Make empymod a hard dependency (#324)

Make empymod a hard dependency. This removes duplication of code (`EMArray`, and in the future potentially more, e.g., with regards to noise generation) and streamlines things. It also brings in `scooby`, which is good for user support / helping with issues.
emsig · Mar 4, 2024 · 8750f85 · 8750f85
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diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -43,7 +43,7 @@ jobs:
           - python-version: "3.10"
             name: full
             os: ubuntu
-            conda: "numba scipy xarray empymod h5py scooby discretize matplotlib"  # tqdm
+            conda: "numba scipy xarray h5py discretize matplotlib"  # tqdm
           - python-version: "3.10"
             name: plain
             os: ubuntu
@@ -55,15 +55,15 @@ jobs:
           - python-version: "3.11"
             name: full
             os: ubuntu
-            conda: "numba scipy xarray tqdm empymod h5py scooby discretize matplotlib"
+            conda: "numba scipy xarray tqdm h5py discretize matplotlib"
           - python-version: "3.12"
             name: plain
             os: ubuntu
             conda: "numba scipy"
           - python-version: "3.12"
             name: full
             os: ubuntu
-            conda: "numba scipy xarray tqdm empymod h5py scooby discretize matplotlib"
+            conda: "numba scipy xarray tqdm h5py discretize matplotlib"
 
     env:
       # Used for coveralls flag

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -9,13 +9,16 @@ Changelog
 latest
 ------
 
+TODO: some text about empymod, scooby.
+
 - Maintenance:
 
   - Bumped the minimum requirements to:
 
     - Python 3.9
     - SciPy 1.9
     - Numba 0.53
+    - empymod 2.3.0 (NEW requirement)
 
   - Testing: added Python 3.12, dropped Python 3.8.
 

diff --git a/docs/manual/installation.rst b/docs/manual/installation.rst
@@ -13,8 +13,9 @@ or via ``pip``:
 
    pip install emg3d
 
-Requirements are the modules ``scipy`` and ``numba``. Various other packages
-are recommended or required for some advanced functionalities, namely:
+Requirements are the modules ``scipy``, ``numba``, and ``empymod``. Various
+other packages are recommended or required for some advanced functionalities,
+namely:
 
 - ``xarray``: For the :class:`emg3d.surveys.Survey` and
   :class:`emg3d.simulations.Simulation` classes (model many sources and
@@ -23,16 +24,14 @@ are recommended or required for some advanced functionalities, namely:
   plotting utilities).
 - ``matplotlib``: To use the plotting utilities within ``discretize``.
 - ``h5py``: Save and load data in the HDF5 format.
-- ``empymod``: Time-domain modelling (:class:`emg3d.time.Fourier`).
-- ``scooby``: For the version and system report (:class:`emg3d.utils.Report`).
 - ``tqdm``: For nice progress bars when computing many sources and frequencies.
 
 All soft dependencies are also available both on ``conda-forge`` and ``pip``.
 To get therefore the complete experience use one of the following options:
 
 .. code-block:: console
 
-   conda install -c conda-forge emg3d empymod discretize xarray matplotlib h5py tqdm scooby
+   conda install -c conda-forge emg3d discretize xarray matplotlib h5py tqdm
 
 or via ``pip``:
 

diff --git a/docs/manual/usage.rst b/docs/manual/usage.rst
@@ -342,5 +342,4 @@ high-level class ``Simulation``. It has to be carried out by using
 above. Have a look at the repo https://github.com/emsig/article-TDEM.
 
 
-*Note:* In addition to ``emg3d`` this requires the soft dependency ``empymod``
-(``discretize`` is recommended).
+*Note:* In addition to ``emg3d``, the soft dependency ``discretize`` is recommended for this.
diff --git a/emg3d/time.py b/emg3d/time.py
@@ -19,24 +19,17 @@
 
 import warnings
 
+import empymod
 import numpy as np
 import scipy as sp
 
-try:
-    import empymod
-except ImportError:
-    empymod = None
-
-from emg3d import utils
-
 __all__ = ['Fourier', ]
 
 
 def __dir__():
     return __all__
 
 
-@utils._requires('empymod')
 class Fourier:
     r"""Time-domain CSEM computation.
 
@@ -68,12 +61,6 @@ class Fourier:
       with cubic spline interpolation (on a log-scale) using
       :class:`scipy.interpolate.InterpolatedUnivariateSpline`.
 
-    .. note::
-
-        The package ``empymod`` has to be installed in order to use
-        ``Fourier``:
-        ``pip install empymod`` or ``conda install -c conda-forge empymod``.
-
 
     Parameters
     ----------
@@ -106,7 +93,7 @@ class Fourier:
         - If ``ft='dlf'``:
 
            - ``dlf``: string of filter name in :mod:`empymod.filters` or the
-             filter method itself; default: ``'key_201_CosSin_2012'``.
+             filter method itself; default: ``'key_201_2012'``.
            - ``pts_per_dec``: points per decade; default: -1.
 
               - If 0: Standard DLF;

diff --git a/emg3d/utils.py b/emg3d/utils.py
@@ -24,12 +24,8 @@
 from datetime import datetime, timedelta
 
 import numpy as np
-
-try:
-    from scooby import Report as ScoobyReport
-except ImportError:
-    class ScoobyReport:
-        """Dummy placeholder."""
+from empymod import EMArray
+from scooby import Report as ScoobyReport
 
 # Version: We take care of it here instead of in __init__, so we can use it
 # within the package itself (logs).
@@ -121,7 +117,6 @@ def passer(*args, **kwargs):
 
 
 # PUBLIC UTILS
-@_requires('scooby')
 class Report(ScoobyReport):
     r"""Print date, time, and version information.
 
@@ -138,11 +133,6 @@ class Report(ScoobyReport):
 
     All modules provided in ``add_pckg`` are also shown.
 
-    .. note::
-
-        The package ``scooby`` has to be installed in order to use ``Report``:
-        ``pip install scooby`` or ``conda install -c conda-forge scooby``.
-
 
     Parameters
     ----------
@@ -165,94 +155,16 @@ def __init__(self, add_pckg=None, ncol=3, text_width=80, sort=False):
         """Initiate a scooby.Report instance."""
 
         # Mandatory packages.
-        core = ['numpy', 'scipy', 'numba', 'emg3d']
+        core = ['numpy', 'scipy', 'numba', 'emg3d', 'empymod']
 
         # Optional packages.
-        optional = ['empymod', 'xarray', 'discretize', 'h5py', 'matplotlib',
+        optional = ['xarray', 'discretize', 'h5py', 'matplotlib',
                     'tqdm', 'IPython']
 
         super().__init__(additional=add_pckg, core=core, optional=optional,
                          ncol=ncol, text_width=text_width, sort=sort)
 
 
-class EMArray(np.ndarray):
-    r"""An EM-ndarray adds the methods `amp` (amplitude) and `pha` (phase).
-
-    Parameters
-    ----------
-    data : ndarray
-        Data to which to add ``.amp`` and ``.pha`` attributes.
-
-
-    Examples
-    --------
-
-    .. ipython::
-
-       In [1]: import numpy as np
-          ...: from empymod.utils import EMArray
-          ...: emvalues = EMArray(np.array([1+1j, 1-4j, -1+2j]))
-
-       # Amplitudes
-       In [2]: emvalues.amp()
-       Out[2]: EMArray([1.41421356, 4.12310563, 2.23606798])
-
-       # Phase in radians
-       In [3]: emvalues.pha()
-       Out[3]: EMArray([ 0.78539816, -1.32581766, -4.24874137])
-
-       # Phase in degrees
-       In [4]: emvalues.pha(deg=True)
-       Out[4]: EMArray([  45.        ,  -75.96375653, -243.43494882])
-
-       # Phase in degrees, lead defined
-       In [5]: emvalues.pha(deg=True, lag=False)
-       Out[5]: EMArray([-45.        ,  75.96375653, 243.43494882])
-
-    """
-
-    def __new__(cls, data):
-        r"""Create a new EMArray."""
-        return np.asarray(data).view(cls)
-
-    def amp(self):
-        """Amplitude of the electromagnetic field."""
-        return np.abs(self.view())
-
-    def pha(self, deg=False, unwrap=True, lag=True):
-        """Phase of the electromagnetic field.
-
-        Parameters
-        ----------
-        deg : bool, default: False
-            The returned phase is in degrees if True, else in radians.
-
-        unwrap : bool, default: True
-            The returned phase is unwrapped if True.
-
-        lag : bool, default: True
-            The returned phase is lag defined if True, else lead defined.
-
-        """
-        # Get phase, lead or lag defined.
-        if lag:
-            pha = np.angle(self.view())
-        else:
-            pha = np.angle(np.conj(self.view()))
-
-        # Unwrap if `unwrap`.
-        # np.unwrap removes the EMArray class;
-        # for consistency, we wrap it in EMArray again.
-        if unwrap and self.size > 1:
-            pha = EMArray(np.unwrap(pha))
-
-        # Convert to degrees if `deg`.
-        if deg:
-            pha *= 180/np.pi
-
-        return pha
-
-
 class Timer:
     """Class for timing (now; runtime)."""
 

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -4,10 +4,7 @@
 # SOFT DEPENDENCIES
 tqdm
 h5py
-scooby
 xarray
-empymod
-cython
 discretize
 matplotlib
 

diff --git a/setup.py b/setup.py
@@ -30,16 +30,15 @@
     install_requires=[
         "scipy>=1.9",
         "numba>=0.53",
+        "empymod>=2.3.0",
     ],
     extras_require={
-        'full': [
-            'tqdm',
-            'h5py',
-            'scooby',
-            'xarray',
-            'empymod',
-            'discretize>=0.7.3',
-            'matplotlib',
+        "full": [
+            "tqdm",
+            "h5py",
+            "xarray",
+            "discretize",
+            "matplotlib",
         ],
     },
     use_scm_version={

diff --git a/tests/test_multiprocessing.py b/tests/test_multiprocessing.py
@@ -5,6 +5,7 @@
 from numpy.testing import assert_allclose
 
 import emg3d
+import empymod
 from emg3d import _multiprocessing as _mp
 
 try:
@@ -13,9 +14,9 @@
     tqdm = None
 
 try:
-    import empymod
+    import xarray
 except ImportError:
-    empymod = None
+    xarray = None
 
 # Data generated with tests/create_data/regression.py
 REGRES = emg3d.load(join(dirname(__file__), 'data', 'regression.npz'))
@@ -74,7 +75,7 @@ def test__solve():
     assert_allclose(dat['Fresult'].field, efield.field)
 
 
-@pytest.mark.skipif(empymod is None, reason="empymod not installed.")
+@pytest.mark.skipif(xarray is None, reason="xarray not installed.")
 def test_layered():
 
     src = emg3d.TxElectricDipole((-2000, 0, 200, 20, 5))
@@ -157,7 +158,6 @@ def test_layered():
     assert np.all(out[::2, 1:, 1, :] != 0.0)
 
 
-@pytest.mark.skipif(empymod is None, reason="empymod not installed.")
 def test_empymod_fwd():
     # Simple check for status quo.
     empymod_inp = {
@@ -203,7 +203,7 @@ class DummySrcRec:
     assert out['p1'] == rec.center
 
 
-@pytest.mark.skipif(empymod is None, reason="empymod not installed.")
+@pytest.mark.skipif(xarray is None, reason="xarray not installed.")
 def test_fd_gradient():
 
     res = np.array([0.9876, ])

diff --git a/tests/test_time.py b/tests/test_time.py
@@ -1,16 +1,11 @@
 import pytest
+import empymod
 import numpy as np
 from numpy.testing import assert_allclose
 
 from emg3d import time
 
-try:
-    import empymod
-except ImportError:
-    empymod = None
 
-
-@pytest.mark.skipif(empymod is None, reason="empymod not installed.")
 class TestFourier:
     def test_defaults(self, capsys):
         times = np.logspace(-2, 2)
@@ -33,7 +28,7 @@ def test_defaults(self, capsys):
         assert Fourier.signal == 0        # Impulse respons
         assert_allclose(times, Fourier.time, 0, 0)
         assert Fourier.verb == 3          # Verbose by default
-        assert 'key' in out.lower()
+        assert 'key' in out
         assert 'Req. freq' in out
         assert 'Calc. freq' in out
         assert Fourier.freq_compute.min() >= fmin
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,10 +4,7 @@ @@
     # SOFT DEPENDENCIES
     tqdm
     h5py
-    scooby
     xarray
-    empymod
-    cython
     discretize
     matplotlib
@@ Expand Down @@