Repository: Noble-Lab/casanovo (language: python)

Issue:
precursor_mass_tol is being ignored
I can't seem to change the behavior of the precursor mass filter, even if I set the precursor_mass_tol to a ridiculously large value.  Here is a small example where I set it to 1e10, and there are still negative scores.

We should also provide (or document, if it exists) a way to turn off the filter entirely.

Also, separately, it seems like the auto-download of the model only works for the `train` command.  When I try it with `sequence` I get `ValueError: A model file must be provided`.

[sample.mztab.txt](https://github.com/Noble-Lab/casanovo/files/12684785/sample.mztab.txt)
[sample.mgf.txt](https://github.com/Noble-Lab/casanovo/files/12684786/sample.mgf.txt)
[sample.log.txt](https://github.com/Noble-Lab/casanovo/files/12684787/sample.log.txt)
[casanovo.yaml.txt](https://github.com/Noble-Lab/casanovo/files/12684788/casanovo.yaml.txt)



Discussion / hints:

Fix patch:
diff --git a/.github/workflows/screenshots.yml b/.github/workflows/screenshots.yml
index 3b646efa..a9bcf896 100644
--- a/.github/workflows/screenshots.yml
+++ b/.github/workflows/screenshots.yml
@@ -11,15 +11,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
 
       - name: Install your custom tools
-        run: pip install .
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
 
       - name: Generate terminal images with rich-codex
         uses: ewels/rich-codex@v1
diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py
index 992cf566..0a1c3618 100644
--- a/casanovo/casanovo.py
+++ b/casanovo/casanovo.py
@@ -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:
@@ -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:
@@ -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:
@@ -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
 
 
 def _get_model_weights() -> str:
diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py
index 852860d3..e16f4d5b 100644
--- a/casanovo/denovo/model_runner.py
+++ b/casanovo/denovo/model_runner.py
@@ -5,6 +5,7 @@
 import os
 import tempfile
 import uuid
+import warnings
 from pathlib import Path
 from typing import Iterable, List, Optional, Union
 
@@ -217,6 +218,7 @@ def initialize_model(self, train: bool) -> None:
             max_charge=self.config.max_charge,
             precursor_mass_tol=self.config.precursor_mass_tol,
             isotope_error_range=self.config.isotope_error_range,
+            min_peptide_len=self.config.min_peptide_len,
             n_beams=self.config.n_beams,
             top_match=self.config.top_match,
             n_log=self.config.n_log,
@@ -229,6 +231,24 @@ def initialize_model(self, train: bool) -> None:
             calculate_precision=self.config.calculate_precision,
         )
 
+        # Reconfigurable non-architecture related parameters for a loaded model
+        loaded_model_params = dict(
+            max_length=self.config.max_length,
+            precursor_mass_tol=self.config.precursor_mass_tol,
+            isotope_error_range=self.config.isotope_error_range,
+            n_beams=self.config.n_beams,
+            min_peptide_len=self.config.min_peptide_len,
+            top_match=self.config.top_match,
+            n_log=self.config.n_log,
+            tb_summarywriter=self.config.tb_summarywriter,
+            warmup_iters=self.config.warmup_iters,
+            max_iters=self.config.max_iters,
+            lr=self.config.learning_rate,
+            weight_decay=self.config.weight_decay,
+            out_writer=self.writer,
+            calculate_precision=self.config.calculate_precision,
+        )
+
         from_scratch = (
             self.config.train_from_scratch,
             self.model_filename is None,
@@ -247,20 +267,38 @@ def initialize_model(self, train: bool) -> None:
             )
             raise FileNotFoundError("Could not find the model weights file")
 
-        # First try loading model details from the weithgs file,
-        # otherwise use the provided configuration.
+        # First try loading model details from the weights file, otherwise use
+        # the provided configuration.
         device = torch.empty(1).device  # Use the default device.
         try:
             self.model = Spec2Pep.load_from_checkpoint(
-                self.model_filename,
-                map_location=device,
+                self.model_filename, map_location=device, **loaded_model_params
             )
-        except RuntimeError:
-            self.model = Spec2Pep.load_from_checkpoint(
-                self.model_filename,
-                map_location=device,
-                **model_params,
+
+            architecture_params = set(model_params.keys()) - set(
+                loaded_model_params.keys()
             )
+            for param in architecture_params:
+                if model_params[param] != self.model.hparams[param]:
+                    warnings.warn(
+                        f"Mismatching {param} parameter in "
+                        f"model checkpoint ({self.model.hparams[param]}) "
+                        f"vs config file ({model_params[param]}); "
+                        "using the checkpoint."
+                    )
+        except RuntimeError:
+            # This only doesn't work if the weights are from an older version
+            try:
+                self.model = Spec2Pep.load_from_checkpoint(
+                    self.model_filename,
+                    map_location=device,
+                    **model_params,
+                )
+            except RuntimeError:
+                raise RuntimeError(
+                    "Weights file incompatible with the current version of "
+                    "Casanovo. "
+                )
 
     def initialize_data_module(
         self,
diff --git a/docs/images/configure-help.svg b/docs/images/configure-help.svg
index fc4e6305..d5dd7aa8 100644
--- a/docs/images/configure-help.svg
+++ b/docs/images/configure-help.svg
@@ -19,62 +19,63 @@
         font-weight: 700;
     }
 
-    .terminal-241098124-matrix {
+    .terminal-2285289330-matrix {
         font-family: Fira Code, monospace;
         font-size: 20px;
         line-height: 24.4px;
         font-variant-east-asian: full-width;
     }
 
-    .terminal-241098124-title {
+    .terminal-2285289330-title {
         font-size: 18px;
         font-weight: bold;
         font-family: arial;
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-    .terminal-241098124-r1 { fill: #c5c8c6 }
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+.terminal-2285289330-r7 { fill: #d0b344;font-weight: bold }
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Test patch:
diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py
index 663e3b3b..6be91831 100644
--- a/tests/unit_tests/test_runner.py
+++ b/tests/unit_tests/test_runner.py
@@ -56,6 +56,8 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config):
     # Try changing model arch:
     other_config = Config(tiny_config)
     other_config.n_layers = 50  # lol
+    other_config.n_beams = 12
+    other_config.max_iters = 2
     with torch.device("meta"):
         # Now load the weights into a new model
         # The device should be meta for all the weights.
@@ -64,6 +66,8 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config):
 
     obs_layers = runner.model.encoder.transformer_encoder.num_layers
     assert obs_layers == 1  # Match the original arch.
+    assert runner.model.n_beams == 12  # Match the config
+    assert runner.model.max_iters == 2  # Match the config
     assert next(runner.model.parameters()).device == torch.device("meta")
 
     # If the Trainer correctly moves the weights to the accelerator,