Merge branch 'main' into alias-system

Author: seisman

.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: |
@@ -104,13 +104,14 @@ jobs:
             geopandas<1.0
             ipython
             pyarrow
+            rasterio<1.4.3
             rioxarray
             make
             pip
             python-build
             myst-nb
             panel
-            sphinx
+            sphinx>=6.2
             sphinx-autodoc-typehints
             sphinx-copybutton
             sphinx-design

.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: |
@@ -61,6 +61,7 @@ jobs:
             geopandas
             ipython
             pyarrow
+            rasterio<1.4.3
             rioxarray
             make
             pip

.github/workflows/ci_tests.yaml

@@ -73,13 +73,13 @@ jobs:
             numpy-version: '1.24'
             pandas-version: '=2.0'
             xarray-version: '=2023.04'
-            optional-packages: ' contextily geopandas<1 ipython pyarrow rioxarray sphinx-gallery'
+            optional-packages: ' contextily geopandas<1 ipython pyarrow rasterio<1.4.3 rioxarray sphinx-gallery'
           # Python 3.12 + core packages (latest versions) + optional packages
           - python-version: '3.12'
             numpy-version: '2.1'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' contextily geopandas>=1.0 ipython pyarrow rioxarray sphinx-gallery'
+            optional-packages: ' contextily geopandas>=1.0 ipython pyarrow rasterio<1.4.3 rioxarray sphinx-gallery'
           # Python 3.11 + core packages (Linux only)
           - os: 'ubuntu-latest'
             python-version: '3.11'
@@ -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: |
@@ -176,7 +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: |
@@ -152,7 +152,7 @@ jobs:
           python -m pip install --pre --prefer-binary \
                         --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
                         numpy pandas xarray netCDF4 packaging \
-                        build contextily dvc geopandas ipython pyarrow rioxarray \
+                        build contextily dvc geopandas ipython pyarrow 'rasterio<1.4.3' rioxarray \
                         pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures \
                         sphinx-gallery
 

.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: |
@@ -71,6 +71,7 @@ jobs:
             geopandas
             ipython
             pyarrow
+            rasterio<1.4.3
             rioxarray
             sphinx-gallery
             make