Merge branch 'main' into python-3.13

Author: weiji14

.github/workflows/benchmarks.yml

@@ -34,7 +34,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/cache_data.yaml

@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/check-links.yml

@@ -23,12 +23,12 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         ref: gh-pages
         path: documentation

.github/workflows/ci_docs.yml

@@ -69,7 +69,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -139,7 +139,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_doctests.yaml

@@ -35,7 +35,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/ci_tests.yaml

@@ -103,7 +103,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/ci_tests_dev.yaml

@@ -46,7 +46,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -89,7 +89,7 @@ jobs:
 
       # Checkout current GMT repository
       - name: Checkout the GMT source from ${{ matrix.gmt_git_ref }} branch
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           repository: 'GenericMappingTools/gmt'
           ref: ${{ matrix.gmt_git_ref }}

.github/workflows/ci_tests_legacy.yaml

@@ -44,7 +44,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/dvc-diff.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         # fetch all history so that dvc diff works
         fetch-depth: 0

.github/workflows/format-command.yml

@@ -18,7 +18,7 @@ jobs:
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/[email protected].0
+      - uses: actions/[email protected].1
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}

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

@@ -45,7 +45,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0

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

@@ -23,7 +23,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
 
     - name: Setup data version control (DVC)
       uses: iterative/[email protected]

.github/workflows/style_checks.yaml

@@ -24,7 +24,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
 
       # Setup Python
       - name: Set up Python

.github/workflows/type_checks.yml

@@ -33,7 +33,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
 
       # Setup Python
       - name: Set up Python

doc/install.md

@@ -85,7 +85,7 @@ We recommend following the instructions further on to install GMT 6.
 
 ## Dependencies
 
-PyGMT requires the following libraries to be installed:
+PyGMT requires the following packages to be installed:
 
 - [numpy](https://numpy.org)
 - [pandas](https://pandas.pydata.org)
@@ -97,19 +97,10 @@ PyGMT requires the following libraries to be installed:
 For the minimum supported versions of the dependencies, please see [](minversions.md).
 :::
 
-The following are optional dependencies:
-
-- [IPython](https://ipython.org): For embedding the figures in Jupyter notebooks (recommended).
-- [Contextily](https://contextily.readthedocs.io): For retrieving tile maps from the internet.
-- [GeoPandas](https://geopandas.org): For using and plotting GeoDataFrame objects.
-- [RioXarray](https://corteva.github.io/rioxarray): For saving multi-band rasters to GeoTIFFs.
-
 :::{note}
-If you have [PyArrow](https://arrow.apache.org/docs/python/index.html) installed, PyGMT
-does have some initial support for `pandas.Series` and `pandas.DataFrame` objects with
-Apache Arrow-backed arrays. Specifically, only uint/int/float and date32/date64 dtypes
-are supported for now. Support for string Arrow dtypes is still a work in progress.
-For more details, see [issue #2800](https://github.com/GenericMappingTools/pygmt/issues/2800).
+Some optional dependencies (e.g., [IPython](https://ipython.readthedocs.io/en/stable/),
+[GeoPandas](https://geopandas.org/en/stable/)) add more functionality to PyGMT.
+For a complete list of the optional dependencies, refer to [](ecosystem.md).
 :::
 
 ## Installing GMT and other dependencies
@@ -165,6 +156,25 @@ conda activate pygmt
 From now on, all commands will take place inside the virtual environment called `pygmt`
 and won't affect your default `base` installation.
 
+::::: {tip}
+You can also enable more PyGMT functionality by installing PyGMT's optional dependencies in the environment.
+:::: {tab-set}
+::: {tab-item} mamba
+:sync: mamba
+```
+mamba install contextily geopandas ipython pyarrow rioxarray
+```
+:::
+
+::: {tab-item} conda
+:sync: conda
+```
+conda install contextily geopandas ipython pyarrow rioxarray
+```
+:::
+::::
+:::::
+
 ## Installing PyGMT
 
 Now that you have GMT installed and your virtual environment activated, you can install

pygmt/_show_versions.py

@@ -1,15 +1,14 @@
 """
-Utility methods to print system info for debugging.
+Utility methods to print system information for debugging.
 
 Adapted from :func:`rioxarray.show_versions` and :func:`pandas.show_versions`.
 """
 
-import importlib
 import platform
 import shutil
 import subprocess
 import sys
-from importlib.metadata import version
+from importlib.metadata import PackageNotFoundError, requires, version
 from typing import TextIO
 
 from packaging.requirements import Requirement
@@ -25,25 +24,17 @@ def _get_clib_info() -> dict[str, str]:
     """
     Get information about the GMT shared library.
     """
-    with Session() as ses:
-        return ses.info
+    with Session() as lib:
+        return lib.info
 
 
 def _get_module_version(modname: str) -> str | None:
     """
     Get version information of a Python module.
     """
     try:
-        if modname in sys.modules:
-            module = sys.modules[modname]
-        else:
-            module = importlib.import_module(modname)
-
-        try:
-            return module.__version__
-        except AttributeError:
-            return module.version
-    except ImportError:
+        return version(modname)
+    except PackageNotFoundError:
         return None
 
 
@@ -85,13 +76,12 @@ def _check_ghostscript_version(gs_version: str | None) -> str | None:
                 f"Ghostscript v{gs_version} has known bugs. "
                 "Please consider upgrading to version v10.02 or later."
             )
-        case v if v >= Version("10.02"):
-            if Version(__gmt_version__) < Version("6.5.0"):
-                return (
-                    f"GMT v{__gmt_version__} doesn't support Ghostscript "
-                    f"v{gs_version}. Please consider upgrading to GMT>=6.5.0 or "
-                    "downgrading to Ghostscript v9.56."
-                )
+        case v if v >= Version("10.02") and Version(__gmt_version__) < Version("6.5.0"):
+            return (
+                f"GMT v{__gmt_version__} doesn't support Ghostscript v{gs_version}. "
+                "Please consider upgrading to GMT>=6.5.0 or downgrading to Ghostscript "
+                "v9.56."
+            )
     return None
 
 
@@ -109,22 +99,14 @@ def show_versions(file: TextIO | None = sys.stdout):
     It also warns users if the installed Ghostscript version has serious bugs or is
     incompatible with the installed GMT version.
     """
-
     sys_info = {
         "python": sys.version.replace("\n", " "),
         "executable": sys.executable,
         "machine": platform.platform(),
     }
-    dep_info = {
-        Requirement(v).name: _get_module_version(Requirement(v).name)
-        for v in importlib.metadata.requires("pygmt")  # type: ignore[union-attr]
-    }
-    dep_info.update(
-        {
-            "gdal": _get_module_version("osgeo.gdal"),
-            "ghostscript": _get_ghostscript_version(),
-        }
-    )
+    requirements = [Requirement(v).name for v in requires("pygmt")] + ["gdal"]  # type: ignore[union-attr]
+    dep_info = {name: _get_module_version(name) for name in requirements}
+    dep_info.update({"ghostscript": _get_ghostscript_version()})
 
     lines = []
     lines.append("PyGMT information:")