From 22f26c77817c0218297b6a6dce6cea15f7e0573a Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 21 Jun 2024 21:22:38 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- docs/images/configure-help.svg | 160 +++++++++++++++------- docs/images/evaluate-help.svg | 191 +++++++++++++------------- docs/images/help.svg | 219 +++++++++++++----------------- docs/images/sequence-help.svg | 191 +++++++++++++------------- docs/images/train-help.svg | 237 +++++++++++++-------------------- 5 files changed, 493 insertions(+), 505 deletions(-) diff --git a/docs/images/configure-help.svg b/docs/images/configure-help.svg index d5dd7aa8..4092bce3 100644 --- a/docs/images/configure-help.svg +++ b/docs/images/configure-help.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ 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 +Traceback (most recent call last): +  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/casanovo", line 5, in <module> +    from casanovo.casanovo import main +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/casanovo/casanovo.py", line 32, in <module> +    import depthcharge +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/__init__.py", line 3, in <module> +    from . import components +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/__init__.py", line 2, in <module> +    from .transformers import SpectrumEncoder, PeptideDecoder +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/transformers.py", line 8, in <module> +    from .. import utils +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/utils.py", line 5, in <module> +    from tensorboard.backend.event_processing.event_accumulator import ( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_accumulator.py", line 24, in <module> +    from tensorboard.backend.event_processing import event_file_loader +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_file_loader.py", line 21, in <module> +    from tensorboard import dataclass_compat +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/dataclass_compat.py", line 33, in <module> +    from tensorboard.plugins.hparams import metadata as hparams_metadata +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/plugins/hparams/metadata.py", line 32, in <module> +    NULL_TENSOR = tensor_util.make_tensor_proto( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/util/tensor_util.py", line 405, in make_tensor_proto +    numpy_dtype = dtypes.as_dtype(nparray.dtype) +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py", line 677, in as_dtype +    if type_value.type == np.string_ or type_value.type == np.unicode_: +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/numpy/__init__.py", line 397, in __getattr__ +    raise AttributeError( +AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'? diff --git a/docs/images/evaluate-help.svg b/docs/images/evaluate-help.svg index e220664b..d86b2497 100644 --- a/docs/images/evaluate-help.svg +++ b/docs/images/evaluate-help.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + + + - + - + - - $ 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.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo evaluate --help +Traceback (most recent call last): +  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/casanovo", line 5, in <module> +    from casanovo.casanovo import main +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/casanovo/casanovo.py", line 32, in <module> +    import depthcharge +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/__init__.py", line 3, in <module> +    from . import components +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/__init__.py", line 2, in <module> +    from .transformers import SpectrumEncoder, PeptideDecoder +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/transformers.py", line 8, in <module> +    from .. import utils +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/utils.py", line 5, in <module> +    from tensorboard.backend.event_processing.event_accumulator import ( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_accumulator.py", line 24, in <module> +    from tensorboard.backend.event_processing import event_file_loader +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_file_loader.py", line 21, in <module> +    from tensorboard import dataclass_compat +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/dataclass_compat.py", line 33, in <module> +    from tensorboard.plugins.hparams import metadata as hparams_metadata +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/plugins/hparams/metadata.py", line 32, in <module> +    NULL_TENSOR = tensor_util.make_tensor_proto( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/util/tensor_util.py", line 405, in make_tensor_proto +    numpy_dtype = dtypes.as_dtype(nparray.dtype) +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py", line 677, in as_dtype +    if type_value.type == np.string_ or type_value.type == np.unicode_: +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/numpy/__init__.py", line 397, in __getattr__ +    raise AttributeError( +AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'? diff --git a/docs/images/help.svg b/docs/images/help.svg index 42180a3f..dfb1039c 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - + + - + - + - - $ 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 +Traceback (most recent call last): +  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/casanovo", line 5, in <module> +    from casanovo.casanovo import main +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/casanovo/casanovo.py", line 32, in <module> +    import depthcharge +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/__init__.py", line 3, in <module> +    from . import components +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/__init__.py", line 2, in <module> +    from .transformers import SpectrumEncoder, PeptideDecoder +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/transformers.py", line 8, in <module> +    from .. import utils +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/utils.py", line 5, in <module> +    from tensorboard.backend.event_processing.event_accumulator import ( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_accumulator.py", line 24, in <module> +    from tensorboard.backend.event_processing import event_file_loader +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_file_loader.py", line 21, in <module> +    from tensorboard import dataclass_compat +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/dataclass_compat.py", line 33, in <module> +    from tensorboard.plugins.hparams import metadata as hparams_metadata +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/plugins/hparams/metadata.py", line 32, in <module> +    NULL_TENSOR = tensor_util.make_tensor_proto( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/util/tensor_util.py", line 405, in make_tensor_proto +    numpy_dtype = dtypes.as_dtype(nparray.dtype) +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py", line 677, in as_dtype +    if type_value.type == np.string_ or type_value.type == np.unicode_: +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/numpy/__init__.py", line 397, in __getattr__ +    raise AttributeError( +AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'? diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index d493e2b2..b9b96d74 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.                                                                       - -╭─ 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.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help +Traceback (most recent call last): +  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/casanovo", line 5, in <module> +    from casanovo.casanovo import main +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/casanovo/casanovo.py", line 32, in <module> +    import depthcharge +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/__init__.py", line 3, in <module> +    from . import components +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/__init__.py", line 2, in <module> +    from .transformers import SpectrumEncoder, PeptideDecoder +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/transformers.py", line 8, in <module> +    from .. import utils +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/utils.py", line 5, in <module> +    from tensorboard.backend.event_processing.event_accumulator import ( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_accumulator.py", line 24, in <module> +    from tensorboard.backend.event_processing import event_file_loader +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_file_loader.py", line 21, in <module> +    from tensorboard import dataclass_compat +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/dataclass_compat.py", line 33, in <module> +    from tensorboard.plugins.hparams import metadata as hparams_metadata +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/plugins/hparams/metadata.py", line 32, in <module> +    NULL_TENSOR = tensor_util.make_tensor_proto( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/util/tensor_util.py", line 405, in make_tensor_proto +    numpy_dtype = dtypes.as_dtype(nparray.dtype) +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py", line 677, in as_dtype +    if type_value.type == np.string_ or type_value.type == np.unicode_: +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/numpy/__init__.py", line 397, in __getattr__ +    raise AttributeError( +AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'? diff --git a/docs/images/train-help.svg b/docs/images/train-help.svg index 82c30122..a71b8915 100644 --- a/docs/images/train-help.svg +++ b/docs/images/train-help.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - + - - $ 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.                  │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo train --help +Traceback (most recent call last): +  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/casanovo", line 5, in <module> +    from casanovo.casanovo import main +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/casanovo/casanovo.py", line 32, in <module> +    import depthcharge +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/__init__.py", line 3, in <module> +    from . import components +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/__init__.py", line 2, in <module> +    from .transformers import SpectrumEncoder, PeptideDecoder +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/components/transformers.py", line 8, in <module> +    from .. import utils +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/depthcharge/utils.py", line 5, in <module> +    from tensorboard.backend.event_processing.event_accumulator import ( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_accumulator.py", line 24, in <module> +    from tensorboard.backend.event_processing import event_file_loader +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/backend/event_processing/event_file_loader.py", line 21, in <module> +    from tensorboard import dataclass_compat +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/dataclass_compat.py", line 33, in <module> +    from tensorboard.plugins.hparams import metadata as hparams_metadata +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/plugins/hparams/metadata.py", line 32, in <module> +    NULL_TENSOR = tensor_util.make_tensor_proto( +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/util/tensor_util.py", line 405, in make_tensor_proto +    numpy_dtype = dtypes.as_dtype(nparray.dtype) +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py", line 677, in as_dtype +    if type_value.type == np.string_ or type_value.type == np.unicode_: +  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/numpy/__init__.py", line 397, in __getattr__ +    raise AttributeError( +AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'?