Merge branch 'main' into python-3.13

Author: seisman

.github/workflows/benchmarks.yml

@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         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/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         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/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         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/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_tests.yaml

@@ -114,7 +114,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.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@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

.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@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |

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

@@ -75,10 +75,10 @@ jobs:
         ls -lh dist/
 
     - name: Publish to Test PyPI
-      uses: pypa/[email protected].2
+      uses: pypa/[email protected].3
       with:
         repository-url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/[email protected].2
+      uses: pypa/[email protected].3

pygmt/clib/conversion.py

@@ -123,7 +123,7 @@ def dataarray_to_matrix(grid):
         inc = [abs(i) for i in inc]
         grid = grid.sortby(variables=list(grid.dims), ascending=True)
 
-    matrix = as_c_contiguous(grid[::-1].to_numpy())
+    matrix = np.ascontiguousarray(grid[::-1].to_numpy())
     region = [float(i) for i in region]
     inc = [float(i) for i in inc]
     return matrix, region, inc
@@ -200,53 +200,11 @@ def vectors_to_arrays(vectors):
     for vector in vectors:
         vec_dtype = str(getattr(vector, "dtype", ""))
         array = np.asarray(a=vector, dtype=dtypes.get(vec_dtype))
-        arrays.append(as_c_contiguous(array))
+        arrays.append(np.ascontiguousarray(array))
 
     return arrays
 
 
-def as_c_contiguous(array):
-    """
-    Ensure a numpy array is C contiguous in memory.
-
-    If the array is not C contiguous, a copy will be necessary.
-
-    Parameters
-    ----------
-    array : 1-D array
-        The numpy array
-
-    Returns
-    -------
-    array : 1-D array
-        Array is C contiguous order.
-
-    Examples
-    --------
-
-    >>> import numpy as np
-    >>> data = np.array([[1, 2], [3, 4], [5, 6]])
-    >>> x = data[:, 0]
-    >>> x
-    array([1, 3, 5])
-    >>> x.flags.c_contiguous
-    False
-    >>> new_x = as_c_contiguous(x)
-    >>> new_x
-    array([1, 3, 5])
-    >>> new_x.flags.c_contiguous
-    True
-    >>> x = np.array([8, 9, 10])
-    >>> x.flags.c_contiguous
-    True
-    >>> as_c_contiguous(x).flags.c_contiguous
-    True
-    """
-    if not array.flags.c_contiguous:
-        return array.copy(order="C")
-    return array
-
-
 def sequence_to_ctypes_array(
     sequence: Sequence | None, ctype, size: int
 ) -> ctp.Array | None:

pygmt/clib/session.py

@@ -19,7 +19,6 @@
 import xarray as xr
 from pygmt.clib.conversion import (
     array_to_datetime,
-    as_c_contiguous,
     dataarray_to_matrix,
     sequence_to_ctypes_array,
     strings_to_ctypes_array,
@@ -1499,7 +1498,7 @@ def virtualfile_from_matrix(self, matrix):
         # collected and the memory freed. Creating it in this context manager
         # guarantees that the copy will be around until the virtual file is
         # closed.
-        matrix = as_c_contiguous(matrix)
+        matrix = np.ascontiguousarray(matrix)
         rows, columns = matrix.shape
 
         family = "GMT_IS_DATASET|GMT_VIA_MATRIX"