DTM-13285 Fixed error handling

Description
Error messages from authentication provide useful messages
Related Issue
https://jira.corp.adobe.com/browse/DTM-13285
How Has This Been Tested?
Unit test coverage has been updated
Types of changes

[ X] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

[ ] I have signed the Adobe Open Source CLA.
[ X] My code follows the code style of this project.
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[ ] I have read the CONTRIBUTING document.
[ X] I have added tests to cover my changes.
[X ] All new and existing tests passed.

Published in v2.1.2.


Change assert statement when not for invariant in mypy check, include recommendation for using -O with CPython in production

High Level Overview of Change

Closes #270
Context of Change
See #270.
When running this script:
closing (with ^C, a KeyboardInterrupt closes the socket as quickly as the implementation using websockets when running python -O ... but not as quick when running python ....
This may result in sending another KeyboardInterrupt which isn't what you want to do.

Type of Change

[X] Refactor (non-breaking change that only restructures code)

Before / After
Before

An assert statement that is used for raising when an import doesn't have a requirement
no runtime recommendations

After

An assert in a __init__ was also dropped for ImportError as it is an error as a result of an import :D
runtime recommendation to include -O in production or in development when running locally with CPython, assert statements are dropped with -O

Test Plan

use the test suite as-is for the ImportError change
feedback on relevant documentation changes.

first glance looks like dropping some # mypy statements caused the type checks to fail; looking into it

Yes @yyolk - those assert statements annotated with mypy are for the type checker. They can't be removed. Changing the assert into an import error should be ok I suppose.

@ledhed2222 gotcha. I suppose the reason is to pass mypy type checks for when there's an invariants only and -O should be used in production, I'm ok with that.
There's quite a bit a slowdown when running without -O, at least in the slow-down I experience which could be unrelated, but only happens without the changes in https://github.com/yyolk/xrpl-py/tree/309a915e57ea6d675f8711ffbfe93409786d1562 or for complete clarity when you don't run without -O to illustrate, the assert statements are completely dropped:
$ cat script.py
assert False

$ python -O script.py
$ echo $?
0
$ python script.py
Traceback (most recent call last):
  File "script.py", line 1, in <module>
    assert False
AssertionError
$ echo $?
1

I'll go ahead and revert the drop assert statements that I now understand are for mypy, (which were commented as such before. I didn't know about
 via https://mypy.readthedocs.io/en/stable/cheat_sheet.html?highlight=assert#built-in-types
 via https://mypy.readthedocs.io/en/stable/common_issues.html#unexpected-errors-about-none-and-or-optional-types
I think to close the issue this references, I could also include an update the appropriate docs to recommend running with -O at runtime when using this library, at least using CPython.

Love the idea of adding documentation on this! Would you please add something? That would make this PR more complete IMO.
Overall, xrpl-py isn't optimized for performance. It's trying to optimize usability and access to features. In my opinion, the developer that needs to optimize xrpl performance is sophisticated enough and has reason enough to run their own xrpl node.

A quick update on my dive into the referenced issue, it's been a while; I apologize for the delay.
I'm sometimes seeing this to work when passing the -O flag, it also seems to happen sometimes even with that flag, which I'd rather dive into more thoroughly with a debugger before recommending just the -O to fix the issue I'm experiencing.
I don't think I'm going to include the option for -O since I'm not always seeing it work and would like to dive in further before seeing why it sometimes does work.
I appreciate you mentioning library's goal to optimize usability and access to features; I definitely agree with this and also take this into account with recommendations.
To your other point; I see what you're saying re: running a node for development. Would be happy to add this to the doc!
This would certainly alleviate my concern of terminating the slow thread taking care of the cleanup of the websocket (which could be to public node). It could be to my development node. I wouldn't so much killing the thread to close the websocket properly if I'm being impatient. I may also suggest running that development mode on the testnet.

Closing this :cold_sweat:    sorry for the cruft! :bow:


Color gradient

This is just a feature suggestion for Metro4, it is not due to any issues.
Maybe you could include a color gradient facilitator. I'm not sure how to do it, maybe something like this:

Thank you Olson for your work, Metro4 is really easy, stylish and complete.

new in 4.4.1, added component gradient-box
Example: https://codepen.io/olton/pen/GRqZXvv

Wow! That was fast.
Thank you very much!!!

Hi! In 4.4.2 gradient-box attributes will change, but all options will be described in docs after release.


UI Limit of 30 keys appear in a collection ( table and new form )

I've noticed collections have a max of 30 keys (29 + _id) in the UI

This is true for the table, on the collection view.
It is also true for  a "New" document.
Seems a bit arbitrary which keys are present and which are truncated.

As a UI suggestion:
New document form: it could be nice to have the keys be a dropdown combo. This would avoid having to list all the possible keys.
Also it's missing the ability to create a new/arbitrary, key.

What? This is a command-line utility and gem. There's no UI.


Intending to upgrade a WSL1 instance to WSL2 by running wsl.exe from inside a WSL instance crashes the terminal.

Please fill out the below information:

Your Windows build number:  (Type ver at a Windows Command Prompt)
Version 1903 (OS Build 18932.1000)

What you're doing and what's happening:  (Copy&paste the full set of specific command-line steps necessary to reproduce the behavior, and their output. Include screen shots if that helps demonstrate the problem.)
Running wsl --set-version Ubuntu-18.04 2 from inside the Ubuntu WSL instance

What's wrong / what should be happening instead:
When running this same command from a PowerShell instance, the first error that was given was that the Virual Machine Platform feature needed to be installed. This should have been what was displayed in the Ubuntu terminal, rather than crashing the instance first. After that, either the terminal should be shut down, upgraded and then restarted, or the user should be instructed to run this command outside of a WSL instance.

Strace of the failing command, if applicable:  (If some_command is failing, then run strace -o some_command.strace -f some_command some_args, and link the contents of some_command.strace in a gist here).

For WSL launch issues, please collect detailed logs.

See our contributing instructions for assistance.

You can't do that. To upgrade a WSL1 distribution, it must not have any running session.

Please run the command outside of the WSL distribution that you're trying to upgrade. This is something that is created by design. Thanks for filing the issue!


Add Github Actions

Nit: Unfortunately the Github Actions aren't enabled for any repository of the organization

BTW in the future please use commit messages that adhere to the established style

BTW in the future please use commit messages that adhere to the established style

Ok, sorry. Feel free to force push the repository adding this commit message:
ci: add github actions

Too busy to do it, just for the future

Too busy to do it, just for the future

If you give me the push access to all the repos, I could do it, don't worry.


Error in installing by Developer installer

Hi
Thanks for your work in alphapeptdeep!
I followed the instruction in Developer installer section to install alphapeptdeep in my linux server. Because the size of the /home folder is very small, so I intend to install in the /tools folder. Following is my cmd:
(peptdeep) user@linux:/tools/alphapeptdeep/project/alphapeptdeep$ sudo pip install -e ".[development]" -t /tools/anaconda3/envs/peptdeep/bin
then I got an error like this:

Please help  how to fix this problem. Thanks very much!
Best
Xiaoxiang

Do not use sudo, as sudo may have its own python env

Thanks for your help ! very appreciated.
I removed the virtual environment created by conda and redo by
conda create --name peptdeep python=3.9 -y
conda activate peptdeep
(peptdeep) user@linux:/tools/alphapeptdeep/project/alphapeptdeep$  pip install -e ".[development]"
after that, I got an error like this:

following is the entire info:
Obtaining file:///tools/alphapeptdeep/project/alphapeptdeep
Preparing metadata (setup.py) ... done
Collecting click
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
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Using cached types_python_dateutil-<IP_ADDRESS>40106-py3-none-any.whl (9.7 kB)
Installing collected packages: wget, webencodings, wcwidth, snowballstemmer, pytz, python-decouple, pyteomics, pure-eval, ptyprocess, nh3, mpmath, json5, fastjsonschema, altgraph, zipp, xxhash, widgetsnbextension, websocket-client, webcolors, watchdog, validators, urllib3, uri-template, tzlocal, tzdata, typing-extensions, types-python-dateutil, traitlets, tqdm, tornado, toolz, tomli, toml, tinycss2, threadpoolctl, tenacity, sympy, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, smmap, six, send2trash, safetensors, rpds-py, rfc3986-validator, rfc3986, regex, pyzstd, pyzmq, pyyaml, python-json-logger, pyparsing, Pygments, pycparser, pyahocorasick, psutil, protobuf, prompt-toolkit, prometheus-client, platformdirs, pkginfo, pipdeptree, pillow, pexpect, parso, pandocfilters, packaging, overrides, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, nest-asyncio, more-itertools, mistune, mdurl, MarkupSafe, lxml, locket, llvmlite, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, joblib, jeepney, imagesize, idna, greenlet, fsspec, fqdn, fonttools, filelock, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, cycler, contextlib2, contextfilter, cloudpickle, click, charset-normalizer, certifi, cachetools, bump2version, blinker, babel, attrs, alabaster, triton, terminado, sqlalchemy, scipy, rfc3339-validator, requests, referencing, readme-renderer, qtpy, python-dateutil, pyarrow, partd, nvidia-cusparse-cu12, nvidia-cudnn-cu12, numba, matplotlib-inline, markdown-it-py, jupyter-core, jinja2, jedi, jaraco.classes, importlib-resources, importlib-metadata, h5py, gitdb, fastcore, contourpy, comm, cffi, bumpversion, bleach, biopython, beautifulsoup4, async-lru, astunparse, asttokens, anyio, stack-data, sphinx, scikit-learn, rich, requests-toolbelt, pyinstaller-hooks-contrib, pydeck, pandas, nvidia-cusolver-cu12, mdit-py-plugins, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, huggingface-hub, gitpython, ghapi, dask, cryptography, arrow, argon2-cffi-bindings, torch, tokenizers, sphinx-basic-ng, SecretStorage, seaborn, pyinstaller, myst_parser, jsonschema, isoduration, ipython, autodocsumm, argon2-cffi, alphatims, alphabase, transformers, nbformat, keyring, ipykernel, furo, execnb, altair, alpharaw, twine, streamlit, qtconsole, nbclient, jupyter-events, jupyter-console, ipywidgets, streamlit-aggrid, nbdev, nbconvert, peptdeep, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter
Running setup.py develop for peptdeep
error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
    running develop
    /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` and ``easy_install``.
            Instead, use pypa/build, pypa/installer or other
            standards-based tools.

            See https://github.com/pypa/setuptools/issues/917 for details.
            ********************************************************************************

    !!
      easy_install.initialize_options(self)
    /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` directly.
            Instead, use pypa/build, pypa/installer or other
            standards-based tools.

            See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
            ********************************************************************************

    !!
      self.initialize_options()
    running egg_info
    error: Cannot update time stamp of directory 'peptdeep.egg-info'
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
running develop
/tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!
        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  easy_install.initialize_options(self)
/tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running egg_info
error: Cannot update time stamp of directory 'peptdeep.egg-info'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
(peptdeep) xhuang@R740:/tools/alphapeptdeep/project/alphapeptdeep$ packet_write_wait: Connection to <IP_ADDRESS> port 30181: Broken pipe
(base) hxx@ubuntu:~$

Thanks for your help ! very appreciated.
I removed the virtual environment created by conda and redo by
conda create --name peptdeep python=3.9 -y
conda activate peptdeep
(peptdeep) user@linux:/tools/alphapeptdeep/project/alphapeptdeep$  pip install -e ".[development]"
after that, I got an error like this:

following is the entire info:
Obtaining file:///tools/alphapeptdeep/project/alphapeptdeep
Preparing metadata (setup.py) ... done
Collecting click
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting pandas
Using cached pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting numpy
Using cached numpy-1.26.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting torch
Using cached torch-2.1.2-cp39-cp39-manylinux1_x86_64.whl.metadata (25 kB)
Collecting tqdm
Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)
Collecting numba
Using cached numba-0.58.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
Collecting psutil
Using cached psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting biopython
Using cached biopython-1.83-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting transformers
Using cached transformers-4.36.2-py3-none-any.whl.metadata (126 kB)
Collecting scikit-learn
Using cached scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting streamlit
Using cached streamlit-1.30.0-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting streamlit-aggrid
Using cached streamlit_aggrid-0.3.4.post3-py3-none-any.whl (3.4 MB)
Collecting lxml
Using cached lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB)
Collecting pyteomics
Using cached pyteomics-4.6.3-py2.py3-none-any.whl.metadata (6.5 kB)
Collecting alphabase
Using cached alphabase-1.2.0-py3-none-any.whl.metadata (13 kB)
Collecting alpharaw
Using cached alpharaw-0.4.2-py3-none-any.whl.metadata (13 kB)
Collecting jupyter
Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Collecting twine
Using cached twine-4.0.2-py3-none-any.whl (36 kB)
Collecting bumpversion
Using cached bumpversion-0.6.0-py2.py3-none-any.whl (8.4 kB)
Collecting pipdeptree
Using cached pipdeptree-2.13.2-py3-none-any.whl.metadata (15 kB)
Collecting ipykernel
Using cached ipykernel-6.29.0-py3-none-any.whl.metadata (6.0 kB)
Collecting wget
Using cached wget-3.2-py3-none-any.whl
Collecting nbdev
Using cached nbdev-2.3.13-py3-none-any.whl.metadata (10 kB)
Collecting pyinstaller
Using cached pyinstaller-6.3.0-py3-none-manylinux2014_x86_64.whl.metadata (8.3 kB)
Collecting seaborn
Using cached seaborn-0.13.1-py3-none-any.whl.metadata (5.4 kB)
Collecting matplotlib
Using cached matplotlib-3.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting autodocsumm
Using cached autodocsumm-0.2.12-py3-none-any.whl.metadata (5.5 kB)
Collecting myst_parser
Using cached myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB)
Collecting sphinx
Using cached sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB)
Collecting nbsphinx
Using cached nbsphinx-0.9.3-py3-none-any.whl.metadata (2.1 kB)
Collecting jinja2
Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
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Installing collected packages: wget, webencodings, wcwidth, snowballstemmer, pytz, python-decouple, pyteomics, pure-eval, ptyprocess, nh3, mpmath, json5, fastjsonschema, altgraph, zipp, xxhash, widgetsnbextension, websocket-client, webcolors, watchdog, validators, urllib3, uri-template, tzlocal, tzdata, typing-extensions, types-python-dateutil, traitlets, tqdm, tornado, toolz, tomli, toml, tinycss2, threadpoolctl, tenacity, sympy, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, smmap, six, send2trash, safetensors, rpds-py, rfc3986-validator, rfc3986, regex, pyzstd, pyzmq, pyyaml, python-json-logger, pyparsing, Pygments, pycparser, pyahocorasick, psutil, protobuf, prompt-toolkit, prometheus-client, platformdirs, pkginfo, pipdeptree, pillow, pexpect, parso, pandocfilters, packaging, overrides, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, nest-asyncio, more-itertools, mistune, mdurl, MarkupSafe, lxml, locket, llvmlite, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, joblib, jeepney, imagesize, idna, greenlet, fsspec, fqdn, fonttools, filelock, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, cycler, contextlib2, contextfilter, cloudpickle, click, charset-normalizer, certifi, cachetools, bump2version, blinker, babel, attrs, alabaster, triton, terminado, sqlalchemy, scipy, rfc3339-validator, requests, referencing, readme-renderer, qtpy, python-dateutil, pyarrow, partd, nvidia-cusparse-cu12, nvidia-cudnn-cu12, numba, matplotlib-inline, markdown-it-py, jupyter-core, jinja2, jedi, jaraco.classes, importlib-resources, importlib-metadata, h5py, gitdb, fastcore, contourpy, comm, cffi, bumpversion, bleach, biopython, beautifulsoup4, async-lru, astunparse, asttokens, anyio, stack-data, sphinx, scikit-learn, rich, requests-toolbelt, pyinstaller-hooks-contrib, pydeck, pandas, nvidia-cusolver-cu12, mdit-py-plugins, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, huggingface-hub, gitpython, ghapi, dask, cryptography, arrow, argon2-cffi-bindings, torch, tokenizers, sphinx-basic-ng, SecretStorage, seaborn, pyinstaller, myst_parser, jsonschema, isoduration, ipython, autodocsumm, argon2-cffi, alphatims, alphabase, transformers, nbformat, keyring, ipykernel, furo, execnb, altair, alpharaw, twine, streamlit, qtconsole, nbclient, jupyter-events, jupyter-console, ipywidgets, streamlit-aggrid, nbdev, nbconvert, peptdeep, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter
Running setup.py develop for peptdeep
error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
    running develop
    /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` and ``easy_install``.
            Instead, use pypa/build, pypa/installer or other
            standards-based tools.

            See https://github.com/pypa/setuptools/issues/917 for details.
            ********************************************************************************

    !!
      easy_install.initialize_options(self)
    /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` directly.
            Instead, use pypa/build, pypa/installer or other
            standards-based tools.

            See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
            ********************************************************************************

    !!
      self.initialize_options()
    running egg_info
    error: Cannot update time stamp of directory 'peptdeep.egg-info'
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
running develop
/tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!
        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  easy_install.initialize_options(self)
/tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running egg_info
error: Cannot update time stamp of directory 'peptdeep.egg-info'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

Oh, I tried the installation described in the second installation section 'pip'. And finally success.
Thanks very much!

Does pip install -e . work? "development" just add some additional packages for developers, you can install them after pip install -e .

I followed you advice and tried the cmd 'pip install -e .'
Unfortunately, it reported the same error as above.

Then how did you install it?

I firstly installed anaconda3 with python3.9. And then installed peptdeep in this existing python environment by 'pip install peptdeep'.

I see, just pip install -e . does not work, hmmm..