Merge branch 'master' of https://github.com/GenericMappingTools/gmt

.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 }}
@@ -67,6 +73,10 @@ jobs:
           path: C:\vcpkg\installed\
         if: runner.os == 'Windows'
 
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        if: runner.os == 'macOS'
+
       - name: Install GMT dependencies
         run: |
           # $RUNNER_OS can be Linux, macOS or Windows

.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'
@@ -12,12 +19,14 @@ jobs:
   check_links:
     name: Check Links
     runs-on: ubuntu-latest
+    if: github.repository == 'GenericMappingTools/gmt'
 
     steps:
     - name: Checkout the repository
       uses: actions/[email protected]
 
     - name: Link Checker
+      id: lychee
       uses: lycheeverse/[email protected]
       with:
         # 429: Too many requests
@@ -43,15 +52,15 @@ jobs:
           **/*.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/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
 

.github/workflows/docker.yml

@@ -9,12 +9,17 @@ on:
       - master
       - 6.[0-9]+
     paths:
-      - 'src/**'
+      - 'ci/**'
       - 'cmake/**'
+      - 'src/**'
       - '**/CMakeLists.txt'
       - '.github/workflows/docker.yml'
   pull_request:
     paths:
+      - 'ci/**'
+      - 'cmake/**'
+      - 'src/**'
+      - '**/CMakeLists.txt'
       - '.github/workflows/docker.yml'
 
 defaults:

.github/workflows/docs.yml

@@ -10,17 +10,18 @@ on:
       - master
       - 6.[0-9]+
     paths:
-      - 'doc/**'
-      - '.github/workflows/**'
       - 'ci/**'
+      - 'doc/**'
+      - '**/CMakeLists.txt'
+      - '.github/workflows/docs.yml'
   release:
     types:
       - published
 
 defaults:
   run:
     # default to use bash shell
-    shell: bash
+    shell: bash -el {0}
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -66,6 +67,10 @@ jobs:
           path: C:\vcpkg\installed\
         if: runner.os == 'Windows'
 
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        if: runner.os == 'macOS'
+
       - name: Install GMT dependencies
         run: |
           # $RUNNER_OS can be Linux, macOS or Windows

.github/workflows/dvc-diff.yml

@@ -30,7 +30,7 @@ jobs:
       uses: iterative/[email protected]
 
     - name: Setup continuous machine learning (CML)
-      uses: iterative/setup-cml@v2.0.1
+      uses: iterative/setup-cml@v3
 
     - name: Setup Micromamba
       uses: mamba-org/[email protected]

.github/workflows/lint-checker.yml

@@ -3,6 +3,7 @@
 on:
   # enable pull request for debugging
   # pull_request:
+  workflow_dispatch:
   # Schedule runs daily
   schedule:
     - cron: '0 0 * * *'

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

@@ -14,6 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'GenericMappingTools/gmt'
 
+    permissions:
+      # To write assets to GitHub release
+      contents: write
+
     steps:
     - name: Checkout
       uses: actions/[email protected]
@@ -39,7 +43,6 @@ jobs:
         shasum -a 256 baseline-images.zip
 
     - name: Upload baseline image as a release asset
-      uses: shogo82148/[email protected]
-      with:
-        upload_url: ${{ github.event.release.upload_url }}
-        asset_path: baseline-images.zip
+      run: gh release upload ${{ github.ref_name }} baseline-images.zip
+      env:
+        GH_TOKEN: ${{ github.token }}

.github/workflows/remind.yml

@@ -1,8 +1,15 @@
+#
+# Create an issue to remind us some important things.
+#
+# It's scheduled to run every 6 months.
+#
 name: Reminders
 
 on:
+  workflow_dispatch:
+  # Scheduled to run at midnight on the 1st day every 6 months
   schedule:
-    - cron: '0 0 1 */6 *' # Runs at midnight on the 1st day every 6th month
+    - cron: '0 0 1 */6 *'
 
 jobs:
   review-known-failures:
@@ -14,19 +21,13 @@ jobs:
 
     - name: Find and report known failures
       run: |
-        # Get the list of known failures
-        KNOWN_FAILURES=$(grep -rl 'GMT_KNOWN_FAILURE' test/**/*.sh)
+        title="Review GMT's known failures"
 
-        # If there are known failures, create an issue
-        if [ -n "$KNOWN_FAILURES" ]; then
-          title="Review GMT's known failures"
-
-          echo "The following tests are marked as GMT_KNOWN_FAILURE and need review:" > report.md
-          echo "" >> report.md
-          while IFS= read -r line ; do echo "1. $line"; done <<< $KNOWN_FAILURES >> report.md
+        bash admin/list_known_failures.sh > report.md
 
+        if [ -s "report.md" ]; then
           gh issue create --title "$title" --body-file report.md
         fi
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/scm-check.yml

@@ -8,6 +8,7 @@ name: SCM Check
 on:
   # uncomment the 'pull_request' line to test the workflow in PRs
   # pull_request:
+  workflow_dispatch:
   schedule:
     # weekly cron job
     - cron: '0 0 * * 0'

.github/workflows/tests.yml

@@ -4,24 +4,28 @@
 name: Tests
 
 on:
-  pull_request:
   push:
     branches:
       - master
       - 6.[0-9]+
     paths:
       - 'src/**'
       - 'test/**'
-      - 'share/**'
       - 'doc/examples/**'
       - 'doc/scripts/**'
-      - '.github/workflows/**'
-      - 'ci/**'
+      - '.github/workflows/tests.yml'
+  pull_request:
+    paths:
+      - 'src/**'
+      - 'test/**'
+      - 'doc/examples/**'
+      - 'doc/scripts/**'
+      - '.github/workflows/tests.yml'
 
 defaults:
   run:
     # default to use bash shell
-    shell: bash
+    shell: bash -el {0}
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -66,6 +70,10 @@ jobs:
           path: C:\vcpkg\installed\
         if: runner.os == 'Windows'
 
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        if: runner.os == 'macOS'
+
       - name: Install GMT dependencies
         run: |
           # $RUNNER_OS can be Linux, macOS or Windows

admin/list_known_failures.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+#
+# Report the list of known failures.
+#
+
+if [ ! -d cmake ]; then
+    echo "Must be run from top-level gmt directory"
+    exit 1
+fi
+
+known_failures=$(grep -rl "GMT_KNOWN_FAILURE" test/**/*.sh doc/**/*.sh)
+if [ -n "$known_failures" ]; then
+    echo "The following tests are marked as GMT_KNOWN_FAILURE and need review:"
+    echo ""
+    while IFS= read -r line; do
+        echo "- $line"
+    done <<< $known_failures
+fi

doc/rst/requirements.txt

@@ -4,7 +4,7 @@
 #
 #   pip install -r doc/rst/requirements.txt
 #
-sphinx_rtd_theme==1.3.0
+sphinx_rtd_theme==2.0.0
 sphinx-copybutton==0.5.2
 sphinx-design==0.5.0
 sphinx-jinja==2.0.2

doc/rst/source/grd2xyz.rst

@@ -41,7 +41,7 @@ precision of the ASCII output format by editing the
 **--FORMAT_FLOAT_OUT**\ =\ *format* on the command line, or choose binary
 output using single or double precision storage. As an option you may
 output z-values without the (*x, y*) coordinates (see |-Z| below) or you can
-save the grid in the STL format for 3-D printers. Also, by giving a CPT via
+save the grid in the STL format for 3-D printers with |-T|. Also, by giving a CPT via
 |-C| we will add *r*, *g*, *b*, *a* columns to the output based on *z* values.
 
 Required Arguments

doc/rst/source/mapproject.rst

@@ -251,27 +251,27 @@ Optional Arguments
 **-W**\ [**b**\|\ **B**\|\ **e**\|\ **E**\|\ **g**\|\ **h**\|\ **j**\|\ **m**\|\ **M**\|\ **n**\|\ **o**\|\ **O**\|\ **r**\|\ **R**\|\ **w**\|\ **x**][**+n**\ [*nx*\ [/*ny*]]]
     Report a variety of plot dimensions or map regions in projected or geographic units.
     No input files are read. With no argument we report the map width and height.
-    The chosen unit of reported plot dimensions may be changed via |-D|.  For
+    The chosen unit of reported plot dimensions may be changed via |-D|. For
     other results, select from these directives:
 
     - **b** - Get the bounding box in longitude and latitude.
     - **B** - Same, but get the result in -Rw/e/s/n string format returned as trailing text.
     - **e** - Return the coordinates of the rectangular area encompassing the non-rectangular
-      area defined by your |-R| |-J|
+      area defined by your |-R| |-J|.
     - **E** - Same, but in -Rw/e/s/n string format returned as trailing text.
     - **g** - Output the plot coordinates of the appended map point *lon*/*lat*.
     - **h** - Only output the height of the map.
     - **j** - Output the map coordinates of a reference point by appending its *code* (with
       standard two-character justification codes).
     - **n** - Same, but appended reference point *rx*/*ry* is given as normalized positions
-      in the 0-1 range,.
+      in the 0-1 range.
     - **o** - If an oblique domain is set via |-R|\ *xmin/xmax/ymin/ymax*\ **+u**\ *unit* then
-      return the diagonal corner coordinates in degrees (in the order *llx urx lly ury*) 
+      return the diagonal corner coordinates in degrees (in the order *llx urx lly ury*).
     - **O** - Same, but get the equivalent |-R| string format returned as trailing text.
     - **m** - Get the rectangular region in projected plot coordinates instead.
     - **M** - Same, but returned in |-R| string format returned as trailing text.
     - **r** - Output the rectangular domain that covers an oblique area as defined by |-R| |-J|.
-    - **R** - Same, but get the result in -R| string format returned as trailing text.
+    - **R** - Same, but get the result in |-R| string format returned as trailing text.
     - **w** - Only output the width of the map in current plot units.
     - **x** - Output the map coordinates of the specific plot reference point *px*/*py*.