Merge branch 'main' into wrap-grdvolume

Author: willschlitzer

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -21,24 +21,24 @@ assignees: ''
   - [ ] 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-python-and-gmt-versions
-  - [ ] Copy draft changelog from Release Drafter and edit it to look nice
+  - [ ] 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**:
 - [ ] 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 file to https://zenodo.org/deposit, ensure that it is filed under the correct reserved DOI
+- [ ] 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)
-  - [ ] [Twitter](https://twitter.com/gmt_dev)
+  - [ ] [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/config.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/workflows/cache_data.yaml

@@ -17,34 +17,36 @@ jobs:
         shell: bash -l {0}
 
     steps:
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v2.3.4
+        with:
+          # fecth all history so that setuptools-scm works
+          fetch-depth: 0
+
       # Setup Miniconda
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           channels: conda-forge
           miniconda-version: "latest"
 
-      # Install GMT
-      - name: Install GMT
-        run: conda install -c conda-forge/label/dev gmt=6.2.0rc2
+      # 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
         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
-          # Download one tile of the 03s srtm data.
-          # @N35E135.earth_relief_03s_g.nc is for internal use only.
-          # The naming scheme may change.
-          # DO NOT USE IT IN SCRIPTS.
-          gmt which -Ga @N35E135.earth_relief_03s_g.nc
-          # @srtm_tiles.nc is needed for 03s and 01s relief data
-          gmt which -Ga @srtm_tiles.nc
-          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 @fractures_06.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/ci_docs.yml

@@ -4,7 +4,7 @@ name: Docs
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
     types: [opened, reopened, synchronize, ready_for_review]
     paths-ignore:
@@ -43,7 +43,7 @@ jobs:
     steps:
       # Cancel previous runs that are not completed
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.9.0
+        uses: styfle/cancel-workflow-action@0.9.1
         with:
           access_token: ${{ github.token }}
 
@@ -66,8 +66,7 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install conda-forge/label/dev::gmt=6.2.0rc2 \
-                        numpy pandas xarray netCDF4 packaging \
+          conda install gmt=6.2.0 numpy pandas xarray netCDF4 packaging \
                         ipython make myst-parser \
                         sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme
 
@@ -77,7 +76,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.0
+        uses: dawidd6/action-download-artifact@v2.14.1
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -115,7 +114,7 @@ jobs:
 
       - name: Push the built HTML to gh-pages
         run: |
-          # Detect if this is a release or from the master branch
+          # Detect if this is a release or from the main branch
           if [[ "${GITHUB_EVENT_NAME}" == "release" ]]; then
               # Get the tag name without the "refs/tags/" part
               version="${GITHUB_REF#refs/*/}"

.github/workflows/ci_tests.yaml

@@ -4,7 +4,7 @@ name: Tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
     types: [opened, reopened, synchronize, ready_for_review]
     paths-ignore:
@@ -44,15 +44,15 @@ jobs:
           # - os: ubuntu-latest
           #   python-version: 3.7
           #   isDraft: true
-        # Pair Python 3.7 with NumPy 1.17 and Python 3.9 with NumPy 1.20
-        # Only install optional packages on Python 3.9/NumPy 1.20
+        # 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
         include:
           - python-version: 3.7
-            numpy-version: '1.17'
+            numpy-version: '1.18'
             optional-packages: ''
           - python-version: 3.9
-            numpy-version: '1.20'
-            optional-packages: ''  # 'geopandas'
+            numpy-version: '1.21'
+            optional-packages: 'geopandas'
     defaults:
       run:
         shell: bash -l {0}
@@ -66,7 +66,7 @@ jobs:
     steps:
       # Cancel previous runs that are not completed
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.9.0
+        uses: styfle/cancel-workflow-action@0.9.1
         with:
           access_token: ${{ github.token }}
 
@@ -89,8 +89,7 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install conda-forge/label/dev::gmt=6.2.0rc2 \
-                        numpy=${{ matrix.numpy-version }} \
+          conda install gmt=6.2.0 numpy=${{ matrix.numpy-version }} \
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
                         codecov coverage[toml] dvc ipython make \
@@ -103,7 +102,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.0
+        uses: dawidd6/action-download-artifact@v2.14.1
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -145,7 +144,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1.5.0
+        uses: codecov/codecov-action@v2.0.2
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.github/workflows/ci_tests_dev.yaml

@@ -4,7 +4,7 @@ name: GMT Dev Tests
 
 on:
   # push:
-  #   branches: [ master ]
+  #   branches: [ main ]
   pull_request:
     types: [ready_for_review]
     paths-ignore:
@@ -23,7 +23,7 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  test_gmt_master:
+  test_gmt_dev:
     name: ${{ matrix.os }} - GMT ${{ matrix.gmt_git_ref }}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -39,7 +39,7 @@ jobs:
     steps:
       # Cancel previous runs that are not completed
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.9.0
+        uses: styfle/cancel-workflow-action@0.9.1
         with:
           access_token: ${{ github.token }}
 
@@ -83,10 +83,11 @@ jobs:
       # Install dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install ninja cmake libblas libcblas liblapack fftw gdal=3.2 geopandas \
+          conda install ninja cmake libblas libcblas liblapack fftw gdal geopandas \
                         ghostscript libnetcdf hdf5 zlib curl pcre make dvc
           pip install --pre numpy pandas xarray netCDF4 packaging \
-                            ipython pytest-cov pytest-mpl pytest>=6.0 sphinx-gallery
+                            ipython pytest-cov pytest-mpl pytest>=6.0 sphinx-gallery \
+                            tomli
 
       # Build and install latest GMT from GitHub
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Linux/macOS)
@@ -102,7 +103,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.0
+        uses: dawidd6/action-download-artifact@v2.14.1
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/dvc-diff.yml

@@ -22,7 +22,7 @@ jobs:
       uses: iterative/setup-dvc@v1.0.3
 
     - name: Setup continuous machine learning (CML)
-      uses: iterative/setup-cml@v1.0.0
+      uses: iterative/setup-cml@v1.0.3
 
     - name: Pull image data from cloud storage
       run: dvc pull --remote upstream
@@ -44,7 +44,7 @@ jobs:
       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
-        dvc diff --show-md master HEAD >> report.md
+        dvc diff --show-md main HEAD >> report.md
 
         # Get just the filename of the added and modified image from the report
         awk 'NF==5 && NR>=7 && $2=="added" {print $4}' report.md > added_files.txt
@@ -68,8 +68,8 @@ jobs:
           cml-publish --title $line --md "$line" >> modified_images_new.md < /dev/null
         done < modified_files.txt
 
-        # Pull images in the master branch from cloud storage
-        git checkout master
+        # Pull images in the main branch from cloud storage
+        git checkout main
         dvc pull --remote upstream
         # Upload old images
         while IFS= read -r line; do

.github/workflows/publish-to-pypi.yml

@@ -2,18 +2,18 @@
 
 name: Publish to PyPI
 
-# Only run for pushes to the master branch and releases.
+# Only run for pushes to the main branch and releases.
 on:
   push:
     branches:
-      - master
+      - main
   release:
     types:
       - published
   # Runs for pull requests should be disabled other than for testing purposes
   #pull_request:
   #  branches:
-  #    - master
+  #    - main
 
 jobs:
   publish-pypi:

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

@@ -0,0 +1,40 @@
+# Upload the ZIP archive of baseline images as a release asset
+
+name: Upload baseline images
+
+# Only run for releases
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  upload-baseline:
+    name: Upload baseline images
+    runs-on: ubuntu-latest
+    if: github.repository == 'GenericMappingTools/pygmt'
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2.3.4
+
+    - name: Setup data version control (DVC)
+      uses: iterative/setup-dvc@v1.0.3
+
+    - name: Pull baseline image data from dvc remote
+      run: |
+        dvc pull
+        ls -lhR pygmt/tests/baseline/
+
+    - name: Create the baseline image asset in zip format
+      run: |
+        mkdir baseline-images
+        mv pygmt/tests/baseline/*.png baseline-images/
+        zip -r baseline-images.zip baseline-images
+        shasum -a 256 baseline-images.zip
+
+    - name: Upload baseline image as a release asset
+      uses: shogo82148/actions-upload-release-asset@v1.3.1
+      with:
+        upload_url: ${{ github.event.release.upload_url }}
+        asset_path: baseline-images.zip

.github/workflows/release-drafter.yml

@@ -4,13 +4,13 @@ on:
   push:
     # branches to consider in the event; optional, defaults to all
     branches:
-      - master
+      - main
 
 jobs:
   update_release_draft:
     runs-on: ubuntu-latest
     steps:
-      # Drafts your next Release notes as Pull Requests are merged into "master"
+      # Drafts your next Release notes as Pull Requests are merged into "main"
       - uses: release-drafter/release-drafter@v5.15.0
         with:
           # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml