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Add support for Python 3.13 #3490

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merged 16 commits into from
Dec 19, 2024
Merged

Add support for Python 3.13 #3490

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f7462f6
Add support for Python 3.13
weiji14 Oct 7, 2024
92d5945
Add conda-forge/label/python_rc channel
weiji14 Oct 7, 2024
bfcec3a
Merge branch 'main' into python-3.13
seisman Oct 9, 2024
f545e17
Merge branch 'main' into python-3.13
weiji14 Oct 21, 2024
40545a0
Merge branch 'main' into python-3.13
weiji14 Oct 22, 2024
47eaad8
Merge branch 'main' into python-3.13
weiji14 Nov 11, 2024
642a538
Revert "Add conda-forge/label/python_rc channel"
weiji14 Nov 11, 2024
6e74524
Don't install optional pyarrow package in Python 3.13 CI build
weiji14 Nov 11, 2024
a06f906
Temporarily invalidate cache
weiji14 Nov 11, 2024
ada48f3
Revert "Temporarily invalidate cache"
weiji14 Nov 11, 2024
90d9b42
Reapply "Add conda-forge/label/python_rc channel"
weiji14 Nov 11, 2024
f9fa6d7
Merge branch 'main' into python-3.13
weiji14 Dec 2, 2024
742980e
Revert "Reapply "Add conda-forge/label/python_rc channel""
weiji14 Dec 2, 2024
df35168
Merge branch 'main' into python-3.13
seisman Dec 16, 2024
93273cd
Merge branch 'main' into python-3.13
seisman Dec 19, 2024
631444f
Update .github/workflows/ci_docs.yml
weiji14 Dec 19, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/benchmarks.yml
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Expand Up @@ -58,7 +58,7 @@ jobs:
cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
create-args: >-
gmt=6.5.0
python=3.12
python=3.13
numpy
pandas
xarray
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2 changes: 1 addition & 1 deletion .github/workflows/cache_data.yaml
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Expand Up @@ -51,7 +51,7 @@ jobs:
- conda-forge
- nodefaults
create-args: >-
python=3.12
python=3.13
gmt=6.5.0
numpy
pandas
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4 changes: 2 additions & 2 deletions .github/workflows/ci_docs.yml
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Expand Up @@ -55,7 +55,7 @@ jobs:
# Is it a draft Pull Request (true or false)?
isDraft:
- ${{ github.event.pull_request.draft }}
# Only run one job (Ubuntu + Python 3.12) for draft PRs
# Only run one job (Ubuntu + Python 3.13) for draft PRs
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exclude:
- os: macos-latest
isDraft: true
Expand Down Expand Up @@ -92,7 +92,7 @@ jobs:
# environment cache is persistent for one week.
cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
create-args: >-
python=3.12
python=3.13
gmt=6.5.0
ghostscript=10.04.0
numpy
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2 changes: 1 addition & 1 deletion .github/workflows/ci_doctests.yaml
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Expand Up @@ -50,7 +50,7 @@ jobs:
- conda-forge
- nodefaults
create-args: >-
python=3.12
python=3.13
gmt=6.5.0
numpy
pandas
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14 changes: 7 additions & 7 deletions .github/workflows/ci_tests.yaml
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Expand Up @@ -54,36 +54,36 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.10', '3.12']
python-version: ['3.10', '3.13']
os: [ubuntu-latest, macos-latest, windows-latest]
# Is it a draft Pull Request (true or false)?
isDraft:
- ${{ github.event.pull_request.draft }}
# Only run two jobs (Ubuntu + Python 3.10/3.12) for draft PRs
# Only run two jobs (Ubuntu + Python 3.10/3.13) for draft PRs
exclude:
- os: macos-latest
isDraft: true
- os: windows-latest
isDraft: true
# Pair Python 3.10 with the minimum supported versions of NumPy, pandas, Xarray
# and Python 3.12 with the latest versions of NumPy, pandas, Xarray
# Only install optional packages on Python 3.12
# and Python 3.13 with the latest versions of NumPy, pandas, Xarray
# Only install optional packages on Python 3.13
include:
- python-version: '3.10'
numpy-version: '1.24'
pandas-version: '=2.0'
xarray-version: '=2023.04'
optional-packages: ''
- python-version: '3.12'
- python-version: '3.13'
numpy-version: '2.1'
pandas-version: ''
xarray-version: ''
optional-packages: ' contextily geopandas ipython pyarrow rioxarray sphinx-gallery'
optional-packages: ' contextily geopandas ipython rioxarray sphinx-gallery'
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@weiji14 weiji14 Nov 11, 2024 •
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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?

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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.

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@weiji14 weiji14 Nov 11, 2024 •
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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.

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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);

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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.

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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.

# The job below is for testing GeoPandas v0.x on Ubuntu.
# The python-version here can't be the versions in the matrix.python-version
# defined above. Otherwise, other jobs will be overridden by this one.
- os: 'ubuntu-latest'
python-version: '3.11' # Can't be 3.10 or 3.12.
python-version: '3.11' # Can't be 3.10 or 3.13.
numpy-version: '1.24'
pandas-version: '=2.1'
xarray-version: ''
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2 changes: 1 addition & 1 deletion .github/workflows/ci_tests_dev.yaml
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Expand Up @@ -69,7 +69,7 @@ jobs:
# environment cache is persistent for one week.
cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
create-args: >-
python=3.12
python=3.13
cmake
make
ninja
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2 changes: 1 addition & 1 deletion .github/workflows/format-command.yml
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Expand Up @@ -27,7 +27,7 @@ jobs:
# Setup Python environment
- uses: actions/[email protected]
with:
python-version: '3.12'
python-version: '3.13'

# Install formatting tools
- name: Install formatting tools
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2 changes: 1 addition & 1 deletion .github/workflows/publish-to-pypi.yml
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Expand Up @@ -53,7 +53,7 @@ jobs:
- name: Set up Python
uses: actions/[email protected]
with:
python-version: '3.12'
python-version: '3.13'

- name: Install dependencies
run: python -m pip install build
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2 changes: 1 addition & 1 deletion .github/workflows/style_checks.yaml
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Expand Up @@ -30,7 +30,7 @@ jobs:
- name: Set up Python
uses: actions/[email protected]
with:
python-version: '3.12'
python-version: '3.13'

- name: Install packages
run: |
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2 changes: 1 addition & 1 deletion .github/workflows/type_checks.yml
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Expand Up @@ -39,7 +39,7 @@ jobs:
- name: Set up Python
uses: actions/[email protected]
with:
python-version: '3.12'
python-version: '3.13'

- name: Install packages
run: |
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2 changes: 1 addition & 1 deletion ci/requirements/docs.yml
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Expand Up @@ -4,7 +4,7 @@ channels:
- nodefaults
dependencies:
# Required dependencies
- python=3.12
- python=3.13
- gmt=6.5.0
- ghostscript=10.04.0
- numpy
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4 changes: 2 additions & 2 deletions doc/install.md
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Expand Up @@ -128,14 +128,14 @@ installed (we'll call it `pygmt` but feel free to change it to whatever you want
::: {tab-item} mamba
:sync: mamba
```
mamba create --name pygmt python=3.12 numpy pandas xarray netcdf4 packaging gmt
mamba create --name pygmt python=3.13 numpy pandas xarray netcdf4 packaging gmt
```
:::

::: {tab-item} conda
:sync: conda
```
conda create --name pygmt python=3.12 numpy pandas xarray netcdf4 packaging gmt
conda create --name pygmt python=3.13 numpy pandas xarray netcdf4 packaging gmt
```
:::
::::
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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -3,7 +3,7 @@ channels:
- conda-forge
- nodefaults
dependencies:
- python=3.12
- python>=3.10
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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).

# Required dependencies
- gmt=6.5.0
- ghostscript=10.04.0
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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -27,6 +27,7 @@ classifiers = [
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"License :: OSI Approved :: BSD License",
]
dependencies = [
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