Merge branch 'main' into pep621

Author: seisman

.github/ISSUE_TEMPLATE/bump_gmt_checklist.md

@@ -14,16 +14,23 @@ assignees: ''
 
 <!-- Please add specific checklist items for the tests, xfail pytest markers, and deprecated syntax that need to be updated. -->
 
-**To-Do**:
-- [ ] Bump the minimum required GMT version (1 PR)
+**To-Do for bumping the GMT version in CI**:
+
+- [ ] Bump the GMT version in CI (1 PR)
   - [ ] Update `.github/workflows/cache_data.yaml`
   - [ ] Update `.github/workflows/ci_docs.yml`
   - [ ] Update `.github/workflows/ci_tests.yaml`
-  - [ ] Update `doc/install.rst`
+  - [ ] Update `ci/requirements/docs.yml`
   - [ ] Update `environment.yml`
+- [ ] Fix failing tests (1 or more PRs)
+- [ ] Fix [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
+
+**To-Do for bumping the minimum required GMT version**:
+
+- [ ] Bump the minimum required GMT version (1 PR)
+  - [ ] Update `doc/install.rst`
   - [ ] Update `required_version` in `pygmt/clib/session.py`
   - [ ] Update `test_get_default` in `pygmt/tests/test_clib.py`
   - [ ] Update compatibility table in `README.rst`
-- [ ] Fix failing tests (1 or more PRs)
 - [ ] Remove [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
 - [ ] Update deprecated syntax in source code and examples based on the [GMT Changelog](https://docs.generic-mapping-tools.org/latest/changes.html)

.github/config.yml

@@ -2,13 +2,13 @@
 ########################################################################################
 # Comment to be posted to on first time issues
 newIssueWelcomeComment: |
-  👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our [contributing guidelines](https://github.com/GenericMappingTools/pygmt/blob/main/CONTRIBUTING.md) and [code of conduct](https://github.com/GenericMappingTools/pygmt/blob/main/CODE_OF_CONDUCT.md).
+  👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our [contributing guidelines](https://github.com/GenericMappingTools/pygmt/blob/main/CONTRIBUTING.md) and [code of conduct](https://github.com/GenericMappingTools/.github/blob/main/CODE_OF_CONDUCT.md).
 
 # Comment to be posted to on PRs from first time contributors in your repository
 newPRWelcomeComment: |
   💖 Thanks for opening this pull request! 💖
 
-  Please make sure you read our [contributing guidelines](https://github.com/GenericMappingTools/pygmt/blob/main/CONTRIBUTING.md) and abide by our [code of conduct](https://github.com/GenericMappingTools/pygmt/blob/main/CODE_OF_CONDUCT.md).
+  Please make sure you read our [contributing guidelines](https://github.com/GenericMappingTools/pygmt/blob/main/CONTRIBUTING.md) and abide by our [code of conduct](https://github.com/GenericMappingTools/.github/blob/main/CODE_OF_CONDUCT.md).
 
   A few things to keep in mind:
 

.github/readme-example.png

@@ -38,7 +38,7 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          mamba install gmt=6.3.0 numpy pandas xarray netCDF4 packaging \
+          mamba install gmt=6.4.0 numpy pandas xarray netCDF4 packaging \
                         build
 
       # Install the package that we want to test

.github/workflows/cache_data.yaml

@@ -26,7 +26,7 @@ jobs:
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/[email protected].0
+      uses: lycheeverse/[email protected].1
       with:
         # 429: Too many requests
         args: >
@@ -45,6 +45,7 @@ jobs:
           --exclude "^https://hackmd.io/@pygmt"
           --exclude "^https://doi.org"
           --exclude "^https://www.researchgate.net/project/"
+          --exclude "^https://test.pypi.org/simple/"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"

.github/workflows/check-links.yml

@@ -70,7 +70,7 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          mamba install gmt=6.3.0 numpy pandas xarray netCDF4 packaging \
+          mamba install gmt=6.4.0 numpy pandas xarray netCDF4 packaging \
                         build ipython make myst-parser geopandas \
                         sphinx sphinx-copybutton sphinx-design sphinx-gallery sphinx_rtd_theme
 
@@ -80,7 +80,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.21.1
+        uses: dawidd6/action-download-artifact@v2.22.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/ci_docs.yml

@@ -90,7 +90,7 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          mamba install gmt=6.3.0 numpy=${{ matrix.numpy-version }} \
+          mamba install gmt=6.4.0 numpy=${{ matrix.numpy-version }} \
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
                         build dvc make pytest>=6.0 \
@@ -102,7 +102,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.21.1
+        uses: dawidd6/action-download-artifact@v2.22.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/ci_tests.yaml

@@ -108,13 +108,8 @@ jobs:
       - name: Pull baseline image data from dvc remote
         if: github.event_name == 'schedule'
         run: |
-          ORIGINAL_BRANCH=$(git branch --show-current)
-          # Pull down GMT 6.4 baseline images from the gmt-6.4 branch
-          # https://github.com/GenericMappingTools/pygmt/pull/1883
-          git checkout gmt-6.4
           dvc pull
           ls -lhR pygmt/tests/baseline/
-          git checkout ${ORIGINAL_BRANCH}
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
@@ -137,7 +132,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.21.1
+        uses: dawidd6/action-download-artifact@v2.22.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/ci_tests_dev.yaml

@@ -22,7 +22,7 @@ jobs:
       uses: iterative/[email protected]
 
     - name: Setup continuous machine learning (CML)
-      uses: iterative/setup-cml@v1.1.3
+      uses: iterative/setup-cml@v1.2.0
 
     - name: Pull image data from cloud storage
       run: dvc pull --remote upstream

.github/workflows/dvc-diff.yml

@@ -21,7 +21,9 @@ jobs:
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/[email protected]
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.10'
 
       # Install formatting tools
       - name: Install formatting tools