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ADD: trac from classo - individual w Classo #16

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merged 30 commits into from
May 23, 2024
Merged

ADD: trac from classo - individual w Classo #16

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3a57c11
classo exploration
adamovanja May 1, 2024
1d1c798
implement calculation of matrix A
adamovanja May 2, 2024
b2bd2a5
good enough version - hopefully working
adamovanja May 2, 2024
659a60a
working trac version to be implemented in ritme
adamovanja May 3, 2024
cd0ab5b
wip to setup trac in ritme
adamovanja May 3, 2024
6e0398c
newest conda env setup
adamovanja May 3, 2024
dc40d3c
add trac model
adamovanja May 3, 2024
9ab31be
update trac search space
adamovanja May 3, 2024
b605fea
2nd committee meeting setup + best hyperparams range
adamovanja May 17, 2024
b353309
starting to debug evaluation
adamovanja May 21, 2024
9195392
fix empty tax + phylo
adamovanja May 21, 2024
5fb4c83
testing individual classo model
adamovanja May 21, 2024
aaaefa4
add trac as individual model no CV
adamovanja May 21, 2024
da5c767
updated env
adamovanja May 22, 2024
7762018
adding tests
adamovanja May 22, 2024
69a04a2
try to fix test
adamovanja May 22, 2024
e2c36ec
try to fix test with updated GHAs
adamovanja May 22, 2024
b51c22f
consistent update of GHA
adamovanja May 22, 2024
57326a2
correct node labelling in trac
adamovanja May 22, 2024
5a1a221
try to fix GHA
adamovanja May 22, 2024
cb742ce
fix node naming in df_a
adamovanja May 22, 2024
5fdd54b
modularize trac model
adamovanja May 22, 2024
4dabf2d
rename model_space
adamovanja May 22, 2024
4306535
fix import
adamovanja May 22, 2024
920dfcd
try to fix GHA error
adamovanja May 23, 2024
342e7d6
try to fix GHA error again
adamovanja May 23, 2024
5ddcff2
adding unit tests
adamovanja May 23, 2024
167918b
merge main into branch
adamovanja May 23, 2024
139100a
merge main into branch
adamovanja May 23, 2024
378d4ad
remove codecov line comments in PR
adamovanja May 23, 2024
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1 change: 1 addition & 0 deletions .github/codecov.yml
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@@ -0,0 +1 @@
comment: off
5 changes: 5 additions & 0 deletions ci/recipe/meta.yaml
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Expand Up @@ -22,9 +22,11 @@ requirements:
- importlib-metadata
- qiime2 {{ qiime2_epoch }}.*
- q2-feature-table {{ qiime2_epoch }}.*
- q2-phylogeny {{ qiime2_epoch }}.*
- lightning
- mlflow
- numpy
- packaging
- pandas
- pip
- pytorch
Expand All @@ -44,6 +46,9 @@ requirements:
run_constrained:
- pip:
- coral_pytorch
- c-lasso
# grpcio pinned due to incompatibility with ray caused by c-lasso
- grpcio==1.51.1


test:
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