NumPy v2 (#344)

- Update for NumPy v2 (replace np.infty by np.inf)
- Fix warnings
- Bump minimum Python to 3.10
- Bump minimum SciPy to 1.10
- No more restriction on Numba version
- Docs need new pickleshare

Author: prisae

.github/workflows/linux.yml

@@ -36,34 +36,26 @@ jobs:
       matrix:
         os: [ubuntu, ]  # macos, windows]  # Only Linux currently.
         case:
-          - python-version: "3.9"
-            name: minimal
-            os: ubuntu
-            conda: "'scipy=1.9' 'numba=0.53' 'numpy<2.0' 'empymod>=2.3'"
-          - python-version: "3.10"
-            name: full
-            os: ubuntu
-            conda: "numba scipy xarray h5py discretize matplotlib 'numpy<2.0' 'empymod>=2.3'"  # tqdm
           - python-version: "3.10"
-            name: plain
+            name: minimal
             os: ubuntu
-            conda: "numba scipy 'numpy<2.0' 'empymod>=2.3'"
+            conda: "'scipy=1.10' numba 'empymod>=2.3.2'"
           - python-version: "3.11"
             name: plain
             os: ubuntu
-            conda: "numba scipy 'numpy<2.0' 'empymod>=2.3'"
+            conda: "scipy numba 'empymod>=2.3.2'"
           - python-version: "3.11"
             name: full
             os: ubuntu
-            conda: "numba scipy xarray tqdm h5py discretize matplotlib 'numpy<2.0' 'empymod>=2.3'"
+            conda: "scipy numba 'empymod>=2.3.2' xarray tqdm h5py discretize matplotlib"
           - python-version: "3.12"
             name: plain
             os: ubuntu
-            conda: "numba scipy 'numpy<2.0' 'empymod>=2.3'"
+            conda: "scipy numba 'empymod>=2.3.2'"
           - python-version: "3.12"
             name: full
             os: ubuntu
-            conda: "numba scipy xarray tqdm h5py discretize matplotlib 'numpy<2.0' 'empymod>=2.3'"
+            conda: "scipy numba 'empymod>=2.3.2' xarray tqdm h5py discretize matplotlib"
 
     env:
       # Used for coveralls flag
@@ -95,8 +87,6 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.case.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
-          use-mamba: true
 
       - name: Install dependencies
         shell: bash -l {0}
@@ -118,7 +108,8 @@ jobs:
       - name: Test with pytest
         shell: bash -l {0}
         run: |
-          python -m pip install --no-build-isolation --no-deps .
+          python -m pip install --upgrade pip
+          make install
           pytest --cov=emg3d
 
       - name: Coveralls

.github/workflows/macos_windows.yml

@@ -62,8 +62,6 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
-          use-mamba: true
 
       - name: Install dependencies
         shell: bash -l {0}
@@ -72,7 +70,7 @@ jobs:
           conda config --show-sources
           conda config --show
           conda info -a
-          conda install numba scipy pytest pytest-console-scripts scooby setuptools-scm
+          conda install scipy numba empymod pytest pytest-console-scripts setuptools-scm
 
       - name: Conda list
         shell: bash -l {0}
@@ -81,5 +79,5 @@ jobs:
       - name: Test with pytest
         shell: bash -l {0}
         run: |
-          python -m pip install .
+          make install
           pytest

CHANGELOG.rst

@@ -6,13 +6,27 @@ Changelog
 """"""""""
 
 
-latest
-------
+v1.8.4 : NumPy v2
+-----------------
+
+**2024-10-09**
+
+The code is now compatible with NumPy v2.
+
 
 - Created foundation for new module ``inversion``.
 
-Maintenance
+- Bumped the minimum requirements to:
+
+  - Python 3.10
+  - SciPy 1.10
+  - empymod 2.3.2
+  - Numba (without minimum version)
+
+- Maintenance
 
+  - Testing: dropped Python 3.9 (Python 3.13 not added yet).
+  - Update for NumPy v2: mainly ``np.infty -> np.inf``.
   - Add notes for ``ipympl`` (interactive plots in modern Jupyter).
   - Reduce code by making use of new SciPy new features (complex-valued
     map_coordinate; lazy loading).

CREDITS.rst

@@ -1,17 +1,22 @@
 Credits
 #######
 
-This project was started by **Dieter Werthmüller** at
-`Delft University of Technology <https://www.tudelft.nl>`_ as part of the
-*Gitaro.JIM* project (till 05/2021, emg3d v1.0.0), funded through
-`MarTERA <https://www.martera.eu>`_ as part of Horizon 2020, a funding scheme
-of the European Research Area. Dieter would like to thank his current employers
-who allow him to maintain and further develop the code after the initial
-funding ended, namely:
-
-- 2021-today: `Delft University of Technology <https://www.tudelft.nl>`_,
-  funded through the `Delphi Consortium <https://www.delphi-consortium.com>`_
-- 2021-today: `TERRASYS Geophysics GmbH & Co. KG <https://www.terrasysgeo.com>`_
+This project was started by **Dieter Werthmüller** at TUD as part of the
+*Gitaro.JIM* project (see below).
+Dieter would like to thank his past and current employers who allowed and allow
+him to maintain and further develop the code after the initial funding ended,
+namely:
+
+- 2018-2021: `Delft University of Technology <https://www.tudelft.nl>`_;
+  through the *Gitaro.JIM* project (till 05/2021, emg3d v1.0.0), funded by
+  `MarTERA <https://www.martera.eu>`_ as part of Horizon 2020, a funding scheme
+  of the European Research Area.
+- 2021-2024: `Delft University of Technology <https://www.tudelft.nl>`_ through
+  the `Delphi Consortium <https://www.delphi-consortium.com>`_.
+- 2021-2022: `TERRASYS Geophysics GmbH & Co. KG
+  <https://www.terrasysgeo.com>`_.
+- 2024-today: `ETH Zurich <https://ethz.ch>`_ through the group `Geothermal
+  Energy and Geofluids <https://geg.ethz.ch>`_.
 
 For a list of code contributors see
 https://github.com/emsig/emg3d/graphs/contributors.

Makefile

@@ -13,10 +13,10 @@ help:
 	@echo ""
 
 install:
-	python -m pip install --no-build-isolation --no-deps -e .
+	python -m pip install --no-build-isolation --use-pep517 --no-deps -e .
 
 dev-install:
-	python -m pip install -r requirements-dev.txt && python -m pip install --no-build-isolation --no-deps -e .
+	python -m pip install -r requirements-dev.txt && python -m pip install --no-build-isolation --use-pep517 --no-deps -e .
 
 pytest:
 	rm -rf .coverage htmlcov/ .pytest_cache/ && pytest --cov=emg3d && coverage html

README.rst

@@ -10,7 +10,7 @@
 .. image:: https://img.shields.io/conda/v/conda-forge/emg3d.svg
    :target: https://anaconda.org/conda-forge/emg3d/
    :alt: conda-forge
-.. image:: https://img.shields.io/badge/python-3.8+-blue.svg
+.. image:: https://img.shields.io/badge/python-3.10+-blue.svg
    :target: https://www.python.org/downloads/
    :alt: Supported Python Versions
 .. image:: https://img.shields.io/badge/platform-linux,win,osx-blue.svg

docs/dev/contributing.rst

@@ -11,7 +11,7 @@ Good places to get started is to browse the existing issues, check out the
 roadmap, or have a look at any open PR:
 
 - `Issues <https://github.com/emsig/emg3d/issues>`_;
-- `Roadmap-project <https://github.com/emsig/emg3d/projects/1>`_;
+- `Roadmap <https://github.com/emsig/emg3d/issues/343>`_;
 - `PR's <https://github.com/emsig/emg3d/pulls>`_.
 
 There are various different ways to get in touch, see

docs/manual/cli.rst

@@ -124,7 +124,7 @@ remove the comment signs to use them.
   [noise_opts]
   # add_noise = True      # Set to False to switch noise off.
   # min_offset = 0.0      # off < min_off set to NaN.
-  # max_offset = np.infty # off > max_off set to NaN.
+  # max_offset = np.inf   # off > max_off set to NaN.
   # mean_noise = 0.0      # Mean of the noise.
   # ntype = white_noise   # Type of the noise.
 

emg3d/fields.py

@@ -696,9 +696,9 @@ def point_source(xx, yy, zz, coo, s):
         nx, ny, nz = s.shape
 
         # Get indices of cells in which source resides.
-        ix = max(0, np.where(coo[0] < np.r_[xx, np.infty])[0][0]-1)
-        iy = max(0, np.where(coo[1] < np.r_[yy, np.infty])[0][0]-1)
-        iz = max(0, np.where(coo[2] < np.r_[zz, np.infty])[0][0]-1)
+        ix = max(0, np.where(coo[0] < np.r_[xx, np.inf])[0][0]-1)
+        iy = max(0, np.where(coo[1] < np.r_[yy, np.inf])[0][0]-1)
+        iz = max(0, np.where(coo[2] < np.r_[zz, np.inf])[0][0]-1)
 
         def get_index_and_strength(ic, nc, csrc, cc):
             """Return index and field strength in c-direction."""
@@ -864,8 +864,8 @@ def min_max_ind(vector, i):
         """Return [min, max]-index of cells in which points resides."""
         vmin = min(points[:, i])
         vmax = max(points[:, i])
-        return [max(0, np.where(vmin < np.r_[vector, np.infty])[0][0]-1),
-                max(0, np.where(vmax < np.r_[vector, np.infty])[0][0]-1)]
+        return [max(0, np.where(vmin < np.r_[vector, np.inf])[0][0]-1),
+                max(0, np.where(vmax < np.r_[vector, np.inf])[0][0]-1)]
 
     rix = min_max_ind(nodes_x, 0)
     riy = min_max_ind(nodes_y, 1)

emg3d/models.py

@@ -468,7 +468,7 @@ def extract_1d(self, method, p0, p1=None, ellipse=None, merge=False,
             # Find corresponding indices, limit to grid.
             def index(nodes, coo):
                 """Return index for interval btw nodes in which coo resides."""
-                x = np.asarray(coo < np.r_[nodes, np.infty]).nonzero()[0][0]-1
+                x = np.asarray(coo < np.r_[nodes, np.inf]).nonzero()[0][0]-1
                 return np.clip(x, 0, nodes.size-2)
 
             # Start and end indices.

emg3d/surveys.py

@@ -619,7 +619,7 @@ def add_noise(self, min_offset=0.0, min_amplitude='half_nf',
             dataset it will create a dataset of zeroes. You can use that to
             obtain the pure noise.
 
-        max_offset : float, default: np.infty
+        max_offset : float, default: np.inf
             Data points in ``data.observed`` where the offset > max_offset are
             set to NaN.
 
@@ -639,8 +639,8 @@ def add_noise(self, min_offset=0.0, min_amplitude='half_nf',
             self.data[add_to].data[cut_amp] = np.nan + 1j*np.nan
 
         # Set offsets below min_offset and above max_offset to NaN.
-        max_offset = kwargs.pop('max_offset', np.infty)
-        if min_offset > 0.0 or max_offset < np.infty:
+        max_offset = kwargs.pop('max_offset', np.inf)
+        if min_offset > 0.0 or max_offset < np.inf:
             for ks, s in self.sources.items():
                 for kr, r in self.receivers.items():
                     off = np.linalg.norm(r.center_abs(s) - s.center)

requirements-dev.txt

@@ -1,6 +1,9 @@
 # GLOBAL REQUIREMENTS.
 -r requirements.txt
 
+# Fix numpy<2 until discretize is ready for 2.0
+numpy<2
+
 # SOFT DEPENDENCIES
 tqdm
 h5py
@@ -22,6 +25,7 @@ sphinx_numfig
 pydata_sphinx_theme
 sphinx_automodapi
 ipykernel
+pickleshare
 
 # FOR TESTING
 asv

setup.py

@@ -26,12 +26,11 @@
             "emg3d=emg3d.cli.main:main",
         ],
     },
-    python_requires=">=3.9",
+    python_requires=">=3.10",
     install_requires=[
-        "scipy>=1.9",
-        "numpy<2.0",
-        "numba>=0.53",
-        "empymod>=2.3.0",
+        "scipy>=1.10",
+        "numba",
+        "empymod>=2.3.2",
     ],
     extras_require={
         "full": [

tests/alternatives.py

@@ -241,7 +241,7 @@ def alt_volume_average(edges_x, edges_y, edges_z, values,
     """
 
     # Get cell indices.
-    # First and last edges ignored => first and last cells extend to +/- infty.
+    # First and last edges ignored => first and last cells extend to +/- inf.
     ix_l = np.searchsorted(edges_x[1:-1], new_edges_x, 'left')
     ix_r = np.searchsorted(edges_x[1:-1], new_edges_x, 'right')
     iy_l = np.searchsorted(edges_y[1:-1], new_edges_y, 'left')
@@ -353,9 +353,9 @@ def point_source(xx, yy, zz, src, s):
         nx, ny, nz = s.shape
 
         # Get indices of cells in which source resides.
-        ix = max(0, np.where(src[0] < np.r_[xx, np.infty])[0][0]-1)
-        iy = max(0, np.where(src[1] < np.r_[yy, np.infty])[0][0]-1)
-        iz = max(0, np.where(src[2] < np.r_[zz, np.infty])[0][0]-1)
+        ix = max(0, np.where(src[0] < np.r_[xx, np.inf])[0][0]-1)
+        iy = max(0, np.where(src[1] < np.r_[yy, np.inf])[0][0]-1)
+        iz = max(0, np.where(src[2] < np.r_[zz, np.inf])[0][0]-1)
 
         def get_index_and_strength(ic, nc, csrc, cc):
             """Return index and field strength in c-direction."""

tests/test_fields.py

@@ -78,7 +78,7 @@ def test_dtype(self):
         with pytest.raises(ValueError, match="must be f>0"):
             _ = fields.Field(self.grid, frequency=0.0)
 
-        with pytest.warns(np.ComplexWarning, match="Casting complex values"):
+        with pytest.warns(np.exceptions.ComplexWarning, match="Casting compl"):
             lp = fields.Field(self.grid, self.field, frequency=-1)
         assert lp.field.dtype == np.float64
 

tests/test_meshes.py

@@ -346,14 +346,14 @@ def test_domain_vector(self):
 
         vector2 = np.array([-1, 0, 1])
         x02, hx2 = meshes.origin_and_widths(vector=vector2, **inp)
-        assert np.in1d(vector2, x02 + np.cumsum(hx2)).all()
+        assert np.isin(vector2, x02 + np.cumsum(hx2)).all()
 
         vector3 = np.array([-2, -1, 0, 1, 2])
         x03, hx3 = meshes.origin_and_widths(  # vector will be cut
                 domain=[-1, 1], vector=vector3, **inp)
-        assert np.in1d(vector3[1:-1], x03 + np.cumsum(hx3)).all()
-        assert not np.in1d(vector3[0], x03 + np.cumsum(hx3))
-        assert not np.in1d(vector3[-1], x03 + np.cumsum(hx3))
+        assert np.isin(vector3[1:-1], x03 + np.cumsum(hx3)).all()
+        assert not np.isin(vector3[0], x03 + np.cumsum(hx3))
+        assert not np.isin(vector3[-1], x03 + np.cumsum(hx3))
 
         x04, hx4 = meshes.origin_and_widths(  # vector will be cut
                 distance=[1.0, 1.0], vector=vector3, **inp)
@@ -362,7 +362,7 @@ def test_domain_vector(self):
 
         x05, hx5 = meshes.origin_and_widths(  # vector will be expanded
                 distance=[2.0, 2.0], vector=vector2, **inp)
-        assert np.in1d(np.array([-2, -1, 0, 1, 2]), x05 + np.cumsum(hx5)).all()
+        assert np.isin(np.array([-2, -1, 0, 1, 2]), x05 + np.cumsum(hx5)).all()
 
     def test_seasurface(self):
         inp = {'frequency': 1/np.pi, 'properties': 9*mu_0, 'domain': [-1, 2],

tests/test_multiprocessing.py

@@ -27,6 +27,7 @@ def dummy(inp):
     return inp
 
 
+@pytest.mark.filterwarnings("ignore:.*lead to deadlocks*:DeprecationWarning")
 def test_process_map():
 
     # Parallel

tests/test_simulations.py

@@ -28,6 +28,7 @@
 rng = np.random.default_rng()
 
 
+@pytest.mark.filterwarnings("ignore:.*lead to deadlocks*:DeprecationWarning")
 @pytest.mark.skipif(xarray is None, reason="xarray not installed.")
 class TestSimulation():
     if xarray is not None:
@@ -695,6 +696,7 @@ def test_compute_1d(self):
         assert grad.shape == self.model.shape
 
 
+@pytest.mark.filterwarnings("ignore:.*lead to deadlocks*:DeprecationWarning")
 @pytest.mark.skipif(xarray is None, reason="xarray not installed.")
 def test_misfit():
     data = 1