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Dockerize spt cggnn train (redo) #282

Merged
merged 32 commits into from
Jan 8, 2024
Merged

Dockerize spt cggnn train (redo) #282

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1d1c099
localize dgl and torch usage to histocartography and cg_gnn_helper
CarlinLiao Dec 11, 2023
9871102
bug fixes
CarlinLiao Dec 13, 2023
972dcb6
clean up unused imports
CarlinLiao Dec 13, 2023
411e894
use dockerized cg-gnn
CarlinLiao Dec 13, 2023
5bc5162
remove torch from toml
CarlinLiao Dec 13, 2023
5028380
Add option to force rebuilding of cached docker layers.
jimmymathews Dec 13, 2023
75296b9
use dockerized cg-gnn
CarlinLiao Dec 13, 2023
9be2448
remove torch from toml
CarlinLiao Dec 13, 2023
1948a05
Merge branch 'issue275' of github.com:nadeemlab/SPT into issue275
CarlinLiao Dec 14, 2023
458c300
update docker image repo
CarlinLiao Dec 14, 2023
4b1e782
expose cggnn cuda option in workflow
CarlinLiao Dec 14, 2023
591d0ba
Merge branch 'main' into issue275
CarlinLiao Dec 14, 2023
806479b
sketch docker-in-nextflow-docker
CarlinLiao Dec 15, 2023
3e700fd
Merge branch 'main' into issue275
CarlinLiao Dec 15, 2023
ca0d541
use virtualenv
CarlinLiao Dec 15, 2023
cdc9d87
remove training script now that it's dockerized
CarlinLiao Dec 15, 2023
19fc43e
undo docker-in-docker changes
CarlinLiao Dec 15, 2023
e305119
sketch no docker test
CarlinLiao Dec 15, 2023
9392d7a
add new rule to make
CarlinLiao Dec 16, 2023
bece9ef
add docker network to nextflow
CarlinLiao Dec 16, 2023
588a3bd
update training command
CarlinLiao Dec 16, 2023
9720bdb
save adj separately
CarlinLiao Dec 17, 2023
2b46c77
Merge branch 'issue279' into issue275
CarlinLiao Dec 17, 2023
8ac70d4
Merge branch 'main' into issue275
CarlinLiao Dec 20, 2023
29eae3f
update pickled test graphs
CarlinLiao Dec 21, 2023
118c884
Fix test target name stuff.
jimmymathews Dec 21, 2023
aa3ad1e
Start separating spt part and external part in test.
jimmymathews Dec 21, 2023
d90a92f
Fix path
jimmymathews Dec 21, 2023
dd18c20
finish integrating partially-outside-docker cggnn test
CarlinLiao Dec 21, 2023
98bec17
remove unused file
CarlinLiao Dec 21, 2023
cb4529b
Deprecate unused test target.
jimmymathews Jan 8, 2024
efb0dfb
Formality of merging after a couple unintentional actions.
jimmymathews Jan 8, 2024
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