CLI Reference¶
This page provides documentation for our command line tools.
graphium¶
Usage:
graphium [OPTIONS] COMMAND [ARGS]...
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--version |
boolean | Show the version and exit. | False |
--help |
boolean | Show this message and exit. | False |
data¶
Graphium datasets.
Usage:
graphium data [OPTIONS] COMMAND [ARGS]...
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--help |
boolean | Show this message and exit. | False |
download¶
Download a Graphium dataset.
Usage:
graphium data download [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
-n, --name |
text | Name of the graphium dataset to download. | _required |
-o, --output |
text | Where to download the Graphium dataset. | _required |
--progress |
boolean | Whether to extract the dataset if it's a zip file. | False |
--help |
boolean | Show this message and exit. | False |
list¶
List available Graphium dataset.
Usage:
graphium data list [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--help |
boolean | Show this message and exit. | False |
finetune¶
Utility CLI for extra fine-tuning utilities.
Usage:
graphium finetune [OPTIONS] COMMAND [ARGS]...
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--help |
boolean | Show this message and exit. | False |
admet¶
Utility CLI to easily fine-tune a model on (a subset of) the benchmarks in the TDC ADMET group. The results are saved to the SAVE_DIR.
Usage:
graphium finetune admet [OPTIONS] SAVE_DIR
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--wandb / --no-wandb |
boolean | Whether to log to Weights & Biases. | True |
--name, -n |
text | One or multiple benchmarks to filter on. See also --inclusive-filter/--exclusive-filter. | None |
--inclusive-filter / --exclusive-filter |
boolean | Whether to include or exclude the benchmarks specified by --name. |
True |
--help |
boolean | Show this message and exit. | False |