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WIP: Test lowest versions of all required and optional dependencies #3639

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WIP: Test lowest versions of all required and optional dependencies #3639

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3a5d6da
Use uv package manager to test lowest versions in ci_tests_legacy.yaml
weiji14 Nov 21, 2024
f303964
Temporarily enable ci_tests_legacy.yaml
weiji14 Nov 21, 2024
3f6909d
Pin to netCDF>=1.7
weiji14 Nov 21, 2024
788fc46
Pin contextily>=1, IPython>=8, pyarrow>=14
weiji14 Nov 21, 2024
4139f4e
Pin geopandas>=0.14, rioxarray>=0.14
weiji14 Nov 21, 2024
1263075
Add --color=yes to test_no_images addopts
weiji14 Nov 21, 2024
d1fa38d
Pin packaging>=22.0
weiji14 Nov 21, 2024
1c69406
Test with pytest-mpl and pytest-doctestplus
weiji14 Nov 21, 2024
3b7b777
Install into uv venv
weiji14 Nov 21, 2024
6120bbe
Pin contextily>=1.2
weiji14 Nov 21, 2024
3299229
Pin pyarrow>=16
weiji14 Nov 21, 2024
0584459
Merge branch 'main' into uv/resolution-lowest
weiji14 Nov 22, 2024
7d542a9
Update wording on ci_tests_legacy.yaml header comment
weiji14 Nov 22, 2024
4733bda
Pin pyarrow>=13 and use pytest.mark.skipif on string_view type test
weiji14 Nov 22, 2024
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39 changes: 15 additions & 24 deletions .github/workflows/ci_tests_legacy.yaml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# Test PyGMT with GMT legacy versions on Linux/macOS/Windows
# Test PyGMT with GMT legacy versions and old Python dependencies on Linux/macOS/Windows
#
# This workflow runs regular PyGMT tests with GMT legacy versions. Due to the minor
# baseline image changes between GMT versions, the workflow only runs the tests but
# doesn't do image comparisons.
# This workflow runs regular PyGMT tests with GMT legacy versions and old versions of
# all optional Python dependencies. Due to the minor baseline image changes between GMT
# versions, the workflow only runs the tests but doesn't do image comparisons.
#
# It is scheduled to run every Tuesday on the main branch.
#
Expand All @@ -12,7 +12,7 @@ on:
# push:
# branches: [ main ]
# Uncomment the 'pull_request' line below to trigger the workflow in PR
# pull_request:
pull_request:
# types: [ready_for_review]
# paths:
# - 'pygmt/**'
Expand Down Expand Up @@ -62,23 +62,6 @@ jobs:
python=3.10
gmt=${{ matrix.gmt_version }}
ghostscript<10
numpy
pandas
xarray
netCDF4
packaging
contextily
geopandas
ipython
pyarrow
rioxarray
sphinx-gallery
make
pip
python-build
pytest
pytest-doctestplus
pytest-mpl

# Download cached remote files (artifacts) from GitHub
- name: Download remote data from GitHub
Expand All @@ -95,10 +78,18 @@ jobs:
env:
GH_TOKEN: ${{ github.token }}

# Install uv package manager
- name: Install uv
uses: astral-sh/setup-uv@v3

# Install the package that we want to test
- name: Install the package
run: make install
run: |
uv run --with pip==23 --resolution lowest-direct --all-extras --dev make install
uv pip list
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Using --resolution lowest-direct for now, because --resolution lowest grabs many other transitive dependencies that may be hard to install (e.g. missing wheels for newer Python versions, so requires compilation from source). We could switch to --resolution lowest once the Python ecosystem does lower bound pins a bit more thoroughly (which may take years).


# Run the tests but skip images
- name: Run tests
run: make test_no_images PYTEST_EXTRA="-r P"
run: uv run --with pytest==8 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
env:
GMT_LIBRARY_PATH: $CONDA_PREFIX/lib
12 changes: 6 additions & 6 deletions pyproject.toml
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Expand Up @@ -33,18 +33,18 @@ dependencies = [
"numpy>=1.24",
"pandas>=2.0",
"xarray>=2023.04",
"netCDF4",
"netCDF4>=1.7",
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We discussed making NetCDF an optional dependency before in #429. Maybe we could revisit that discussion?

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@seisman seisman Nov 22, 2024 •
edited
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That's a good point. NetCDF4 was needed by xarray when reading and writing netCDF files. As mentioned in #239 (comment), previously, our load_xxx functions (e.g., load_earth_relief) called xarray.load_dataarray to load local netCDF grids into an xarray.DataArray object, making netCDF a highly "required" dependency.

After we refactor our load_xxx function in #3120, we no longer call xarray.load_dataarray, so netCDF should be no longer highly needed by PyGMT.

I've opened PR #3643 to see how the PyGMT relies on the netCDF package.

Edit: There are only 14 failures in the Python 3.11 + Ubuntu CI job after removing netCDF entirely (see https://github.com/GenericMappingTools/pygmt/actions/runs/11968416461/job/33367210857?pr=3643) and most of them are caused by load_static_earth_relief.

"packaging",
]
dynamic = ["version"]

[project.optional-dependencies]
all = [
"contextily",
"geopandas",
"IPython", # 'ipython' is not the correct module name.
"pyarrow",
"rioxarray",
"contextily>=1",
"geopandas>=0.14",
"IPython>=8", # 'ipython' is not the correct module name.
"pyarrow>=14",
"rioxarray>=0.14",
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@weiji14 weiji14 Nov 21, 2024 •
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Setting lower bounds here, otherwise uv will try to install super old versions that may not work anymore, some which actually go back to Python 2! For e.g., it tried to install rioxarray=0.0.1 at https://github.com/GenericMappingTools/pygmt/actions/runs/11945100244/job/33297179010#step:7:45. Happy to reconsider some of these version pins if needed.

Edit see comments at #3639 (comment) and #3639 (comment) below.

]

[project.urls]
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