From 645a33fc020a5db94ce2de3d483eb5fcdc7c2a92 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 30 Aug 2024 23:51:54 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- docs/images/sequence-help.svg | 222 ++++++++++++++++++---------------- docs/images/train-help.svg | 204 +++++++++++++++---------------- 2 files changed, 221 insertions(+), 205 deletions(-) diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index a707a97c..ea6ff078 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + - + - + - - $ 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. If evaluate is set to True PEAK_PATH must be one or more annotated    - MGF file.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--evaluate-e  Run in evaluation mode. When  │ -│                                                this flag is set the peptide  │ -│                                                and amino acid precision will │ -│                                                be calculated and logged at   │ -│                                                the end of the sequencing     │ -│                                                run. All input files must be  │ -│                                                annotated MGF files if        │ -│                                                running in evaluation mode.   │ -│--model-mTEXT                        Either the model weights      │ -│                                                (.ckpt file) or a URL         │ -│                                                pointing to the model weights │ -│                                                file. If not provided,        │ -│                                                Casanovo will try to download │ -│                                                the latest release            │ -│                                                automatically.                │ -│--output_dir-fPATH                        The destination directory for │ -│                                                output files                  │ -│--output_root-oFILE                        The root name for all output  │ -│                                                files                         │ -│--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'.    │ -│--overwrite-d  Whether to overwrite output   │ -│                                                files.                        │ -│--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. If evaluate is set to True PEAK_PATH must be one or more annotated    + MGF file.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--evaluate-e  Run in evaluation mode.    │ +│                                                   When this flag is set the  │ +│                                                   peptide and amino acid     │ +│                                                   precision will be          │ +│                                                   calculated and logged at   │ +│                                                   the end of the sequencing  │ +│                                                   run. All input files must  │ +│                                                   be annotated MGF files if  │ +│                                                   running in evaluation      │ +│                                                   mode.                      │ +│--model-mTEXT                       Either the model weights   │ +│                                                   (.ckpt file) or a URL      │ +│                                                   pointing to the model      │ +│                                                   weights file. If not       │ +│                                                   provided, Casanovo will    │ +│                                                   try to download the latest │ +│                                                   release automatically.     │ +│--output_dir-dPATH                       The destination directory  │ +│                                                   for output files           │ +│--output_root-oFILE                       The root name for all      │ +│                                                   output files               │ +│--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'.                │ +│--force_overwrite-f  Whether to overwrite       │ +│                                                   output files.              │ +│--help-h  Show this message and      │ +│                                                   exit.                      │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/train-help.svg b/docs/images/train-help.svg index f5fd20a7..783a0660 100644 --- a/docs/images/train-help.svg +++ b/docs/images/train-help.svg @@ -19,162 +19,162 @@ font-weight: 700; } - .terminal-249329225-matrix { + .terminal-2920970231-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-249329225-title { + .terminal-2920970231-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-249329225-r1 { fill: #c5c8c6 } -.terminal-249329225-r2 { fill: #d0b344 } -.terminal-249329225-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-249329225-r4 { fill: #68a0b3;font-weight: bold } -.terminal-249329225-r5 { fill: #868887 } -.terminal-249329225-r6 { fill: #cc555a } -.terminal-249329225-r7 { fill: #d0b344;font-weight: bold } -.terminal-249329225-r8 { fill: #8a4346 } -.terminal-249329225-r9 { fill: #98a84b;font-weight: bold } -.terminal-249329225-r10 { fill: #8d7b39;font-weight: bold } + .terminal-2920970231-r1 { fill: #c5c8c6 } +.terminal-2920970231-r2 { fill: #d0b344 } +.terminal-2920970231-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2920970231-r4 { fill: #68a0b3;font-weight: bold } +.terminal-2920970231-r5 { fill: #868887 } +.terminal-2920970231-r6 { fill: #cc555a } +.terminal-2920970231-r7 { fill: #d0b344;font-weight: bold } +.terminal-2920970231-r8 { fill: #8a4346 } +.terminal-2920970231-r9 { fill: #98a84b;font-weight: bold } +.terminal-2920970231-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -186,53 +186,53 @@ - + - - $ 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_path-pFILE                    An annotated MGF file    │ -│                                                     for validation, like     │ -│                                                     from MassIVE-KB. Use     │ -│                                                     this option multiple     │ -│                                                     times to specify         │ -│                                                     multiple files.          │ -│--model-mTEXT                    Either the model weights │ -│                                                     (.ckpt file) or a URL    │ -│                                                     pointing to the model    │ -│                                                     weights file. If not     │ -│                                                     provided, Casanovo will  │ -│                                                     try to download the      │ -│                                                     latest release           │ -│                                                     automatically.           │ -│--output_dir-fPATH                    The destination          │ -│                                                     directory for output     │ -│                                                     files                    │ -│--output_root-oFILE                    The root name for all    │ -│                                                     output files             │ -│--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'.   │ -│--overwrite-d  Whether to overwrite     │ -│                                                     output files.            │ -│--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_path-pFILE                    An annotated MGF file    │ +│                                                     for validation, like     │ +│                                                     from MassIVE-KB. Use     │ +│                                                     this option multiple     │ +│                                                     times to specify         │ +│                                                     multiple files.          │ +│--model-mTEXT                    Either the model weights │ +│                                                     (.ckpt file) or a URL    │ +│                                                     pointing to the model    │ +│                                                     weights file. If not     │ +│                                                     provided, Casanovo will  │ +│                                                     try to download the      │ +│                                                     latest release           │ +│                                                     automatically.           │ +│--output_dir-dPATH                    The destination          │ +│                                                     directory for output     │ +│                                                     files                    │ +│--output_root-oFILE                    The root name for all    │ +│                                                     output files             │ +│--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'.   │ +│--force_overwrite-f  Whether to overwrite     │ +│                                                     output files.            │ +│--help-h  Show this message and    │ +│                                                     exit.                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +