Merge pull request #80 from ericpre/pyodide_install

Make `numexpr` an optional dependency to allow installation in pyodide

.github/workflows/tests.yml

@@ -15,13 +15,22 @@ jobs:
         os: [ubuntu, windows, macos]
         PYTHON_VERSION: ['3.9', '3.11']
         LABEL: ['']
+        PIP_SELECTOR: ['[tests, speed]']
         include:
           - os: ubuntu
             PYTHON_VERSION: '3.8'
+            PIP_SELECTOR: '[tests, speed]'
           - os: ubuntu
             PYTHON_VERSION: '3.10'
+            PIP_SELECTOR: '[tests, speed]'
           - os: ubuntu
             PYTHON_VERSION: '3.12'
+            PIP_SELECTOR: '[tests, speed]'
+          # test minimum requirement
+          - os: ubuntu
+            PYTHON_VERSION: '3.9'
+            LABEL: '-minimum'
+            PIP_SELECTOR: '[tests]'
 
     steps:
       - uses: actions/checkout@v4
@@ -52,7 +61,7 @@ jobs:
 
       - name: Install
         run: |
-          pip install -e .[tests]
+          pip install -e '.${{ matrix.PIP_SELECTOR }}'
 
       - name: Pip list
         run: |

doc/user_guide/eels.rst

@@ -394,16 +394,17 @@ edge functionalities:
 
 .. _eels.fine_structure:
 
-Fine structure analysis
-^^^^^^^^^^^^^^^^^^^^^^^
+Fine structure analysis using a spline function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The fine structure of an EELS ionization edge manifests as distinct features within
 the first few tens of eVs energy. It is due to variations in the electron's energy
 loss probability caused by the interactions with the material's electronic structure.
 It offers insights into the material's electronic properties, bonding, and local environments.
 Therefore, we cannot model them from first-principles because i) the material is usually unknown
-ii) HyperSpy only supports Hydrogenic and Hartree-Slater EELS core-loss models. Instead, the
-:py:class:`~.components.EELSCLEdge` component includes features
+ii) HyperSpy supports Hydrogenic, Hartree-Slater EELS, DFT and Dirac core-loss models, which don't
+include modeling of the fine structure - see :ref:`eels.GOS` and :class:`~.components.EELSCLEdge`
+for more information. Instead, the :py:class:`~.components.EELSCLEdge` component includes features
 for EELS fine structure modelling and analysis using functions to mimic the fine structure
 features. The most basic consists in modelling
 the fine structure of ionization edges using a spline function. You can activate this feature
@@ -483,8 +484,8 @@ structure width. It is possible to suspend this feature by calling
 To resume it use
 :py:meth:`~.models.EELSModel.suspend_auto_fine_structure_width`
 
-Fine structure analysis
-"""""""""""""""""""""""
+Fine structure analysis using Gaussian functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Fine structure analysis consists on measuring different features of the fine structure
 (e.g., peak position, area, ...). Often, these features can be related to the ionized atom environment.

doc/user_guide/install.rst

@@ -95,7 +95,35 @@ and install it using (requires ``pip``):
 
 Required dependencies will be installed automatically.
 
+Optional dependencies
+---------------------
 
+Optional dependencies can be installed using the
+`extras <https://packaging.python.org/en/latest/specifications/dependency-specifiers/#extras>`_.
+To install all optional dependencies:
+
+.. code-block:: bash
+
+    pip install exspy[all]
+
+The list of *extras*:
+
++------------------+-----------------------------+------------------------------------------------------------+
+| Extra            | Dependencies                | Usage                                                      |
++==================+=============================+============================================================+
+| ``speed``        | ``numexpr``                 | To speed up fitting with components supporting ``numexpr`` |
++------------------+-----------------------------+------------------------------------------------------------+
+| ``gui-jupyter``  | ``hyperspy_gui_ipywidgets`` | To use the ``ipywidgets`` user interface                   |
++------------------+-----------------------------+------------------------------------------------------------+
+| ``gui-traitsui`` | ``hyperspy_gui_traitsui``   | To use the ``qt`` user interface                           |
++------------------+-----------------------------+------------------------------------------------------------+
+
+And for development, the following *extras* are available (see ``pyproject.toml`` for more information):
+
+- tests
+- doc
+- dev
+
 Updating the package
 ====================
 

exspy/_utils.py

@@ -0,0 +1,36 @@
+# -*- coding: utf-8 -*-
+# Copyright 2007-2024 The eXSpy developers
+#
+# This file is part of eXSpy.
+#
+# eXSpy is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# eXSpy is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with eXSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+import importlib
+import logging
+
+_logger = logging.getLogger(__name__)
+
+
+def parse_component_module(module):
+    """Check if numexpr is installed, if not fall back to numpy"""
+    if module == "numexpr":
+        numexpr_spec = importlib.util.find_spec("numexpr")
+        if numexpr_spec is None:
+            module = "numpy"
+            _logger.warning(
+                "Numexpr is not installed, falling back to numpy, "
+                "which is slower to calculate model."
+            )
+
+    return module

exspy/components/eels_double_power_law.py

@@ -22,6 +22,8 @@
 from hyperspy.docstrings.parameters import FUNCTION_ND_DOCSTRING
 import hyperspy.api as hs
 
+from exspy._utils import parse_component_module
+
 
 class DoublePowerLaw(hs.model.components1D.Expression):
     r"""Double power law component for EELS spectra.
@@ -87,7 +89,7 @@ def __init__(
             left_cutoff=left_cutoff,
             position="origin",
             autodoc=False,
-            module=module,
+            module=parse_component_module(module),
             compute_gradients=compute_gradients,
             linear_parameter_list=["A"],
             check_parameter_linearity=False,

exspy/components/pes_see.py

@@ -22,6 +22,8 @@
 
 import hyperspy.api as hs
 
+from exspy._utils import parse_component_module
+
 
 _logger = logging.getLogger(__name__)
 
@@ -77,7 +79,7 @@ def __init__(
             Phi=Phi,
             B=B,
             position="Phi",
-            module=module,
+            module=parse_component_module(module),
             autodoc=False,
             compute_gradients=compute_gradients,
             linear_parameter_list=["A"],

exspy/components/volume_plasmon_drude.py

@@ -20,6 +20,8 @@
 
 import hyperspy.api as hs
 
+from exspy._utils import parse_component_module
+
 
 class VolumePlasmonDrude(hs.model.components1D.Expression):
     r"""
@@ -72,7 +74,7 @@ def __init__(
             plasmon_energy=plasmon_energy,
             fwhm=fwhm,
             position="plasmon_energy",
-            module=module,
+            module=parse_component_module(module),
             autodoc=False,
             compute_gradients=compute_gradients,
             linear_parameter_list=["intensity"],

exspy/tests/components/test_double_power_law.py

@@ -31,8 +31,10 @@ def test_function():
     g.origin.value = 1
     g.shift.value = 2
     g.ratio.value = 2
-    assert np.isinf(g.function(1))
-    assert np.isinf(g.function(3))
+    if g._module == "numexpr":
+        # numpy raises a ZeroDivisionError
+        assert np.isinf(g.function(1))
+        assert np.isinf(g.function(3))
     assert g.function(-1) == 0
     assert g.function(0) == 0
     assert g.function(2) == 9

pyproject.toml

@@ -42,7 +42,6 @@ dependencies = [
   "dask[array]",
   "hyperspy>=2.0rc0",
   "matplotlib",
-  "numexpr",
   "numpy",
   "pint",
   "pooch",
@@ -74,17 +73,19 @@ file = "LICENSE"
   # unpin when sphinxcontrib-towncrier support more recent version to towncrier
   "towncrier<24",
 ]
+"speed" = ["numexpr"]
 "tests" = [
   "pytest     >= 5.0",
   "pytest-mpl",
   "pytest-cov >= 2.8.1",
   "pytest-xdist",
   "setuptools-scm",
 ]
-"dev" = ["black"]
+"dev" = ["ruff"]
 "all" = [
   "exspy[gui-jupyter]",
-  "exspy[gui-traitsui]"
+  "exspy[gui-traitsui]",
+  "exspy[speed]"
 ]
 
 [project.urls]

upcoming_changes/80.enhancements.rst

@@ -0,0 +1 @@
+Make ``numexpr`` an optional dependency to allow installation in pyodide.