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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
e24a6c2
Merge branch 'main' into uv/resolution-lowest
weiji14 Dec 2, 2024
52c78fa
Remove unused import _get_module_version
weiji14 Dec 2, 2024
d64087e
Merge branch 'main' into uv/resolution-lowest
weiji14 Jan 2, 2025
af01f75
Bump astral-sh/setup-uv from 3 to 5.1.0
weiji14 Jan 2, 2025
3cb017c
Merge branch 'main' into uv/resolution-lowest
weiji14 Mar 23, 2025
fe0caf2
Merge branch 'main' into uv/resolution-lowest
weiji14 Apr 14, 2025
15da090
Merge branch 'main' into uv/resolution-lowest
weiji14 Apr 14, 2025
170fb09
Remove note about testing min versions on optional deps in ci_tests.yaml
weiji14 Apr 14, 2025
b1e26da
Merge branch 'main' into uv/resolution-lowest
weiji14 Apr 29, 2025
b079acc
Bump astral-sh/setup-uv from 5.1.0 to 6.0.0
weiji14 Apr 29, 2025
b7814ed
Merge branch 'main' into uv/resolution-lowest
weiji14 Apr 29, 2025
fe20756
Merge branch 'main' into uv/resolution-lowest
weiji14 Jun 9, 2025
2cc4ba2
Bump astral-sh/setup-uv from 6.0.0 to 6.1.0
weiji14 Jun 9, 2025
f54d002
Temporarily pin to rioxarray>=0.19
weiji14 Jun 9, 2025
834be64
Revert "Temporarily pin to rioxarray>=0.19"
weiji14 Jun 9, 2025
8ce0755
Merge branch 'main' into uv/resolution-lowest
weiji14 Jun 13, 2025
4540a5d
Try install pyproj from conda-forge instead of PyPI
weiji14 Jun 13, 2025
668cbe1
Merge branch 'main' into uv/resolution-lowest
weiji14 Sep 15, 2025
f5db0ad
:arrow_up: Bump astral-sh/setup-uv from 6.1.0 to 6.7.0
weiji14 Sep 15, 2025
0d8ec91
Edit comment in ci_tests.yaml
weiji14 Sep 15, 2025
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43 changes: 19 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 +78,22 @@ 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 venv
source .venv/bin/activate
uv run --with pip==23 --resolution lowest-direct --all-extras --dev make install
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@weiji14 weiji14 Nov 21, 2024

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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).

uv pip list

# Run the tests but skip images
- name: Run tests
run: make test_no_images PYTEST_EXTRA="-r P"
run: |
source .venv/bin/activate
uv run --with pytest==8,pytest-mpl==0.17,pytest-doctestplus==1.2 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
env:
GMT_LIBRARY_PATH: $CONDA_PREFIX/lib
2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -55,7 +55,7 @@ doctest: _runtest
# run tests without image comparisons
# run pytest without the --mpl option to disable image comparisons
# use '-o addopts' to override 'addopts' settings in pyproject.toml file
test_no_images: PYTEST_ARGS=-o addopts="--verbose --durations=0 --durations-min=0.2 --doctest-modules"
test_no_images: PYTEST_ARGS=-o addopts="--verbose --color=yes --durations=0 --durations-min=0.2 --doctest-modules"
test_no_images: _runtest

format:
Expand Down
14 changes: 7 additions & 7 deletions pyproject.toml
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Expand Up @@ -33,18 +33,18 @@ dependencies = [
"numpy>=1.24",
"pandas>=2.0",
"xarray>=2023.04",
"netCDF4",
"packaging",
"netCDF4>=1.7",
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@weiji14 weiji14 Nov 21, 2024

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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 •
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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.

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@weiji14 weiji14 Apr 15, 2025 •
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There is another error that popped up on Ubuntu-22.04-ARM64 at https://github.com/GenericMappingTools/pygmt/actions/runs/14457975280/job/40545076044?pr=3639#step:7:1079, related to static_earth_relief too:

==================================== ERRORS ====================================
__________________ ERROR at setup of test_clib_read_data_grid __________________

self = CachingFileManager(<class 'netCDF4._netCDF4.Dataset'>, '/home/runner/.gmt/cache/static_earth_relief.nc', mode='r', kwa...r': True, 'diskless': False, 'persist': False, 'format': 'NETCDF4'}, manager_id='26bc1ee9-cb26-4f6f-bcea-ac669a2faa62')
needs_lock = True

    def _acquire_with_cache_info(self, needs_lock=True):
        """Acquire a file, returning the file and whether it was cached."""
        with self._optional_lock(needs_lock):
            try:
>               file = self._cache[self._key]

../.venv/lib/python3.11/site-packages/xarray/backends/file_manager.py:210: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <xarray.backends.lru_cache.LRUCache object at 0xff802d7a2b80>
key = [<class 'netCDF4._netCDF4.Dataset'>, ('/home/runner/.gmt/cache/static_earth_relief.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), '26bc1ee9-cb26-4f6f-bcea-ac669a2faa62']

    def __getitem__(self, key: K) -> V:
        # record recent use of the key by moving it to the front of the list
        with self._lock:
>           value = self._cache[key]
E           KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('/home/runner/.gmt/cache/static_earth_relief.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), '26bc1ee9-cb26-4f6f-bcea-ac669a2faa62']

../.venv/lib/python3.11/site-packages/xarray/backends/lru_cache.py:56: KeyError

During handling of the above exception, another exception occurred:

    @pytest.fixture(scope="module", name="expected_xrgrid")
    def fixture_expected_xrgrid():
        """
        The expected xr.DataArray object for the static_earth_relief.nc file.
        """
>       return load_dataarray(which("@static_earth_relief.nc"))

../pygmt/tests/test_clib_read_data.py:30: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../pygmt/io.py:44: in load_dataarray
    with xr.open_dataarray(filename_or_obj, **kwargs) as dataarray:
../.venv/lib/python3.11/site-packages/xarray/backends/api.py:686: in open_dataarray
    dataset = open_dataset(
../.venv/lib/python3.11/site-packages/xarray/backends/api.py:525: in open_dataset
    backend_ds = backend.open_dataset(
../.venv/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:588: in open_dataset
    store = NetCDF4DataStore.open(
../.venv/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:389: in open
    return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose)
../.venv/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:336: in __init__
    self.format = self.ds.data_model
../.venv/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:398: in ds
    return self._acquire()
../.venv/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:392: in _acquire
    with self._manager.acquire_context(needs_lock) as root:
../../../../.local/share/uv/python/cpython-3.11.12-linux-aarch64-gnu/lib/python3.11/contextlib.py:137: in __enter__
    return next(self.gen)
../.venv/lib/python3.11/site-packages/xarray/backends/file_manager.py:198: in acquire_context
    file, cached = self._acquire_with_cache_info(needs_lock)
../.venv/lib/python3.11/site-packages/xarray/backends/file_manager.py:216: in _acquire_with_cache_info
    file = self._opener(*self._args, **kwargs)
src/netCDF4/_netCDF4.pyx:2489: in netCDF4._netCDF4.Dataset.__init__
    ???
src/netCDF4/_netCDF4.pyx:2092: in netCDF4._netCDF4._get_vars
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   RuntimeError: only endian='native' allowed for NETCDF3 files, got 'big' (variable 'lon', group '/')

src/netCDF4/_netCDF4.pyx:4062: RuntimeError

This seems to be fixed in Unidata/netcdf4-python#1355, released in netcdf4=1.7.2. So we can either set the minimum version to netCDF4>=1.7.2 and/or remove netCDF4 in #3643. Would prefer the latter, because netCDF4=1.7.2 is the latest version released on Oct 2024, so not very old.

Edit: netCDF4 is no longer a required dependency of PyGMT since #3643, so no need to worry about this anymore.

"packaging>=22.0",
]
dynamic = ["version"]

[project.optional-dependencies]
all = [
"contextily",
"geopandas",
"IPython", # 'ipython' is not the correct module name.
"pyarrow",
"rioxarray",
"contextily>=1.2",
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@weiji14 weiji14 Nov 21, 2024

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Need to pin to contextily>=1.2, otherwise this code block won't work as expected (there is a chance that an ImportError will be raised if contextily=1.1 is installed, but xyzservices is not installed, breaking the _HAS_CONTEXTILY logic):

pygmt/pygmt/datasets/tile_map.py

Lines 12 to 19 in 97185e8

try:
import contextily
from xyzservices import TileProvider
_HAS_CONTEXTILY = True
except ImportError:
TileProvider = None
_HAS_CONTEXTILY = False

Xref geopandas/contextily#183, where xyzservices was included as a requirement of contextily (in v1.2.0)

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@seisman seisman Nov 22, 2024

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Good to know that we require contexily>=1.2

"geopandas>=0.14",
"IPython>=8", # 'ipython' is not the correct module name.
"pyarrow>=14",
"rioxarray>=0.14",
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@weiji14 weiji14 Jun 9, 2025 •
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Getting this test failure on windows-2022 at https://github.com/GenericMappingTools/pygmt/actions/runs/15524973929/job/43703740279?pr=3639#step:7:1095:

_______________ [doctest] pygmt.datasets.tile_map.load_tile_map _______________
118     >>> raster.sizes
119     Frozen({'band': 3, 'y': 256, 'x': 512})
120     >>> raster.coords  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
121     Coordinates:
122       * band         (band) uint8... 1 2 3
123       * y            (y) float64... -7.081e-10 -7.858e+04 ... -1.996e+07 -2.004e+07
124       * x            (x) float64... -2.004e+07 -1.996e+07 ... 1.996e+07 2.004e+07
125         spatial_ref  int... 0
126     >>> # CRS is set only if rioxarray is available
127     >>> if hasattr(raster, "rio"):
Expected:
    'EPSG:3857'
Got:
    'PROJCS["WGS 84 / Pseudo-Mercator",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Mercator_1SP"],PARAMETER["central_meridian",0],PARAMETER["scale_factor",1],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1],AXIS["Easting",EAST],AXIS["Northing",NORTH],EXTENSION["PROJ4","+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs"],AUTHORITY["EPSG","3857"]]'

D:\a\pygmt\pygmt\pygmt\datasets\tile_map.py:127: DocTestFailure

Similar situation to the one reported at #3575. We could perhaps pin to a rioxarray version that requires rasterio>=1.4.2? E.g. rioxarray=0.19.0 pins to rasterio>=1.4.3 (corteva/rioxarray#850). However, that version was released too recently on 22 Apr 2025 (<2 months).

Suggestions on what to do?

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@seisman seisman Jun 9, 2025

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The actual error messages are

ERROR 1: PROJ: proj_create_from_database: C:\Users\runneradmin\micromamba\envs\pygmt/Library/share/proj\proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 3 whereas a number >= 4 is expected. It comes from another PROJ installation.
ERROR 1: PROJ: proj_identify: C:\Users\runneradmin\micromamba\envs\pygmt/Library/share/proj\proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 3 whereas a number >= 4 is expected. It comes from another PROJ installation.

Some related discussions are in corteva/rioxarray#447. I'm unsure if pin rioxarray>=0.19.0 can solve the issue, but please give it a try first.

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@weiji14 weiji14 Jun 9, 2025

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Hmm you're right, got the same ERROR 1: PROJ: ... message even with rioxarray>0.19.0. Probably because we are using uv/PyPI installed packages with incompatible PROJ versions, instead of conda-forge packages where packages are compiled with the same PROJ lib.

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@seisman seisman Jun 13, 2025 •
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The dependency tree GMT->GDAL->PROJ installs PROJ 9.4.0, while uv/pypi installs pyproj 3.7.1 which contains PROJ 9.5.1.

Perhaps we can install pyproj via micromamba instead?

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@weiji14 weiji14 Jun 13, 2025

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Perhaps we can install pyproj via micromamba instead?

Tried at commit 4540a5d, same error 😢

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@seisman seisman Jun 24, 2025

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What happens if setting env PROJ_WHEEL=YES?

xref: https://pyproj4.github.io/pyproj/dev/installation.html#setup-pyproj

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@weiji14 weiji14 Jun 24, 2025

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PROJ_WHEEL seems to be relevant only when building the pyproj wheel, but since we're pulling a compiled version of pyproj from PyPI/conda-forge, it probably doesn't do anything.

]

[project.urls]
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