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Merged
seisman merged 12 commits into from
Nov 7, 2023
Merged

Add support for Python 3.12 #2711

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fc5c445
Add support for Python 3.12
weiji14 Oct 2, 2023
6bded07
Add conda-forge/label/python_rc channel
weiji14 Oct 2, 2023
caa65d3
Merge branch 'main' into python-3.12
weiji14 Oct 11, 2023
534bc30
Merge branch 'main' into python-3.12
weiji14 Oct 15, 2023
654e8be
Revert "Add conda-forge/label/python_rc channel"
weiji14 Oct 15, 2023
5c0d900
Merge branch 'main' into python-3.12
weiji14 Oct 24, 2023
a22dfd5
Merge branch 'main' into python-3.12
weiji14 Oct 25, 2023
d1b01c3
Fix DeprecationWarning with use of datetime.utcnow() on Python 3.12
weiji14 Oct 25, 2023
a048c86
Pretend to be on macOS instead of Windows
weiji14 Oct 26, 2023
90a3a49
Use datetime.timezone.utc instead of Python 3.11+ only datetime.UTC
weiji14 Oct 26, 2023
486c37a
Merge branch 'main' into python-3.12
weiji14 Nov 7, 2023
99fdbf8
Pretend to be on macOS if running on Linux, and vice versa
weiji14 Nov 7, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/cache_data.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ jobs:
- conda-forge
- nodefaults
create-args: >-
python=3.11
python=3.12
gmt=6.4.0
numpy
pandas
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4 changes: 2 additions & 2 deletions .github/workflows/ci_docs.yml
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Expand Up @@ -44,7 +44,7 @@ jobs:
# Is it a draft Pull Request (true or false)?
isDraft:
- ${{ github.event.pull_request.draft }}
# Only run one job (Ubuntu + Python 3.11) for draft PRs
# Only run one job (Ubuntu + Python 3.12) for draft PRs
exclude:
- os: macos-latest
isDraft: true
Expand Down Expand Up @@ -75,7 +75,7 @@ jobs:
cache-downloads: true
cache-environment: true
create-args: >-
python=3.11
python=3.12
gmt=6.4.0
numpy
pandas
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2 changes: 1 addition & 1 deletion .github/workflows/ci_doctests.yaml
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Expand Up @@ -48,7 +48,7 @@ jobs:
- conda-forge
- nodefaults
create-args: >-
python=3.11
python=3.12
gmt=6.4.0
numpy
pandas
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10 changes: 5 additions & 5 deletions .github/workflows/ci_tests.yaml
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Expand Up @@ -52,24 +52,24 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9', '3.11']
python-version: ['3.9', '3.12']
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 3.9/3.11) for draft PRs
# Only run two jobs (Ubuntu + Python 3.9/3.12) for draft PRs
exclude:
- os: macos-latest
isDraft: true
- os: windows-latest
isDraft: true
# Pair Python 3.9 with NumPy 1.22 and Python 3.11 with NumPy 1.26
# Only install optional packages on Python 3.11/NumPy 1.26
# Pair Python 3.9 with NumPy 1.22 and Python 3.12 with NumPy 1.26
# Only install optional packages on Python 3.12/NumPy 1.26
include:
- python-version: '3.9'
numpy-version: '1.22'
optional-packages: ''
- python-version: '3.11'
- python-version: '3.12'
numpy-version: '1.26'
optional-packages: ' contextily geopandas ipython rioxarray sphinx-gallery'

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2 changes: 1 addition & 1 deletion .github/workflows/ci_tests_dev.yaml
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Expand Up @@ -100,7 +100,7 @@ jobs:
cache-downloads: true
cache-environment: true
create-args: >-
python=3.11
python=3.12

@weiji14 weiji14 Oct 26, 2023

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GMT Dev Tests failing because pygit2 doesn't have Python 3.12 wheels, and building from source fails at https://github.com/GenericMappingTools/pygmt/actions/runs/6648200102/job/18064869372#step:7:570:

  Building wheel for pygit2 (pyproject.toml): started
  Building wheel for pygit2 (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Building wheel for pygit2 (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [66 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-312
      creating build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/index.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/ffi.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/submodule.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/credentials.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/_run.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/utils.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/config.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/errors.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/_build.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/refspec.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/repository.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/blame.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/packbuilder.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/remote.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/callbacks.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/settings.py -> build/lib.linux-x86_64-cpython-312/pygit2
      copying pygit2/__init__.py -> build/lib.linux-x86_64-cpython-312/pygit2
      creating build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/transport.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/errors.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/blame.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/net.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/merge.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/diff.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/graph.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/describe.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/commit.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/revert.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/config.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/common.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/oid.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/attr.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/repository.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/remote.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/types.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/pack.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/clone.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/stash.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/index.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-cpython-312/pygit2/decl
      copying pygit2/_pygit2.pyi -> build/lib.linux-x86_64-cpython-312/pygit2
      running build_ext
      generating cffi module 'build/temp.linux-x86_64-cpython-312/pygit2._libgit2.c'
      creating build/temp.linux-x86_64-cpython-312
      building 'pygit2._pygit2' extension
      creating build/temp.linux-x86_64-cpython-312/src
      gcc -pthread -B /home/runner/micromamba/envs/pygmt/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/runner/micromamba/envs/pygmt/include -fPIC -O2 -isystem /home/runner/micromamba/envs/pygmt/include -fPIC -I/usr/local/include -I/home/runner/micromamba/envs/pygmt/include/python3.12 -c src/blob.c -o build/temp.linux-x86_64-cpython-312/src/blob.o
      In file included from src/blob.c:30:
      src/diff.h:33:10: fatal error: git2.h: No such file or directory
         33 | #include <git2.h>
            |          ^~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pygit2
  Building wheel for frozenlist (pyproject.toml): started
  Building wheel for frozenlist (pyproject.toml): finished with status 'done'
  Created wheel for frozenlist: filename=frozenlist-1.4.0-cp312-cp312-linux_x86_64.whl size=53997 sha256=39bb8d4c56a724d4cd9ed87de83b7de69e78a79763d0d9f5ae5e95f8497b5b83
  Stored in directory: /home/runner/.cache/pip/wheels/f1/9c/94/9386cb0ea511a93226456388d41d35f1c24ba15a62ffd7b1ef
  Building wheel for multidict (pyproject.toml): started
  Building wheel for multidict (pyproject.toml): finished with status 'done'
  Created wheel for multidict: filename=multidict-6.0.4-cp312-cp312-linux_x86_64.whl size=34743 sha256=b99632e55f0994365432703c422b45c7b80332be4690bfa943602cb30e69d013
  Stored in directory: /home/runner/.cache/pip/wheels/f6/d8/ff/3c14a64b8f2ab1aa94ba2888f5a988be6ab446ec5c8d1a82da
  Building wheel for yarl (pyproject.toml): started
  Building wheel for yarl (pyproject.toml): finished with status 'done'
  Created wheel for yarl: filename=yarl-1.9.2-cp312-cp312-linux_x86_64.whl size=70034 sha256=d286d55089432e38d0441fa83a86e4a994b9537a62cec71e97187e4d2d41a9ec
  Stored in directory: /home/runner/.cache/pip/wheels/84/e3/6a/7d0fa1abee8e4aa39922b5bd54689b4b5e4269b2821f482a32
Successfully built antlr4-python3-runtime dulwich frozenlist multidict yarl
Failed to build pygit2
ERROR: Could not build wheels for pygit2, which is required to install pyproject.toml-based projects

Might need to wait for libgit2/pygit2#1240.

@weiji14 weiji14 Oct 31, 2023

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Rather than waiting for pygit2 to release Python 3.12 wheels, we could also keep the GMT Dev Tests on Python 3.11 for now?

Suggested change
python=3.12
python=3.11

@seisman seisman Oct 31, 2023

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OK to me.

@weiji14 weiji14 Nov 7, 2023

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Looks like pygit2 has Python 3.12 wheels now - https://pypi.org/project/pygit2/1.13.2/#files

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/setup-python@v4.7.1
with:
python-version: '3.11'
python-version: '3.12'

# 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 @@ -46,7 +46,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v4.7.1
with:
python-version: '3.11'
python-version: '3.12'

- 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/setup-python@v4.7.1
with:
python-version: '3.11'
python-version: '3.12'

- name: Install packages
run: |
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4 changes: 2 additions & 2 deletions doc/install.rst
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Expand Up @@ -132,14 +132,14 @@ want):

::

mamba create --name pygmt python=3.11 numpy pandas xarray netcdf4 packaging gmt
mamba create --name pygmt python=3.12 numpy pandas xarray netcdf4 packaging gmt

.. tab-item:: conda
:sync: conda

::

conda create --name pygmt python=3.11 numpy pandas xarray netcdf4 packaging gmt
conda create --name pygmt python=3.12 numpy pandas xarray netcdf4 packaging gmt

Activate the environment by running the following (**do not forget this step!**):

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2 changes: 1 addition & 1 deletion pygmt/tests/test_clib_loading.py
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Expand Up @@ -72,7 +72,7 @@ def test_load_libgmt_fails(monkeypatch):
be found.
"""
with monkeypatch.context() as mpatch:
mpatch.setattr(sys, "platform", "win32") # pretend to be on Windows
mpatch.setattr(sys, "platform", "darwin") # pretend to be on macOS

@weiji14 weiji14 Oct 26, 2023

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Ok, this workaround I applied in a048c86 doesn't actually work on macOS...

@weiji14 weiji14 Nov 7, 2023 •
edited
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Your workaround a048c86 fails on macOS CI, because on macOS, PyGMT will find the gmt.dylib successfully in the system default path (I think conda's lib path is in the default search path)

Two possible workarounds:

1. Monkeypatch `sys.platform` so it always returns the wrong platform, e.g., return `linux` on macOS/Windows and `darwin` on Linux

2. Instead of monkeypatching `sys.platform`, we can monkeypath `clib_names` to return invalid library names.

Ok, trying out Option 1 in 99fdbf8. Edit: Yep, it worked!

mpatch.setattr(
subprocess, "check_output", lambda cmd, encoding: "libfakegmt.so"
)
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4 changes: 2 additions & 2 deletions pygmt/tests/test_clib_put_vector.py
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@@ -1,8 +1,8 @@
"""
Test the functions that put vector data into GMT.
"""
import datetime
import itertools
from datetime import datetime

import numpy as np
import numpy.testing as npt
Expand Down Expand Up @@ -122,7 +122,7 @@ def test_put_vector_string_dtype():
"2021-02-03T00:00:00",
"2021-02-03T04:00:00",
"2021-02-03T04:05:06",
f"{datetime.utcnow().strftime('%Y-%m-%d')}T04:50:06",
f"{datetime.datetime.now(tz=datetime.UTC).strftime('%Y-%m-%d')}T04:50:06",
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],
]

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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -28,6 +28,7 @@ classifiers = [
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: BSD License",
]
dependencies = [
Expand Down