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Use config options and auto-downloaded weights #246

Merged
merged 14 commits into from
Dec 12, 2023
Merged

Use config options and auto-downloaded weights #246

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0d312e6
Use auto-downloaded weights
melihyilmaz Sep 22, 2023
0ea1b7d
Use config options in model init
melihyilmaz Sep 22, 2023
4ab4728
Fix linting
melihyilmaz Sep 22, 2023
d906679
Fix missing return value
melihyilmaz Sep 22, 2023
b6b374f
Merge branch 'dev' into fix-modelrunner-inputs
melihyilmaz Nov 28, 2023
bfb168e
Override mismatching params with ckpt
melihyilmaz Nov 28, 2023
0e3bcb8
Handle corrupt ckpt
melihyilmaz Nov 29, 2023
4d1e91f
Add test case for parameter mismatch
melihyilmaz Nov 29, 2023
6f77c4d
Merge branch 'dev' into fix-modelrunner-inputs
wfondrie Dec 11, 2023
f2fa7f9
Add Python version to screenshot action
wfondrie Dec 11, 2023
9a1df46
Generate new screengrabs with rich-codex
github-actions[bot] Dec 11, 2023
bb548ac
Fix import order
bittremieux Dec 12, 2023
05adba6
Minor reformatting
bittremieux Dec 12, 2023
8c88a71
Merge branch 'fix-modelrunner-inputs' of github.com:Noble-Lab/casanov…
bittremieux Dec 12, 2023
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8 changes: 4 additions & 4 deletions casanovo/casanovo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ def sequence(
to sequence peptides.
"""
output = setup_logging(output, verbosity)
config = setup_model(model, config, output, False)
config, model = setup_model(model, config, output, False)
with ModelRunner(config, model) as runner:
logger.info("Sequencing peptides from:")
for peak_file in peak_path:
Expand Down Expand Up @@ -164,7 +164,7 @@ def evaluate(
such as those provided by MassIVE-KB.
"""
output = setup_logging(output, verbosity)
config = setup_model(model, config, output, False)
config, model = setup_model(model, config, output, False)
with ModelRunner(config, model) as runner:
logger.info("Sequencing and evaluating peptides from:")
for peak_file in annotated_peak_path:
Expand Down Expand Up @@ -207,7 +207,7 @@ def train(
provided by MassIVE-KB, from which to train a new Casnovo model.
"""
output = setup_logging(output, verbosity)
config = setup_model(model, config, output, True)
config, model = setup_model(model, config, output, True)
with ModelRunner(config, model) as runner:
logger.info("Training a model from:")
for peak_file in train_peak_path:
Expand Down Expand Up @@ -378,7 +378,7 @@ def setup_model(
for key, value in config.items():
logger.debug("%s = %s", str(key), str(value))

return config
return config, model
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def _get_model_weights() -> str:
Expand Down
7 changes: 3 additions & 4 deletions casanovo/denovo/model_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -255,12 +255,11 @@ def initialize_model(self, train: bool) -> None:
self.model = Spec2Pep.load_from_checkpoint(
self.model_filename,
map_location=device,
**model_params,
)
except RuntimeError:
self.model = Spec2Pep.load_from_checkpoint(
self.model_filename,
map_location=device,
**model_params,
raise RuntimeError(
"Mismatching parameters between loaded model and config file"
)

def initialize_data_module(
Expand Down
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