Merge pull request #3255 from ericpre/pyodide

HyperSpy on pyodide (and jupyterlite)

.github/workflows/build.yml

@@ -0,0 +1,75 @@
+name: Build
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron:  '0 0 * * 0'
+  pull_request:
+    types: [labeled, ready_for_review, reopened]
+
+jobs:
+  build:
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'run-packaging') || github.event_name == 'workflow_dispatch'  || github.event_name == 'schedule' }}
+    name: Build
+    runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: '3.11'
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Display version
+        run: |
+          python --version
+          pip --version
+
+      - name: Install pypa/build
+        run: |
+          pip install build
+
+      - name: Build a binary wheel and a source tarball
+        run: |
+          python -m build
+
+      - name: Display content dist folder
+        run: |
+          ls -shR dist/
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./dist/*
+          name: dist
+
+  test:
+    name: Test Packaging
+    needs: build
+    runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: '3.11'
+    steps:
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: actions/download-artifact@v3
+
+      - name: Display content working folder
+        run: |
+          ls -R
+
+      - name: Install distribution
+        run: |
+          pip install --pre --find-links dist hyperspy[all,tests]
+
+      - name: Pip list
+        run: |
+          pip list
+
+      - name: Test distribution
+        run: |
+          pytest --pyargs hyperspy --reruns 3 -n 2

doc/user_guide/install.rst

@@ -172,15 +172,14 @@ use:
 
 See the following list of selectors to select the installation of optional
 dependencies required by specific functionalities:
-
+* ``ipython`` for integration with the `ipython` terminal and parallel processing using `ipyparallel`,
 * ``learning`` for some machine learning features,
 * ``gui-jupyter`` to use the `Jupyter widgets <https://ipywidgets.readthedocs.io/en/stable/>`_
   GUI elements,
 * ``gui-traitsui`` to use the GUI elements based on `traitsui <https://docs.enthought.com/traitsui/>`_,
-* ``mrcz`` to read mrcz file,
-* ``speed`` to speed up some functionalities,
-* ``usid`` to read usid file,
+* ``speed`` install numba and numexpr to speed up some functionalities,
 * ``tests`` to install required libraries to run HyperSpy's unit tests,
+* ``coverage`` to coverage statistics when running the tests,
 * ``build-doc`` to install required libraries to build HyperSpy's documentation,
 * ``dev`` to install all the above,
 * ``all`` to install all the above except the development requirements

hyperspy/_components/bleasdale.py

@@ -24,30 +24,34 @@ class Bleasdale(Expression):
 
     r"""Bleasdale function component.
 
-    Also called the Bleasdale-Nelder function. Originates from the description of the yield-density relationship in crop growth.
+    Also called the Bleasdale-Nelder function. Originates from
+    the description of the yield-density relationship in crop growth.
 
     .. math::
 
         f(x) = \left(a+b\cdot x\right)^{-1/c}
 
     Parameters
-    -----------
-        a : Float
-
-        b : Float
-
-        c : Float
-
-        **kwargs
-            Extra keyword arguments are passed to the
-            :py:class:`~._components.expression.Expression` component.
-
+    ----------
+    a : float, default=1.0
+        The value of Parameter a.
+    b : float, default=1.0
+        The value of Parameter b.
+    c : float, default=1.0
+        The value of Parameter c.        
+    **kwargs
+        Extra keyword arguments are passed to
+        :py:class:`~.api.model.components1D.Expression`.
+
+    Note
+    ----
     For :math:`(a+b\cdot x)\leq0`, the component will be set to 0.
+
     """
 
-    def __init__(self, a=1., b=1., c=1., module="numexpr", **kwargs):
+    def __init__(self, a=1., b=1., c=1., module=None, **kwargs):
         super().__init__(
-            expression="where((a + b * x) > 0, (a + b * x) ** (-1 / c), 0)",
+            expression="where((a + b * x) > 0, pow(a + b * x, -1 / c), 0)",
             name="Bleasdale",
             a=a,
             b=b,
@@ -58,6 +62,12 @@ def __init__(self, a=1., b=1., c=1., module="numexpr", **kwargs):
             linear_parameter_list=['b'],
             check_parameter_linearity=False,
             **kwargs)
+        module = self._whitelist['module'][1]
+        if module in ("numpy", "scipy"):
+            # Issue with calculating component at 0...
+            raise ValueError(
+                f"{module} is not supported for this component, use numexpr instead."
+                )
 
     def grad_a(self, x):
         """

hyperspy/_components/exponential.py

@@ -52,7 +52,7 @@ class Exponential(Expression):
         :py:class:`~._components.expression.Expression` component.
     """
 
-    def __init__(self, A=1., tau=1., module="numexpr", **kwargs):
+    def __init__(self, A=1., tau=1., module=None, **kwargs):
         super().__init__(
             expression="A * exp(-x / tau)",
             name="Exponential",

hyperspy/_components/expression.py

@@ -17,6 +17,7 @@
 # along with HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
 
 from functools import wraps
+import logging
 import numpy as np
 import sympy
 
@@ -26,6 +27,9 @@
 from hyperspy.docstrings.parameters import FUNCTION_ND_DOCSTRING
 
 
+_logger = logging.getLogger(__name__)
+
+
 _CLASS_DOC = \
     """%s component (created with Expression).
 
@@ -87,9 +91,10 @@ class docstring.
         applicable. It enables interative adjustment of the position of the
         component in the model. For 2D components, a tuple must be passed
         with the name of the two parameters e.g. `("x0", "y0")`.
-    module : {"numpy", "numexpr", "scipy"}, default "numpy"
+    module : {"numpy", "numexpr", "scipy", None}, default "numpy"
         Module used to evaluate the function. numexpr is often faster but
         it supports fewer functions and requires installing numexpr.
+        If None, the "numexpr" will be used if installed.
     add_rotation : bool, default False
         This is only relevant for 2D components. If `True` it automatically
         adds `rotation_angle` parameter.
@@ -114,10 +119,10 @@ class docstring.
         parameters.
     check_parameter_linearity : bool
         If `True`, automatically check if each parameter is linear and set
-        its corresponding attribute accordingly. If `False`, the default is to 
+        its corresponding attribute accordingly. If `False`, the default is to
         set all parameters, except for those who are specified in
         ``linear_parameter_list``.
-        
+
     **kwargs
         Keyword arguments can be used to initialise the value of the
         parameters.
@@ -162,6 +167,17 @@ def __init__(self, expression, name, position=None, module="numpy",
                  linear_parameter_list=None, check_parameter_linearity=True,
                  **kwargs):
 
+        if module is None:
+            try:
+                import numexpr
+                module = "numexpr"
+            except ImportError:
+                module = "numpy"
+                _logger.warning(
+                    "Numexpr is not installed, falling back to numpy, "
+                    "which is slower to calculate model."
+                )
+
         if linear_parameter_list is None:
             linear_parameter_list = []
         self._add_rotation = add_rotation
@@ -224,13 +240,13 @@ def __init__(self, expression, name, position=None, module="numpy",
                 if p.name not in linear_parameter_list:
                     # _parsed_expr used "non public" parameter name and we
                     # need to use the correct parameter name by using
-                    # _rename_pars_inv 
+                    # _rename_pars_inv
                     p._linear = _check_parameter_linearity(
                         self._parsed_expr,
                         self._rename_pars_inv.get(p.name, p.name)
                         )
 
-    def compile_function(self, module="numpy", position=False):
+    def compile_function(self, module, position=False):
         """
         Compile the function and calculate the gradient automatically when
         possible.
@@ -379,7 +395,7 @@ def _separate_pseudocomponents(self):
         Separate an expression into a group of lambdified functions
         that can compute the free parts of the expression, and a single
         lambdified function that computes the fixed parts of the expression
-        
+
         Used by the _compute_expression_part method.
         """
         expr = self._str_expression
@@ -455,4 +471,3 @@ def _check_parameter_linearity(expr, name):
                       "determined automatically.", UserWarning)
         return False
     return True
-

hyperspy/_components/gaussian.py

@@ -105,7 +105,7 @@ class Gaussian(Expression):
     ~._components.gaussianhf.GaussianHF
     """
 
-    def __init__(self, A=1., sigma=1., centre=0., module="numexpr", **kwargs):
+    def __init__(self, A=1., sigma=1., centre=0., module=None, **kwargs):
         super().__init__(
             expression="A * (1 / (sigma * sqrt(2*pi))) * exp(-(x - centre)**2 \
                         / (2 * sigma**2))",

hyperspy/_components/gaussian2d.py

@@ -70,7 +70,7 @@ class Gaussian2D(Expression):
     """
 
     def __init__(self, A=1., sigma_x=1., sigma_y=1., centre_x=0.,
-                 centre_y=0, module="numexpr", **kwargs):
+                 centre_y=0, module=None, **kwargs):
         super().__init__(
             expression="A * (1 / (sigma_x * sigma_y * 2 * pi)) * \
                        exp(-((x - centre_x) ** 2 / (2 * sigma_x ** 2) \

hyperspy/_components/gaussianhf.py

@@ -83,7 +83,7 @@ class GaussianHF(Expression):
 
     """
 
-    def __init__(self, height=1., fwhm=1., centre=0., module="numexpr",
+    def __init__(self, height=1., fwhm=1., centre=0., module=None,
                  **kwargs):
         super().__init__(
             expression="height * exp(-(x - centre)**2 * 4 * log(2)/fwhm**2)",

hyperspy/_components/logistic.py

@@ -57,7 +57,7 @@ class Logistic(Expression):
         :py:class:`~._components.expression.Expression` component.
     """
 
-    def __init__(self, a=1., b=1., c=1., origin=0., module="numexpr", **kwargs):
+    def __init__(self, a=1., b=1., c=1., origin=0., module=None, **kwargs):
         super().__init__(
             expression="a / (1 + b * exp(-c * (x - origin)))",
             name="Logistic",

hyperspy/_components/lorentzian.py

@@ -94,7 +94,7 @@ class Lorentzian(Expression):
     the full-with-half-maximum and height of the distribution, respectively.
     """
 
-    def __init__(self, A=1., gamma=1., centre=0., module="numexpr", **kwargs):
+    def __init__(self, A=1., gamma=1., centre=0., module=None, **kwargs):
         # We use `_gamma` internally to workaround the use of the `gamma`
         # function in sympy
         super().__init__(

hyperspy/_components/polynomial.py

@@ -51,7 +51,7 @@ class Polynomial(Expression):
 
     """
 
-    def __init__(self, order=2, module="numexpr", **kwargs):
+    def __init__(self, order=2, module=None, **kwargs):
         if order == 0:
             raise ValueError("Polynomial of order 0 is not supported.")
         coeff_list = ['{}'.format(o).zfill(len(list(str(order)))) for o in

hyperspy/_components/power_law.py

@@ -61,7 +61,7 @@ class PowerLaw(Expression):
     """
 
     def __init__(self, A=10e5, r=3., origin=0., left_cutoff=0.0,
-                 module="numexpr", compute_gradients=False, **kwargs):
+                 module=None, compute_gradients=False, **kwargs):
         super().__init__(
             expression="where(left_cutoff<x, A*(-origin + x)**-r, 0)",
             name="PowerLaw",

hyperspy/_components/rc.py

@@ -54,7 +54,7 @@ class RC(Expression):
 
     """
 
-    def __init__(self, Vmax=1., V0=0., tau=1., module="numexpr", **kwargs):
+    def __init__(self, Vmax=1., V0=0., tau=1., module=None, **kwargs):
         super().__init__(
             expression="V0 + Vmax * (1 - exp(-x / tau))",
             name="RC",