Remove the dependency of netCDF4 (#3643)

seisman · weiji14 · web-flow · commit 7741d0645293 · 2025-04-29T18:04:53.000+08:00
Co-authored-by: Wei Ji &lt;23487320+weiji14@users.noreply.github.com&gt;
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -60,7 +60,6 @@ jobs:
             numpy
             pandas
             xarray
-            netCDF4
             packaging
             geopandas
             pyarrow-core
diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -55,7 +55,6 @@ jobs:
             numpy
             pandas
             xarray
-            netCDF4
             packaging
             python-build
 
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -96,7 +96,6 @@ jobs:
             numpy
             pandas
             xarray
-            netCDF4
             packaging
             contextily
             geopandas
diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -54,7 +54,6 @@ jobs:
             numpy
             pandas
             xarray
-            netCDF4
             packaging
             contextily
             geopandas
diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -75,13 +75,13 @@ jobs:
             numpy-version: '1.26'
             pandas-version: '=2.1'
             xarray-version: '=2023.07'
-            optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray sphinx-gallery'
+            optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
           # Python 3.13 + core packages (latest versions) + optional packages
           - python-version: '3.13'
             numpy-version: '2.2'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray sphinx-gallery'
+            optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
           # Python 3.12 + core packages (Linux only)
           - os: 'ubuntu-latest'
             python-version: '3.12'
@@ -129,7 +129,6 @@ jobs:
             numpy=${{ matrix.numpy-version }}
             pandas${{ matrix.pandas-version }}
             xarray${{ matrix.xarray-version }}
-            netCDF4
             packaging
             make
             pip
diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -150,10 +150,10 @@ jobs:
         run: |
           python -m pip install --pre --prefer-binary \
                         --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
-                        numpy pandas xarray netCDF4 packaging \
+                        numpy pandas xarray packaging \
                         build contextily dvc geopandas ipython pyarrow rioxarray \
                         pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures \
-                        sphinx-gallery
+                        netCDF4 sphinx-gallery
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
@@ -64,7 +64,6 @@ jobs:
             numpy=1.26
             pandas
             xarray
-            netCDF4
             packaging
             contextily=1.5
             geopandas=1.0
diff --git a/.github/workflows/type_checks.yml b/.github/workflows/type_checks.yml
@@ -53,7 +53,7 @@ jobs:
           # 3. type checker and stub packages
           # 4. other packages that are used somewhere in PyGMT
           python -m pip install \
-            numpy pandas xarray netcdf4 packaging \
+            numpy pandas xarray packaging \
             contextily geopandas ipython pyarrow rioxarray \
             mypy pandas-stubs pyarrow-stubs \
             matplotlib pytest
diff --git a/ci/requirements/docs.yml b/ci/requirements/docs.yml
@@ -10,7 +10,6 @@ dependencies:
     - numpy
     - pandas
     - xarray
-    - netCDF4
     - packaging
     # Optional dependencies
     - contextily
diff --git a/doc/install.md b/doc/install.md
@@ -95,7 +95,6 @@ PyGMT requires the following packages to be installed:
 - [NumPy](https://numpy.org)
 - [pandas](https://pandas.pydata.org)
 - [Xarray](https://xarray.dev/)
-- [netCDF4](https://unidata.github.io/netcdf4-python)
 - [packaging](https://packaging.pypa.io)
 
 :::{note}
@@ -128,14 +127,14 @@ 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=3.13 numpy pandas xarray netcdf4 packaging gmt
+mamba create --name pygmt python=3.13 numpy pandas xarray packaging gmt
 ```
 :::
 
 ::: {tab-item} conda
 :sync: conda
 ```
-conda create --name pygmt python=3.13 numpy pandas xarray netcdf4 packaging gmt
+conda create --name pygmt python=3.13 numpy pandas xarray packaging gmt
 ```
 :::
 ::::
diff --git a/environment.yml b/environment.yml
@@ -10,7 +10,6 @@ dependencies:
     - numpy>=1.26
     - pandas>=2.1
     - xarray>=2023.07
-    - netCDF4
     - packaging
     # Optional dependencies
     - contextily>=1.5
@@ -34,6 +33,7 @@ dependencies:
     - pytest-cov
     - pytest-doctestplus
     - pytest-mpl
+    - netCDF4
     # Dev dependencies (building documentation)
     - geodatasets
     - myst-nb
diff --git a/pygmt/tests/test_io.py b/pygmt/tests/test_io.py
@@ -9,6 +9,8 @@
 from pygmt.helpers import GMTTempFile
 from pygmt.io import load_dataarray
 
+pytest.importorskip("netCDF4")
+
 
 # TODO(PyGMT>=0.20.0): Remove test_io_load_dataarray
 def test_io_load_dataarray():
diff --git a/pygmt/tests/test_xarray_accessor.py b/pygmt/tests/test_xarray_accessor.py
@@ -2,6 +2,7 @@
 Test the behaviour of the GMTDataArrayAccessor class.
 """
 
+import importlib
 import sys
 from pathlib import Path
 
@@ -14,6 +15,8 @@
 from pygmt.enums import GridRegistration, GridType
 from pygmt.exceptions import GMTInvalidInput
 
+_HAS_NETCDF4 = bool(importlib.util.find_spec("netCDF4"))
+
 
 def test_xarray_accessor_gridline_cartesian():
     """
@@ -102,6 +105,7 @@ def test_xarray_accessor_set_invalid_registration_and_gtype():
 
 
 # TODO(GMT>=6.5.0): Remove the xfail marker for GMT>=6.5.0.
+@pytest.mark.skipif(condition=not _HAS_NETCDF4, reason="netCDF4 is not installed")
 @pytest.mark.xfail(
     condition=sys.platform == "win32" and Version(__gmt_version__) < Version("6.5.0"),
     reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/7573",
@@ -119,7 +123,7 @@ def test_xarray_accessor_sliced_datacube():
             "https://github.com/pydata/xarray-data/raw/master/eraint_uvz.nc",
             download="u",
         )
-        with xr.open_dataset(fname) as dataset:
+        with xr.open_dataset(fname, engine="netcdf4") as dataset:
             grid = dataset.sel(level=500, month=1, drop=True).z
 
         assert grid.gmt.registration == GridRegistration.GRIDLINE
diff --git a/pygmt/tests/test_xarray_backend.py b/pygmt/tests/test_xarray_backend.py
@@ -2,6 +2,7 @@
 Tests for xarray 'gmt' backend engine.
 """
 
+import importlib
 import re
 
 import numpy as np
@@ -12,8 +13,11 @@
 from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import GMTTempFile
 
+_HAS_NETCDF4 = bool(importlib.util.find_spec("netCDF4"))
+
 
 @pytest.mark.benchmark
+@pytest.mark.skipif(condition=not _HAS_NETCDF4, reason="netCDF4 is not installed")
 def test_xarray_backend_load_dataarray():
     """
     Check that xarray.load_dataarray works to read a netCDF grid with
diff --git a/pyproject.toml b/pyproject.toml
@@ -38,7 +38,6 @@ dependencies = [
     "numpy>=1.26",
     "pandas>=2.1",
     "xarray>=2023.07",
-    "netCDF4",
     "packaging",
 ]
 dynamic = ["version"]
diff --git a/requirements.txt b/requirements.txt
@@ -2,5 +2,4 @@
 numpy>=1.26
 pandas>=2.1
 xarray>=2023.07
-netCDF4
 packaging
