Merge branch 'main' into gridding/triangulate

Author: weiji14

.github/ISSUE_TEMPLATE/bump_gmt_checklist.md

@@ -0,0 +1,29 @@
+---
+name: Bump GMT version checklist
+about: Checklist for bumping the minimum required GMT version.
+title: Bump to GMT X.Y.Z
+labels: maintenance
+assignees: ''
+
+---
+
+:tada: [GMT X.Y.Z](https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z) has been released! It is installable from the
+[conda-forge channel](https://anaconda.org/conda-forge/gmt/files) using the following command:
+
+`conda install -c conda-forge gmt=X.Y.Z`
+
+<!-- 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)
+  - [ ] Update `.github/workflows/cache_data.yaml`
+  - [ ] Update `.github/workflows/ci_docs.yml`
+  - [ ] Update `.github/workflows/ci_tests.yaml`
+  - [ ] Update `doc/install.rst`
+  - [ ] Update `environment.yml`
+  - [ ] 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/ISSUE_TEMPLATE/feature_request.md

@@ -1,5 +1,5 @@
 ---
-name: Feature request
+name: Feature request - General feature
 about: Request the addition of a new feature/functionality
 title: ''
 labels: feature request

.github/ISSUE_TEMPLATE/module_request.md

@@ -0,0 +1,31 @@
+---
+name: Feature request - Wrap new GMT module
+about: Request PyGMT wrapper for a GMT module
+title: Wrapper for <module-name>
+labels: feature request
+assignees: ''
+
+---
+
+<!-- Please replace <module-name> in the issue title and the description with the name of the requested module and add the description of the module. -->
+
+**Description of the desired module**:
+
+Implement [`<module-name>`](https://docs.generic-mapping-tools.org/latest/<module-name>.html) which `<insert description of the GMT module>`.
+
+<!-- Please be as detailed as you can in your description. If possible, include an example of how you would like to use this feature (even better if it's a code example). -->
+
+
+**Are you willing to help implement and maintain this feature?** Yes/No
+
+<!-- Every feature we add is code that we will have to maintain and keep updated. This takes a lot of effort. If you are willing to be involved in the project and help maintain your feature, it will make it easier for us to accept it. -->
+
+**Checklist for wrapping GMT Module**
+
+<!-- Please do not edit this section when submitting pull requests. This checklist will help track progress on wrapping the module. -->
+
+- [ ] 'Initial feature implementation' Pull Request (PR)
+- [ ] 'Add missing aliases to module' documentation PR
+- [ ] 'Support additional functionality in module' PR (optional)
+- [ ] 'Add gallery example for module' documentation PR
+- [ ] 'Add tutorial for module' documentation PR (optional)

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -16,10 +16,11 @@ assignees: ''
 - [ ] Wrap Y ()
 
 **Before release**:
+- [ ] Run `grep --include="*.py" -r 'remove_version="vX.Y.Z"' pygmt` from the base of the repository to check if any deprecations and related tests should be removed in this version
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
 - [ ] 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
+  - [ ] Update `CITATION.cff` and BibTeX at 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))

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,6 +14,7 @@ Fixes #
 - [ ] Add tests for new features or tests that would have caught the bug that you're fixing.
 - [ ] Add new public functions/methods/classes to `doc/api/index.rst`.
 - [ ] Write detailed docstrings for all functions/methods.
+- [ ] If wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
 - [ ] If adding new functionality, add an example to docstrings or tutorials.
 
 **Slash Commands**

.github/workflows/cache_data.yaml

@@ -19,22 +19,26 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3.0.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/[email protected]
         with:
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.2.0 \
+          mamba install gmt=6.3.0 \
                         numpy pandas xarray netCDF4 packaging matplotlib
 
       # Install the package that we want to test

.github/workflows/check-links.yml

@@ -15,33 +15,32 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v3.0.0
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v3.0.0
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.0.8
+      uses: lycheeverse/lychee-action@v1.3.2
       with:
         # 429: Too many requests
         args: >
           --accept 429
+          --exclude-mail
           --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$"
+          --exclude "^https://docs.generic-mapping-tools.org/latest/%3Cmodule-name%3E.html$"
           --exclude "https://hackmd.io/@pygmt"
           --verbose
           "repository/**/*.rst"
@@ -51,8 +50,12 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+    - name: Get current date
+      id: date
+      run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
+
     - name: Create Issue From File
       uses: peter-evans/create-issue-from-file@v3
       with:
-        title: Link Checker Report
+        title: Link Checker Report on ${{ steps.date.outputs.date }}
         content-filepath: ./lychee/out.md

.github/workflows/ci_docs.yml

@@ -13,7 +13,6 @@ on:
       - '*.json'
       - 'LICENSE.txt'
       - '.gitignore'
-      - '.pylintrc'
   release:
     types:
       - published
@@ -25,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: ['3.9']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -36,6 +35,7 @@ jobs:
             isDraft: true
           - os: windows-latest
             isDraft: true
+    timeout-minutes: 30
     defaults:
       run:
         shell: bash -l {0}
@@ -49,34 +49,38 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3.0.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/[email protected]
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.2.0 numpy pandas xarray netCDF4 packaging \
+          mamba install gmt=6.3.0 numpy pandas xarray netCDF4 packaging \
                         ipython make myst-parser geopandas \
                         sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: conda list
+        run: mamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.1
+        uses: dawidd6/action-download-artifact@v2.17.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -103,7 +107,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@28c7f3d2b5162b5ddd3dfd9a45aa55eaf396478b
+        uses: actions/checkout@v3.0.0
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_tests.yaml

@@ -15,7 +15,6 @@ on:
       - 'README.rst'
       - 'LICENSE.txt'
       - '.gitignore'
-      - '.pylintrc'
   release:
     types:
       - published
@@ -30,7 +29,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.9]
+        python-version: ['3.8', '3.9']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -44,15 +43,16 @@ jobs:
           # - os: ubuntu-latest
           #   python-version: 3.7
           #   isDraft: true
-        # Pair Python 3.7 with NumPy 1.18 and Python 3.9 with NumPy 1.21
-        # Only install optional packages on Python 3.9/NumPy 1.21
+        # Pair Python 3.8 with NumPy 1.19 and Python 3.9 with NumPy 1.22
+        # Only install optional packages on Python 3.9/NumPy 1.22
         include:
-          - python-version: 3.7
-            numpy-version: '1.18'
+          - python-version: '3.8'
+            numpy-version: '1.19'
             optional-packages: ''
-          - python-version: 3.9
-            numpy-version: '1.21'
-            optional-packages: 'geopandas'
+          - python-version: '3.9'
+            numpy-version: '1.22'
+            optional-packages: 'geopandas ipython'
+    timeout-minutes: 30
     defaults:
       run:
         shell: bash -l {0}
@@ -72,37 +72,40 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3.0.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/[email protected]
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.2.0 numpy=${{ matrix.numpy-version }} \
+          mamba install gmt=6.3.0 numpy=${{ matrix.numpy-version }} \
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
-                        codecov coverage[toml] dvc ipython make \
-                        pytest-cov pytest-mpl pytest>=6.0 \
-                        sphinx-gallery
+                        dvc make pytest>=6.0 \
+                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery tomli
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: conda list
+        run: mamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.1
+        uses: dawidd6/action-download-artifact@v2.17.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -121,7 +124,7 @@ jobs:
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
         run: |
-          dvc pull
+          dvc pull --verbose
           ls -lhR pygmt/tests/baseline/
 
       # Install the package that we want to test
@@ -144,7 +147,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2.0.3
+        uses: codecov/codecov-action@v2.1.0
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY