to aid in resolving relative paths
@mattheww95
updated manifest to allow for multiple versions of different dbs
b976d92
@mattheww95
updated extract, build, search classes
69131cc
@mattheww95
updated tests
03cbdd6
@mattheww95
fixed merge conflicts
47837a7
@mattheww95
updated tests and and search workflow
593bd36
@mattheww95
updated test data for workflows
51cfd6a
@mattheww95
updated multi db selection for data using a manifest
376a0e0
@mattheww95
added complete workflow tests and updated CI Scripts
3b416ae
@mattheww95
updated CI
3f8ce62
@mattheww95
updated CI
d6e80a0
@mattheww95
Added pytest-workflow to CI
e254fa6
@mattheww95
Added pytest-workflow to CI
3591976
@mattheww95
Added pytest-workflow to CI
a3b5fd7
@mattheww95
altered CI workflow due to tmp dir issues
672567a
@mattheww95
updated manifest test to remove dependency on order
44bd63c
@mattheww95 mattheww95 marked this pull request as ready for review May 2, 2024 18:52
@mattheww95 mattheww95 merged commit 2ffb35c into dev May 2, 2024
1 check passed
@mattheww95 mattheww95 deleted the jr_dev branch May 2, 2024 20:13
@mattheww95 mattheww95 restored the jr_dev branch May 2, 2024 20:13
@mattheww95 mattheww95 deleted the jr_dev branch May 2, 2024 20:13
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3 participants
@mattheww95 @ChristyPeterson @jrober84