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Merged
merged 12 commits into from
Nov 20, 2025
Merged

Model versioning #46

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ce25370
versining
Nov 10, 2025
e79417a
versioning new version
Nov 13, 2025
208d6f6
fix testcases
Nov 13, 2025
2d28550
fetch metadata data version from model if metadata is not passed and …
Nov 14, 2025
4ec6c14
correct assert and fixes #39
Nov 14, 2025
b1cd400
Merge branch 'main' into model-versioning
MuhammedHasan Nov 14, 2025
2a34fb7
notebook updates
Nov 14, 2025
69f5cfd
host config
Nov 15, 2025
25aeb05
fix caching names
Nov 15, 2025
8ef71d5
versining support and dependecny updates
Nov 18, 2025
d5f1b8b
bug fix in metadata callback
Nov 18, 2025
152a625
modisco version conflict
Nov 19, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -186,3 +186,4 @@ wandb/
docs/api
docs/tutorials/example
docs/wandb
run_tutorial.s*
16 changes: 8 additions & 8 deletions docs/tutorials/1-attribution-motif-discovery.ipynb
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Expand Up @@ -122,7 +122,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -159,7 +159,7 @@
}
],
"source": [
"! decima attributions --model 0 --genes \"SPI1,BRD3\" --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_classical_monoctypes"
"! decima attributions --model v1_rep0 --genes \"SPI1,BRD3\" --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_classical_monoctypes"
]
},
{
Expand Down Expand Up @@ -311,7 +311,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -338,12 +338,12 @@
}
],
"source": [
"! decima attributions-predict --model 0 --genes \"SPI1,BRD3\" --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_classical_monoctypes_0"
"! decima attributions-predict --model v1_rep0 --genes \"SPI1,BRD3\" --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_classical_monoctypes_0"
]
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -370,7 +370,7 @@
}
],
"source": [
"! decima attributions-predict --model 1 --genes \"SPI1,BRD3\" --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_classical_monoctypes_1"
"! decima attributions-predict --model v1_rep1 --genes \"SPI1,BRD3\" --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_classical_monoctypes_1"
]
},
{
Expand Down Expand Up @@ -1005,7 +1005,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -1041,7 +1041,7 @@
}
],
"source": [
"! decima attributions --model 0 --seqs ../tests/data/seqs.fasta --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_custom_seqs"
"! decima attributions --model v1_rep0 --seqs ../tests/data/seqs.fasta --tasks \"cell_type == 'classical monocyte'\" --output-prefix example/output_custom_seqs"
]
},
{
Expand Down
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