Merge branch 'main' into docformatter-1.7.0

Author: weiji14

.github/workflows/check-links.yml

@@ -33,7 +33,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.7.0
+      uses: lycheeverse/lychee-action@v1.8.0
       with:
         # 429: Too many requests
         args: >

.github/workflows/ci_docs.yml

@@ -85,7 +85,7 @@ jobs:
             netCDF4
             packaging
             contextily
-            geopandas
+            geopandas!=0.13.0
             ipython
             rioxarray
             build

.github/workflows/ci_tests.yaml

@@ -164,7 +164,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/[email protected].3
+        uses: codecov/[email protected].4
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.github/workflows/dvc-diff.yml

@@ -27,13 +27,16 @@ jobs:
         fetch-depth: 0
 
     - name: Setup data version control (DVC)
-      uses: iterative/[email protected].1
+      uses: iterative/[email protected].2
 
     - name: Setup continuous machine learning (CML)
       uses: iterative/[email protected]
 
-    - name: Pull image data from cloud storage
-      run: dvc pull --remote upstream
+    # workaround from https://github.com/iterative/cml/issues/1377
+    - name: Setup NodeJS
+      uses: actions/[email protected]
+      with:
+        node-version: '16'
 
     # Produce the markdown diff report, which should look like:
     # ## Summary of changed images
@@ -45,80 +48,59 @@ jobs:
     # | added    | pygmt/tests/baseline/test_image.png |
     # | deleted  | pygmt/tests/baseline/test_image2.png |
     # | modified | pygmt/tests/baseline/test_image3.png |
+    #
+    # ## Image diff(s)
+    #
+    # <details>
+    # ...
+    # </details>
+    #
+    # Report last updated at commit abcdef
     - 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
+
+        # Pull image data from cloud storage
+        dvc pull --remote upstream
         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
         awk 'NF==5 && NR>=7 && $2=="modified" {print $4}' report.md > modified_files.txt
 
+        # Backup new images in the baseline-new directory
+        mkdir pygmt/tests/baseline-new
+        cp pygmt/tests/baseline/*.png pygmt/tests/baseline-new/
+        # Pull images in the main branch from cloud storage
+        git checkout main
+        dvc pull --remote upstream
+
         # 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
+          echo -e "- $(basename $line) \n" >> report.md
+          echo -e "![](${line/baseline/baseline-new})" >> report.md
         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 main branch from cloud storage
-        git checkout main
-        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
+        while IFS= read -r line; do
+          echo -e "| $(basename $line) | ![]($line) | ![](${line/baseline/baseline-new}) |" >> report.md
+        done < modified_files.txt
 
         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
 
-        # Save the report content to the output parameter 'report'
-        echo 'report<<EOF' >> $GITHUB_OUTPUT
-        cat report.md >> $GITHUB_OUTPUT
-        echo 'EOF' >> $GITHUB_OUTPUT
-
-    - name: Find comment with image diff report
-      uses: peter-evans/[email protected]
-      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/[email protected]
-      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/[email protected]
-      with:
-        comment-id: ${{ steps.fc.outputs.comment-id }}
-        body: ${{ steps.image-diff.outputs.report }}
-        edit-mode: replace
+        # create/update PR comment
+        cml comment update report.md

.github/workflows/format-command.yml

@@ -25,7 +25,7 @@ jobs:
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/[email protected].0
+      - uses: actions/[email protected].1
         with:
           python-version: '3.11'
 

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

@@ -44,7 +44,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         python-version: '3.11'
 

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

@@ -22,7 +22,7 @@ jobs:
       uses: actions/[email protected]
 
     - name: Setup data version control (DVC)
-      uses: iterative/[email protected].1
+      uses: iterative/[email protected].2
 
     - name: Pull baseline image data from dvc remote
       run: |

.github/workflows/style_checks.yaml

@@ -28,7 +28,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: '3.11'
 

ci/requirements/docs.yml

@@ -12,7 +12,7 @@ dependencies:
     - packaging
     # Optional dependencies
     - contextily
-    - geopandas
+    - geopandas!=0.13.0
     - ipython
     - rioxarray
     # Development dependencies (general)

doc/contributing.md

@@ -62,9 +62,9 @@ the problem:
   filter the messages to include only the GMT-equivalent commands using a command
   such as:
 
-      python <test>.py 2>&1 | awk -F': ' '$2=="GMT_Call_Command string" {print "gmt", $3}'
+      python <test>.py 2>&1 | awk -F': ' '$2=="GMT_Call_Command string" {print $3}'
 
-  where `<test>` is the name of your test script.
+  where `<test>` is the name of your test script. Note that this script works only with GMT>=6.4
 * If the bug is produced when passing an in-memory data object (e.g., a
   pandas.DataFrame or xarray.DataArray) to a PyGMT function, try writing the
   data to a file (e.g., a NetCDF or ASCII txt file) and passing the data file

examples/gallery/lines/vector_heads_tails.py

@@ -12,20 +12,20 @@
 one at the end). Optionally, append **t** for a terminal line, **c** for a
 circle, **a** for arrow (default), **i** for tail, **A** for plain open
 arrow, and **I** for plain open tail. Further append **l** or **r** (e.g.
-``+bar``) to only draw the left or right half-sides of the selected head/tail
+``"+bar"``) to only draw the left or right half-sides of the selected head/tail
 (default is both sides) or use **+l** or **+r** to apply simultaneously to both
-sides. In this context left and right refer to the side of the vector line
-when viewed from the beginning point to the end point of a line segment.
-The angle of the vector head apex can be set using **+a**\ *angle*
+beginning and end. In this context left and right refer to the side of the
+vector line when viewed from the beginning point to the end point of a line
+segment. The angle of the vector head apex can be set using **+a**\ *angle*
 (default is 30). The shape of the vector head can be adjusted using
-**+h**\ *shape* (e.g. ``+h0.5``).
+**+h**\ *shape* (e.g. ``"+h0.5"``).
 
 For further modifiers see :gmt-docs:`plot.html#vector-attributes`.
 
 In the following we use the :meth:`pygmt.Figure.plot` method to plot vectors
 with individual heads and tails. We must specify the modifiers (together with
-the vector type, here ``v``, see also
-:doc:`Vector types documentation </gallery/lines/vector_styles>`)
+the vector type, here ``"v"`` for Cartesian vector, see also
+:doc:`Vector types example </gallery/lines/vector_styles>`)
 by passing the corresponding shortcuts to the ``style`` parameter.
 
 """

examples/gallery/lines/vector_styles.py

@@ -5,7 +5,7 @@
 The :meth:`pygmt.Figure.plot` method can plot Cartesian, circular, and
 geographic vectors. The ``style`` parameter controls vector attributes.
 See also
-:doc:`Vector attributes documentation </gallery/lines/vector_heads_tails>`.
+:doc:`Vector attributes example </gallery/lines/vector_heads_tails>`.
 
 """
 import numpy as np
@@ -28,7 +28,7 @@
 y = np.linspace(33.5, 42.5, 12)  # y vector coordinates
 direction = np.zeros(x.shape)  # direction of vectors
 length = np.linspace(0.5, 2.4, 12)  # length of vectors
-# Cartesian vectors (v) with red pen and fill (+g, +p), vector head at
+# Cartesian vectors (v) with red fill and pen (+g, +p), vector head at
 # end (+e), and 40 degree angle (+a) with no indentation for vector head (+h)
 style = "v0.2c+e+a40+gred+h0+p1p,red"
 fig.plot(x=x, y=y, style=style, pen="1p,red", direction=[direction, length])

examples/projections/misc/misc_robinson.py

@@ -6,14 +6,23 @@
 Arthur H. Robinson in 1963, is a modified cylindrical projection that is
 neither conformal nor equal-area. Central meridian and all parallels are
 straight lines; other meridians are curved. It uses lookup tables rather than
-analytic expressions to make the world map "look" right 22. The scale is true
-along latitudes 38. The projection was originally developed for use by Rand
-McNally and is currently used by the National Geographic Society.
+analytic expressions to make the world map "look" right [#f1]_.
+The scale is true along latitudes 38° north and south. The projection was
+originally developed for use by Rand McNally and is currently used by the
+National Geographic Society.
 
 **n**\ [*lon0/*]\ *scale* or **N**\ [*lon0/*]\ *width*
 
 The projection is set with **n** or **N**. The central meridian is set with the
 optional *lon0*, and the figure size is set with *scale* or *width*.
+
+.. rubric:: Footnotes
+
+.. [#f1] Robinson provided a table of y-coordinates for latitudes every 5°.
+         To project values for intermediate latitudes one must interpolate
+         the table. Different interpolants may result in slightly different
+         maps. GMT uses the interpolant selected by the parameter
+         :gmt-term:`GMT_INTERPOLANT` in the gmt.conf file.
 """
 import pygmt
 

pygmt/src/meca.py

@@ -79,10 +79,13 @@ def data_format_code(convention, component="full"):
     B="frame",
     C="cmap",
     E="extensionfill",
+    Fr="labelbox",
     G="compressionfill",
     J="projection",
+    L="outline",
     N="no_clip",
     R="region",
+    T="nodal",
     V="verbose",
     W="pen",
     c="panel",
@@ -124,7 +127,7 @@ def meca(
           - Columns 1 and 2: event longitude and latitude
           - Column 3: event depth (in km)
           - Columns 4 to 3+n: focal mechanism parameters. The number of columns
-            *n* depends on the choice of ``convection``, which will be
+            *n* depends on the choice of ``convention``, which will be
             described below.
           - Columns 4+n and 5+n: longitude, latitude at which to place
             beachball. Using ``0 0`` will plot the beachball at the longitude,
@@ -204,32 +207,61 @@ def meca(
     event_name : str or list of str, or 1-D numpy array
         Text string(s), e.g., event name(s) to appear near the beachball(s).
         List must be the same length as the number of events. Will override
-        the ``event_name`` values in ``spec`` if ``spec`` is a dictionary
+        the ``event_name`` labels in ``spec`` if ``spec`` is a dictionary
         or pd.DataFrame.
+    labelbox : bool or str
+        [*fill*].
+        Draw a box behind the label if given. Use *fill* to give a fill color
+        [Default is ``"white"``].
     offset : bool or str
         [**+p**\ *pen*][**+s**\ *size*].
         Offset beachball(s) to longitude(s) and latitude(s) specified in the
         the last two columns of the input file or array, or by
         ``plot_longitude`` and ``plot_latitude`` if provided. A small circle
         is plotted at the initial location and a line connects the beachball
         to the circle. Use **+s**\ *size* to set the diameter of the circle
-        [Default is no circle]. Use **+p**\ *pen* to set the line pen
-        attributes [Default is ``"0.25p"``].
+        [Default is no circle]. Use **+p**\ *pen* to set the pen attributes
+        for this feature [Default is set via ``pen``]. The fill of the
+        circle is set via ``compressionfill`` or ``cmap``, i.e.,
+        corresponds to the fill of the compressive quadrants.
     compressionfill : str
         Set color or pattern for filling compressive quadrants
-        [Default is ``"black"``].
+        [Default is ``"black"``]. This setting also applies to the fill of
+        the circle defined via ``offset``.
     extensionfill : str
         Set color or pattern for filling extensive quadrants
         [Default is ``"white"``].
     pen : str
-        Set pen attributes for outline of beachball
-        [Default is ``"0.25p,black,solid"``].
+        Set pen attributes for all lines related to beachball [Default is
+        ``"0.25p,black,solid"``]. This setting applies to ``outline``,
+        ``nodal``, and ``offset``, unless overruled by arguments passed to
+        those parameters. Draws circumference of beachball.
+    outline : bool or str
+        [*pen*].
+        Draw circumference and nodal planes of beachball. Use *pen* to set
+        the pen attributes for this feature [Default is set via ``pen``].
+    nodal : bool, int, or str
+        [*nplane*][/*pen*].
+        Plot the nodal planes and outline the bubble which is transparent.
+        If *nplane* is
+
+        - ``0`` or ``True``: both nodal planes are plotted [Default].
+        - ``1``: only the first nodal plane is plotted.
+        - ``2``: only the second nodal plane is plotted.
+
+        Use /*pen* to set the pen attributes for this feature [Default is
+        set via ``pen``].
+        For double couple mechanisms, ``nodal`` renders the beachball
+        transparent by drawing only the nodal planes and the circumference.
+        For non-double couple mechanisms, ``nodal=0`` overlays best
+        double couple transparently.
     cmap : str
         File name of a CPT file or a series of comma-separated colors (e.g.,
         *color1,color2,color3*) to build a linear continuous CPT from those
         colors automatically. The color of the compressive quadrants is
         determined by the z-value (i.e., event depth or the third column for
-        an input file).
+        an input file). This setting also applies to the fill of the circle
+        defined via ``offset``.
     no_clip : bool
         Do **not** skip symbols that fall outside the frame boundaries
         [Default is ``False``, i.e., plot symbols inside the frame

pygmt/tests/baseline/test_meca_gcmt_convention.png.dvc

@@ -0,0 +1,4 @@
+outs:
+- md5: fc7c271049fc8583914b508c4bee08fe
+  size: 9830
+  path: test_meca_spec_single_focalmecha.png