Add Python 3.10 support #36

br3ndonland · 2021-07-05T19:14:14Z

Description

This PR will add Python 3.10 support to inboard.

Changes

GitHub Actions

Add Python 3.10 to GitHub Actions workflows
Update to stable Python 3.10 when it is released
Update Python version syntax to enclose version numbers in quotes
- Python versions must now be quoted in YAML. 3.10 (without quotes) is interpreted as a float and becomes 3.1, so "3.10" must be used instead.
- Support 3.10 actions/setup-python#249 (comment)
- https://dev.to/hugovk/the-python-3-1-problem-85g

Poetry

Install Poetry successfully with Python 3.10: Poetry has introduced some breaking changes recently. To help buffer against these breaking changes, and to promote reproducible Poetry installations, Install Poetry with pipx #47 updated Poetry installations to use pipx instead of get-poetry.py or its replacement install-poetry.py. This change eliminated all of the issues seen with get-poetry.py and install-poetry.py.
Install Poetry dependencies successfully with Python 3.10: Installing Poetry with pipx (Install Poetry with pipx #47) eliminated the issues seen when installing dependencies with Python 3.10.
Ensure Python 3.10 classifier is included with Poetry package builds: Fixed as of Poetry 1.1.11 (Include Python 3.10 classifier when running poetry build on 3.10 python-poetry/poetry#4581).

Expand this details element for details on some of the problems seen with get-poetry.py and install-poetry.py on Python 3.10.

The previous get-poetry.py install script is not compatible with Python 3.10. Attempts to install Poetry with Python 3.10 and get-poetry.py may raise ModuleNotFoundError (python-poetry/poetry#3071, python-poetry/poetry#3345) and other errors:

 Traceback (most recent call last):
  File "/opt/poetry/bin/poetry", line 17, in <module>
    from poetry.console import main
  File "/opt/poetry/lib/poetry/console/__init__.py", line 1, in <module>
    from .application import Application
  File "/opt/poetry/lib/poetry/console/application.py", line 3, in <module>
    from cleo import Application as BaseApplication
ModuleNotFoundError: No module named 'cleo'

Poetry 1.1.11 claimed to resolve Python 3.10 issues, but it did not.

The new install-poetry.py script (added in python-poetry/poetry#3706) must therefore be used, but it was problematic when it was introduced.

install-poetry.py did not respect POETRY_VIRTUALENVS_CREATE

As of Poetry 1.1.7, there may be complications when using install-poetry.py without a virtualenv (POETRY_VIRTUALENVS_CREATE=false). When installing dependencies, the following error is frequently seen:

OSError

Could not find a suitable TLS CA certificate bundle, invalid path:
/opt/poetry/venv/lib/python3.9/site-packages/certifi/cacert.pem

at /opt/poetry/venv/lib/python3.9/site-packages/requests/adapters.py:227
in cert_verify

In some situations, Poetry uninstalls its own dependencies. The OSError above occurs because Poetry uninstalls requests and certifi, then complains that it can't find them. See:

Poetry may have also been incorrectly attempting to read from its virtualenv (instead of site-packages) if it was not respecting POETRY_VIRTUALENVS_CREATE. Downstream steps also did not appear to respect POETRY_VIRTUALENVS_CREATE, so the application did not run. See:

Poetry did not install packages correctly with install-poetry.py, POETRY_VIRTUALENVS_CREATE, and Python 3.10

Poetry errored out with a JSONDecodeError when attempting to install packages with Python 3.10. See python-poetry/poetry#4210. This appeared to be resolved as of Poetry 1.2.0a2.

There were also errors with Poetry's own virtualenv when using install-poetry.py, POETRY_VIRTUALENVS_CREATE, and multiple versions of Python, including 3.8 and 3.9. Error tracebacks typically reported a traceback sequence of CalledProcessError -> EnvCommandError -> PoetryException for each package, and appeared to involve virtualenv and pip. These errors may have been related to Poetry's "new installer", which can be disabled with the command poetry config experimental.new-installer false or the environment variable POETRY_EXPERIMENTAL_NEW_INSTALLER=false.

Example traceback from a GitHub Actions run:

  CalledProcessError

  Command '['/opt/poetry/venv/bin/python', '/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip', 'install', '--disable-pip-version-check', '--prefix', '/opt/hostedtoolcache/Python/3.8.11/x64', '--no-deps', 'file:/home/runner/.cache/pypoetry/artifacts/94/aa/c7/f2115774653c0d0bf72ce93092eb73de70854164adf9f00749a952ba9c/websockets-9.1-cp38-cp38-manylinux2010_x86_64.whl']' returned non-zero exit status 1.

  at /opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/subprocess.py:516 in run
       512│             # We don't call process.wait() as .__exit__ does that for us.
       513│             raise
       514│         retcode = process.poll()
       515│         if check and retcode:
    →  516│             raise CalledProcessError(retcode, process.args,
       517│                                      output=stdout, stderr=stderr)
       518│     return CompletedProcess(process.args, retcode, stdout, stderr)
       519│
       520│

The following error occurred when trying to handle this error:


  EnvCommandError

  Command ['/opt/poetry/venv/bin/python', '/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip', 'install', '--disable-pip-version-check', '--prefix', '/opt/hostedtoolcache/Python/3.8.11/x64', '--no-deps', 'file:/home/runner/.cache/pypoetry/artifacts/94/aa/c7/f2115774653c0d0bf72ce93092eb73de70854164adf9f00749a952ba9c/websockets-9.1-cp38-cp38-manylinux2010_x86_64.whl'] errored with the following return code 1, and output:
  Traceback (most recent call last):
    File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/runpy.py", line 194, in _run_module_as_main
      return _run_code(code, main_globals, None,
    File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/runpy.py", line 87, in _run_code
      exec(code, run_globals)
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/__main__.py", line 24, in <module>
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/cli/main.py", line 71, in main
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/commands/__init__.py", line 96, in create_command
    File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/importlib/__init__.py", line 127, in import_module
      return _bootstrap._gcd_import(name[level:], package, level)
    File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/commands/install.py", line 15, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/cli/req_command.py", line 21, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/req/__init__.py", line 8, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/req/req_install.py", line 32, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_internal/pyproject.py", line 4, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_vendor/toml/__init__.py", line 6, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_vendor/toml/encoder.py", line 6, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
    File "<frozen zipimport>", line 259, in load_module
    File "/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl/pip/_vendor/toml/decoder.py", line 7, in <module>
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 971, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 914, in _find_spec
    File "<frozen importlib._bootstrap_external>", line 1407, in find_spec
    File "<frozen importlib._bootstrap_external>", line 1381, in _get_spec
    File "<frozen importlib._bootstrap_external>", line 1362, in _legacy_get_spec
    File "<frozen importlib._bootstrap>", line 414, in spec_from_loader
    File "<frozen importlib._bootstrap_external>", line 709, in spec_from_file_location
    File "<frozen zipimport>", line 191, in get_filename
    File "<frozen zipimport>", line 709, in _get_module_code
    File "<frozen zipimport>", line 536, in _get_data
  FileNotFoundError: [Errno 2] No such file or directory: '/opt/poetry/venv/lib/python3.8/site-packages/virtualenv/seed/wheels/embed/pip-21.0.1-py3-none-any.whl'


  at /opt/poetry/venv/lib/python3.8/site-packages/poetry/utils/env.py:1300 in _run
      1296│                 output = subprocess.check_output(
      1297│                     cmd, stderr=subprocess.STDOUT, env=env, **kwargs
      1298│                 )
      1299│         except CalledProcessError as e:
    → 1300│             raise EnvCommandError(e, input=input_)
      1301│
      1302│         return decode(output)
      1303│
      1304│     def execute(self, bin: str, *args: str, **kwargs: Any) -> Optional[int]:

The following error occurred when trying to handle this error:


  PoetryException

  Failed to install file:/home/runner/.cache/pypoetry/artifacts/94/aa/c7/f2115774653c0d0bf72ce93092eb73de70854164adf9f00749a952ba9c/websockets-9.1-cp38-cp38-manylinux2010_x86_64.whl

  at /opt/poetry/venv/lib/python3.8/site-packages/poetry/utils/pip.py:60 in pip_install
       56│                     *env.get_pip_command(),
       57│                     *args,
       58│                     env={**os.environ, "PYTHONPATH": str(env.purelib)},
       59│                 )
    →  60│         raise PoetryException(f"Failed to install {path.as_posix()}") from e
       61│
       62│
       63│ def pip_editable_install(directory: Path, environment: Env) -> Union[int, str]:
       64│     return pip_install(

May be somewhat related to:

install-poetry.py was not present in stable releases

Poetry 1.1 releases did not include install-poetry.py in their source tree. This could be a problem for projects that fetch install-poetry.py from a specific Git tag, as this project does (#44).

For example:

https://raw.githubusercontent.com/python-poetry/poetry/1.1.11/get-poetry.py returns the get-poetry.py install script
https://raw.githubusercontent.com/python-poetry/poetry/1.1.11/install-poetry.py returns 404

pydantic and typing

Ensure pydantic provides Python package wheels for Python 3.10: Python 3.10 support was added in pydantic 1.9.0.
Ensure pydantic models are compatible with Python 3.10 type annotations:
- The Python 3.10 union operator (the pipe, like str | None) will not be used on pydantic models. This project still supports Python 3.8 and 3.9. If running Python 3.9 or below, pydantic is not compatible with the union operator, even if annotations are imported with from __future__ import annotations.
- PEP 604: Allow writing union types as X | Y
- PEP 604 compatiblity to replace Optional[str] with str | None pydantic/pydantic#2597 (comment)
- feat: support generic types and | operator pydantic/pydantic#2609 (comment)
- Pydantic fails with Python 3.10 new UnionType pydantic/pydantic#3300 (comment)
Update type annotations for Python 3.10 (all except the union types on pydantic model fields)

#36 #44 PR #44 introduced version tests for Poetry. The GitHub Actions workflow builds.yml was matching the version number as a substring anywhere in the output of `poetry -V`, but the hooks.yml and tests.yml workflows were matching the version number at the end of the `poetry -V` output. This would have become an issue if the format of the output was changed, and sure enough, Poetry 1.2.0 changes the format to have parentheses around the version number. This commit will update the hooks.yml and tests.yml workflows to match the version number as a substring anywhere in the output of `poetry -V`.

1d8eee0 884d475 Poetry has a new install script, install-poetry.py, which alters the requirements for adding Poetry to `$PATH`. `$HOME/.local/bin` was already on `$PATH` for pipx, so it seemed like a good option. Commits 1d8eee0 and 884d475 updated `.zshrc` and `script/strap-after-setup` for install-poetry.py and `POETRY_HOME=$HOME/.local`. This made sense initially, because Poetry installs its binaries into `$POETRY_HOME/bin`, and because Poetry doesn't have a `$POETRY_BIN_DIR` configuration variable like pipx does (`$PIPX_BIN_DIR`). Unfortunately, `POETRY_HOME=$HOME/.local` ended up being problematic, because Poetry takes over `$POETRY_HOME`, and doesn't consider other applications installed there. For example, if the get-poetry.py or install-poetry.py scripts were used to install Poetry, they can also be used to uninstall Poetry. Uninstalling with `python install-poetry.py --uninstall` or `python get-poetry.py --uninstall` deletes the entire `$POETRY_HOME` directory, which means it deletes `$HOME/.local`, causing problems for other applications that use `$HOME/.local` (python-poetry/poetry#4625). There have been many other issues with the Poetry custom install scripts get-poetry.py and install-poetry.py (br3ndonland/inboard#36), so other installation methods are be welcome. Poetry is now available through Homebrew, but Homebrew installation is not supported by the Poetry maintainers. Homebrew installation also requires its own custom install script, which creates its own issues. python-poetry/poetry#941 python-poetry/poetry#1765 Homebrew/homebrew-core#48883 Homebrew/homebrew-core#86776 pipx (https://pypa.github.io/pipx/) can also be used to install Poetry. The pipx installation method is suggested in the Poetry docs and GitHub, and pipx is already in use in this repo. python-poetry/poetry#677 python-poetry/poetry#3360 This commit will remove `export POETRY_HOME=$HOME/.local` from `.zshrc`, and will install Poetry with pipx.

br3ndonland/fastenv#7 br3ndonland/inboard#36 Python versions must now be quoted in YAML. `3.10` (without quotes) is interpreted as a float and becomes `3.1`. `"3.10"` will be used instead.

codecov · 2021-10-26T03:16:16Z

Codecov Report

Merging #36 (a1f7241) into develop (97e35b7) will not change coverage.
The diff coverage is n/a.

❗ Current head a1f7241 differs from pull request most recent head f3fd95d. Consider uploading reports for the commit f3fd95d to get more accurate results

@@            Coverage Diff            @@
##           develop       python-poetry/poetry#36   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           10        10           
  Lines          281       264   -17     
=========================================
- Hits           281       264   -17

Flag	Coverage Δ
unit	`100.00% <ø> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
inboard/start.py	`100.00% <0.00%> (ø)`
inboard/logging_conf.py	`100.00% <0.00%> (ø)`
inboard/app/main_fastapi.py	`100.00% <0.00%> (ø)`
inboard/app/utilities_fastapi.py	`100.00% <0.00%> (ø)`

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Beta releases of Python 3.10 were installed with `"3.10.0-beta - 3.10"`. Python 3.10 is now stable, so beta versions are no longer needed. Python versions in YAML must now be quoted. `3.10` is interpreted as a float and becomes `3.1`, so `"3.10"` must be used instead.

The Python version can be customized by using a Docker build argument, such as `--build-arg PYTHON_VERSION=3.9`.

This commit will update type annotation syntax for Python 3.10. The project currently also supports Python 3.8 and 3.9, so the annotations are imported with `from __future__ import annotations`. The Python 3.10 union operator (the pipe, like `str | None`) will not be used on pydantic models. If running Python 3.9 or below, pydantic is not compatible with the union operator, even if annotations are imported with `from __future__ import annotations`. https://peps.python.org/pep-0604/ https://docs.python.org/3/whatsnew/3.10.html pydantic/pydantic#2597 (comment) pydantic/pydantic#2609 (comment) pydantic/pydantic#3300 (comment)

sourcery-ai · 2022-04-02T21:15:36Z

Sourcery Code Quality Report

Merging this PR leaves code quality unchanged.

Quality metrics	Before	After	Change
Complexity	2.07 ⭐	2.07 ⭐	0.00
Method Length	54.31 ⭐	54.27 ⭐	-0.04 👍
Working memory	6.97 🙂	6.97 🙂	0.00
Quality	77.47% ⭐	77.47% ⭐	0.00%

Other metrics	Before	After	Change
Lines	685	693	8

Changed files	Quality Before	Quality After	Quality Change
inboard/gunicorn_conf.py	76.44% ⭐	76.44% ⭐	0.00%
inboard/logging_conf.py	75.15% ⭐	75.15% ⭐	0.00%
inboard/start.py	73.65% 🙂	73.65% 🙂	0.00%
inboard/app/main_base.py	81.09% ⭐	81.09% ⭐	0.00%
inboard/app/utilities_starlette.py	69.55% 🙂	69.55% 🙂	0.00%
tests/test_gunicorn_conf.py	75.65% ⭐	75.65% ⭐	0.00%
tests/app/test_main.py	82.97% ⭐	82.97% ⭐	0.00%

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
tests/test_gunicorn_conf.py	TestGunicornSettings.test_gunicorn_config_with_custom_options	0 ⭐	162 😞	9 🙂	63.76% 🙂	Try splitting into smaller methods
inboard/start.py	run_pre_start_script	5 ⭐	86 🙂	10 😞	66.01% 🙂	Extract out complex expressions
inboard/start.py	_update_uvicorn_config_options	4 ⭐	67 🙂	10 😞	69.84% 🙂	Extract out complex expressions
inboard/start.py	set_uvicorn_options	1 ⭐	70 🙂	11 😞	70.46% 🙂	Extract out complex expressions
inboard/logging_conf.py	LogFilter.set_filters	2 ⭐	32 ⭐	10 😞	77.42% ⭐	Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

⭐ excellent
🙂 good
😞 poor
⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

br3ndonland · 2022-04-02T21:41:45Z

inboard is finally ready to support Python 3.10. Thanks to everyone for their patience over the past nine months.

#36 Type annotations were updated for Python 3.10 in #36. This `from typing import Set` was added in #49 prior to merging #36, and was overlooked when merging the PR. This commit will replace `typing.Set` with a parametrized generic. https://peps.python.org/pep-0585/ https://docs.python.org/3/whatsnew/3.9.html

After creating numerous problems for maintainers by cramming breaking changes into patch releases, Poetry finally released a minor version, 1.2, which should probably have been a major version. In order to upgrade, each project will need to update its pyproject.toml (to support groups), update any references to the install script (which has been moved twice), and make several other associated changes. This commit will set an upper bound on the `pipx install poetry` command to avoid upgrading to Poetry 1.2. br3ndonland/inboard#36 br3ndonland/inboard#44 br3ndonland/inboard#47 https://python-poetry.org/blog/announcing-poetry-1.2.0/

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Pin and test Poetry version #44

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This was referenced Oct 23, 2021

Pin and test Poetry version br3ndonland/fastenv#6

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Add Python 3.10 support br3ndonland/fastenv#7

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Install Poetry with pipx #47

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br3ndonland force-pushed the python-3.10 branch from 0957b2f to 363a2ff Compare November 6, 2021 17:29

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br3ndonland force-pushed the python-3.10 branch from 363a2ff to a1f7241 Compare December 31, 2021 21:27

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iamleeg mentioned this pull request Mar 1, 2022

Log batch job failures to Slack globaldothealth/list#2561

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br3ndonland added 3 commits April 2, 2022 16:55

Use Python 3.10 as default version in Dockerfile

760c071

The Python version can be customized by using a Docker build argument, such as `--build-arg PYTHON_VERSION=3.9`.

br3ndonland force-pushed the python-3.10 branch from a1f7241 to f3fd95d Compare April 2, 2022 21:15

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br3ndonland marked this pull request as ready for review April 2, 2022 21:26

br3ndonland merged commit 7b2fdf6 into develop Apr 2, 2022

br3ndonland deleted the python-3.10 branch April 2, 2022 21:42

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Add Python 3.10 support #36

Add Python 3.10 support #36

br3ndonland commented Jul 5, 2021 •

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br3ndonland commented Apr 2, 2022

Add Python 3.10 support #36

Add Python 3.10 support #36

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br3ndonland commented Jul 5, 2021 •

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