Revert 30 commits

Author: seisman

.github/workflows/benchmarks.yml

@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |
@@ -87,8 +87,8 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.1.0
+        uses: CodSpeedHQ/action@v3.0.1
         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 --override-ini addopts='--verbose'"
+          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed"

.github/workflows/cache_data.yaml

@@ -43,7 +43,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_docs.yml

@@ -80,7 +80,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |
@@ -103,7 +103,6 @@ jobs:
             contextily
             geopandas<1.0
             ipython
-            pyarrow
             rioxarray
             make
             pip
@@ -115,7 +114,7 @@ jobs:
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
-            sphinx_rtd_theme<3.0
+            sphinx_rtd_theme
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_doctests.yaml

@@ -42,7 +42,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_tests.yaml

@@ -1,26 +1,24 @@
 # 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 jobs on Linux are triggered to save on Continuous
-# Integration resources:
+# In draft pull request, only two jobs on Linux are triggered to save on
+# Continuous Integration resources:
 #
-# - 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
+# - 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)
 #
 name: Tests
 
@@ -61,32 +59,35 @@ jobs:
         # Is it a draft Pull Request (true or false)?
         isDraft:
           - ${{ github.event.pull_request.draft }}
-        # Only run three jobs on Ubuntu for draft PRs
+        # Only run two jobs (Ubuntu + Python 3.10/3.12) 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: ' contextily geopandas<1 ipython pyarrow rioxarray sphinx-gallery'
-          # Python 3.12 + core packages (latest versions) + optional packages
+            optional-packages: ''
           - python-version: '3.12'
             numpy-version: '2.1'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' contextily geopandas>=1.0 ipython pyarrow rioxarray sphinx-gallery'
-          # Python 3.11 + core packages (Linux only)
+            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.
           - os: 'ubuntu-latest'
-            python-version: '3.11'
-            numpy-version: ''
+            python-version: '3.11'  # Can't be 3.10 or 3.12.
+            numpy-version: '1.24'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ''
+            optional-packages: ' geopandas<1'
 
     timeout-minutes: 30
     defaults:
@@ -113,7 +114,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_tests_dev.yaml

@@ -57,7 +57,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_tests_legacy.yaml

@@ -51,7 +51,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/publish-to-pypi.yml

@@ -75,10 +75,10 @@ jobs:
         ls -lh dist/
 
     - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.12.2
+      uses: pypa/gh-action-pypi-publish@v1.10.3
       with:
         repository-url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@v1.12.2
+      uses: pypa/gh-action-pypi-publish@v1.10.3

.github/workflows/type_checks.yml

@@ -50,8 +50,8 @@ jobs:
           # 4. other packages that are used somewhere in PyGMT
           python -m pip install \
             numpy pandas xarray netcdf4 packaging \
-            contextily geopandas ipython pyarrow rioxarray \
-            mypy pandas-stubs pyarrow-stubs \
+            contextily geopandas ipython rioxarray \
+            mypy pandas-stubs \
             matplotlib pytest
           python -m pip list
 

README.md

@@ -191,7 +191,14 @@ 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 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.
+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.