Merge branch 'main' into options

Author: seisman

.github/ISSUE_TEMPLATE/bump_gmt_checklist.md

@@ -19,6 +19,7 @@ assignees: ''
 - [ ] Bump the GMT version in CI (1 PR)
   - [ ] Update `environment.yml`
   - [ ] Update `ci/requirements/docs.yml`
+  - [ ] Update `.github/workflows/benchmarks.yml`
   - [ ] Update `.github/workflows/cache_data.yaml`
   - [ ] Update `.github/workflows/ci_doctests.yaml`
   - [ ] Update `.github/workflows/ci_docs.yml`

.github/workflows/benchmarks.yml

@@ -0,0 +1,97 @@
+# Run performance benchmarks
+#
+# Continuous benchmarking using pytest-codspeed. Measures the execution speed
+# of tests marked with @pytest.mark.benchmark decorator.
+
+name: Benchmarks
+
+on:
+  # Run on pushes to the main branch
+  push:
+    branches: [ main ]
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - '.github/workflows/benchmarks.yml'
+  pull_request:
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - '.github/workflows/benchmarks.yml'
+  # `workflow_dispatch` allows CodSpeed to trigger backtest
+  # performance analysis in order to generate initial data.
+  workflow_dispatch:
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  benchmarks:
+    runs-on: ubuntu-22.04
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          # fetch all history so that setuptools-scm works
+          fetch-depth: 0
+
+      # Install Miniconda with conda-forge dependencies
+      - name: Setup Miniconda
+        uses: conda-incubator/[email protected]
+        with:
+          auto-activate-base: true
+          activate-environment: ""  # base environment
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+
+      # Install GMT and dependencies from conda-forge
+      - name: Install dependencies
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          # Preprend $CONDA/bin to $PATH so that conda's python is used over system python
+          echo $CONDA/bin >> $GITHUB_PATH
+          conda install --solver=libmamba gmt=6.4.0 python=3.12 \
+                        numpy pandas xarray netCDF4 packaging \
+                        geopandas pytest pytest-mpl
+          python -m pip install -U pytest-codspeed setuptools
+
+      # Download cached remote files (artifacts) from GitHub
+      - name: Download remote data from GitHub
+        uses: dawidd6/[email protected]
+        with:
+          workflow: cache_data.yaml
+          workflow_conclusion: success
+          name: gmt-cache
+          path: .gmt
+
+      # Move downloaded files to ~/.gmt directory and list them
+      - name: Move and list downloaded remote files
+        run: |
+          mkdir -p ~/.gmt
+          mv .gmt/* ~/.gmt
+          # Change modification times of the two files, so GMT won't refresh it
+          touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
+          ls -lhR ~/.gmt
+
+      # Install the package that we want to test
+      - name: Install the package
+        run: make install
+
+      # Run the benchmark tests
+      - name: Run benchmarks
+        uses: CodSpeedHQ/[email protected]
+        with:
+          run: |
+            python -c "import pygmt; pygmt.show_versions()"
+            PYGMT_USE_EXTERNAL_DISPLAY="false" python -m pytest -r P --pyargs pygmt --codspeed
+        env:
+          GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

.github/workflows/cache_data.yaml

@@ -1,18 +1,21 @@
-# Cache GMT remote data files and uploads as artifacts
+# Cache GMT remote data files and upload as artifacts
 #
 # This workflow downloads data files needed by PyGMT tests/documentation from
 # the GMT data server and uploads as workflow artifacts which can be accessed
 # by other GitHub Actions workflows.
 #
 # It is scheduled to run every Sunday at 12:00 (UTC). If new remote files are
-# needed urgently, maintainers can manually uncomment the 'pull_request:' line
-# below to refresh the cache.
+# needed urgently, maintainers can update the workflow file or
+# 'pygmt/helpers/caching.py' file to refresh the cache.
 #
 name: Cache data
 
 on:
-  # Uncomment the 'pull_request' line below to manually re-cache data artifacts
-  # pull_request:
+  pull_request:
+    # Make any changes to the following files to refresh the cache
+    paths:
+      - 'pygmt/helpers/caching.py'
+      - '.github/workflows/cache_data.yaml'
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -61,11 +64,11 @@ jobs:
       # Download remote files
       - name: Download remote data
         run: |
-          python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
+          python -c "from pygmt.helpers.caching import cache_data; cache_data()"
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: gmt-cache
           path: |

.github/workflows/ci_docs.yml

@@ -72,7 +72,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=3.12

.github/workflows/ci_tests.yaml

@@ -101,7 +101,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}
@@ -141,9 +141,7 @@ jobs:
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
-        run: |
-          dvc pull --verbose
-          ls -lhR pygmt/tests/baseline/
+        run: dvc pull --verbose && ls -lhR pygmt/tests/baseline/
 
       # Install the package that we want to test
       - name: Install the package
@@ -155,7 +153,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: ${{ failure() }}
         with:
           name: artifact-${{ runner.os }}-${{ matrix.python-version }}

.github/workflows/ci_tests_dev.yaml

@@ -95,7 +95,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=3.12
@@ -120,7 +120,7 @@ jobs:
         run: curl https://raw.githubusercontent.com/GenericMappingTools/gmt/master/ci/build-gmt.sh | bash
         env:
           GMT_GIT_REF: ${{ matrix.gmt_git_ref }}
-          GMT_INSTALL_DIR: ${{ github.workspace }}/gmt-install-dir
+          GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
         if: runner.os != 'Windows'
 
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Windows)
@@ -139,13 +139,15 @@ jobs:
             -DGMT_USE_THREADS=TRUE
           cmake --build .
           cmake --build . --target install
+          cd ..
+          rm -rf gmt/
         env:
           GMT_GIT_REF: ${{ matrix.gmt_git_ref }}
-          GMT_INSTALL_DIR: ${{ github.workspace }}/gmt-install-dir
+          GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
         if: runner.os == 'Windows'
 
       - name: Add GMT's bin to PATH
-        run: echo '${{ github.workspace }}/gmt-install-dir/bin' >> $GITHUB_PATH
+        run: echo '${{ runner.temp }}/gmt-install-dir/bin' >> $GITHUB_PATH
 
       # Install dependencies from PyPI
       - name: Install dependencies
@@ -163,9 +165,7 @@ jobs:
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
-        run: |
-          dvc pull
-          ls -lhR pygmt/tests/baseline/
+        run: dvc pull --verbose && ls -lhR pygmt/tests/baseline/
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -193,11 +193,11 @@ jobs:
       - name: Test with pytest
         run: make test PYTEST_EXTRA="-r P"
         env:
-          GMT_LIBRARY_PATH: ${{ github.workspace }}/gmt-install-dir/lib
+          GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: ${{ failure() }}
         with:
           name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}

.github/workflows/ci_tests_legacy.yaml

@@ -59,7 +59,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=3.9
@@ -76,7 +76,6 @@ jobs:
             rioxarray
             sphinx-gallery
             build
-            dvc
             make
             pip
             pytest
@@ -101,12 +100,6 @@ jobs:
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
-      # Pull baseline image data from dvc remote (DAGsHub)
-      - name: Pull baseline image data from dvc remote
-        run: |
-          dvc pull pygmt/tests/baseline/test_logo.png --verbose
-          ls -lhR pygmt/tests/baseline/
-
       # Install the package that we want to test
       - name: Install the package
         run: make install

.github/workflows/format-command.yml

@@ -32,7 +32,7 @@ jobs:
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          python -m pip install blackdoc docformatter ruff
+          python -m pip install docformatter ruff
           python -m pip list
           sudo apt-get install dos2unix
 

.github/workflows/release-baseline-images.yml

@@ -25,9 +25,7 @@ jobs:
       uses: iterative/[email protected]
 
     - name: Pull baseline image data from dvc remote
-      run: |
-        dvc pull
-        ls -lhR pygmt/tests/baseline/
+      run: dvc pull && ls -lhR pygmt/tests/baseline/
 
     - name: Create the baseline image asset in zip format
       run: |

.github/workflows/style_checks.yaml

@@ -34,11 +34,11 @@ jobs:
 
       - name: Install packages
         run: |
-          python -m pip install blackdoc docformatter ruff
+          python -m pip install docformatter ruff
           python -m pip list
           sudo apt-get install dos2unix
 
-      - name: Formatting check (blackdoc, docformatter, ruff)
+      - name: Formatting check (docformatter, ruff)
         run: make check
 
       - name: Ensure files use UNIX line breaks and have 644 permission