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Update dev branch with task5-workflow #55

Merged
merged 51 commits into from
Jun 5, 2024
Merged

Update dev branch with task5-workflow #55

merged 51 commits into from
Jun 5, 2024

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rsgoncalves
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@nguyenank
set up initial workflow to run UK Biobank terms through mapper
568794c
@nguyenank
update workflow to have correct command for calling mapper
f3ba66e
@nguyenank
try adding link to test repo
af95902
@nguyenank
add runs-on to new test job
3bdc0fe
@nguyenank
update job dependencies, enabled github authentication for private repo
f0a43ce
@nguyenank
explicitly git add file
5181db2
@nguyenank
update workflow to use MAPPER_SECRET token
92bbd52
@nguyenank
condense workflow to only test accessing the repository
f98812b
@nguyenank
temporarily remove dependency
dc8a7de
@nguyenank
restore full workflow
02cbc50
@nguyenank
fix nesting
7f0d0ec
@nguyenank
update workflow; remove unnecessary files
066ad04
@nguyenank
update workflow so repos are nested rather than side-by-side
9b302f3
@nguyenank
change reference to test repo and add debug 'ls'
35670be
@nguyenank
make moving into the tests repo a separate step
3afdc7f
@nguyenank
fix typo
5486413
@nguyenank
update paths
aa2c0fa
@nguyenank
don't use relative path for output
dc8dd5b
@nguyenank
update output file reference
e79a3d3
@nguyenank
wrap output path in quotes
869ea95
@nguyenank
add debug 'ls', refactor git add
5a09805
@nguyenank
fix summary path typo
c4536b1
@nguyenank
update to use working-directory attribute
8f9ef88
@nguyenank
correct typo in sumamry_path var name
a217bf4
@nguyenank
fix formatting on start of row
b3e4b06
@nguyenank
set minimum score for mapper tool to 0
38dfcd2
@nguyenank
merge in main
108fefe
@nguyenank
update numpy version
1fccdff
@nguyenank
update testing script to run coverage error script
7cf3a43
@nguyenank
t2t.py -> text2term.py
4843594
nguyenank and others added 21 commits February 6, 2022 23:11
@nguyenank
fix typo in coverage-script running
27540e1
@nguyenank
test summary.csv
e424d44
@nguyenank
adjust working directory for coverage-erro script
20505a1
@nguyenank
update output path
3c282d6
@nguyenank
debug coverage_error script run error
90d96b6
@nguyenank
update coverage_error script to use new column names
b36a996
@nguyenank
add UK Biobank EFO owl version and one error and commit message
ae4e50d
@nguyenank
switch to coverage_one_error script
803db57
@nguyenank
test, escaping commas
741c28b
@nguyenank
test 2, now with fixed variable names
6f21f0b
@nguyenank
test 3, with more quote marks
ea3e124
@nguyenank
add escaping, full pipeline
da9ddc6
@paynejason
Merge pull request #47 from ccb-hms/development
0ec28ce 
Development
@paynejason
Merge pull request #48 from ccb-hms/development
b8eaf76 
Fixing testing
@rsgoncalves
Merge pull request #50 from ccb-hms/development
7faefc9 
Minor improvements and bug fixes
@rsgoncalves
Merge pull request #51 from ccb-hms/development
af66474 
Bump version
@rsgoncalves
Merge pull request #52 from ccb-hms/development
d256539 
Updated README
@rsgoncalves
Merge pull request #53 from ccb-hms/development
cfd5733 
Remove collapsible headers from README
@rsgoncalves
Merge branch 'main' into task5-workflow
0786f8a
@rsgoncalves
Merge pull request #13 from ccb-hms/task5-workflow
a97c99c 
Add Testing Script
@rsgoncalves
Merge pull request #54 from ccb-hms/development
02b1fa2 
Update README
@rsgoncalves rsgoncalves merged commit 84c6f15 into development Jun 5, 2024
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3 participants
@rsgoncalves @nguyenank @paynejason