Merge branch 'main' into add-tutorial-meca

GenericMappingTools · May 2, 2024 · eec5e37 · eec5e37
2 parents 649bf83 + 19edbd3
commit eec5e37
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yaml → .github/ISSUE_TEMPLATE/1-bug_report.yaml b/.github/ISSUE_TEMPLATE/bug_report.yaml → .github/ISSUE_TEMPLATE/1-bug_report.yaml
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yaml → ...hub/ISSUE_TEMPLATE/2-feature_request.yaml b/.github/ISSUE_TEMPLATE/feature_request.yaml → ...hub/ISSUE_TEMPLATE/2-feature_request.yaml
diff --git a/.github/ISSUE_TEMPLATE/module_request.yaml → .github/ISSUE_TEMPLATE/3-module_request.yaml b/.github/ISSUE_TEMPLATE/module_request.yaml → .github/ISSUE_TEMPLATE/3-module_request.yaml
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md → ...hub/ISSUE_TEMPLATE/4-release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md → ...hub/ISSUE_TEMPLATE/4-release_checklist.md
@@ -43,7 +43,7 @@ assignees: ''
 - [ ] Manually upload the pygmt-vX.Y.Z.zip and baseline-images.zip files to https://zenodo.org/deposit, ensure that it is filed under the correct reserved DOI
 
 **After release**:
-- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Done automatically by conda-forge's bot, but remember to pin NEP29 versions]
+- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Done automatically by conda-forge's bot, but remember to pin SPEC0 versions]
 - [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt (after conda-forge update)
 - [ ] Announce the release on:
   - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! draft on https://hackmd.io/@pygmt. requires moderator status)

diff --git a/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md → ...ub/ISSUE_TEMPLATE/5-bump_gmt_checklist.md b/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md → ...ub/ISSUE_TEMPLATE/5-bump_gmt_checklist.md
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -6,7 +6,7 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      # Check for updates to GitHub Actions every weekday
+      # Check for updates to GitHub Actions on Tuesdays
       interval: "weekly"
       day: "tuesday"
     # Allow up to 2 open pull requests at a time

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -37,14 +37,14 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].4
         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].3
+        uses: conda-incubator/[email protected].4
         with:
           auto-activate-base: true
           activate-environment: ""  # base environment
@@ -64,29 +64,25 @@ jobs:
 
       # 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: |
+          gh run download -n gmt-cache -D gmt-cache
+          # Move downloaded files to ~/.gmt directory and list them
           mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          mv gmt-cache/* ~/.gmt
+          rmdir gmt-cache
           # 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
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package
         run: make install
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v2.3.0
+        uses: CodSpeedHQ/action@v2.4.1
         with:
           run: |
             python -c "import pygmt; pygmt.show_versions()"

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].1
+        uses: actions/[email protected].4
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -80,7 +80,7 @@ jobs:
         with:
           name: gmt-cache
           path: |
-              ~/.gmt/cache
-              ~/.gmt/server
-              ~/.gmt/gmt_data_server.txt
-              ~/.gmt/gmt_hash_server.txt
+            ~/.gmt/cache
+            ~/.gmt/server
+            ~/.gmt/gmt_data_server.txt
+            ~/.gmt/gmt_hash_server.txt
diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -23,19 +23,19 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.9.3
+      uses: lycheeverse/lychee-action@v1.10.0
       with:
         # 429: Too many requests
         args: >
@@ -72,4 +72,4 @@ jobs:
         title="Link Checker Report on ${{ steps.date.outputs.date }}"
         gh issue create --title "$title" --body-file ./lychee/out.md
         env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          GH_TOKEN: ${{ github.token }}
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -69,7 +69,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].4
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -112,21 +112,17 @@ jobs:
 
       # 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: |
+          gh run download -n gmt-cache -D gmt-cache
+          # Move downloaded files to ~/.gmt directory and list them
           mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          mv gmt-cache/* ~/.gmt
+          rmdir gmt-cache
           # 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
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package
@@ -139,7 +135,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/[email protected].1
+        uses: actions/[email protected].4
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one
@@ -162,7 +158,7 @@ jobs:
           # to get the right commit hash.
           message="Deploy $version from $(git rev-parse --short HEAD)"
           cd deploy
-          # Need to have this file so that Github doesn't try to run Jekyll
+          # Need to have this file so that GitHub doesn't try to run Jekyll
           touch .nojekyll
           # Delete all the files and replace with our new  set
           echo -e "\nRemoving old files from previous builds of ${version}:"

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].1
+        uses: actions/[email protected].4
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -71,21 +71,17 @@ jobs:
 
       # 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: |
+          gh run download -n gmt-cache -D gmt-cache
+          # Move downloaded files to ~/.gmt directory and list them
           mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          mv gmt-cache/* ~/.gmt
+          rmdir gmt-cache
           # 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
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package

diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -92,7 +92,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].4
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -128,21 +128,17 @@ jobs:
 
       # 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: |
+          gh run download -n gmt-cache -D gmt-cache
+          # Move downloaded files to ~/.gmt directory and list them
           mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          mv gmt-cache/* ~/.gmt
+          rmdir gmt-cache
           # 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
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote

diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -47,7 +47,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].4
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -135,21 +135,17 @@ jobs:
 
       # 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: |
+          gh run download -n gmt-cache -D gmt-cache
+          # Move downloaded files to ~/.gmt directory and list them
           mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          mv gmt-cache/* ~/.gmt
+          rmdir gmt-cache
           # 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
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
@@ -44,7 +44,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].4
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -83,24 +83,20 @@ jobs:
 
       # 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: |
+          gh run download -n gmt-cache -D gmt-cache
+          # Move downloaded files to ~/.gmt directory and list them
           mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          mv gmt-cache/* ~/.gmt
+          rmdir gmt-cache
           # Change modification times of the two files, so GMT won't refresh it
           # The two files are in the `~/.gmt/server` directory for GMT<=6.4, and
           # in the `~/.gmt` directory for GMT>=6.5.
           mv ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt ~/.gmt/server/
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
           ls -lhR ~/.gmt
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package

diff --git a/.github/workflows/dvc-diff.yml b/.github/workflows/dvc-diff.yml
@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         # fetch all history so that dvc diff works
         fetch-depth: 0
@@ -52,7 +52,7 @@ jobs:
     # Report last updated at commit abcdef
     - name: Generate the image diff report
       env:
-        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        repo_token: ${{ github.token }}
       run: |
         echo -e "## Summary of changed images\n" > report.md
         echo -e "This is an auto-generated report of images that have changed on the DVC remote\n" >> report.md

diff --git a/.github/workflows/format-command.yml b/.github/workflows/format-command.yml
@@ -18,7 +18,7 @@ jobs:
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].4
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -48,11 +48,3 @@ jobs:
             git commit -am "[format-command] fixes"
             git push
           fi
-
-      - name: Add reaction
-        uses: peter-evans/[email protected]
-        with:
-          token: ${{ steps.generate-token.outputs.token }}
-          repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
-          comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
-          reactions: hooray
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -45,7 +45,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0