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 }
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-.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 }
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+.terminal-2285289330-r7 { fill: #d0b344;font-weight: bold }
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-
+
-
- $ 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 }
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-.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 }
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+.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 }
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@@ -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 }
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-.terminal-2334127528-r6 { fill: #868887 }
-.terminal-2334127528-r7 { fill: #98a84b;font-weight: bold }
+ .terminal-2243088900-r1 { fill: #c5c8c6 }
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+.terminal-2243088900-r7 { fill: #868887 }
+.terminal-2243088900-r8 { fill: #98a84b;font-weight: bold }
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@@ -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 }
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-.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 }
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+.terminal-2396407494-r9 { fill: #98a84b;font-weight: bold }
+.terminal-2396407494-r10 { fill: #8d7b39;font-weight: bold }
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+
@@ -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 }
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-.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 }
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+.terminal-3340932753-r9 { fill: #98a84b;font-weight: bold }
+.terminal-3340932753-r10 { fill: #8d7b39;font-weight: bold }
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@@ -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. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+