Merge branch 'main' into add-tutorial-meca

GenericMappingTools · May 21, 2024 · 828ef97 · 828ef97
2 parents eec5e37 + 8192ca0
commit 828ef97
Show file tree

Hide file tree

Showing 34 changed files with 406 additions and 290 deletions.
diff --git a/.github/ISSUE_TEMPLATE/4-release_checklist.md b/.github/ISSUE_TEMPLATE/4-release_checklist.md
@@ -23,7 +23,10 @@ assignees: ''
   - [ ] All tests pass in the ["GMT Dev Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml)
   - [ ] All tests pass in the ["Doctests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
   - [ ] Deprecations and related tests are removed for this version by running `grep --include="*.py" -r 'remove_version="vX.Y.Z"' pygmt` from the base of the repository
+- [ ] Update warnings in `pygmt.show_versions()` as well as notes in [Common installation issues](https://www.pygmt.org/dev/install.html#not-working-transparency)
+      and [Testing your install]((https://www.pygmt.org/dev/install.html#testing-your-install) regarding GMT-Ghostscript incompatibility
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
+- [ ] Review the ["PyGMT Team" page](https://www.pygmt.org/dev/team.html)
 - [ ] Finish up 'Changelog entry for v0.x.x' Pull Request:
   - [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
   - [ ] Update `CITATION.cff` and BibTeX at https://github.com/GenericMappingTools/pygmt#citing-pygmt

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -1,7 +1,7 @@
 # Run performance benchmarks
 #
-# Continuous benchmarking using pytest-codspeed. Measures the execution speed
-# of tests marked with @pytest.mark.benchmark decorator.
+# Continuous benchmarking using pytest-codspeed. Measures the execution speed of tests
+# marked with @pytest.mark.benchmark decorator.
 
 name: Benchmarks
 
@@ -15,12 +15,9 @@ on:
   # Run in PRs but only if the PR has the 'run/benchmark' label
   pull_request:
     types: [ opened, reopened, labeled, synchronize ]
-  # `workflow_dispatch` allows CodSpeed to trigger backtest
-  # performance analysis in order to generate initial data.
+  # '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 }}
@@ -37,39 +34,49 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         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 >> $GITHUB_PATH
-          conda install --solver=libmamba gmt=6.5.0 python=3.12 \
-                        numpy pandas xarray netCDF4 packaging \
-                        geopandas pyarrow pytest pytest-mpl
-          python -m pip install -U pytest-codspeed setuptools
+      - name: Get current week number of year
+        id: date
+        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT  # e.g., 2024-W19
 
+      # Install Micromamba with conda-forge dependencies
+      - name: Setup Micromamba
+        uses: mamba-org/[email protected]
+        with:
+          environment-name: pygmt
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+          cache-downloads: false
+          cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
+          create-args: >-
+            gmt=6.5.0
+            python=3.12
+            numpy
+            pandas
+            xarray
+            netCDF4
+            packaging
+            geopandas
+            pyarrow
+            pytest
+            pytest-codspeed
+            pytest-mpl
+            pytest-rerunfailures 
+            pytest-xdist
+            
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
         run: |
-          gh run download -n gmt-cache -D gmt-cache
-          # Move downloaded files to ~/.gmt directory and list them
-          mkdir -p ~/.gmt
-          mv gmt-cache/* ~/.gmt
-          rmdir gmt-cache
+          # Download cached files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
@@ -84,8 +91,6 @@ jobs:
       - 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/
+          # '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"
diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -23,12 +23,12 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].4
+      uses: actions/[email protected].5
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].4
+      uses: actions/[email protected].5
       with:
         ref: gh-pages
         path: documentation
@@ -71,5 +71,5 @@ jobs:
       run: |
         title="Link Checker Report on ${{ steps.date.outputs.date }}"
         gh issue create --title "$title" --body-file ./lychee/out.md
-        env:
-          GH_TOKEN: ${{ github.token }}
+      env:
+        GH_TOKEN: ${{ github.token }}
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -69,11 +69,15 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
+      - name: Get current week number of year
+        id: date
+        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT  # e.g., 2024-W19
+
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
         uses: mamba-org/[email protected]
@@ -85,6 +89,8 @@ jobs:
               - nodefaults
           cache-downloads: false
           cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
             python=3.12
             gmt=6.5.0
@@ -113,11 +119,8 @@ jobs:
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
         run: |
-          gh run download -n gmt-cache -D gmt-cache
-          # Move downloaded files to ~/.gmt directory and list them
-          mkdir -p ~/.gmt
-          mv gmt-cache/* ~/.gmt
-          rmdir gmt-cache
+          # Download cached files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
@@ -135,7 +138,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -35,7 +35,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -72,11 +72,8 @@ jobs:
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
         run: |
-          gh run download -n gmt-cache -D gmt-cache
-          # Move downloaded files to ~/.gmt directory and list them
-          mkdir -p ~/.gmt
-          mv gmt-cache/* ~/.gmt
-          rmdir gmt-cache
+          # Download cached files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt

diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -49,6 +49,8 @@ jobs:
   test:
     name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
     runs-on: ${{ matrix.os }}
+    permissions:
+      id-token: write  # This is required for requesting OIDC token for codecov
     strategy:
       fail-fast: false
       matrix:
@@ -92,11 +94,15 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
+      - name: Get current week number of year
+        id: date
+        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT  # e.g., 2024-W19
+
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
         uses: mamba-org/[email protected]
@@ -108,6 +114,8 @@ jobs:
               - nodefaults
           cache-downloads: false
           cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}
             gmt=6.5.0
@@ -125,15 +133,14 @@ jobs:
             pytest-cov
             pytest-doctestplus
             pytest-mpl
+            pytest-rerunfailures
+            pytest-xdist
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
         run: |
-          gh run download -n gmt-cache -D gmt-cache
-          # Move downloaded files to ~/.gmt directory and list them
-          mkdir -p ~/.gmt
-          mv gmt-cache/* ~/.gmt
-          rmdir gmt-cache
+          # Download files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
@@ -155,17 +162,17 @@ jobs:
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
         uses: actions/upload-artifact@v4
-        if: ${{ failure() }}
+        if: failure()
         with:
           name: artifact-${{ runner.os }}-${{ matrix.python-version }}
           path: tmp-test-dir-with-unique-name
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/[email protected]
+        uses: codecov/[email protected]
+        if: success() || failure()
         with:
+          use_oidc: true
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY
           fail_ci_if_error: false
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -37,7 +37,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-14, windows-2022]
+        os: [ubuntu-24.04, macos-14, windows-2022]
         gmt_git_ref: [master]
     timeout-minutes: 30
     defaults:
@@ -47,11 +47,15 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
+      - name: Get current week number of year
+        id: date
+        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT  # e.g., 2024-W19
+
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
         uses: mamba-org/[email protected]
@@ -63,6 +67,8 @@ jobs:
               - nodefaults
           cache-downloads: false
           cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
             python=3.12
             cmake
@@ -120,9 +126,9 @@ 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<2' pandas xarray netCDF4 packaging \
                         build contextily dvc geopandas ipython pyarrow rioxarray \
-                        'pytest>=6.0' pytest-cov pytest-doctestplus pytest-mpl \
+                        pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures pytest-xdist\
                         sphinx-gallery
 
       # Show installed pkg information for postmortem diagnostic
@@ -136,11 +142,8 @@ jobs:
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
         run: |
-          gh run download -n gmt-cache -D gmt-cache
-          # Move downloaded files to ~/.gmt directory and list them
-          mkdir -p ~/.gmt
-          mv gmt-cache/* ~/.gmt
-          rmdir gmt-cache
+          # Download cached files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt