From 5879b0a93b0b9ef8f13b7c54a16ce32788675087 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Fri, 2 Aug 2024 11:52:26 +0200 Subject: [PATCH 1/6] Update paper reference (#361) --- README.md | 2 +- docs/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 533c76e2..35b7c646 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ If you use Casanovo in your work, please cite the following publications: - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621) +- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) ## Documentation diff --git a/docs/index.md b/docs/index.md index 2283aeb2..3dd77622 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,7 +7,7 @@ If you use Casanovo in your work, please cite the following publications: - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621) +- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) ```{toctree} --- From f792527e07f60f3eebef45773fccc59b4f92614b Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Tue, 6 Aug 2024 08:47:53 +0200 Subject: [PATCH 2/6] Bug report template (#360) * bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit --- .github/ISSUE_TEMPLATE/bug_report_template.md | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug_report_template.md diff --git a/.github/ISSUE_TEMPLATE/bug_report_template.md b/.github/ISSUE_TEMPLATE/bug_report_template.md new file mode 100644 index 00000000..cf4c487c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report_template.md @@ -0,0 +1,55 @@ +--- +name: Bug Report +about: Submit a Casanovo Bug Report +labels: bug +--- + +## Describe the Issue +A clear and concise description of what the issue/bug is. + +## Steps To Reproduce +Steps to reproduce the incorrect behavior. + +## Expected Behavior +A clear and concise description of what you expected to happen. + +## Terminal Output (If Applicable) +Provide any applicable console output in between the tick marks below. + +``` + +``` + +## Environment: +- OS: [e.g. Windows 11, Windows 10, macOS 14, Ubuntu 24.04] +- Casanovo Version: [e.g. 4.2.1] +- Hardware Used (CPU or GPU, if GPU also GPU model and CUDA version): [e.g. GPU: NVIDIA GeForce RTX 2070, CUDA Version: 12.5] + +### Checking GPU Version + +The GPU model can be checked by typing `nvidia-smi` into a terminal/console window. +An example of how to use this command is shown below. +In this case, the CUDA version is 12.5 and the GPU model is GeForce RTX 2070. + + +``` +(casanovo_env) C:\Users\\OneDrive\Documents\casanovo>nvidia-smi +Fri Aug 2 12:34:57 2024 ++-----------------------------------------------------------------------------------------+ +| NVIDIA-SMI 555.99 Driver Version: 555.99 CUDA Version: 12.5 | +|-----------------------------------------+------------------------+----------------------+ +| GPU Name Driver-Model | Bus-Id Disp.A | Volatile Uncorr. ECC | +| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | +| | | MIG M. | +|=========================================+========================+======================| +| 0 NVIDIA GeForce RTX 2070 ... WDDM | 00000000:01:00.0 On | N/A | +| N/A 60C P8 16W / 90W | 1059MiB / 8192MiB | 0% Default | +| | | N/A | ++-----------------------------------------+------------------------+----------------------+ +``` + +## Additional Context +Add any other context about the problem here. + +## Attach Files +Please attach all input files used and the full Casanovo log file. From bf1e5a36b8f3b73805d1354339562aed9051f4de Mon Sep 17 00:00:00 2001 From: Gwenneth Straub Date: Tue, 6 Aug 2024 00:10:59 -0700 Subject: [PATCH 3/6] upgrade codecove to v4 (#364) --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7e79b5a3..1c74a29d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -42,7 +42,7 @@ jobs: run: | pytest --cov=casanovo tests/ - name: Upload coverage to codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true From e6321a7c6d59da5bb48b9e9eabb0b00979d17d01 Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Thu, 19 Sep 2024 12:31:10 -0700 Subject: [PATCH 4/6] Update docs with model weights (#384) * Update docs with model weights * Generate new screengrabs with rich-codex * Fix version and paper link --------- Co-authored-by: github-actions[bot] --- docs/getting_started.md | 9 +- docs/images/configure-help.svg | 64 ++++++------ docs/images/evaluate-help.svg | 123 ++++++++++++----------- docs/images/help.svg | 157 +++++++++++++++-------------- docs/images/sequence-help.svg | 123 ++++++++++++----------- docs/images/train-help.svg | 175 +++++++++++++++++---------------- 6 files changed, 347 insertions(+), 304 deletions(-) diff --git a/docs/getting_started.md b/docs/getting_started.md index 73cbd5f0..78163ac2 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -81,9 +81,12 @@ This model file or a custom one can then be specified using the `--model` comman Not all releases will have a model file included on the [Releases page](https://github.com/Noble-Lab/casanovo/releases), in which case model weights for alternative releases with the same major version number can be used. -The most recent model weights for Casanovo version 3.x are currently provided under [Casanovo v3.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v3.0.0): -- `casanovo_massivekb.ckpt`: Default Casanovo weights to use when analyzing tryptic data. These weights will be downloaded automatically if no weights are explicitly specified. -- `casanovo_non-enzy.checkpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually. +The most recent model weights for Casanovo version 4.2 and above are currently provided under [Casanovo v4.2.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.2.0): +- `casanovo_v4_2_0.ckpt`: Default Casanovo weights to use as described in [Melendez et al.](https://pubs.acs.org/doi/full/10.1021/acs.jproteome.4c00422). These weights will be downloaded automatically if no weights are explicitly specified. + +Alternatively, model weigths for Casanovo version 4.x as described in [Yilmaz et al.](https://www.nature.com/articles/s41467-024-49731-x) are currently provided under [Casanovo v4.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.0.0): +- `casanovo_massivekb.ckpt`: Casanovo weights to use when analyzing tryptic data. These weights need to be downloaded manually. +- `casanovo_nontryptic.ckpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually. ## Running Casanovo diff --git a/docs/images/configure-help.svg b/docs/images/configure-help.svg index 0822927a..b1fcce10 100644 --- a/docs/images/configure-help.svg +++ b/docs/images/configure-help.svg @@ -19,57 +19,63 @@ font-weight: 700; } - .terminal-3936755216-matrix { + .terminal-2766440694-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3936755216-title { + .terminal-2766440694-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3936755216-r1 { fill: #c5c8c6 } + .terminal-2766440694-r1 { fill: #c5c8c6 } +.terminal-2766440694-r2 { fill: #d0b344 } +.terminal-2766440694-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2766440694-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2766440694-r5 { fill: #868887 } +.terminal-2766440694-r6 { fill: #98a84b;font-weight: bold } +.terminal-2766440694-r7 { fill: #d0b344;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + @@ -81,21 +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  -o  FILE  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 b16c4ffd..2f770e2e 100644 --- a/docs/images/evaluate-help.svg +++ b/docs/images/evaluate-help.svg @@ -19,99 +19,108 @@ font-weight: 700; } - .terminal-1284026435-matrix { + .terminal-2215953096-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1284026435-title { + .terminal-2215953096-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1284026435-r1 { fill: #c5c8c6 } + .terminal-2215953096-r1 { fill: #c5c8c6 } +.terminal-2215953096-r2 { fill: #d0b344 } +.terminal-2215953096-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2215953096-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2215953096-r5 { fill: #868887 } +.terminal-2215953096-r6 { fill: #cc555a } +.terminal-2215953096-r7 { fill: #d0b344;font-weight: bold } +.terminal-2215953096-r8 { fill: #8a4346 } +.terminal-2215953096-r9 { fill: #98a84b;font-weight: bold } +.terminal-2215953096-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,35 +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_PATH    FILE  [required]                                   │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --model      -m  FILE                        The model weights (.ckpt file). │ -│                                              If not provided, Casanovo will  │ -│                                              try to download the latest      │ -│                                              release.                        │ -│ --output     -o  FILE                        The mzTab file to which results │ -│                                              will be written.                │ -│ --config     -c  FILE                        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 2e22e2d3..eae8e93d 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -19,126 +19,133 @@ font-weight: 700; } - .terminal-100512290-matrix { + .terminal-771077830-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-100512290-title { + .terminal-771077830-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-100512290-r1 { fill: #c5c8c6 } + .terminal-771077830-r1 { fill: #c5c8c6 } +.terminal-771077830-r2 { fill: #d0b344 } +.terminal-771077830-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-771077830-r4 { fill: #68a0b3;font-weight: bold } +.terminal-771077830-r5 { fill: #d0b344;font-weight: bold } +.terminal-771077830-r6 { fill: #608ab1;text-decoration: underline; } +.terminal-771077830-r7 { fill: #868887 } +.terminal-771077830-r8 { fill: #98a84b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -150,44 +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 f5799766..6635cfaa 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -19,99 +19,108 @@ font-weight: 700; } - .terminal-2359602172-matrix { + .terminal-2906046081-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2359602172-title { + .terminal-2906046081-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2359602172-r1 { fill: #c5c8c6 } + .terminal-2906046081-r1 { fill: #c5c8c6 } +.terminal-2906046081-r2 { fill: #d0b344 } +.terminal-2906046081-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2906046081-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2906046081-r5 { fill: #868887 } +.terminal-2906046081-r6 { fill: #cc555a } +.terminal-2906046081-r7 { fill: #d0b344;font-weight: bold } +.terminal-2906046081-r8 { fill: #8a4346 } +.terminal-2906046081-r9 { fill: #98a84b;font-weight: bold } +.terminal-2906046081-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,35 +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_PATH    FILE  [required]                                             │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --model      -m  FILE                        The model weights (.ckpt file). │ -│                                              If not provided, Casanovo will  │ -│                                              try to download the latest      │ -│                                              release.                        │ -│ --output     -o  FILE                        The mzTab file to which results │ -│                                              will be written.                │ -│ --config     -c  FILE                        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 fccd4140..58251215 100644 --- a/docs/images/train-help.svg +++ b/docs/images/train-help.svg @@ -19,138 +19,147 @@ font-weight: 700; } - .terminal-2430201580-matrix { + .terminal-2982408974-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2430201580-title { + .terminal-2982408974-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2430201580-r1 { fill: #c5c8c6 } + .terminal-2982408974-r1 { fill: #c5c8c6 } +.terminal-2982408974-r2 { fill: #d0b344 } +.terminal-2982408974-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2982408974-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2982408974-r5 { fill: #868887 } +.terminal-2982408974-r6 { fill: #cc555a } +.terminal-2982408974-r7 { fill: #d0b344;font-weight: bold } +.terminal-2982408974-r8 { fill: #8a4346 } +.terminal-2982408974-r9 { fill: #98a84b;font-weight: bold } +.terminal-2982408974-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -162,48 +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_PATH    FILE  [required]                                       │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ *  --validation_peak_pa…  -p  FILE                    An annotated MGF file  │ -│                                                       for validation, like   │ -│                                                       from MassIVE-KB. Use   │ -│                                                       this option multiple   │ -│                                                       times to specify       │ -│                                                       multiple files.        │ -│                                                       [required]             │ -│    --model                -m  FILE                    The model weights      │ -│                                                       (.ckpt file). If not   │ -│                                                       provided, Casanovo     │ -│                                                       will try to download   │ -│                                                       the latest release.    │ -│    --output               -o  FILE                    The mzTab file to      │ -│                                                       which results will be  │ -│                                                       written.               │ -│    --config               -c  FILE                    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.                  │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 27660fc663db5e038624a3ebc1657ba1eafa32cd Mon Sep 17 00:00:00 2001 From: justin-a-sanders <60298590+justin-a-sanders@users.noreply.github.com> Date: Mon, 30 Sep 2024 18:55:25 -0700 Subject: [PATCH 5/6] Update pytorch lightning requirement --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d5c583df..d91bb57a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ classifiers = [ requires-python = ">=3.8" dependencies = [ "appdirs", - "lightning>=2.0", + "lightning>=2.1", "click", "depthcharge-ms>=0.2.3,<0.3.0", "natsort", From 7e7d883785af6de17434a5c23d71d9bfad8e7166 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 29 Oct 2024 16:37:54 +0000 Subject: [PATCH 6/6] Generate new screengrabs with rich-codex --- docs/images/evaluate-help.svg | 4 ---- docs/images/help.svg | 2 -- 2 files changed, 6 deletions(-) diff --git a/docs/images/evaluate-help.svg b/docs/images/evaluate-help.svg index 85c301b7..661f0efe 100644 --- a/docs/images/evaluate-help.svg +++ b/docs/images/evaluate-help.svg @@ -19,7 +19,6 @@ font-weight: 700; } - .terminal-1819499677-matrix { font-family: Fira Code, monospace; font-size: 20px; @@ -27,14 +26,12 @@ font-variant-east-asian: full-width; } - .terminal-1819499677-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1819499677-r1 { fill: #c5c8c6 } .terminal-1819499677-r2 { fill: #d0b344 } .terminal-1819499677-r3 { fill: #c5c8c6;font-weight: bold } @@ -81,7 +78,6 @@ - diff --git a/docs/images/help.svg b/docs/images/help.svg index b4ef53d5..dbdc05e0 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -19,7 +19,6 @@ font-weight: 700; } - .terminal-1998256653-matrix { font-family: Fira Code, monospace; font-size: 20px; @@ -33,7 +32,6 @@ font-family: arial; } - .terminal-1998256653-r1 { fill: #c5c8c6 } .terminal-1998256653-r2 { fill: #d0b344 } .terminal-1998256653-r3 { fill: #c5c8c6;font-weight: bold }