Merge branch 'master' into psconvert-no-file-dup

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -13,6 +13,7 @@ assignees: ''
 
 **Before release**:
 
+- [ ] check if there are new [SCM releases](https://doi.org/10.5281/zenodo.1243862)
 - [ ] check if all tests pass on macOS, Linux and Windows
 - [ ] check if other GMT-derived projects work well
 	- [ ] MB-System (@PaulWessel)

.github/codecov.yml

@@ -0,0 +1,5 @@
+# Codecov configuration file
+#
+# Reference: https://docs.codecov.com/docs/codecovyml-reference
+#
+comment: false

.github/dependabot.yml

@@ -6,9 +6,17 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      # Check for updates to GitHub Actions every weekday
-      interval: "weekly"
-      day: "tuesday"
+      interval: "monthly"
+    # Allow up to 2 open pull requests at a time
+    open-pull-requests-limit: 2
+    # Specify labels for pull requests
+    labels:
+      - "maintenance"
+
+  - package-ecosystem: "pip"
+    directory: "/doc/rst/"
+    schedule:
+      interval: "monthly"
     # Allow up to 2 open pull requests at a time
     open-pull-requests-limit: 2
     # Specify labels for pull requests

.github/workflows/build.yml

@@ -4,22 +4,28 @@
 name: Build
 
 on:
-  pull_request:
-    paths-ignore:
-      - 'doc/**'
-      - '!doc/**/CMakeLists.txt'
   push:
     branches:
       - master
       - 6.[0-9]+
-    paths-ignore:
-      - 'doc/**'
-      - '!doc/**/CMakeLists.txt'
+    paths:
+      - 'ci/**'
+      - 'cmake/**'
+      - 'src/**'
+      - '**/CMakeLists.txt'
+      - '.github/workflows/build.yml'
+  pull_request:
+    paths:
+      - 'ci/**'
+      - 'cmake/**'
+      - 'src/**'
+      - 'CMakeLists.txt'
+      - '.github/workflows/build.yml'
 
 defaults:
   run:
     # default to use bash shell
-    shell: bash
+    shell: bash -el {0}
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -57,15 +63,17 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4.1.6
 
       - name: Setup vcpkg (Windows)
-        uses: dawidd6/action-download-artifact@v3.1.4
-        with:
-          workflow: ci-caches.yml
-          name: vcpkg-cache
-          path: C:\vcpkg\installed\
+        run: gh run download -n vcpkg-cache -D C:/vcpkg/installed/
         if: runner.os == 'Windows'
+        env:
+          GH_TOKEN: ${{ github.token }}
+
+      - name: Setup conda (macOS)
+        uses: conda-incubator/setup-miniconda@v3
+        if: runner.os == 'macOS'
 
       - name: Install GMT dependencies
         run: |
@@ -76,16 +84,10 @@ jobs:
         env:
           EXCLUDE_OPTIONAL: ${{ matrix.EXCLUDE_OPTIONAL }}
 
-      - name: Cache GSHHG and DCW data
-        uses: actions/cache@v4
-        id: cache-coastline
-        with:
-          path: ${{ env.COASTLINEDIR }}
-          key: coastline-${{ hashFiles('ci/download-coastlines.sh') }}
-
-      - name: Download coastlines
-        run: bash ci/download-coastlines.sh
-        if: steps.cache-coastline.outputs.cache-hit != 'true'
+      - name: Download GSHHG and DCW data
+        run: gh run download -n coastline-cache -D coastline
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       - name: Configure GMT
         run: |
@@ -113,27 +115,18 @@ jobs:
           cmake --build .
         if: runner.os == 'Windows'
 
-      - name: Download cached GMT remote data from GitHub Artifacts
-        uses: dawidd6/action-download-artifact@v3.1.4
-        with:
-          workflow: ci-caches.yml
-          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
-          ls -lRh ~/.gmt
-
       - name: Install GMT
         run: |
           cd build
           cmake --build . --target install
           # Add GMT PATH to bin
           echo "${INSTALLDIR}/bin" >> $GITHUB_PATH
 
+      - name: Download cached GMT remote data from GitHub Artifacts
+        run: gh run download -n gmt-cache -D ~/.gmt/static/
+        env:
+          GH_TOKEN: ${{ github.token }}
+
       - name: Check a few simple commands
         run: bash ci/simple-gmt-tests.sh
 

.github/workflows/check-links.yml

@@ -1,9 +1,16 @@
-# This workflow checks the links in plaintext files in the repository
+# Check links in plaintext files in the repository
+#
+# This workflow runs the lychee tool to check all links in plaintext files. It will
+# create an issue if broken links are found.
+#
+# It is scheduled to run weekly at 12 noon every Sunday.
+#
 name: Check Links
 
 on:
   # Uncomment the 'pull_request' line below to trigger the workflow in PR
   # pull_request:
+  workflow_dispatch:
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -12,13 +19,15 @@ jobs:
   check_links:
     name: Check Links
     runs-on: ubuntu-latest
+    if: github.repository == 'GenericMappingTools/gmt'
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v3.6.0
+      uses: actions/checkout@v4.1.6
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.9.3
+      id: lychee
+      uses: lycheeverse/lychee-action@v1.10.0
       with:
         # 429: Too many requests
         args: >
@@ -38,19 +47,20 @@ jobs:
           --exclude ^http://www.eumetsat.int
           --exclude ^http://nsis.sourceforge.io
           --exclude ^https://www.ethnologue.com
+          --exclude ^https://linux.die.net/man/3/printf
           --verbose
           **/*.rst
           **/*.rst_
           **/*.md
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Get current date
       id: date
       run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
 
     - name: Create Issue From File
-      uses: peter-evans/create-issue-from-file@v5
-      with:
-        title: Link Checker Report on ${{ steps.date.outputs.date }}
-        content-filepath: ./lychee/out.md
+      if: env.lychee_exit_code != 0
+      run: |
+        title="Link Checker Report on ${{ steps.date.outputs.date }}"
+        gh issue create --title "$title" --body-file ./lychee/out.md
+      env:
+        GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/ci-caches.yml

@@ -2,15 +2,17 @@
 # Create CI caches for:
 #
 # 1. GMT remote data for building documentation and running tests
-# 2. vcpkg libraries on Windows
+# 2. GMT GSHHG and DCW datasets
+# 3. vcpkg libraries on Windows
 #
 name: GMT CI Caches
 
 on:
-  # Uncomment the "push:" line to manually re-cache data artifacts in pushes
-  #push:
-  # Uncomment the 'pull_request:' line to manually re-cache data artifacts in PRs
-  # pull_request:
+  pull_request:
+    # Make any changes to the following files to refresh the cache in PRs
+    paths:
+      - '.github/workflows/ci-caches.yml'
+  workflow_dispatch:
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -22,12 +24,22 @@ concurrency:
 jobs:
   data_cache:
     name: Cache GMT data
-    # We have to use macOS, because Linux/Windows agents may fail to download
-    runs-on: macOS-latest
+    runs-on: macos-latest
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - name: Install GMT
-        run: brew install gmt
+        uses: mamba-org/setup-micromamba@v1.9.0
+        with:
+          environment-name: gmt
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+          create-args: >-
+            gmt=6.5.0
 
       - name: Download remote data
         run: |
@@ -76,28 +88,54 @@ jobs:
           gmt which -Ga $data
           gmt which -Ga $data
           # Download cache files multiple times to make sure all are downloaded
+          # Workaroud for https://github.com/GenericMappingTools/gmt/issues/8437.
+          mv ~/.gmt/gmt_data_server.txt ~/.gmt/server/
+          mv ~/.gmt/gmt_hash_server.txt ~/.gmt/server/
           gmt get -Dcache
           gmt get -Dcache
           gmt get -Dcache
+          # Workaroud for https://github.com/GenericMappingTools/gmt/issues/8437.
+          mkdir ~/.gmt/static/
+          mv ~/.gmt/server ~/.gmt/static/
+          mv ~/.gmt/cache ~/.gmt/static/
           # check files
-          ls -R ~/.gmt
+          ls -lR ~/.gmt
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
         uses: actions/upload-artifact@v4
         with:
           name: gmt-cache
-          path: |
-            ~/.gmt/cache
-            ~/.gmt/server
+          path: ~/.gmt/static
+
+  coastline_cache:
+    name: Cache GSHHG and DCW datasets
+    runs-on: ubuntu-latest
+    env:
+      COASTLINEDIR: ${{ github.workspace }}/coastline
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4.1.6
+
+      - name: Download GSHHG and DCW datasets
+        run: bash ci/download-coastlines.sh
+        env:
+          COASTLINEDIR: ${{ env.COASTLINEDIR }}
+
+      - name: Upload artifacts to GitHub
+        uses: actions/upload-artifact@v4
+        with:
+          name: coastline-cache
+          path: ${{ env.COASTLINEDIR }}
 
   vcpkg_cache:
     name: Cache vcpkg libraries
     runs-on: windows-latest
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4.1.6
 
       - name: Install vcpkg libraries
         run: bash ci/install-dependencies-windows.sh

.github/workflows/code-validator.yml

@@ -5,10 +5,17 @@ on:
     branches:
       - master
       - '[0-9]+.[0-9]+'
+    paths:
+      - 'src/**'
+      - 'cmake/**'
+      - '**/*.sh'
+      - '.github/workflows/code-validator.yml'
   pull_request:
-    paths-ignore:
-      - 'doc/**'
-      - '!doc/**/CMakeLists.txt'
+    paths:
+      - 'src/**'
+      - 'cmake/**'
+      - '**/*.sh'
+      - '.github/workflows/code-validator.yml'
 
 name: Code Validator
 
@@ -18,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4.1.6
 
       - name: Check PSL_strings.h
         run: |