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Fix some installation things #18

Merged
merged 63 commits into from
Apr 6, 2023
Merged

Fix some installation things #18

merged 63 commits into from
Apr 6, 2023

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jcblemai
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jcblemai and others added 27 commits March 21, 2023 09:59
@jcblemai
fix path install
431555f
@shauntruelove
move setup data and fix build_US_setup.R to read correct parquet fi…
17f07bb 
…les.
@shauntruelove
fix slot reference
a30420d
@shauntruelove
fix paths in data scripts
1a08fc4
@jcblemai
fix argument bug
ad8858d
@jcblemai
Merge branch 'slurm-fixes' of https://github.com/HopkinsIDD/flepiMoP …
5a66f70 
…into slurm-fixes
@shauntruelove
fix data_path issues
70e1da7
@shauntruelove
Merge branch 'slurm-fixes' of https://github.com/HopkinsIDD/flepiMoP …
210ee7d 
…into slurm-fixes
@shauntruelove
fix issue with calls to "spatial_setup::base_path" --> now changed to…
9cdb795 
… "data_path
@shauntruelove
fix spatial_setup::setup_name --> setup_name
68db265
@jcblemai
conda enviroment file
a31ccc0
@saraloo
setup_name to top section
32fce60
@saraloo
Merge branch 'slurm-fixes' of https://github.com/HopkinsIDD/flepiMoP …
4a2aab8 
…into slurm-fixes
@jcblemai
seir integration
f9907a3
@jcblemai
Merge branch 'slurm-fixes' of https://github.com/HopkinsIDD/flepiMoP …
d8ece8f 
…into slurm-fixes
@jcblemai
dttning
e0df3b2
@jcblemai
removing the lecacy configs
50f1a93
@shauntruelove
fix paths in create_seeding.R
5f21749
@shauntruelove
Merge branch 'slurm-fixes' of https://github.com/HopkinsIDD/flepiMoP …
7356be6 
…into slurm-fixes
@shauntruelove
fix reference to fix_negative_counts
13d9c6e
@shauntruelove
fix issues with incidI, Confirmed, etc. move to all "incidX" and "cumX"
285dba7
@shauntruelove
fix data issues
0dc0503
@jcblemai
fixes gempyor for the new configuration setup
3c0a543
@saraloo
add slurm and aws processing
32371b9
@saraloo
Merge branch 'slurm-fixes' of https://github.com/HopkinsIDD/flepiMoP …
fb4ac65 
…into slurm-fixes
@saraloo
fix inference::gt_data_path
9cc0429
@jcblemai
inference job for slurm runs
13e0ace
shauntruelove
shauntruelove previously approved these changes Mar 31, 2023
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@shauntruelove shauntruelove left a comment

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Looks great

saraloo
saraloo previously approved these changes Mar 31, 2023
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kjsato
kjsato reviewed Mar 31, 2023
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added 3 pending comments

batch/SLURM_inference_job.run Show resolved Hide resolved
build/local_install.R Show resolved Hide resolved
batch/postprocessing-scripts.sh Outdated Show resolved Hide resolved
@saraloo saraloo dismissed stale reviews from shauntruelove and themself via 59af283 March 31, 2023 20:23
jcblemai
jcblemai commented Apr 5, 2023
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@jcblemai jcblemai left a comment

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lgtm

kjsato
kjsato approved these changes Apr 6, 2023
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thanks for a lot of modifications!

@shauntruelove shauntruelove merged commit 92ba4ad into main Apr 6, 2023
@jcblemai jcblemai deleted the slurm-fixes branch April 6, 2023 21:07
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@shauntruelove shauntruelove shauntruelove approved these changes

@kjsato kjsato kjsato approved these changes

@saraloo saraloo Awaiting requested review from saraloo

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4 participants
@jcblemai @shauntruelove @kjsato @saraloo