Drop Python 3.9 support and add compatibility for Python 3.13 #721

tomvothecoder · 2025-01-17T21:01:31Z

Description

This pull request focuses on upgrading the minimum supported Python version to 3.10 across the project, adding support for Python 3.13, and modernizing type annotations for improved readability and compliance with newer Python standards.

Closes [DevOps]: Drop Python 3.9 support #710

Python version upgrades:

Updated the Python version in .github/workflows/build_workflow.yml to use 3.12 for setup and added 3.13 to the test matrix. [1] [2]
Increased the minimum required Python version to 3.10 in conda-env/ci.yml, conda-env/dev.yml, and pyproject.toml. [1] [2] [3]
Removed Python 3.9 from the classifiers and added Python 3.13 in pyproject.toml.
Added setuptools explicitly to dev.yml and ci.yml Conda environment files. Required because Python 3.13 requires setuptools to be explicitly installed—it is no longer implicitly available in all environments as in previous versions.

Type annotation modernization:

Replaced Dict, List, Optional, Tuple, and Union with modern PEP 604 and PEP 585 style annotations (e.g., dict, list, |) across multiple files, including xcdat/axis.py, xcdat/bounds.py, and docs/conf.py. [1] [2] [3]

Testing improvements:

Added strict=False to zip calls in tests/test_regrid.py to ensure compatibility with the updated Python versions.

Logic Improvements:

Updated logic in _swap_lon_axis() (axis.py) to check whether coordinates have index with 360 based on GitHub Copilot suggestion
- np.where returns a tuple of arrays; therefore, using 'len(index_with_360)' always yields the number of dimensions rather than the count of matching elements. Consider updating the check to 'if index_with_360[0].size > 0:' to accurately detect if any indices were found.

Checklist

My code follows the style guidelines of this project
I have performed a self-review of my own code
My changes generate no new warnings
Any dependent changes have been merged and published in downstream modules

If applicable:

I have added tests that prove my fix is effective or that my feature works
New and existing unit tests pass with my changes (locally and CI/CD build)
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
I have noted that this is a breaking change for a major release (fix or feature that would cause existing functionality to not work as expected)

codecov · 2025-05-12T17:56:03Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (421e667) to head (6f2d00c).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #721   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           16        16           
  Lines         1711      1702    -9     
=========================================
- Hits          1711      1702    -9

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Copilot

Pull Request Overview

This PR updates the project to drop support for Python 3.9 and add support for newer versions including Python 3.13. It also modernizes type annotations throughout the codebase by replacing legacy typing constructs (e.g. Dict and Tuple) with native PEP 585 generics (e.g. dict and tuple), and updates related tests, documentation, and CI configuration files.

Reviewed Changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 1 comment.

File	Description
pyproject.toml, conda-env/*.yml, workflows	Updated Python version requirements and CI matrix to remove 3.9 and support 3.13
xcdat/*.py	Converted type annotations to modern native types and removed obsolete future imports
tests/test_regrid.py	Adjusted test code (e.g. added strict=False in zip) to accommodate new Python behavior

Comments suppressed due to low confidence (1)

xcdat/regridder/base.py:60

[nitpick] There is a spelling mistake in the docstring: 'xr.Daatset' should be corrected to 'xr.Dataset'.

Returns
-------
    xr.Daatset

.github/workflows/build_workflow.yml

- Update `python >=3.10` constraint in conda-env yml files

- No longer needed with python >=3.10

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull Request Overview

This pull request upgrades the minimum supported Python version to 3.10 (with added testing for Python 3.13) and modernizes type annotations to the newer PEP 585/604 style across the codebase. The changes span configuration files, workflow definitions, and core modules to ensure compatibility with newer Python versions and cleaner type usage.

Reviewed Changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated no comments.

File	Description
xcdat/*	Updated type annotations from typing.Union[...] and related types to the modern union syntax (e.g., “str
pyproject.toml, conda-env/*, .github/workflows/build_workflow.yml	Updated the supported Python versions and test matrix to reflect the new minimum (3.10) and include Python 3.13.

Comments suppressed due to low confidence (1)

xcdat/axis.py:395

np.where returns a tuple of arrays; therefore, using 'len(index_with_360)' always yields the number of dimensions rather than the count of matching elements. Consider updating the check to 'if index_with_360[0].size > 0:' to accurately detect if any indices were found.

if len(index_with_360) > 0:

- Based on GitHub Copilot suggestion

tomvothecoder · 2025-05-12T19:05:47Z

xcdat/axis.py

+            if index_with_360[0].size > 0:
                _if_multidim_dask_array_then_load(new_coords)

                new_coords[index_with_360] = 360


Updated this logic based on Copilot review comment:

np.where returns a tuple of arrays; therefore, using 'len(index_with_360)' always yields the number of dimensions rather than the count of matching elements. Consider updating the check to 'if index_with_360[0].size > 0:' to accurately detect if any indices were found.

Copilot

Pull Request Overview

This PR upgrades the minimum Python version, modernizes type annotations throughout the codebase, and adds compatibility for Python 3.13. Key changes include:

Updating CI/CD, Conda environment, and pyproject configuration to require Python >=3.10 and include Python 3.13.
Converting legacy typing constructs (e.g. Dict, List, Union) to native union and container literals (e.g. dict, list, using the | operator).
Minor logic improvements such as correcting prime meridian index checks in the longitude axis swap function.

Reviewed Changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
xcdat/utils.py & xcdat/tutorial.py	Modernized type annotations and removed unnecessary future imports
xcdat/axis.py	Updated type hints and adjusted the prime meridian check condition
xcdat/regridder/*	Adopted new union syntax for API type annotations and improved parameter consistency
conda-env/*, .github/workflows/build_workflow.yml	Updated Python version requirements and added explicit setuptools dependency
pyproject.toml, docs/conf.py	Modified version constraints and updated type annotations in documentation
Remaining Files	Consistent modernization of type annotations and minor formatting changes

Comments suppressed due to low confidence (1)

.github/workflows/build_workflow.yml:58

The workflow matrix now includes Python 3.13. Please confirm that all dependencies and tests pass under Python 3.13, ensuring full compatibility.

python-version: ["3.10", "3.11", "3.12", "3.13"]

Copilot · 2025-05-12T19:13:54Z

xcdat/axis.py

@@ -425,7 +423,7 @@ def _swap_lon_axis(coords: xr.DataArray, to: Tuple[float, float]) -> xr.DataArra
            # Example with 360 coords: [60, 150, 0] -> [60, 150, 360]
            index_with_360 = np.where(coords == 360)

-            if len(index_with_360) > 0:
+            if index_with_360[0].size > 0:


Changing the condition to 'if index_with_360[0].size > 0:' correctly checks for matching indices in a multidimensional np.where result. Please verify that this new condition is intended and consistently applied across similar cases.

Copilot · 2025-05-12T19:13:54Z

xcdat/regridder/xgcm.py

@@ -18,10 +19,10 @@ def __init__(
        input_grid: xr.Dataset,
        output_grid: xr.Dataset,
        method: XGCMVerticalMethods = "linear",
-        target_data: Optional[Union[str, xr.DataArray]] = None,
-        grid_positions: Optional[Dict[str, str]] = None,
+        target_data: str | xr.DataArray | None = None,


[nitpick] The updated union syntax (using 'str | xr.DataArray | None') improves clarity. Ensure that any downstream modules that depend on this annotation correctly support the new union operator syntax.

tomvothecoder · 2025-05-12T19:23:22Z

FYI @xCDAT/core-developers just merged this PR. The most major code change was replacing all unnecessary from typing import ... with Python 3.10+ syntax (e.g., replace Dict[..] with dict[...]). This change makes the code more future-proof and cleaner.

Adds sparse as a dependency Fixes formatting Updates docstrings [PR]: Enable `skipna` for spatial and temporal mean operations (#655) Co-authored-by: Tom Vo <tomvothecoder@gmail.com> Removes pdb import Fix incorrect dimension used for temporal weights generation (#749) Adds mask creation to create_grid and fixes aligning grid dimension for xesmf Lifting src mask generation Adds create_nan_mask argument to regrid2 Adds docstring to create_mask Add weight threshold option for spatial averaging (#672) - Add parameter `min_weight` to `SpatialAccessor.average()` Replace support section with endorsements (#757) Drop Python 3.9 support and add compatibility for Python 3.13 (#721) Fixes typings Fixes spelling error Fixes black formatting issue Adds scipy dependency Add `.zenodo.json` and `CITATION.cff` to cite core authors (#759) Refactors create_nan_mask Adds tests and fixes mask dimension ordering Fixes variable name Adds create_nan_mask support to xesmf Chunk weights before broadcasting/masking in _group_average (#767) Use the median of the delta instead of min for time freq inference (#768) Co-authored-by: Tom Vo <tomvothecoder@gmail.com> Adds missing test

github-actions bot added type: devops Testing, CI/CD, systems configuration type: docs Updates to documentation labels Jan 17, 2025

tomvothecoder self-assigned this Jan 23, 2025

tomvothecoder added this to the FY25Q2 (01/01/25 - 03/31/25) milestone Jan 23, 2025

tomvothecoder modified the milestones: FY25Q2 (01/01/25 - 03/31/25), FY25Q3 (04/01/25 - 06/30/25) Apr 14, 2025

tomvothecoder moved this from In Progress to Next Up in xCDAT Development Apr 14, 2025

tomvothecoder changed the title ~~Drop Python 3.9 support (after v0.8.0)~~ Drop Python 3.9 support (pending E3SM Unified) Apr 16, 2025

tomvothecoder force-pushed the devops/drop-python-3.9 branch from 33c4bee to 5b9627c Compare May 12, 2025 17:53

tomvothecoder changed the title ~~Drop Python 3.9 support (pending E3SM Unified)~~ Drop Python 3.9 support May 12, 2025

tomvothecoder changed the title ~~Drop Python 3.9 support~~ Drop Python 3.9 support and add support for Python 3.13 May 12, 2025

tomvothecoder requested a review from Copilot May 12, 2025 18:44

Copilot AI reviewed May 12, 2025

View reviewed changes

.github/workflows/build_workflow.yml Outdated Show resolved Hide resolved

tomvothecoder changed the title ~~Drop Python 3.9 support and add support for Python 3.13~~ Update min support to Python 3.10 and add support for Python 3.13. May 12, 2025

tomvothecoder changed the title ~~Update min support to Python 3.10 and add support for Python 3.13.~~ Update min support to Python 3.10 and add support for Python 3.13 May 12, 2025

tomvothecoder changed the title ~~Update min support to Python 3.10 and add support for Python 3.13~~ Update min Python to 3.10 and add support for Python 3.13 May 12, 2025

tomvothecoder and others added 10 commits May 12, 2025 11:48

Drop Python 3.9 support

6a27095

- Update `python >=3.10` constraint in conda-env yml files

Remove Python 3.9 from build workflow

2d916a6

Revert notebook change

ddcee20

Fix ruff issue with strict=False in zip()

5f082d7

Update python version used in build workflow

09fc920

Add support for Python 3.13

1e20685

Remove from __future__ import annotations

65ea8e9

- No longer needed with python >=3.10

Update all use of typing library to python 3.10+ syntax

2600d17

Update .github/workflows/build_workflow.yml

694f451

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Fix type annotation spelling mistake in _drop_axis()

f031653

tomvothecoder force-pushed the devops/drop-python-3.9 branch from f45e84f to f031653 Compare May 12, 2025 18:48

tomvothecoder requested a review from Copilot May 12, 2025 18:48

Copilot AI reviewed May 12, 2025

View reviewed changes

tomvothecoder changed the title ~~Update min Python to 3.10 and add support for Python 3.13~~ Modernize Python Support: Remove 3.9, Add 3.13 Compatibility May 12, 2025

tomvothecoder changed the title ~~Modernize Python Support: Remove 3.9, Add 3.13 Compatibility~~ Drop Python 3.9 support, add compatibility for Python 3.13 May 12, 2025

tomvothecoder added 2 commits May 12, 2025 12:02

Remove numpy constraint in build workflow

fd14f6b

Update logic to check if index_with_360 is > 0

645ff36

- Based on GitHub Copilot suggestion

tomvothecoder commented May 12, 2025

View reviewed changes

Add setuptools as dependencies in conda envs

6f2d00c

tomvothecoder changed the title ~~Drop Python 3.9 support, add compatibility for Python 3.13~~ Drop Python 3.9 support and add compatibility for Python 3.13 May 12, 2025

tomvothecoder requested a review from Copilot May 12, 2025 19:12

tomvothecoder moved this from Next Up to In Progress in xCDAT Development May 12, 2025

Copilot AI reviewed May 12, 2025

View reviewed changes

tomvothecoder merged commit 14f876b into main May 12, 2025
10 checks passed

github-project-automation bot moved this from In Progress to Done in xCDAT Development May 12, 2025

tomvothecoder deleted the devops/drop-python-3.9 branch May 12, 2025 19:18

tomvothecoder mentioned this pull request May 12, 2025

Adds ability to infer target data for vertical regridding #756

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Drop Python 3.9 support and add compatibility for Python 3.13 #721

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Description

Python version upgrades:

Type annotation modernization:

Testing improvements:

Logic Improvements:

Checklist

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