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Surface the basic configuration with the user before proceeding with validation checking - Issue #196 #321

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Surface the basic configuration with the user before proceeding with validation checking - Issue #196 #321

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8b2f149
Update cli.py
sambujangfofana Apr 26, 2024
5cd74c2
Update config.py
sambujangfofana Apr 26, 2024
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43 changes: 43 additions & 0 deletions zamba/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ def train(

If an argument is specified in both the command line and in a yaml file, the command line input will take precedence.
"""

if config is not None:
with config.open() as f:
config_dict = yaml.safe_load(f)
Expand Down Expand Up @@ -128,6 +129,27 @@ def train(
if skip_load_validation is not None:
train_dict["skip_load_validation"] = skip_load_validation

# surface the configuration before validation checking
msg = f"""Review the following configuration before proceeding with validation checking:

Config file: {config_file}
Data directory: {data_dir if data_dir is not None else config_dict["train_config"].get("data_dir")}
Labels csv: {labels if labels is not None else config_dict["train_config"].get("labels")}
Checkpoint: {checkpoint if checkpoint is not None else config_dict["train_config"].get("checkpoint")}
"""

if yes:
typer.echo(f"{msg}\n\nSkipping confirmation and proceeding to validation checking.")
else:
yes = typer.confirm(
f"{msg}\n\nIs this correct?",
abort=False,
default=True,
)
if not yes:
print("\n\nPlease review and adjust the configuration and run the command again.")
return

try:
manager = ModelManager(
ModelConfig(
Expand Down Expand Up @@ -321,6 +343,27 @@ def predict(
if overwrite is not None:
predict_dict["overwrite"] = overwrite

# surface the configuration before validation checking
msg = f"""Review the following configuration before proceeding with validation checking:

Config file: {config_file}
Data directory: {data_dir if data_dir is not None else config_dict["predict_config"].get("data_dir")}
Filepath csv: {filepaths if filepaths is not None else config_dict["predict_config"].get("filepaths")}
Checkpoint: {checkpoint if checkpoint is not None else config_dict["predict_config"].get("checkpoint")}
"""

if yes:
typer.echo(f"{msg}\n\nSkipping confirmation and proceeding to validation checking.")
else:
yes = typer.confirm(
f"{msg}\n\nIs this correct?",
abort=False,
default=True,
)
if not yes:
print("\n\nPlease review and adjust the configuration and run the command again.")
return

try:
manager = ModelManager(
ModelConfig(
Expand Down
12 changes: 7 additions & 5 deletions zamba/models/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -524,11 +524,13 @@ def validate_filepaths_and_labels(cls, values):
)

elif values["split_proportions"] is not None:
logger.warning(
"Labels contains split column yet split_proportions are also provided. Split column in labels takes precedence."
)
# set to None for clarity in final configuration.yaml
values["split_proportions"] = None
# Check to see if split_proportions contains the default values
if values.get("split_proportions") != {"train": 3, "val": 1, "holdout": 1}:
logger.warning(
"Labels contains split column yet split_proportions are also provided. Split column in labels takes precedence."
)
# set to None for clarity in final configuration.yaml
values["split_proportions"] = None

# error if labels are entirely null
null_labels = labels.label.isnull()
Expand Down