Merge branch 'master' into filename-with-spaces

.github/workflows/cache_data.yaml

@@ -19,7 +19,7 @@ jobs:
     steps:
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.0
+        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@v1.0.8
       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@v2.1.0
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -66,17 +66,18 @@ 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=0.5.1
+                        sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
         run: conda list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.13.0
+        uses: dawidd6/action-download-artifact@v2.14.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/ci_tests.yaml

@@ -63,7 +63,7 @@ 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 }}
 
@@ -76,7 +76,7 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.0
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -86,7 +86,8 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.1.1 numpy=${{ matrix.numpy-version }} \
+          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 \
@@ -98,7 +99,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.13.0
+        uses: dawidd6/action-download-artifact@v2.14.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -140,7 +141,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1.3.1
+        uses: codecov/codecov-action@v1.5.0
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.github/workflows/ci_tests_dev.yaml

@@ -39,7 +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 }}
 
@@ -73,7 +73,7 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.0
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -102,7 +102,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.13.0
+        uses: dawidd6/action-download-artifact@v2.14.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/dvc-diff.yml

@@ -24,6 +24,9 @@ jobs:
     - 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
     #
@@ -32,32 +35,52 @@ jobs:
     # | Status   | Path                                |
     # |----------|-------------------------------------|
     # | added    | pygmt/tests/baseline/test_image.png |
-    - name: Put list of images that were added or changed into report
+    # | 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
-        cat report.md
 
-    - name: Pull image data from cloud storage
-      run: dvc pull --remote upstream
-
-    - name: Put image diff(s) into report
-      env:
-        repo_token: ${{ secrets.GITHUB_TOKEN }}
-      id: image-diff
-      run: |
-        # Get just the filename of the changed image from the report
-        awk 'NF==5 && NR>=7 {print $4}' report.md > diff_files.txt
+        # 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 < diff_files.txt
+        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
 

.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/slash-command-dispatch.yml

@@ -6,6 +6,7 @@ on:
     # types: [created, edited]
 jobs:
   slashCommandDispatch:
+    if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot

.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

CONTRIBUTING.md

@@ -181,13 +181,17 @@ When editing documentation, use the following standards to demonstrate the examp
 
 1. Python arguments, such as import statements, Boolean expressions, and function
    arguments should be wrapped as ``code`` by using \`\` on both sides of the code.
-   Example: \`\`import pygmt\`\` results in ``import pygmt``.
+   Examples: \`\`import pygmt\`\` results in ``import pygmt``, \`\`True\`\` results in `True`,
+    \`\`style="v"\`\` results in `style="v"`.
 2. Literal GMT arguments should be **bold** by wrapping the arguments with \*\*
    (two asterisks) on both sides. The argument description should be in *italicized*
    with \* (single asterisk) on both sides.
-   Example: `**+l**\ *label*` results in **+l***label*.
-3. Optional arguments are placed wrapped with [ ] (square brackets).
+   Examples: `**+l**\ *label*` results in **+l***label*, `**05m**` results in **05m**.
+3. Optional arguments are wrapped with [ ] (square brackets).
 4. Arguments that are mutually exclusive are separated with a | (bar) to denote "or".
+5. Default arguments for parameters and configuration settings are wrapped
+   with [ ] (square brackers) with the prefix "Default is". Example: [Default is
+   **p**].
 
 ## Contributing Code
 
@@ -215,7 +219,7 @@ General guidelines for pull requests (PRs):
   do.
 * Each pull request should consist of a **small** and logical collection of changes.
 * Larger changes should be broken down into smaller components and integrated
-  separately.
+  separately. For example, break the wrapping of aliases into multiple pull requests.
 * Bug fixes should be submitted in separate PRs.
 * Use underscores for all Python (*.py) files as per [PEP8](https://www.python.org/dev/peps/pep-0008/),
   not hyphens. Directory names should also use underscores instead of hyphens.
@@ -299,6 +303,12 @@ warn us and you can make a new commit with the formatted code.
 Even better, you can just write `/format` in the first line of any comment in a
 Pull Request to lint the code automatically.
 
+When wrapping a new alias, use an underscore to separate words bridged by vowels
+(aeiou), such as `no_skip` and `z_only`. Do not use an underscore to separate
+words bridged only by consonants, such as `distcalc`, and `crossprofile`. This
+convention is not applied by the code checking tools, but the PyGMT maintainers
+will comment on any pull requests as needed.
+
 We also use [flake8](http://flake8.pycqa.org/en/latest/) and
 [pylint](https://www.pylint.org/) to check the quality of the code and quickly catch
 common errors.

MANIFEST.in

@@ -7,7 +7,6 @@ exclude .gitignore
 exclude .pylintrc
 exclude AUTHORSHIP.md
 exclude CONTRIBUTING.md
-exclude MAINTENANCE.md
 exclude Makefile
 exclude environment.yml
 exclude package.json

Makefile

@@ -36,7 +36,7 @@ test:
 	@echo ""
 	@cd $(TESTDIR); python -c "import $(PROJECT); $(PROJECT).show_versions()"
 	@echo ""
-	cd $(TESTDIR); pytest $(PYTEST_COV_ARGS) $(PROJECT)
+	cd $(TESTDIR); PYGMT_USE_EXTERNAL_DISPLAY="false" pytest $(PYTEST_COV_ARGS) $(PROJECT)
 	cp $(TESTDIR)/coverage.xml .
 	cp -r $(TESTDIR)/htmlcov .
 	rm -r $(TESTDIR)

doc/Makefile

@@ -31,7 +31,8 @@ html: api
 	@echo
 	@echo "Building HTML files."
 	@echo
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	# Set PYGMT_USE_EXTERNAL_DISPLAY to "false" to disable external display
+	PYGMT_USE_EXTERNAL_DISPLAY="false" $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

doc/_static/style.css

@@ -89,6 +89,32 @@ p {
     max-width: 1000px;
 }
 
+/* Format parameters section similar to sphinx_rtd_theme v4.x.x (not a grid) */
+html.writer-html5 .rst-content dl.field-list {
+    display: initial;
+}
+
+/* Add a grey box around parameters similar to sphinx_rtd_theme v4.x.x) */
+.rst-content dl:not(.docutils) dl dt {
+    margin-bottom: 4px;
+    border: none;
+    border-left: solid 3px #ccc;
+    background: #f0f0f0;
+    color: #555;
+}
+
+.rst-content dl:not(.docutils) dt {
+    display: table;
+    margin: 6px 0;
+    font-size: 90%;
+    line-height: normal;
+    background: #e7f2fa;
+    color: #2980B9;
+    border-top: solid 3px #6ab0de;
+    padding: 6px;
+    position: relative;
+}
+
 /* Remove the padding from the Parameters table */
 .rst-content table.field-list .field-name {
     padding-left: 0px;