Merge pull request #227 from GeoStat-Framework/meshio5.1_fix

Field: make Field.mesh compatible with meshio v5.1+

Author: MuellerSeb

.github/workflows/main.yml

@@ -66,7 +66,7 @@ jobs:
           fetch-depth: '0'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.2.2
+        uses: pypa/cibuildwheel@v2.3.1
         env:
           CIBW_ARCHS: ${{ matrix.cfg.arch }}
         with:

CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to **GSTools** will be documented in this file.
 
 
+## [1.3.5] - Pure Pink - ?
+
+### Bugfixes
+- `Field.mesh` was not compatible with [meshio](https://github.com/nschloe/meshio) v5.1+ [#227](https://github.com/GeoStat-Framework/GSTools/pull/227)
+
+
 ## [1.3.4] - Pure Pink - 2021-11
 
 ### Enhancements
@@ -321,7 +327,7 @@ See: [#197](https://github.com/GeoStat-Framework/GSTools/issues/197)
 First release of GSTools.
 
 
-[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.4...HEAD
+[1.3.5]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.4...HEAD
 [1.3.4]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.3...v1.3.4
 [1.3.3]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.2...v1.3.3
 [1.3.2]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.1...v1.3.2

README.md

@@ -338,10 +338,10 @@ in memory for immediate 3D plotting in Python.
 
 - [NumPy >= 1.14.5](https://www.numpy.org)
 - [SciPy >= 1.1.0](https://www.scipy.org/scipylib)
-- [hankel >= 1.0.2](https://github.com/steven-murray/hankel)
+- [hankel >= 1.0.0](https://github.com/steven-murray/hankel)
 - [emcee >= 3.0.0](https://github.com/dfm/emcee)
 - [pyevtk >= 1.1.1](https://github.com/pyscience-projects/pyevtk)
-- [meshio>=4.0.3, <5.0](https://github.com/nschloe/meshio)
+- [meshio >= 4.0.0](https://github.com/nschloe/meshio)
 
 ### Optional
 

docs/source/index.rst

@@ -407,10 +407,10 @@ Requirements
 
 - `Numpy >= 1.14.5 <http://www.numpy.org>`_
 - `SciPy >= 1.1.0 <http://www.scipy.org>`_
-- `hankel >= 1.0.2 <https://github.com/steven-murray/hankel>`_
+- `hankel >= 1.0.0 <https://github.com/steven-murray/hankel>`_
 - `emcee >= 3.0.0 <https://github.com/dfm/emcee>`_
 - `pyevtk >= 1.1.1 <https://github.com/pyscience-projects/pyevtk>`_
-- `meshio>=4.0.3, <5.0 <https://github.com/nschloe/meshio>`_
+- `meshio >= 4.0.0 <https://github.com/nschloe/meshio>`_
 
 
 Optional

examples/03_variogram/01_find_best_model.py

@@ -55,12 +55,9 @@
 ###############################################################################
 # Create a ranking based on the score and determine the best models
 
-ranking = [
-    (k, v)
-    for k, v in sorted(scores.items(), key=lambda item: item[1], reverse=True)
-]
-print("RANKING")
+ranking = sorted(scores.items(), key=lambda item: item[1], reverse=True)
+print("RANKING by Pseudo-r2 score")
 for i, (model, score) in enumerate(ranking, 1):
-    print(i, model, score)
+    print(f"{i:>6}. {model:>15}: {score:.5}")
 
 plt.show()

examples/04_vector_field/01_3d_vector_field.py

@@ -16,8 +16,8 @@
 
 ###############################################################################
 # create a uniform grid with PyVista
-dim, spacing, origin = (40, 30, 10), (1, 1, 1), (-10, 0, 0)
-mesh = pv.UniformGrid(dim, spacing, origin)
+dims, spacing, origin = (40, 30, 10), (1, 1, 1), (-10, 0, 0)
+mesh = pv.UniformGrid(dims=dims, spacing=spacing, origin=origin)
 
 ###############################################################################
 # create an incompressible random 3d velocity field on the given mesh

gstools/field/tools.py

@@ -22,6 +22,9 @@
 __all__ = ["fmt_mean_norm_trend", "to_vtk_helper", "generate_on_mesh"]
 
 
+MESHIO_VERSION = list(map(int, meshio.__version__.split(".")[:2]))
+
+
 def _fmt_func_val(f_cls, func_val):  # pragma: no cover
     if func_val is None:
         return str(None)
@@ -190,7 +193,8 @@ def generate_on_mesh(
                 raise ValueError("Field.mesh: mesh dimension too low!")
             pnts = np.empty((0, mesh_dim), dtype=np.double)
             for cell in mesh.cells:
-                pnt = np.mean(mesh.points[cell[1]], axis=1)
+                cell_points = cell[1] if MESHIO_VERSION < [5, 1] else cell.data
+                pnt = np.mean(mesh.points[cell_points], axis=1)
                 offset.append(pnts.shape[0])
                 length.append(pnt.shape[0])
                 pnts = np.vstack((pnts, pnt))

pyproject.toml

@@ -81,6 +81,6 @@ test-command = "pytest -v {package}/tests"
 test-skip = "*-macosx_arm64 *-macosx_universal2:arm64"
 
 [[tool.cibuildwheel.overrides]]
-# use manylinux2014 for py3.10
-select = "cp310-*"
-manylinux-x86_64-image = "manylinux2014"
+select = "*manylinux_i686"
+# no wheels for 32 bit anymore
+before-test = "pip install 'numpy<1.22'"

setup.cfg

@@ -47,12 +47,12 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    emcee>=3.0.0,<4
-    hankel>=1.0.2,<2
-    meshio>=4.0.3,<6
-    numpy>=1.14.5,<2
-    pyevtk>=1.1.1,<2
-    scipy>=1.1.0,<2
+    emcee>=3.0.0
+    hankel>=1.0.0
+    meshio>=4.0.0
+    numpy>=1.14.5
+    pyevtk>=1.1.1
+    scipy>=1.1.0
 python_requires = >=3.6
 zip_safe = False