Merge remote-tracking branch 'upstream/master'

Author: michaelgrund

.github/workflows/cache_data.yaml

@@ -19,7 +19,7 @@ jobs:
     steps:
       # 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"

.github/workflows/check-links.yml

@@ -26,7 +26,7 @@ jobs:
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.0.6
+      uses: lycheeverse/lychee-action@v1.0.7
       with:
         # 429: Too many requests
         args: >
@@ -52,7 +52,7 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Create Issue From File
-      uses: peter-evans/create-issue-from-file@v2.3.2
+      uses: peter-evans/create-issue-from-file@v3
       with:
         title: Link Checker Report
         content-filepath: ./lychee/out.md

.github/workflows/ci_docs.yml

@@ -43,7 +43,7 @@ jobs:
     steps:
       # Cancel previous runs that are not completed
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.8.0
+        uses: styfle/cancel-workflow-action@0.9.0
         with:
           access_token: ${{ github.token }}
 
@@ -56,7 +56,7 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -66,9 +66,10 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
+          conda install -c conda-forge/label/dev gmt=6.2.0rc1
+          conda install numpy pandas xarray netCDF4 packaging \
                         ipython make myst-parser \
-                        sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme=0.4.3
+                        sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages

.github/workflows/ci_tests.yaml

@@ -25,12 +25,12 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9]
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -41,25 +41,29 @@ jobs:
             isDraft: true
           - os: windows-latest
             isDraft: true
-          - os: ubuntu-latest
-            python-version: 3.7
-            isDraft: true
-          - os: ubuntu-latest
-            python-version: 3.8
-            isDraft: true
+          # - 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
+        include:
+          - python-version: 3.7
+            numpy-version: '1.17'
+          - python-version: 3.9
+            numpy-version: '1.20'
     defaults:
       run:
         shell: bash -l {0}
 
-    # environmental variables used in coverage
+    # Environment variables used by codecov
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
+      NUMPY: ${{ matrix.numpy-version }}
 
     steps:
       # Cancel previous runs that are not completed
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.8.0
+        uses: styfle/cancel-workflow-action@0.9.0
         with:
           access_token: ${{ github.token }}
 
@@ -72,7 +76,7 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -82,7 +86,9 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
+          conda install -c conda-forge/label/dev gmt=6.2.0rc1
+          conda install numpy=${{ matrix.numpy-version }} \
+                        pandas xarray netCDF4 packaging \
                         codecov coverage[toml] dvc ipython make \
                         pytest-cov pytest-mpl pytest>=6.0 \
                         sphinx-gallery
@@ -135,8 +141,8 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1.2.2
+        uses: codecov/codecov-action@v1.4.1
         with:
           file: ./coverage.xml # optional
-          env_vars: OS,PYTHON
+          env_vars: OS,PYTHON,NUMPY
           fail_ci_if_error: false

.github/workflows/ci_tests_dev.yaml

@@ -1,5 +1,4 @@
-# This workflow installs PyGMT dependencies, builds documentation and runs tests on GMT dev version
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# This workflow installs PyGMT and runs tests on GMT dev version
 
 name: GMT Dev Tests
 
@@ -10,10 +9,13 @@ on:
     types: [ready_for_review]
     paths-ignore:
       - 'doc/**'
+      - 'examples/**'
       - '*.md'
       - '*.json'
       - 'README.rst'
       - 'LICENSE.txt'
+      - '.gitignore'
+      - '.pylintrc'
   repository_dispatch:
     types: [test-gmt-dev-command]
   # Schedule daily tests
@@ -28,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.9]
-        os: [ubuntu-20.04, macOS-10.15, windows-latest]
+        os: [ubuntu-latest, macOS-11.0, windows-latest]
         gmt_git_ref: [master]
     defaults:
       run:
@@ -37,7 +39,7 @@ jobs:
     steps:
       # Cancel previous runs that are not completed
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.8.0
+        uses: styfle/cancel-workflow-action@0.9.0
         with:
           access_token: ${{ github.token }}
 
@@ -71,8 +73,9 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
+          activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
           miniconda-version: "latest"
@@ -81,8 +84,9 @@ jobs:
       - name: Install dependencies
         run: |
           conda install ninja cmake libblas libcblas liblapack fftw gdal \
-                        ghostscript libnetcdf hdf5 zlib curl pcre ipython \
-                        dvc pytest pytest-cov pytest-mpl
+                        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
 
       # Build and install latest GMT from GitHub
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Linux/macOS)

.github/workflows/dvc-diff.yml

@@ -0,0 +1,118 @@
+# Checks for image diffs in a Pull Request and adds a GitHub comment showing the diff
+name: DVC image diff
+
+on:
+  pull_request:
+    paths:
+      - 'pygmt/tests/baseline/*.png.dvc'
+
+jobs:
+  dvc-diff:
+    name: DVC image diff
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2.3.4
+      with:
+        # fetch all history so that dvc diff works
+        fetch-depth: 0
+
+    - name: Setup data version control (DVC)
+      uses: iterative/setup-dvc@v1.0.2
+
+    - name: Setup continuous machine learning (CML)
+      uses: iterative/setup-cml@v1.0.0
+
+    - name: Pull image data from cloud storage
+      run: dvc pull --remote upstream
+
+    # Produce the markdown diff report, which should look like:
+    # ## Summary of changed images
+    #
+    # This is an auto-generated report of images that have changed on the DVC remote
+    #
+    # | Status   | Path                                |
+    # |----------|-------------------------------------|
+    # | added    | pygmt/tests/baseline/test_image.png |
+    # | deleted  | pygmt/tests/baseline/test_image2.png |
+    # | modified | pygmt/tests/baseline/test_image3.png |
+    - name: Generate the image diff report
+      env:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+      id: image-diff
+      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
+
+        # 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
+        awk 'NF==5 && NR>=7 && $2=="modified" {print $4}' report.md > modified_files.txt
+
+        # Append each image to the markdown report
+        echo -e "## Image diff(s)\n" >> report.md
+        echo -e "<details>\n" >> report.md
+
+        # Added images
+        echo -e "### Added images\n" >> report.md
+        while IFS= read -r line; do
+          echo -e "- $line \n" >> report.md
+          cml-publish --title $line --md "$line" >> report.md < /dev/null
+        done < added_files.txt
+
+        # Modified images
+        echo -e "### Modified images\n" >> report.md
+        # Upload new images
+        while IFS= read -r line; do
+          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
+        dvc pull --remote upstream
+        # Upload old images
+        while IFS= read -r line; do
+          cml-publish --title $line --md "$line" >> modified_images_old.md < /dev/null
+        done < modified_files.txt
+
+        # Append image report for modified images
+        echo -e "| Path | Old | New |" >> report.md
+        echo -e "|---|---|---|" >> report.md
+        paste modified_files.txt modified_images_old.md modified_images_new.md -d"|" |
+          awk -F"|" 'function basename(file) {sub(".*/", "", file); return file} {printf("| %s | %s | %s |\n",  basename($1), $2, $3)}' >> report.md
+
+        echo -e "</details>\n" >> report.md
+
+        # Mention git commit SHA in the report
+        echo -e "Report last updated at commit ${{ github.event.pull_request.head.sha }}" >> report.md
+
+        # Format report to escape newlines before publishing as GitHub comment
+        report=$(cat report.md)
+        report="${report//'%'/'%25'}"
+        report="${report//$'\n'/'%0A'}"
+        report="${report//$'\r'/'%0D'}"
+        echo ::set-output name=report::$report
+
+    - name: Find comment with image diff report
+      uses: peter-evans/find-comment@v1.2.0
+      id: fc
+      with:
+        issue-number: ${{ github.event.pull_request.number }}
+        comment-author: 'github-actions[bot]'
+        body-includes: 'This is an auto-generated report of images that have changed on the DVC remote'
+
+    - name: Create comment with image diff report
+      if: steps.fc.outputs.comment-id == ''
+      uses: peter-evans/create-or-update-comment@v1.4.4
+      with:
+        issue-number: ${{ github.event.pull_request.number }}
+        body: ${{ steps.image-diff.outputs.report }}
+
+    - name: Update comment with new image diff report
+      if: steps.fc.outputs.comment-id != ''
+      uses: peter-evans/create-or-update-comment@v1.4.4
+      with:
+        comment-id: ${{ steps.fc.outputs.comment-id }}
+        body: ${{ steps.image-diff.outputs.report }}
+        edit-mode: replace

.github/workflows/format-command.yml

@@ -21,7 +21,7 @@ jobs:
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/setup-python@v2.2.1
+      - uses: actions/setup-python@v2.2.2
 
       # Install formatting tools
       - name: Install formatting tools

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

@@ -29,7 +29,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v2.2.1
+      uses: actions/setup-python@v2.2.2
       with:
         python-version: 3.9
 

.github/workflows/style_checks.yaml

@@ -20,7 +20,7 @@ jobs:
 
       # Setup Miniconda
       - name: Set up Python
-        uses: actions/setup-python@v2.2.1
+        uses: actions/setup-python@v2.2.2
         with:
           python-version: 3.9
 

AUTHORS.md

@@ -8,6 +8,7 @@ Manoa.
 The following people have contributed code and/or documentation to the project
 (alphabetical by name) and are considered to be "PyGMT Developers":
 
+* [Abhishek Anant](https://twitter.com/itsabhianant) | [0000-0002-5751-2010](https://orcid.org/0000-0002-5751-2010) | Unaffiliated
 * [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | Michigan State University
 * [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University
 * [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey