Merge branch 'main' into to_numpy/pandas_numeric

Author: seisman

.github/workflows/benchmarks.yml

@@ -91,4 +91,4 @@ jobs:
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.
-          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed"
+          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed --override-ini addopts='--verbose'"

.github/workflows/check-links.yml

@@ -35,7 +35,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v2.0.2
+      uses: lycheeverse/lychee-action@v2.1.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md

.github/workflows/ci_tests.yaml

@@ -1,24 +1,26 @@
 # Test PyGMT on Linux/macOS/Windows
 #
-# This workflow runs regular PyGMT tests and uploads test coverage reports stored
-# in `.coverage.xml` to https://app.codecov.io/gh/GenericMappingTools/pygmt
-# via the [Codecov GitHub Action](https://github.com/codecov/codecov-action).
-# More codecov related configurations are stored in `.github/codecov.yml`.
-# If any tests fail, it also uploads the diff images as workflow artifacts.
+# This workflow runs regular PyGMT tests and uploads test coverage reports stored in
+# `.coverage.xml` to https://app.codecov.io/gh/GenericMappingTools/pygmt via the
+# [Codecov GitHub Action](https://github.com/codecov/codecov-action). More codecov
+# related configurations are stored in `.github/codecov.yml`. If any tests fail, it also
+# uploads the diff images as workflow artifacts.
 #
 # It is run:
 # 1. on every commit to the main branch
-# 2. on every commit to the pull request branches, unless the pull requests only
-#    contain non-code changes.
+# 2. on every commit to the pull request branches, unless the pull requests only contain
+#    non-code changes.
 # 3. when a new release is published
 #
 # It is also scheduled to run daily on the main branch.
 #
-# In draft pull request, only two jobs on Linux are triggered to save on
-# Continuous Integration resources:
+# In draft pull request, only jobs on Linux are triggered to save on Continuous
+# Integration resources:
 #
-# - Minimum supported Python, NumPy, pandas, Xarray versions following [SPEC 0](https://scientific-python.org/specs/spec-0000/)
-# - Latest Python, NumPy versions + optional packages (e.g. GeoPandas)
+# - Minimum supported Python + core packages (minimum supported versions)
+#   + optional packages (minimum supported versions if any)
+# - Latest Python + core packages (latest versions) + optional packages
+# - Last release before the latest Python + core packages
 #
 name: Tests
 
@@ -59,35 +61,32 @@ jobs:
         # 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 three jobs on Ubuntu 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
         include:
+          # Python 3.10 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
           - python-version: '3.10'
             numpy-version: '1.24'
             pandas-version: '=2.0'
             xarray-version: '=2023.04'
-            optional-packages: ''
+            optional-packages: ' contextily geopandas<1 ipython pyarrow rioxarray sphinx-gallery'
+          # Python 3.12 + core packages (latest versions) + optional packages
           - python-version: '3.12'
             numpy-version: '2.1'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' contextily geopandas ipython pyarrow rioxarray sphinx-gallery'
-          # 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.
+            optional-packages: ' contextily geopandas>=1.0 ipython pyarrow rioxarray sphinx-gallery'
+          # Python 3.11 + core packages (Linux only)
           - os: 'ubuntu-latest'
-            python-version: '3.11'  # Can't be 3.10 or 3.12.
-            numpy-version: '1.24'
-            pandas-version: '=2.1'
+            python-version: '3.11'
+            numpy-version: ''
+            pandas-version: ''
             xarray-version: ''
-            optional-packages: ' geopandas<1 pyarrow'
+            optional-packages: ''
 
     timeout-minutes: 30
     defaults:
@@ -143,7 +142,6 @@ jobs:
             pytest-doctestplus
             pytest-mpl
             pytest-rerunfailures
-            pytest-xdist
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -166,7 +164,7 @@ jobs:
 
       # Run the regular tests
       - name: Run tests
-        run: make test PYTEST_EXTRA="-r P -n auto --reruns 2"
+        run: make test PYTEST_EXTRA="-r P --reruns 2"
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
@@ -178,10 +176,10 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.3
         if: success() || failure()
         with:
           use_oidc: true
-          file: ./coverage.xml # optional
+          files: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY
           fail_ci_if_error: false

.github/workflows/ci_tests_dev.yaml

@@ -153,7 +153,7 @@ jobs:
                         --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
                         numpy pandas xarray netCDF4 packaging \
                         build contextily dvc geopandas ipython pyarrow rioxarray \
-                        pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures pytest-xdist\
+                        pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures \
                         sphinx-gallery
 
       # Show installed pkg information for postmortem diagnostic
@@ -181,7 +181,7 @@ jobs:
 
       # Run the tests
       - name: Test with pytest
-        run: make test PYTEST_EXTRA="-r P -n auto --reruns 2"
+        run: make test PYTEST_EXTRA="-r P --reruns 2"
         env:
           GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib
 

.github/workflows/ci_tests_legacy.yaml

@@ -62,7 +62,7 @@ jobs:
             python=3.10
             gmt=${{ matrix.gmt_version }}
             ghostscript<10
-            numpy
+            numpy<2
             pandas
             xarray
             netCDF4

Makefile

@@ -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:

README.md

@@ -191,14 +191,7 @@ Other official wrappers for GMT:
 ## Minimum supported versions
 
 PyGMT has adopted [SPEC 0](https://scientific-python.org/specs/spec-0000/) alongside the
-rest of the scientific Python ecosystem, and therefore:
-
-- Support for Python versions be dropped 3 years after their initial release.
-- Support for core package dependencies (NumPy, pandas, Xarray) be dropped 2 years after
-  their initial release.
-
-Similarly, the PyGMT team has decided to discontinue support for GMT versions 3 years
-after their initial release.
-
-Please see [Minimum Supported Versions](https://www.pygmt.org/dev/minversions.html) for
-the minimum supported versions of GMT, Python and core package dependencies.
+rest of the scientific Python ecosystem, and made a few extensions based on the needs of
+the project. Please see [Minimum Supported Versions](https://www.pygmt.org/dev/minversions.html)
+for the detailed policy and the minimum supported versions of GMT, Python and core
+package dependencies.

doc/Makefile

@@ -55,7 +55,5 @@ server:
 clean:
 	rm -rf $(BUILDDIR)
 	rm -rf api/generated
-	rm -rf intro
-	rm -rf tutorials
-	rm -rf gallery
-	rm -rf projections
+	rm -rf intro tutorials gallery projections
+	rm -rf sg_execution_times.rst

doc/maintenance.md

@@ -120,18 +120,25 @@ made to our documentation website every time we make a commit in a pull request.
 The service has a configuration file `.readthedocs.yaml`, with a list of options
 to change the default behaviour at <https://docs.readthedocs.io/en/stable/config-file/index.html>.
 
+## Continuous Benchmarking
 
-## Dependencies Policy
+We use the [CodSpeed](https://codspeed.io) service to continuously track PyGMT's
+performance. The `pytest-codspeed` plugin collects benchmark data and uploads it to the
+CodSpeed server, where results are available at <https://codspeed.io/GenericMappingTools/pygmt>.
 
-PyGMT has adopted [SPEC 0](https://scientific-python.org/specs/spec-0000/) alongside the
-rest of the scientific Python ecosystem, and therefore:
+Benchmarking is handled through the `benchmarks.yml` GitHub Actions workflow. It's
+automatically executed when a pull request is merged into the main branch. To trigger
+benchmarking in a pull request, add the `run/benchmark` label to the pull request.
 
-* Support for Python versions be dropped 3 years after their initial release.
-* Support for core package dependencies (NumPy, pandas, Xarray) be dropped 2 years after
-  their initial release.
+To include a new test in the benchmark suite, apply the `@pytest.mark.benchmark`
+decorator to a test function.
 
-Similarly, the PyGMT team has decided to discontinue support for GMT versions 3 years
-after their initial release.
+## Dependencies Policy
+
+PyGMT has adopted [SPEC 0](https://scientific-python.org/specs/spec-0000/) alongside the
+rest of the scientific Python ecosystem, and made a few extensions based on the needs of
+the project. Please see [Minimum Supported Versions](minversions.md) for the detailed
+policy and the minimum supported versions of GMT, Python and core package dependencies.
 
 In `pyproject.toml`, the `requires-python` key should be set to the minimum supported
 version of Python. Minimum supported versions of GMT, Python and core package

doc/minversions.md

@@ -18,14 +18,25 @@ myst:
 # Minimum Supported Versions
 
 PyGMT has adopted [SPEC 0](https://scientific-python.org/specs/spec-0000/) alongside the
-rest of the scientific Python ecosystem, and therefore:
+rest of the scientific Python ecosystem, and will therefore:
 
-- Support for Python versions be dropped 3 years after their initial release.
-- Support for core package dependencies (NumPy, pandas, Xarray) be dropped 2 years after
-  their initial release.
+- Drop support for Python versions 3 years after their initial release.
+- Drop support for core package dependencies (NumPy, pandas, Xarray) 2 years after their
+  initial release.
 
-Similarly, the PyGMT team has decided to discontinue support for GMT versions 3 years
-after their initial release.
+In addition to the above, the PyGMT team has also decided to:
+
+- Drop support for GMT versions 3 years after their initial release, while ensuring at
+  least two latest minor versions remain supported.
+- Maintain support for [optional dependencies](/ecosystem.md#pygmt-dependencies) for at
+  least 1 year after their initial release. Users are encouraged to use the most
+  up-to-date optional dependencies where possible.
+
+:::{note}
+The SPEC 0 policy is enforced on a best-effort basis, and the PyGMT team may decide to
+drop support for core (and optional) package dependencies earlier than recommended for
+compatibility reasons.
+:::
 
 | PyGMT Version | GMT | Python | NumPy | pandas | Xarray |
 |---|---|---|---|---|---|