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; } - .terminal-241098124-r1 { fill: #c5c8c6 } -.terminal-241098124-r2 { fill: #c5c8c6;font-weight: bold } -.terminal-241098124-r3 { fill: #d0b344;font-weight: bold } -.terminal-241098124-r4 { fill: #68a0b3;font-weight: bold } -.terminal-241098124-r5 { fill: #868887 } -.terminal-241098124-r6 { fill: #98a84b;font-weight: bold } + .terminal-2285289330-r1 { fill: #c5c8c6 } +.terminal-2285289330-r2 { fill: #d0b344 } +.terminal-2285289330-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2285289330-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2285289330-r5 { fill: #868887 } +.terminal-2285289330-r6 { fill: #98a84b;font-weight: bold } +.terminal-2285289330-r7 { fill: #d0b344;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + @@ -86,21 +87,21 @@ - + - - $ casanovo configure --help - -Usage: casanovo configure [OPTIONS] - - Generate a Casanovo configuration file to customize.                            - The casanovo configuration file is in the YAML format.                          - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--output-oFILE  The output configuration file.                           │ -│--help-h  Show this message and exit.                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo configure --help + +Usage:casanovo configure [OPTIONS]                                             + + Generate a Casanovo configuration file to customize.                            + The casanovo configuration file is in the YAML format.                          + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--output-oFILE  The output configuration file.                           │ +│--help-h  Show this message and exit.                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/evaluate-help.svg b/docs/images/evaluate-help.svg index d4832c98..e220664b 100644 --- a/docs/images/evaluate-help.svg +++ b/docs/images/evaluate-help.svg @@ -19,107 +19,108 @@ font-weight: 700; } - .terminal-1106939395-matrix { + .terminal-1788431117-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1106939395-title { + .terminal-1788431117-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1106939395-r1 { fill: #c5c8c6 } -.terminal-1106939395-r2 { fill: #c5c8c6;font-weight: bold } -.terminal-1106939395-r3 { fill: #d0b344;font-weight: bold } -.terminal-1106939395-r4 { fill: #68a0b3;font-weight: bold } -.terminal-1106939395-r5 { fill: #868887 } -.terminal-1106939395-r6 { fill: #cc555a } -.terminal-1106939395-r7 { fill: #8a4346 } -.terminal-1106939395-r8 { fill: #98a84b;font-weight: bold } -.terminal-1106939395-r9 { fill: #8d7b39;font-weight: bold } + .terminal-1788431117-r1 { fill: #c5c8c6 } +.terminal-1788431117-r2 { fill: #d0b344 } +.terminal-1788431117-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-1788431117-r4 { fill: #68a0b3;font-weight: bold } +.terminal-1788431117-r5 { fill: #868887 } +.terminal-1788431117-r6 { fill: #cc555a } +.terminal-1788431117-r7 { fill: #d0b344;font-weight: bold } +.terminal-1788431117-r8 { fill: #8a4346 } +.terminal-1788431117-r9 { fill: #98a84b;font-weight: bold } +.terminal-1788431117-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,35 +132,35 @@ - + - - $ casanovo evaluate --help - -Usage: casanovo evaluate [OPTIONS] ANNOTATED_PEAK_PATH... - - Evaluate de novo peptide sequencing performance.                                - ANNOTATED_PEAK_PATH must be one or more annoated MGF files, such as those       - provided by MassIVE-KB.                                                         - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*ANNOTATED_PEAK_PATHFILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--model-mFILE                        The model weights (.ckpt file). │ -│                                              If not provided, Casanovo will  │ -│                                              try to download the latest      │ -│                                              release.                        │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo evaluate --help + +Usage:casanovo evaluate [OPTIONS] ANNOTATED_PEAK_PATH...                       + + Evaluate de novo peptide sequencing performance.                                + ANNOTATED_PEAK_PATH must be one or more annoated MGF files, such as those       + provided by MassIVE-KB.                                                         + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  ANNOTATED_PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--model-mFILE                        The model weights (.ckpt file). │ +│                                              If not provided, Casanovo will  │ +│                                              try to download the latest      │ +│                                              release.                        │ +│--output-oFILE                        The mzTab file to which results │ +│                                              will be written.                │ +│--config-cFILE                        The YAML configuration file     │ +│                                              overriding the default options. │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ +│                                              logging messages. Log files are │ +│                                              always set to 'debug'.          │ +│--help-h  Show this message and exit.     │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/help.svg b/docs/images/help.svg index 72d06a85..42180a3f 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -19,132 +19,133 @@ font-weight: 700; } - .terminal-2334127528-matrix { + .terminal-2243088900-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2334127528-title { + .terminal-2243088900-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2334127528-r1 { fill: #c5c8c6 } -.terminal-2334127528-r2 { fill: #c5c8c6;font-weight: bold } -.terminal-2334127528-r3 { fill: #d0b344;font-weight: bold } -.terminal-2334127528-r4 { fill: #68a0b3;font-weight: bold } -.terminal-2334127528-r5 { fill: #1984e9 } -.terminal-2334127528-r6 { fill: #868887 } -.terminal-2334127528-r7 { fill: #98a84b;font-weight: bold } + .terminal-2243088900-r1 { fill: #c5c8c6 } +.terminal-2243088900-r2 { fill: #d0b344 } +.terminal-2243088900-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2243088900-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2243088900-r5 { fill: #d0b344;font-weight: bold } +.terminal-2243088900-r6 { fill: #608ab1;text-decoration: underline; } +.terminal-2243088900-r7 { fill: #868887 } +.terminal-2243088900-r8 { fill: #98a84b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -156,44 +157,44 @@ - + - - $ casanovo --help - -Usage: casanovo [OPTIONS] COMMAND [ARGS]... - - ╔════════════════════════════════════════════════════════════════════════════╗  - ║                                  Casanovo                                  ║  - ╚════════════════════════════════════════════════════════════════════════════╝  - Casanovo de novo sequences peptides from tandem mass spectra using a            - Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   - de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  - training new models.                                                            - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io - • Official code repository: https://github.com/Noble-Lab/casanovo - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   -mass spectrometry peptide sequencing with a transformer model. Proceedings   -of the 39th International Conference on Machine Learning - ICML '22 (2022)   -doi:10.1101/2022.02.07.479481.                                               - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo de novo sequences peptides from tandem mass spectra using a            + Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   + de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  + training new models.                                                            + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io + • Official code repository: https://github.com/Noble-Lab/casanovo + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022)   +doi:10.1101/2022.02.07.479481.                                               + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│evaluate  Evaluate de novo peptide sequencing performance.                  │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index 01b002fd..d493e2b2 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -19,107 +19,108 @@ font-weight: 700; } - .terminal-485984700-matrix { + .terminal-2396407494-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-485984700-title { + .terminal-2396407494-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-485984700-r1 { fill: #c5c8c6 } -.terminal-485984700-r2 { fill: #c5c8c6;font-weight: bold } -.terminal-485984700-r3 { fill: #d0b344;font-weight: bold } -.terminal-485984700-r4 { fill: #68a0b3;font-weight: bold } -.terminal-485984700-r5 { fill: #868887 } -.terminal-485984700-r6 { fill: #cc555a } -.terminal-485984700-r7 { fill: #8a4346 } -.terminal-485984700-r8 { fill: #98a84b;font-weight: bold } -.terminal-485984700-r9 { fill: #8d7b39;font-weight: bold } + .terminal-2396407494-r1 { fill: #c5c8c6 } +.terminal-2396407494-r2 { fill: #d0b344 } +.terminal-2396407494-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2396407494-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2396407494-r5 { fill: #868887 } +.terminal-2396407494-r6 { fill: #cc555a } +.terminal-2396407494-r7 { fill: #d0b344;font-weight: bold } +.terminal-2396407494-r8 { fill: #8a4346 } +.terminal-2396407494-r9 { fill: #98a84b;font-weight: bold } +.terminal-2396407494-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,35 +132,35 @@ - + - - $ casanovo sequence --help - -Usage: casanovo sequence [OPTIONS] PEAK_PATH... - - De novo sequence peptides from tandem mass spectra.                             - PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which to sequence  - peptides.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*PEAK_PATHFILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--model-mFILE                        The model weights (.ckpt file). │ -│                                              If not provided, Casanovo will  │ -│                                              try to download the latest      │ -│                                              release.                        │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help + +Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 + + De novo sequence peptides from tandem mass spectra.                             + PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which to sequence  + peptides.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--model-mFILE                        The model weights (.ckpt file). │ +│                                              If not provided, Casanovo will  │ +│                                              try to download the latest      │ +│                                              release.                        │ +│--output-oFILE                        The mzTab file to which results │ +│                                              will be written.                │ +│--config-cFILE                        The YAML configuration file     │ +│                                              overriding the default options. │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ +│                                              logging messages. Log files are │ +│                                              always set to 'debug'.          │ +│--help-h  Show this message and exit.     │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/train-help.svg b/docs/images/train-help.svg index e70940ed..82c30122 100644 --- a/docs/images/train-help.svg +++ b/docs/images/train-help.svg @@ -19,146 +19,147 @@ font-weight: 700; } - .terminal-889313671-matrix { + .terminal-3340932753-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-889313671-title { + .terminal-3340932753-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-889313671-r1 { fill: #c5c8c6 } -.terminal-889313671-r2 { fill: #c5c8c6;font-weight: bold } -.terminal-889313671-r3 { fill: #d0b344;font-weight: bold } -.terminal-889313671-r4 { fill: #68a0b3;font-weight: bold } -.terminal-889313671-r5 { fill: #868887 } -.terminal-889313671-r6 { fill: #cc555a } -.terminal-889313671-r7 { fill: #8a4346 } -.terminal-889313671-r8 { fill: #98a84b;font-weight: bold } -.terminal-889313671-r9 { fill: #8d7b39;font-weight: bold } + .terminal-3340932753-r1 { fill: #c5c8c6 } +.terminal-3340932753-r2 { fill: #d0b344 } +.terminal-3340932753-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-3340932753-r4 { fill: #68a0b3;font-weight: bold } +.terminal-3340932753-r5 { fill: #868887 } +.terminal-3340932753-r6 { fill: #cc555a } +.terminal-3340932753-r7 { fill: #d0b344;font-weight: bold } +.terminal-3340932753-r8 { fill: #8a4346 } +.terminal-3340932753-r9 { fill: #98a84b;font-weight: bold } +.terminal-3340932753-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -170,48 +171,48 @@ - + - - $ casanovo train --help - -Usage: casanovo train [OPTIONS] TRAIN_PEAK_PATH... - - Train a Casanovo model on your own data.                                        - TRAIN_PEAK_PATH must be one or more annoated MGF files, such as those provided  - by MassIVE-KB, from which to train a new Casnovo model.                         - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*TRAIN_PEAK_PATHFILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│*--validation_peak_pa…-pFILE                    An annotated MGF file  │ -│                                                       for validation, like   │ -│                                                       from MassIVE-KB. Use   │ -│                                                       this option multiple   │ -│                                                       times to specify       │ -│                                                       multiple files.        │ -│[required]            │ -│--model-mFILE                    The model weights      │ -│                                                       (.ckpt file). If not   │ -│                                                       provided, Casanovo     │ -│                                                       will try to download   │ -│                                                       the latest release.    │ -│--output-oFILE                    The mzTab file to      │ -│                                                       which results will be  │ -│                                                       written.               │ -│--config-cFILE                    The YAML configuration │ -│                                                       file overriding the    │ -│                                                       default options.       │ -│--verbosity-v[debug|info|warning|er  Set the verbosity of   │ -│ror]  console logging        │ -│                                                       messages. Log files    │ -│                                                       are always set to      │ -│                                                       'debug'.               │ -│--help-h  Show this message and  │ -│                                                       exit.                  │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo train --help + +Usage:casanovo train [OPTIONS] TRAIN_PEAK_PATH...                              + + Train a Casanovo model on your own data.                                        + TRAIN_PEAK_PATH must be one or more annoated MGF files, such as those provided  + by MassIVE-KB, from which to train a new Casnovo model.                         + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  TRAIN_PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│*--validation_peak_pa…-pFILE                    An annotated MGF file  │ +│                                                       for validation, like   │ +│                                                       from MassIVE-KB. Use   │ +│                                                       this option multiple   │ +│                                                       times to specify       │ +│                                                       multiple files.        │ +│[required]            │ +│--model-mFILE                    The model weights      │ +│                                                       (.ckpt file). If not   │ +│                                                       provided, Casanovo     │ +│                                                       will try to download   │ +│                                                       the latest release.    │ +│--output-oFILE                    The mzTab file to      │ +│                                                       which results will be  │ +│                                                       written.               │ +│--config-cFILE                    The YAML configuration │ +│                                                       file overriding the    │ +│                                                       default options.       │ +│--verbosity-v[debug|info|warning|er  Set the verbosity of   │ +│ror]  console logging        │ +│                                                       messages. Log files    │ +│                                                       are always set to      │ +│                                                       'debug'.               │ +│--help-h  Show this message and  │ +│                                                       exit.                  │ +╰──────────────────────────────────────────────────────────────────────────────╯ + 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,