Merge branch 'main' into pyarrow/string

weiji14 · weiji14 · commit 44d01ed16fbd · 2024-11-15T13:48:17.000+13:00
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -43,7 +43,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -80,7 +80,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
@@ -115,7 +115,7 @@ jobs:
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
-            sphinx_rtd_theme
+            sphinx_rtd_theme<3.0
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -42,7 +42,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -85,9 +85,9 @@ jobs:
           - os: 'ubuntu-latest'
             python-version: '3.11'  # Can't be 3.10 or 3.12.
             numpy-version: '1.24'
-            pandas-version: ''
+            pandas-version: '=2.1'
             xarray-version: ''
-            optional-packages: ' geopandas<1'
+            optional-packages: ' geopandas<1 pyarrow'
 
     timeout-minutes: 30
     defaults:
@@ -114,7 +114,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -57,7 +57,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
@@ -51,7 +51,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -75,10 +75,10 @@ jobs:
         ls -lh dist/
 
     - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.12.0
+      uses: pypa/gh-action-pypi-publish@v1.12.2
       with:
         repository-url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@v1.12.0
+      uses: pypa/gh-action-pypi-publish@v1.12.2
diff --git a/ci/requirements/docs.yml b/ci/requirements/docs.yml
@@ -30,4 +30,4 @@ dependencies:
     - sphinx-copybutton
     - sphinx-design
     - sphinx-gallery
-    - sphinx_rtd_theme
+    - sphinx_rtd_theme<3.0
diff --git a/environment.yml b/environment.yml
@@ -42,7 +42,7 @@ dependencies:
     - sphinx-copybutton
     - sphinx-design
     - sphinx-gallery>=0.17.0
-    - sphinx_rtd_theme
+    - sphinx_rtd_theme<3.0
     # Dev dependencies (type hints)
     - mypy
     - pandas-stubs
diff --git a/pygmt/clib/conversion.py b/pygmt/clib/conversion.py
@@ -157,10 +157,15 @@ def _to_numpy(data: Any) -> np.ndarray:
     array
         The C contiguous NumPy array.
     """
-    # Mapping of unsupported dtypes to the expected NumPy dtype.
-    dtypes: dict[str, type] = {
-        "date32[day][pyarrow]": np.datetime64,
-        "date64[ms][pyarrow]": np.datetime64,
+    # Mapping of unsupported dtypes to expected NumPy dtypes.
+    dtypes: dict[str, type | str] = {
+        # For string dtypes.
+        "large_string": np.str_,  # pa.large_string and pa.large_utf8
+        "string": np.str_,  # pa.string and pa.utf8
+        "string_view": np.str_,  # pa.string_view
+        # For datetime dtypes.
+        "date32[day][pyarrow]": "datetime64[D]",
+        "date64[ms][pyarrow]": "datetime64[ms]",
     }
 
     if (
@@ -174,7 +179,7 @@ def _to_numpy(data: Any) -> np.ndarray:
         # we can remove the workaround in PyGMT v0.17.0.
         array = np.ascontiguousarray(data.astype(float))
     else:
-        vec_dtype = str(getattr(data, "dtype", ""))
+        vec_dtype = str(getattr(data, "dtype", getattr(data, "type", "")))
         array = np.ascontiguousarray(data, dtype=dtypes.get(vec_dtype))
     return array
 
diff --git a/pygmt/src/plot.py b/pygmt/src/plot.py
@@ -213,7 +213,8 @@ def plot(
     if kind == "empty":  # Add more columns for vectors input
         # Parameters for vector styles
         if (
-            kwargs.get("S") is not None
+            isinstance(kwargs.get("S"), str)
+            and len(kwargs["S"]) >= 1
             and kwargs["S"][0] in "vV"
             and is_nonstr_iter(direction)
         ):
diff --git a/pygmt/src/plot3d.py b/pygmt/src/plot3d.py
@@ -197,7 +197,8 @@ def plot3d(
     if kind == "empty":  # Add more columns for vectors input
         # Parameters for vector styles
         if (
-            kwargs.get("S") is not None
+            isinstance(kwargs.get("S"), str)
+            and len(kwargs["S"]) >= 1
             and kwargs["S"][0] in "vV"
             and is_nonstr_iter(direction)
         ):
diff --git a/pygmt/tests/baseline/test_figure_shift_origin.png.dvc b/pygmt/tests/baseline/test_figure_shift_origin.png.dvc
diff --git a/pygmt/tests/baseline/test_shift_origin.png.dvc b/pygmt/tests/baseline/test_shift_origin.png.dvc
@@ -0,0 +1,5 @@
+outs:
+- md5: 39b241fdd879271cf1e8cf1f73454706
+  size: 9910
+  hash: md5
+  path: test_shift_origin.png
diff --git a/pygmt/tests/test_clib_to_numpy.py b/pygmt/tests/test_clib_to_numpy.py
diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
diff --git a/pygmt/tests/test_shift_origin.py b/pygmt/tests/test_shift_origin.py

-Original file line number
+Diff line change
         ls -lh dist/
     - name: Publish to Test PyPI
 -      uses: pypa/[email protected].0
 +      uses: pypa/[email protected].2
       with:
         repository-url: https://test.pypi.org/legacy/
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
 -      uses: pypa/[email protected].0
 +      uses: pypa/[email protected].2