Merge branch 'main' into mambaforge

Author: weiji14

.codecov.yml

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvc/.gitignore

@@ -0,0 +1,4 @@
+[core]
+    remote = upstream
+['remote "upstream"']
+    url = https://dagshub.com/GenericMappingTools/pygmt.dvc

.dvc/config

@@ -0,0 +1,3 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.dvcignore

@@ -1,33 +1,44 @@
 ---
 name: PyGMT release checklist
 about: Checklist for a new PyGMT release.
-title: Release PyGMT x.x.x
+title: Release PyGMT vX.Y.Z
 labels: maintenance
 assignees: ''
 
 ---
 
-**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/0.x.x)
+**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
 **Scheduled Date**: YYYY/MM/DD
+**Pull request due date**: YYYY/MM/DD
+
+**Priority PRs/issues to complete prior to release**
+- [ ] Wrap X ()
+- [ ] Wrap Y ()
 
 **Before release**:
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
-- [ ] Update Changelog
-- [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
-- [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
+- [ ] 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 information https://github.com/GenericMappingTools/pygmt#citing-pygmt
+  - [ ] Add the documentation link https://github.com/GenericMappingTools/pygmt#documentation-for-other-versions
+  - [ ] Add compatibility information https://github.com/GenericMappingTools/pygmt#compatibility-with-gmt-and-pythonnumpy-versions
+  - [ ] Copy draft changelog from Release Drafter and edit it to look nice ([see maintainers guide for details](https://www.pygmt.org/dev/maintenance.html#updating-the-changelog))
 
 **Release**:
-- [ ] Go to [GitHub Release](https://github.com/GenericMappingTools/pygmt/releases) and make a release, this will automatically create a tag too
-- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, make sure you file it under the correct reserved DOI
+- [ ] At the [PyGMT release page on GitHub](https://github.com/GenericMappingTools/pygmt/releases):
+  - [ ] Edit the draft release notes with the finalized changelog
+  - [ ] Set the tag version and release title to vX.Y.Z
+  - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
+- [ ] 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) [Usually done automatically by conda-forge's bot]
-- [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt
+- [ ] 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/)
+  - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! draft on https://hackmd.io/@pygmt. requires moderator status)
   - [ ] [Major/Minor releases only] GMT [website](https://github.com/GenericMappingTools/website) (News)
-  - [ ] [ResearchGate](https://www.researchgate.net/project/PyGMT-A-Python-interface-for-the-Generic-Mapping-Tools)
-
+  - [ ] [ResearchGate](https://www.researchgate.net/project/PyGMT-A-Python-interface-for-the-Generic-Mapping-Tools) (after forum announcement)
+  - [ ] [Twitter](https://twitter.com/gmt_dev) (after forum announcement)
 ---
 
 - [ ] Party :tada: (don't tick before all other checkboxes are ticked!)

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,19 @@
+codecov:
+  notify:
+    require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto  # increase overall coverage on each pull request
+        threshold: 0.25%  # Allow the coverage to drop by X%
+        if_not_found: success
+        if_ci_failed: failure
+    patch:
+      default:
+        target: 90%  # >=90% of new changes should be tested
+        if_not_found: success
+        if_ci_failed: failure
+
+comment: off

.github/codecov.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/master/CONTRIBUTING.md) and [code of conduct](https://github.com/GenericMappingTools/pygmt/blob/master/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/pygmt/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/master/CONTRIBUTING.md) and abide by our [code of conduct](https://github.com/GenericMappingTools/pygmt/blob/master/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/pygmt/blob/main/CODE_OF_CONDUCT.md).
 
   A few things to keep in mind:
 

.github/config.yml

@@ -1,30 +1,38 @@
-name-template: 'v$NEXT_PATCH_VERSION'
-tag-template: 'v$NEXT_PATCH_VERSION'
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+version-resolver:
+  minor:
+    labels:
+      - 'feature'
+  default: patch
 categories:
   - title: 'New Features'
     label: 'feature'
   - title: 'Enhancements'
     label: 'enhancement'
-  - title: 'Documentation'
-    label: 'documentation'
+  - title: 'Deprecations'
+    label: 'deprecation'
   - title: 'Bug Fixes'
     label: 'bug'
+  - title: 'Documentation'
+    label: 'documentation'
   - title: 'Maintenance'
     label: 'maintenance'
-  - title: 'Deprecations'
-    label: 'deprecation'
 exclude-labels:
   - 'skip-changelog'
-change-template: '* $TITLE (#$NUMBER)'
+category-template: '### $TITLE'
+change-template: '* $TITLE ([#$NUMBER]($URL))'
 template: |
-  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3781524.svg)](https://doi.org/10.5281/zenodo.3781524)
+  ## Release v$RESOLVED_VERSION (20YY/MM/DD)
+
+  [![Digital Object Identifier for PyGMT v$RESOLVED_VERSION](https://zenodo.org/badge/DOI/10.5281/zenodo.3781524.svg)](https://doi.org/10.5281/zenodo.3781524)
 
-  ## Highlights
+  ### Highlights
 
   *
 
   $CHANGES
 
-  ## Contributors
+  ### Contributors
 
   $CONTRIBUTORS

.github/release-drafter.yml

@@ -12,31 +12,41 @@ jobs:
   gmt_cache:
     name: Cache GMT artifacts
     runs-on: macOS-latest
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          # fecth all history so that setuptools-scm works
+          fetch-depth: 0
+
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           channels: conda-forge
           miniconda-version: "latest"
 
-      # Install GMT
-      - name: Install GMT
-        shell: bash -l {0}
-        run: conda install -c conda-forge gmt=6.1.1
+      # Install GMT and other required dependencies from conda-forge
+      - name: Install dependencies
+        run: |
+          conda install gmt=6.2.0 \
+                        numpy pandas xarray netCDF4 packaging matplotlib
+
+      # Install the package that we want to test
+      - name: Install the package
+        run: |
+          python setup.py sdist --formats=zip
+          pip install dist/*
 
       # Download remote files
       - name: Download remote data
-        shell: bash -l {0}
         run: |
-          gmt which -Ga @earth_relief_10m_p @earth_relief_10m_g \
-                        @earth_relief_30m_p @earth_relief_30m_g \
-                        @earth_relief_01d_p @earth_relief_01d_g \
-                        @earth_relief_05m_p @earth_relief_05m_g
-          gmt which -Ga @ridge.txt @Table_5_11.txt @test.dat.nc \
-                        @tut_bathy.nc @tut_quakes.ngdc @tut_ship.xyz \
-                        @usgs_quakes_22.txt
+          python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub

.github/workflows/cache_data.yaml

@@ -0,0 +1,58 @@
+# This workflow checks the links in plaintext and HTML files
+name: Check Links
+
+on:
+  # Uncomment the 'pull_request' line below to trigger the workflow in PR
+  # pull_request:
+  # Schedule runs on 12 noon every Sunday
+  schedule:
+    - cron: '0 12 * * 0'
+
+jobs:
+  check_links:
+    name: Check Links
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout the repository
+      uses: actions/[email protected]
+      with:
+        path: repository
+
+    - name: Checkout the documentation
+      uses: actions/[email protected]
+      with:
+        ref: gh-pages
+        path: documentation
+
+    - name: Link Checker
+      uses: lycheeverse/[email protected]
+      with:
+        # 429: Too many requests
+        args: >
+          --accept 429
+          --exclude "^https://doi.org/10.5281/zenodo$"
+          --exclude "^https://zenodo.org/badge/DOI/$"
+          --exclude "^https://zenodo.org/badge/DOI/10.5281/zenodo$"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
+          --exclude "^https://www.generic-mapping-tools.org/_static/gmt-logo.png/$"
+          --exclude "^https://www.generic-mapping-tools.org/_static/gmt-logo.png/n/n$"
+          --exclude "^``@ridge.txt$"
+          --exclude "^git"
+          --exclude "^file://"
+          --exclude "^https://docs.generic-mapping-tools.org/latest/%s$"
+          --exclude "https://hackmd.io/@pygmt"
+          --verbose
+          "repository/**/*.rst"
+          "repository/**/*.md"
+          "repository/**/*.py"
+          "documentation/dev/**/*.html"
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Create Issue From File
+      uses: peter-evans/create-issue-from-file@v3
+      with:
+        title: Link Checker Report
+        content-filepath: ./lychee/out.md