Merge branch 'main' into add-tut-symbols

.github/ISSUE_TEMPLATE/1-bug_report.yaml

@@ -1,28 +1,30 @@
 name: Bug report
-description: Report a problem/bug to help us improve
+description: Report a problem/bug to help us improve.
 labels: bug
 body:
   - type: markdown
     attributes:
-      value: |
+      value: >
         Thanks for taking the time to fill out this bug report!
   - type: textarea
     attributes:
       label: "Description of the problem"
-      description: |
+      description: >
         Please be as detailed as you can when describing an issue.
         The more information we have, the easier it will be for us to track this down.
     validations:
       required: true
   - type: textarea
     attributes:
       label: "Minimal Complete Verifiable Example"
-      description: |
+      description: >
         So that we can understand and fix the issue quickly and efficiently, please provide
         a minimal, self-contained copy-pastable example that demonstrates the issue.
+
         For more details, check out:
 
         - [Minimal Complete Verifiable Examples](https://stackoverflow.com/help/mcve)
+
         - [Craft Minimal Bug Reports](https://matthewrocklin.com/minimal-bug-reports)
 
       placeholder: "PASTE CODE HERE"
@@ -40,9 +42,11 @@ body:
   - type: textarea
     attributes:
       label: "System information"
-      description: |
-        Please paste the output of `python -c "import pygmt; pygmt.show_versions()"`
-        If this command is not successful, please describe your operating system, how you installed PyGMT, how you installed GMT, and paste the full error message.
+      description: >
+        Please paste the output of `python -c "import pygmt; pygmt.show_versions()"`.
+
+        If this command is not successful, please describe your operating system,
+        how you installed PyGMT, how you installed GMT, and paste the full error message.
       placeholder: "PASTE THE OUTPUT HERE"
       render: bash
     validations:

.github/ISSUE_TEMPLATE/2-feature_request.yaml

@@ -5,16 +5,17 @@ body:
   - type: textarea
     attributes:
       label: "Description of the desired feature"
-      description: |
-        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).
+      description: >
+        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).
   - type: dropdown
     id: help
     attributes:
       label: Are you willing to help implement and maintain this feature?
-      description: |
-        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.
+      description: >
+        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.
       options:
         - "No"
         - "Yes"

.github/ISSUE_TEMPLATE/3-module_request.yaml

@@ -5,23 +5,29 @@ labels: ["feature request"]
 body:
   - type: markdown
     attributes:
-      value: |
-        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.
+      value: >
+        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.
   - type: textarea
     id: which-module
     attributes:
       label: Description of the desired module
-      description: 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).
-      placeholder: Implement [`<module-name>`](https://docs.generic-mapping-tools.org/latest/<module-name>.html) which `<insert description of the GMT module>`.
+      description: >
+        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).
+      placeholder: >
+        Implement [`<module-name>`](https://docs.generic-mapping-tools.org/latest/<module-name>.html)
+        which `<insert description of the GMT module>`.
     validations:
       required: true
   - type: dropdown
     id: help
     attributes:
       label: Are you willing to help implement and maintain this feature?
-      description: |
-        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.
+      description: >
+        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.
       options:
         - "No"
         - "Yes"
@@ -30,5 +36,6 @@ body:
       required: true
   - type: markdown
     attributes:
-      value: |
-        Progress on wrapping the module will be tracked in the [project board](https://github.com/GenericMappingTools/pygmt/projects/9).
+      value: >
+        Progress on wrapping the module will be tracked in the
+        [project board](https://github.com/orgs/GenericMappingTools/projects/3).

.github/workflows/benchmarks.yml

@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/cache_data.yaml

@@ -43,7 +43,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_docs.yml

@@ -80,7 +80,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_doctests.yaml

@@ -42,7 +42,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_tests.yaml

@@ -113,7 +113,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |
@@ -142,7 +142,6 @@ jobs:
             pytest-doctestplus
             pytest-mpl
             pytest-rerunfailures
-            pytest-xdist
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -165,7 +164,7 @@ jobs:
 
       # Run the regular tests
       - name: Run tests
-        run: make test PYTEST_EXTRA="-r P -n auto --reruns 2"
+        run: make test PYTEST_EXTRA="-r P --reruns 2"
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
@@ -177,7 +176,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/[email protected].3
+        uses: codecov/[email protected].7
         if: success() || failure()
         with:
           use_oidc: true

.github/workflows/ci_tests_dev.yaml

@@ -57,7 +57,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |
@@ -153,7 +153,7 @@ jobs:
                         --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
                         numpy pandas xarray netCDF4 packaging \
                         build contextily dvc geopandas ipython pyarrow rioxarray \
-                        pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures pytest-xdist\
+                        pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures \
                         sphinx-gallery
 
       # Show installed pkg information for postmortem diagnostic
@@ -181,7 +181,7 @@ jobs:
 
       # Run the tests
       - name: Test with pytest
-        run: make test PYTEST_EXTRA="-r P -n auto --reruns 2"
+        run: make test PYTEST_EXTRA="-r P --reruns 2"
         env:
           GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib
 

.github/workflows/ci_tests_legacy.yaml

@@ -51,7 +51,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

doc/Makefile

@@ -55,7 +55,5 @@ server:
 clean:
 	rm -rf $(BUILDDIR)
 	rm -rf api/generated
-	rm -rf intro
-	rm -rf tutorials
-	rm -rf gallery
-	rm -rf projections
+	rm -rf intro tutorials gallery projections
+	rm -rf sg_execution_times.rst

examples/gallery/histograms/scatter_and_histograms.py

@@ -2,70 +2,75 @@
 Scatter plot with histograms
 ============================
 
-To create a scatter plot with histograms at the sides of the plot one
-can use :meth:`pygmt.Figure.plot` in combination with
-:meth:`pygmt.Figure.histogram`. The positions of the histograms are plotted
-by offsetting them from the main scatter plot figure using
-:meth:`pygmt.Figure.shift_origin`.
+To create a scatter plot with histograms at the sides of the plot one can use
+:meth:`pygmt.Figure.plot` in combination with :meth:`pygmt.Figure.histogram`. The
+positions of the histograms are plotted by offsetting them from the main scatter plot
+using :meth:`pygmt.Figure.shift_origin`.
 """
 
 # %%
 import numpy as np
 import pygmt
 
-# Generate random data from a standard normal distribution centered on 0
-# with a standard deviation of 1
-rng = np.random.default_rng(seed=19680801)
+# Generate random x, y coordinates from a standard normal distribution.
+# x values are centered on 0 with a standard deviation of 1, and y values are centered
+# on 30 with a standard deviation of 2.
+rng = np.random.default_rng()
 x = rng.normal(loc=0, scale=1, size=1000)
-y = rng.normal(loc=0, scale=1, size=1000)
+y = rng.normal(loc=30, scale=2, size=1000)
 
-# Get axis limits
-xymax = max(np.max(np.abs(x)), np.max(np.abs(y)))
+# Get axis limits from the data limits. Extend the limits by 0.5 to add some margin.
+xmin = np.floor(x.min()) - 0.5
+xmax = np.ceil(x.max()) + 0.5
+ymin = np.floor(y.min()) - 0.5
+ymax = np.ceil(y.max()) + 0.5
 
+# Set fill color for symbols and bars.
+fill = "seagreen"
+
+# Set the dimensions of the scatter plot.
+width, height = 10, 8
 
 fig = pygmt.Figure()
 fig.basemap(
-    region=[-xymax - 0.5, xymax + 0.5, -xymax - 0.5, xymax + 0.5],
-    projection="X10c/10c",
-    frame=["WSrt", "a1"],
+    region=[xmin, xmax, ymin, ymax],
+    projection=f"X{width}/{height}",
+    frame=["WSrt", "af"],
 )
 
-fillcol = "seagreen"
-
-# Plot data points as circles with a diameter of 0.15 centimeters
-fig.plot(x=x, y=y, style="c0.15c", fill=fillcol, transparency=50)
+# Plot data points as circles with a diameter of 0.15 centimeters and set transparency
+# level for all circles to deal with overplotting.
+fig.plot(x=x, y=y, style="c0.15c", fill=fill, transparency=50)
 
-# Shift the plot origin and add top margin histogram
-fig.shift_origin(yshift="10.25c")
+# Shift the plot origin and add top margin histogram.
+fig.shift_origin(yshift=height + 0.25)
 
 fig.histogram(
-    projection="X10c/2c",
-    frame=["Wsrt", "xf1", "y+lCounts"],
-    # Give the same value for ymin and ymax to have ymin and ymax
-    # calculated automatically
-    region=[-xymax - 0.5, xymax + 0.5, 0, 0],
+    projection=f"X{width}/3",
+    frame=["Wsrt", "xf", "yaf+lCounts"],
+    # Give the same value for ymin and ymax to have them calculated automatically.
+    region=[xmin, xmax, 0, 0],
     data=x,
-    fill=fillcol,
+    fill=fill,
     pen="0.1p,white",
     histtype=0,
-    series=0.1,
+    series=0.2,
 )
 
-# Shift the plot origin and add right margin histogram
-fig.shift_origin(yshift="-10.25c", xshift="10.25c")
+# Shift the plot origin and add right margin histogram.
+fig.shift_origin(yshift=-height - 0.25, xshift=width + 0.25)
 
+# Plot the horizontal histogram.
 fig.histogram(
     horizontal=True,
-    projection="X2c/10c",
-    # Note that the y-axis annotation "Counts" is shown in x-axis direction
-    # due to the rotation caused by horizontal=True
-    frame=["wSrt", "xf1", "y+lCounts"],
-    region=[-xymax - 0.5, xymax + 0.5, 0, 0],
+    projection=f"X3/{height}",
+    # Note that the x- and y-axis are flipped, with the y-axis plotted horizontally.
+    frame=["wSrt", "xf", "yaf+lCounts"],
+    region=[ymin, ymax, 0, 0],
     data=y,
-    fill=fillcol,
+    fill=fill,
     pen="0.1p,white",
     histtype=0,
-    series=0.1,
+    series=0.2,
 )
-
 fig.show()

examples/tutorials/advanced/cartesian_histograms.py

@@ -79,9 +79,8 @@
     fill="red3",
     pen="1p,darkgray,solid",
     histtype=0,
-    # Use horizontal bars
-    # Please note the flip of the x and y axes regarding annotations, ticks, gridlines,
-    # and labels
+    # Use horizontal bars. Note that the x- and y-axis are flipped, with the x-axis
+    # plotted vertically and the y-axis plotted horizontally.
     horizontal=True,
 )