NumPy v2 (#221)

- Update for NumPy v2 (replace np.infty by np.inf; np.float_ by np.float64)
- Bump minimum Python to 3.10
- Bump minimum SciPy to 1.10
- No more restriction on Numba version
- Docs need new pickleshare
- Fixes to address warnings regarding the deprecated conversion of an array with ndim > 0 to a scalar.

.github/workflows/linux.yml

@@ -36,40 +36,30 @@ jobs:
       matrix:
         os: [ubuntu, ]  # macos, windows]  # Only Linux currently.
         case:
-          - python-version: "3.9"
-            name: minimal
-            os: ubuntu
-            conda: "'numba=0.53' 'scipy=1.9' scooby libdlf"
-            test: ""
           - python-version: "3.10"
-            name: plain
+            name: minimal
             os: ubuntu
-            conda: "numba scipy scooby libdlf"
+            conda: "numba 'scipy=1.10' scooby libdlf"
             test: ""
-          - python-version: "3.10"
-            name: full
-            os: ubuntu
-            conda: "numba scipy scooby libdlf matplotlib pytest-mpl"
-            test: "--mpl"
           - python-version: "3.11"
             name: plain
             os: ubuntu
-            conda: "numba scipy scooby libdlf"
+            conda: "numba 'scipy>=1.10' scooby libdlf"
             test: ""
           - python-version: "3.11"
             name: full
             os: ubuntu
-            conda: "numba scipy scooby libdlf matplotlib pytest-mpl"
+            conda: "numba 'scipy>=1.10' scooby libdlf matplotlib pytest-mpl"
             test: "--mpl"
           - python-version: "3.12"
             name: plain
             os: ubuntu
-            conda: "numba scipy scooby libdlf"
+            conda: "numba 'scipy>=1.10' scooby libdlf"
             test: ""
           - python-version: "3.12"
             name: full
             os: ubuntu
-            conda: "numba scipy scooby libdlf matplotlib pytest-mpl"
+            conda: "numba 'scipy>=1.10' scooby libdlf matplotlib pytest-mpl"
             test: "--mpl"
 
     env:
@@ -125,7 +115,8 @@ jobs:
       - name: Test with pytest
         shell: bash -l {0}
         run: |
-          python -m pip install .
+          python -m pip install --upgrade pip
+          make install
           cp ./tests/matplotlibrc ./.
           pytest --cov=empymod ${{ matrix.case.test }}
 

.github/workflows/macos_windows.yml

@@ -81,5 +81,5 @@ jobs:
       - name: Test with pytest
         shell: bash -l {0}
         run: |
-          python -m pip install .
+          make install
           pytest

CHANGELOG.rst

@@ -10,15 +10,34 @@ v2.3.x
 """"""
 
 
-latest
-------
+v2.3.2: NumPy v2
+----------------
+
+**2024-10-09**
+
+The code is now compatible with NumPy v2.
 
 - Gallery Update Part I:
+
   - Update for Jupyterlab (ipympl/widget) 
   - Replaced implicit by explicit pyplots
   - Use by default a positiv z-upwards coordinate system
   - Part I: frequency domain; reproducing; published
 
+- Bumped the minimum requirements to:
+
+  - Python 3.9
+  - SciPy 1.10
+  - Numba, libdlf, scooby (without minimum version)
+
+- Maintenance:
+
+  - Testing: dropped Python 3.9 (Python 3.13 not added yet).
+  - Update for NumPy v2: mainly ``np.infty -> np.inf``,
+    ``np.float_ -> np.float64``.
+  - Some fixes to address warnings regarding the deprecated conversion of an
+    array with ndim > 0 to a scalar.
+
 
 v2.3.1: Julia wrapper
 ---------------------
@@ -58,7 +77,7 @@ dependency.
 - Maintenance:
 
   - Bumped the minimum requirements to:
-  
+
     - Python 3.9
     - SciPy 1.9
     - Numba 0.53

Makefile

@@ -14,10 +14,10 @@ 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 .
 
 .ONESHELL:
 pytest:

README.rst

@@ -10,7 +10,7 @@
 .. image:: https://img.shields.io/conda/v/conda-forge/empymod.svg
    :target: https://anaconda.org/conda-forge/empymod/
    :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/conf.py

@@ -142,6 +142,10 @@
 # is responsible for resolving them.
 linkcheck_ignore = [
     "https://doi.org/*",  # DOIs should be permanent (their entire purpose)
-    "https://conahcyt.mx",  # Check fails; check later again!
-    "https://software.seg.org",  # Page cannot be reached.
+    # Pages which fail with linkcheck, but can be reached manually
+    # How do we check these?
+    "https://conahcyt.mx",
+    "https://software.seg.org",
+    "https://wiki.seg.org/wiki",                # Requires human-check
+    "https://www.cambridge.org/9781107058620",
 ]

docs/dev/contributing.rst

@@ -11,9 +11,11 @@ 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/empymod/issues>`_;
-- `Roadmap-project <https://github.com/emsig/empymod/projects/3>`_;
 - `PR's <https://github.com/emsig/empymod/pulls>`_.
 
+.. GOT DELETED BY GITHUB
+   `Roadmap-project <https://github.com/emsig/empymod/projects/3>`_;
+
 There are various different ways to get in touch, see
 `emsig.xyz#contributing-contact <https://emsig.xyz/#contributing-contact>`_.
 

docs/manual/references.rst

@@ -33,7 +33,7 @@ References
    power spectrum: Monthly Notices of the Royal Astronomical Society, 312,
    pages 257--284; DOI: `10.1046/j.1365-8711.2000.03071.x
    <https://doi.org/10.1046/j.1365-8711.2000.03071.x>`_; Website of FFTLog:
-   `casa.colorado.edu/~ajsh/FFTLog <http://casa.colorado.edu/~ajsh/FFTLog>`_.
+   `jila.colorado.edu/~ajsh/FFTLog <https://jila.colorado.edu/~ajsh/FFTLog>`_.
 .. [HuTS15] Hunziker, J., J. Thorbecke, and E. Slob, 2015, The electromagnetic
    response in a layered vertical transverse isotropic medium: A new look at an
    old problem: Geophysics, 80(1), F1--F18; DOI: `10.1190/geo2013-0411.1

docs/manual/transforms.rst

@@ -60,8 +60,8 @@ FFTLog
 
 FFTLog is the logarithmic analogue to the Fast Fourier Transform FFT originally
 proposed by [Talm78]_. The code used by ``empymod`` was published in Appendix B
-of [Hami00]_ and is publicly available at `casa.colorado.edu/~ajsh/FFTLog
-<http://casa.colorado.edu/~ajsh/FFTLog>`_. From the ``FFTLog``-website:
+of [Hami00]_ and is publicly available at `jila.colorado.edu/~ajsh/FFTLog
+<https://jila.colorado.edu/~ajsh/FFTLog>`_. From the ``FFTLog``-website:
 
 *FFTLog is a set of fortran subroutines that compute the fast Fourier or Hankel
 (= Fourier-Bessel) transform of a periodic sequence of logarithmically spaced

empymod/scripts/fdesign.py

@@ -638,10 +638,10 @@ def plot_result(filt, full, prntres=True):
         else:   # (c) if several spacing and several shift values
             field = np.ma.masked_where(np.isinf(minfield), field)
             plt.pcolormesh(shift, spacing, field, cmap=cmap, shading='nearest')
-            plt.xlim([shift[0]-np.diff(shift[:2])/2,
-                      shift[-1]+np.diff(shift[-2:])/2])
-            plt.ylim([spacing[0]-np.diff(spacing[:2])/2,
-                      spacing[-1]+np.diff(spacing[-2:])/2])
+            plt.xlim([shift[0]-np.diff(shift[:2])[0]/2,
+                      shift[-1]+np.diff(shift[-2:])[0]/2])
+            plt.ylim([spacing[0]-np.diff(spacing[:2])[0]/2,
+                      spacing[-1]+np.diff(spacing[-2:])[0]/2])
             plt.ylabel('Spacing')
             plt.xlabel('Shift')
             plt.colorbar()

empymod/transform.py

@@ -658,7 +658,7 @@ def fourier_fftlog(fEM, time, freq, ftarg):
 
     FFTLog is the logarithmic analogue to the Fast Fourier Transform FFT.
     FFTLog was presented in Appendix B of [Hami00]_ and published at
-    https://casa.colorado.edu/~ajsh/FFTLog.
+    https://jila.colorado.edu/~ajsh/FFTLog.
 
     This function uses a simplified version of `pyfftlog`, which is a
     python-version of `FFTLog`. For more details regarding `pyfftlog` see

empymod/utils.py

@@ -695,7 +695,7 @@ def check_model(depth, res, aniso, epermH, epermV, mpermH, mpermV, xdirect,
     Returns
     -------
     depth : array
-        Depths of layer interfaces, adds -infty at beginning if not present.
+        Depths of layer interfaces, adds -inf at beginning if not present.
 
     res : array
         As input, checked for size.
@@ -736,13 +736,13 @@ def check_model(depth, res, aniso, epermH, epermV, mpermH, mpermV, xdirect,
     # Add -infinity at the beginning
     # => The top-layer (-infinity to first interface) is layer 0.
     if depth.size == 0:
-        depth = np.array([-np.infty, ])
+        depth = np.array([-np.inf, ])
     else:
-        if depth[0] != -np.infty:
-            depth = np.r_[-np.infty, depth]
+        if depth[0] != -np.inf:
+            depth = np.r_[-np.inf, depth]
 
-        # Remove +np.infty (can be used to define 2-layer coordinate system).
-        if depth[-1] == np.infty:
+        # Remove +np.inf (can be used to define 2-layer coordinate system).
+        if depth[-1] == np.inf:
             depth = depth[:-1]
 
     # Check if the user provided a model for etaH/etaV/zetaH/zetaV
@@ -1479,9 +1479,9 @@ def get_layer_nr(inp, depth):
     """
     zinp = np.array(inp[2], dtype=np.float64)
 
-    #  depth = [-infty : last interface]; create additional depth-array
-    # pdepth = [fist interface : +infty]
-    pdepth = np.concatenate((depth[1:], np.array([np.infty])))
+    #  depth = [-inf : last interface]; create additional depth-array
+    # pdepth = [fist interface : +inf]
+    pdepth = np.concatenate((depth[1:], np.array([np.inf])))
 
     # Broadcast arrays
     b_zinp = np.atleast_1d(zinp)[:, None]

examples/educational/coordinate_system.py

@@ -103,11 +103,11 @@
 
   In a two-layer scenario with only one interface ``depth = z`` it always
   assumes a **LHS**, as it is not possible to detect the direction from only
-  one interface. To force a **RHS** you have to add ``-np.infty`` for the
+  one interface. To force a **RHS** you have to add ``-np.inf`` for the
   down-most interface:
 
-  - **LHS**: ``depth = z`` (+z down); default, corresponds to ``[z, np.infty]``
-  - **RHS**: ``depth = [z, -np.infty]`` (+z up)
+  - **LHS**: ``depth = z`` (+z down); default, corresponds to ``[z, np.inf]``
+  - **RHS**: ``depth = [z, -np.inf]`` (+z up)
 
 
 In this example we first create a sketch of the LHS and RHS for visualization,

requirements-dev.txt

@@ -18,6 +18,7 @@ pydata_sphinx_theme
 sphinx_automodapi
 ipykernel
 ipympl
+pickleshare
 
 # FOR TESTING
 asv

setup.py

@@ -28,11 +28,10 @@
             "empymod=empymod.__main__:main",
         ],
     },
-    python_requires=">=3.9",
+    python_requires=">=3.10",
     install_requires=[
-        "scipy>=1.9",
-        "numpy<2.0",
-        "numba>=0.53",
+        "scipy>=1.10",
+        "numba",
         "libdlf",
         "scooby",
     ],

tests/create_data/kernel.py

@@ -47,7 +47,7 @@
 zetaV = np.outer(2j*np.pi*freq, mpermV*mu_0)
 filt = filters.Hankel().key_51_2012
 lambd = filt.base/np.array([0.001, 1, 100, 10000])[:, None]
-depth = np.array([-np.infty, 0, 150, 300, 500, 600])
+depth = np.array([-np.inf, 0, 150, 300, 500, 600])
 inp1 = {'zsrc': 100.,
         'zrec': 650.,
         'lsrc': np.array(1),

tests/create_data/transform.py

@@ -262,10 +262,12 @@ def test_time(res, off, t, signal):
 sPJ0br = iuSpline(np.log(ilambd), PJ0b.real)
 sPJ0bi = iuSpline(np.log(ilambd), PJ0b.imag)
 ang_fact = kernel.angle_factor(angle, ab, msrc, mrec)
-iinp = {'a': a, 'b': b, 'epsabs': atol, 'epsrel': rtol, 'limit': limit}
+iinp = {'a': float(a), 'b': float(b), 'epsabs': float(atol),
+        'epsrel': float(rtol), 'limit': int(limit)}
 quad = {'inp': {'sPJ0r': sPJ0r, 'sPJ0i': sPJ0i, 'sPJ1r': sPJ1r, 'sPJ1i': sPJ1i,
-                'sPJ0br': sPJ0br, 'sPJ0bi': sPJ0bi, 'ab': ab, 'off': off,
-                'ang_fact': ang_fact, 'iinp': iinp},
+                'sPJ0br': sPJ0br, 'sPJ0bi': sPJ0bi, 'ab': ab,
+                'off': float(off[0]), 'ang_fact': float(ang_fact[0]),
+                'iinp': iinp},
         'res': np.squeeze(freqres)}
 
 # # I -- Store data # #

tests/test_io.py

@@ -115,7 +115,7 @@ def test_ComplexNumPyEncoder():
 
     # NumPy types
     assert type(test.default(np.int_(1))) is int
-    assert type(test.default(np.float_(1))) is float
+    assert type(test.default(np.float64(1))) is float
     assert type(test.default(np.bool_(1))) is bool
     assert type(test.default(np.array([[1., 1.], [1., 1.]]))) is list
 

tests/test_model.py

@@ -735,17 +735,17 @@ def test_coordinate_systems():
         orig = dipole(depth=z0, res=[air, hs], **inpLHS, **inp)
 
         # Alternatives LHS: low to high and high to low
-        LHSl2h = dipole(depth=[z0, np.infty], res=[air, hs], **inpLHS, **inp)
-        LHSh2l = dipole(depth=[np.infty, z0], res=[hs, air], **inpLHS, **inp)
+        LHSl2h = dipole(depth=[z0, np.inf], res=[air, hs], **inpLHS, **inp)
+        LHSh2l = dipole(depth=[np.inf, z0], res=[hs, air], **inpLHS, **inp)
 
         assert_allclose(orig, LHSl2h)
         assert_allclose(orig, LHSh2l)
 
         # Alternatives LHS: low to high and high to low
         RHSlth = sign*dipole(
-            depth=[-np.infty, -z0], res=[hs, air], **inpRHS, **inp)
+            depth=[-np.inf, -z0], res=[hs, air], **inpRHS, **inp)
         RHSh2l = sign*dipole(
-            depth=[-z0, -np.infty], res=[air, hs], **inpRHS, **inp)
+            depth=[-z0, -np.inf], res=[air, hs], **inpRHS, **inp)
 
         assert_allclose(orig, RHSlth, rtol=5e-6)
         assert_allclose(orig, RHSh2l, rtol=5e-6)

tests/test_tmtemod.py

@@ -21,7 +21,7 @@
 zeta = np.outer(2j*np.pi*freq, mperm*mu_0)
 filt = filters.Hankel().key_201_2012
 lambd = filt.base/np.array([0.001, 1, 100, 10000])[:, None]
-depth = np.array([-np.infty, 0, 150, 300, 500, 600, 800])
+depth = np.array([-np.inf, 0, 150, 300, 500, 600, 800])
 
 
 def test_dipole():

tests/test_utils.py

@@ -414,7 +414,7 @@ def test_check_model(capsys):
     out, _ = capsys.readouterr()
     assert "* WARNING :: Parameter aniso < " in out
     assert "   direct field    :  Comp. in frequency domain" in out
-    assert_allclose(depth, [-np.infty, 0])
+    assert_allclose(depth, [-np.inf, 0])
     assert_allclose(res, [1e20, 20])
     assert_allclose(aniso, [1, np.sqrt(1e-20/20)])
     assert_allclose(epermH, [0, 1])
@@ -435,13 +435,13 @@ def test_check_model(capsys):
     out, _ = capsys.readouterr()
     assert "   direct field    :  Not calculated (secondary field)" in out
 
-    # Check -np.infty is added to depth
+    # Check -np.inf is added to depth
     out = utils.check_model([], 2, 1, 1, 1, 1, 1, True, 1)
-    assert_allclose(out[0], -np.infty)
+    assert_allclose(out[0], -np.inf)
 
-    # Check -np.infty is not added if it is already in depth
-    out = utils.check_model(-np.infty, 2, 1, 1, 1, 1, 1, True, 1)
-    assert_allclose(out[0], -np.infty)
+    # Check -np.inf is not added if it is already in depth
+    out = utils.check_model(-np.inf, 2, 1, 1, 1, 1, 1, True, 1)
+    assert_allclose(out[0], -np.inf)
 
     # Check verbosity and fullspace
     utils.check_model(0, [1, 1], [2, 2], [10, 10], [1, 1], None, [3, 3], True,
@@ -932,15 +932,15 @@ def test_get_geo_fact():
 
 def test_get_layer_nr():
     bip = np.array([0, 0, 300])
-    lbip, zbip = utils.get_layer_nr(bip, np.array([-np.infty, 500]))
+    lbip, zbip = utils.get_layer_nr(bip, np.array([-np.inf, 500]))
     assert lbip == 0
     assert zbip == 300
-    lbip, _ = utils.get_layer_nr(bip, np.array([-np.infty, 0, 300, 500]))
+    lbip, _ = utils.get_layer_nr(bip, np.array([-np.inf, 0, 300, 500]))
     assert lbip == 1
-    lbip, _ = utils.get_layer_nr(bip, np.array([-np.infty, 0, 200]))
+    lbip, _ = utils.get_layer_nr(bip, np.array([-np.inf, 0, 200]))
     assert lbip == 2
     bip = np.array([np.zeros(4), np.zeros(4), np.arange(4)*100])
-    lbip, _ = utils.get_layer_nr(bip, np.array([-np.infty, 0, 200]))
+    lbip, _ = utils.get_layer_nr(bip, np.array([-np.inf, 0, 200]))
     assert_allclose(lbip, [0, 1, 1, 2])