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Fix/minors and typos #11

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63e71db
Fix CLI help strings and remove unused --verbose argument
1WojciechNowak May 20, 2026
5928342
Replace old microbiome_gpt/microbiome-gpt references with gut_former/…
1WojciechNowak May 20, 2026
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -55,7 +55,7 @@ temp/
anas-ntbs/

# WIP scripts
src/microbiome_gpt/run_data_preparation.py
src/gut_former/run_data_preparation.py

# Personal notes
TODO.md
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -54,7 +54,7 @@ fix:
# -----------------------------------------

kernel:
poetry run python -m ipykernel install --user --name=microbiome-gpt --display-name "Python (microbiome-gpt)"
poetry run python -m ipykernel install --user --name=gut-former --display-name "Python (gut-former)"

jupyter:
poetry run jupyter notebook
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8 changes: 4 additions & 4 deletions notebooks/figure1a_data_overview.ipynb
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Expand Up @@ -15,7 +15,7 @@
},
"cell_type": "code",
"source": [
"from microbiome_gpt.utils.fig_style import apply_style\n",
"from gut_former.utils.fig_style import apply_style\n",
"\n",
"apply_style(font_family=\"DejaVu Serif\", base_font_size=16)"
],
Expand Down Expand Up @@ -55,7 +55,7 @@
},
"cell_type": "code",
"source": [
"from microbiome_gpt.utils.project_paths import find_data_path, find_figures_path\n",
"from gut_former.utils.project_paths import find_data_path, find_figures_path\n",
"\n",
"data_path = find_data_path()\n",
"figures_path = find_figures_path()"
Expand Down Expand Up @@ -618,9 +618,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python (microbiome-gpt)",
"display_name": "Python (gut-former)",
"language": "python",
"name": "microbiome-gpt"
"name": "gut-former"
},
"language_info": {
"codemirror_mode": {
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10 changes: 5 additions & 5 deletions notebooks/figure1b_model_eval.ipynb
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Expand Up @@ -18,7 +18,7 @@
}
},
"source": [
"from microbiome_gpt.utils.fig_style import apply_style\n",
"from gut_former.utils.fig_style import apply_style\n",
"\n",
"apply_style(font_family=\"DejaVu Serif\", base_font_size=16)"
],
Expand Down Expand Up @@ -48,7 +48,7 @@
}
},
"source": [
"from microbiome_gpt.utils.project_paths import find_data_path, find_figures_path\n",
"from gut_former.utils.project_paths import find_data_path, find_figures_path\n",
"\n",
"data_path = find_data_path()\n",
"figures_path = find_figures_path()\n",
Expand Down Expand Up @@ -131,7 +131,7 @@
},
"cell_type": "code",
"source": [
"from microbiome_gpt.utils.analysis import get_pcoa_coords, get_disparity\n",
"from gut_former.utils.analysis import get_pcoa_coords, get_disparity\n",
"\n",
"fig, axes = plt.subplots(1, 2, figsize=(10, 4))\n",
"\n",
Expand Down Expand Up @@ -272,9 +272,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python (microbiome-gpt)",
"display_name": "Python (gut-former)",
"language": "python",
"name": "microbiome-gpt"
"name": "gut-former"
},
"language_info": {
"name": "python",
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4 changes: 2 additions & 2 deletions notebooks/figure2_signatures.ipynb
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Expand Up @@ -18,7 +18,7 @@
}
},
"source": [
"from microbiome_gpt.utils.fig_style import apply_style\n",
"from gut_former.utils.fig_style import apply_style\n",
"\n",
"apply_style(font_family=\"DejaVu Serif\", base_font_size=16)"
],
Expand Down Expand Up @@ -54,7 +54,7 @@
}
},
"source": [
"from microbiome_gpt.utils.project_paths import find_data_path, find_figures_path\n",
"from gut_former.utils.project_paths import find_data_path, find_figures_path\n",
"\n",
"data_path = find_data_path()\n",
"output_path = find_data_path().parent / \"output\"\n",
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2 changes: 1 addition & 1 deletion src/gut_former/run_data_preparation.py
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Expand Up @@ -15,7 +15,7 @@ def main():
# Handling Args
p = argparse.ArgumentParser()

p.add_argument("--dataset", type=str, default="raw", help="TODO")
p.add_argument("--dataset", type=str, default="raw", help="Dataset name; expects taxonomy_relab_{dataset}.csv, pathways_relab_{dataset}.csv, and metadata_{dataset}.csv in the data directory, with sample ID as the (optionally unnamed) first column")

args = p.parse_args()

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8 changes: 4 additions & 4 deletions src/gut_former/run_inference.py
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Expand Up @@ -19,11 +19,11 @@ def main():
# Handling Args
p = argparse.ArgumentParser()

p.add_argument("--dataset", type=str, default="sample", help="TODO")
p.add_argument("--embedding_dim", type=int, default=128, help="TODO")
p.add_argument("--latent_dim", type=int, default=64, help="TODO")
p.add_argument("--dataset", type=str, default="sample", help="Dataset name; expects taxonomy_{dataset}.csv and pathways_{dataset}.csv in the data directory, with sample ID as the (optionally unnamed) first column")
p.add_argument("--embedding_dim", type=int, default=128, help="Embedding dimension for the model")
p.add_argument("--latent_dim", type=int, default=64, help="Latent space dimension; controls the size of the learned representation")
output_path = find_output_path()
p.add_argument("--checkpoint", type=str, default=f"{output_path}/checkpoint_sample.pt", help="TODO")
p.add_argument("--checkpoint", type=str, default=f"{output_path}/checkpoint_sample.pt", help="Path to model checkpoint file to load for inference")
args = p.parse_args()

# Loading & Preparing Data
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13 changes: 6 additions & 7 deletions src/gut_former/run_training.py
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Expand Up @@ -29,13 +29,12 @@ def main():

p = argparse.ArgumentParser()

p.add_argument("--dataset", type=str, default="sample", help="TODO")
p.add_argument("--embedding_dim", type=int, default=128, help="TODO")
p.add_argument("--latent_dim", type=int, default=64, help="TODO")
p.add_argument("--batch_size", type=int, default=16, help="TODO")
p.add_argument("--learning_rate", type=float, default=1.893292917167e-4, help="TODO")
p.add_argument("--epochs", type=int, default=55, help="TODO")
p.add_argument("--verbose", type=bool, default=True, help="TODO")
p.add_argument("--dataset", type=str, default="sample", help="Dataset name; expects taxonomy_{dataset}.csv, pathways_{dataset}.csv, and metadata_{dataset}.csv in the data directory, with sample ID as the (optionally unnamed) first column")
p.add_argument("--embedding_dim", type=int, default=128, help="Embedding dimension for the model")
p.add_argument("--latent_dim", type=int, default=64, help="Latent space dimension; controls the size of the learned representation")
p.add_argument("--batch_size", type=int, default=16, help="Mini-batch size for training")
p.add_argument("--learning_rate", type=float, default=1.893292917167e-4, help="Learning rate for the Adam optimizer")
p.add_argument("--epochs", type=int, default=55, help="Number of training epochs")

p.add_argument("--checkpoint", type=str, default=None, help="Path to checkpoint to resume training from")
args = p.parse_args()
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