Add support for Python 3.13

[weiji14]

Description of proposed changes

Python 3.13 has been released on 7 Oct 2024, changelog is at https://docs.python.org/3.13/whatsnew/3.13.html

Previous PR for Python 3.12 at #2711

Fixes #

Reminders

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• Add tests for new features or tests that would have caught the bug that you're fixing.
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• Write detailed docstrings for all functions/methods.
• If wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
• If adding new functionality, add an example to docstrings or tutorials.
• Use underscores (not hyphens) in names of Python files and directories.

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[weiji14]

Still waiting on a few packages upstream to add Python 3.13 support:

• netcdf4 - New post release to create Python 3.13 wheels Unidata/netcdf4-python#1370
• pyarrow - according to https://conda-forge.org/status/migration/?name=python313, this is waiting on sparse which is waiting on numba, see Rebuild for python 3.13 conda-forge/numba-feedstock#148 Edit: There is a Python 3.13 build of pyarrow that doesn't require sparse anymore, see Rebuild for python 3.13 conda-forge/pyarrow-feedstock#139

[seisman]

Also need to revert the changes in 92d5945.

[weiji14]

Since we're including PyArrow in the Python 3.11 CI build as of #3605, let's just remove PyArrow here until it supports Python 3.13 to not hold up #3606?

[seisman]

We can't remove PyArrow in the Python 3.13 job, because we need both pandas<2.2+pyarrow (in Python 3.11) and pandas>=2.2+pyarrow (in Python 3.12 or 3.13) to test the behavior changes in pands 2.2.

[weiji14]

I was thinking we could do (after #3606) Python 3.11+pandas=2.1+pyarrow; Python 3.12+pandas=2.2+pyarrow, but anyways, this won't work yet because mamba install is still complaining about some incompatible depedencies (looks like something on dvc):

The following packages are incompatible
├─ dvc >=3.56.0  is installable and it requires
|    ...
│  └─ scmrepo >=3.3.8,<4 , which requires
│     └─ asyncssh >=2.13.1,<3 , which requires
│        └─ python-gssapi >=1.2.0  with the potential options
│           ├─ python-gssapi [1.6.10|1.6.11|1.6.12|1.6.13|1.6.9] would require
│           │  └─ python_abi 3.6 *_pypy36_pp73, which can be installed (as previously explained);
│           ├─ python-gssapi [1.6.10|1.6.11|...|1.7.0] would require
│           │  └─ python >=3.6,<3.7.0a0 , which can be installed;
│           ├─ python-gssapi [1.6.10|1.6.11|...|1.8.1] would require
│           │  └─ python >=3.7,<3.8.0a0 , which can be installed;
│           ├─ python-gssapi [1.6.10|1.6.11|...|1.8.3] would require
│           │  └─ python >=3.8,<3.9.0a0 , which can be installed;
│           ├─ python-gssapi [1.6.10|1.6.11|...|1.9.0] would require
│           │  └─ python >=3.9,<3.10.0a0 , which can be installed;
│           ├─ python-gssapi [1.6.12|1.6.13|...|1.7.3] would require
│           │  └─ python_abi 3.7 *_pypy37_pp73, which can be installed (as previously explained);
│           ├─ python-gssapi [1.7.2|1.7.3|...|1.9.0] would require
│           │  └─ python >=3.10,<3.11.0a0 , which can be installed;
│           ├─ python-gssapi [1.7.3|1.8.0|1.8.1|1.8.2] would require
│           │  └─ python_abi 3.8 *_pypy38_pp73, which can be installed (as previously explained);
│           ├─ python-gssapi [1.7.3|1.8.0|1.8.1|1.8.2|1.8.3] would require
│           │  ├─ pypy3.9 >=7.3.13 , which can be installed (as previously explained);
│           │  └─ python_abi 3.9 *_pypy39_pp73, which can be installed (as previously explained);
│           ├─ python-gssapi [1.8.2|1.8.3|1.9.0] would require
│           │  └─ python >=3.11,<3.12.0a0 , which can be installed;
│           ├─ python-gssapi [1.8.2|1.8.3|1.9.0] would require
│           │  └─ python_abi 3.12.* *_cp312, which can be installed (as previously explained);
│           ├─ python-gssapi 1.8.2 would require
│           │  └─ pypy3.8 >=7.3.11 , which can be installed (as previously explained);
│           └─ python-gssapi 1.8.2 would require
│              └─ pypy3.9 >=7.3.11 , which can be installed (as previously explained);
└─ python 3.13**  is not installable because there are no viable options
   ├─ python 3.13.0 conflicts with any installable versions previously reported;
   └─ python [3.13.0rc1|3.13.0rc2|3.13.0rc3] would require
      └─ _python_rc, which does not exist (perhaps a missing channel).

Wait for conda-forge/python-gssapi-feedstock#32.

[weiji14]

Also need to wait for conda-forge/kombu-feedstock#78:

error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ dvc =* * is installable with the potential options
    ...
    │  └─ dvc [3.49.0|3.50.0|...|3.58.0] would require
    │     └─ celery =* * with the potential options
    ...
    │        ├─ celery [5.3.0|5.3.1|5.3.4] would require
    │        │  └─ kombu [>=5.3.0,<6.0 *|>=5.3.1,<6.0 *|>=5.3.2,<6.0 *] with the potential options
    │        │     ├─ kombu [5.3.0|5.3.1|...|5.4.1] would require
    │        │     │  └─ python >=3.10,<3.11.0a0 * with the potential options
    │        │     │     ├─ python [3.10.7|3.10.8|3.11.0|3.9.14|3.9.15], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.0|3.10.1|...|3.9.9], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.4|3.9.12], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.5|3.9.13], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.0|3.10.1|...|3.10.9], which can be installed;
    │        │     │     └─ python [3.10.6|3.11.0], which can be installed (as previously explained);
    │        │     ├─ kombu [5.3.0|5.3.1|...|5.4.1] would require
    │        │     │  └─ python >=3.11,<3.12.0a0 * with the potential options
    │        │     │     ├─ python [3.10.7|3.10.8|3.11.0|3.9.14|3.9.15], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.6|3.11.0], which can be installed (as previously explained);
    │        │     │     └─ python [3.11.0|3.11.1|...|3.11.9], which can be installed;
    │        │     ├─ kombu [5.3.0|5.3.1|5.3.2] would require
    │        │     │  └─ python_abi ==3.8 *_pypy38_pp73, which can be installed (as previously explained);
    │        │     ├─ kombu [4.6.10|4.6.11|...|5.4.0] would require
    │        │     │  └─ python >=3.8,<3.9.0a0 *, which can be installed;
    │        │     ├─ kombu [5.3.0|5.3.1|...|5.4.0] would require
    │        │     │  └─ python_abi ==3.9 *_pypy39_pp73, which can be installed (as previously explained);
    │        │     ├─ kombu [5.3.0|5.3.1|...|5.4.1] would require
    │        │     │  └─ python >=3.9,<3.10.0a0 * with the potential options
    │        │     │     ├─ python [3.10.7|3.10.8|3.11.0|3.9.14|3.9.15], which can be installed (as previously explained);
    │        │     │     ├─ python [3.9.10|3.9.12|...|3.9.9], which can be installed;
    │        │     │     ├─ python [3.9.0|3.9.1], which can be installed (as previously explained);
    │        │     │     ├─ python 3.9.1, which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.0|3.10.1|...|3.9.9], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.4|3.9.12], which can be installed (as previously explained);
    │        │     │     ├─ python [3.10.5|3.9.13], which can be installed (as previously explained);
    │        │     │     ├─ python 3.9.2, which can be installed (as previously explained);
    │        │     │     └─ python [3.9.4|3.9.5|3.9.6|3.9.7], which can be installed (as previously explained);
    │        │     └─ kombu [5.3.2|5.3.3|...|5.4.1] would require
    │        │        └─ python_abi =3.12 *_cp312, which can be installed (as previously explained);

[seisman]

conda-forge/python-gssapi-feedstock#32 has been superseded by conda-forge/python-gssapi-feedstock#33.

So we still need to wait for conda-forge/kombu-feedstock#78. kombu's Python 3.13 support was added in celery/kombu#2052, which first appeared in kombu v5.5.0rc2.

kombu v5.5.0rc2 was released two months ago, and there is still no kombu v5.5.0 out. Not sure how long we have to wait.

[weiji14]

Ok, for reference, we applied a workaround for dvc in #3695, and pyarrow now has a Python 3.13 build since conda-forge/pyarrow-feedstock#139.

[weiji14]

Note that this has changed from python=3.12 to python>=3.10 to folllow SPEC 0 (same with NumPy, pandas and xarray lines below).

[seisman]

This PR should be good to merge after all CI passes, except one minor comment above.

[weiji14]

Thanks @seisman! Just tracking our time to support new Python versions, still hoping we can keep this to under 2 months:

• Python 3.13 (Add support for Python 3.13 #3490) - 2024Oct07 to 2024Dec19 (2months 12days)
• Python 3.12 (Add support for Python 3.12 #2711) - 2023Oct02 to 2023Nov08 (1month 6days)
• Python 3.11 (Add support for Python 3.11 #2172) - 2022Oct24 to 2022Dec22 (1month 28days)
• Python 3.12 (Support Python 3.10 #1591) - 2021Oct07 to 2021Oct28 (21days)